ChapterPDF Available

Abstract and Figures

Bananas and plantains are one of the most important crops in the world, yet very few hybrids are cultivated. Bananas face considerable pressure from multiple biotic and abiotic stresses, but its genetic improvement is impeded by constraints on seed set due to multiple physiological and reproductive issues. The triploid nature of almost all commercially important bananas requires a complicated breeding scheme involving cross hybridization across ploidy levels and results in poor seed set that reduces the probability of obtaining favorable recombination. The poor seed set is further complicated by issues of parthenocarpy and partial to complete female and male sterility that are not fully understood. While the introduction of genomic resources of this perennial long cycling crop promises to hasten the development of improved cultivars, there is a need to maintain vigorous and committed long-term international breeding programs.
Content may be subject to copyright.
219© Springer International Publishing AG 2017
H. Campos, P.D.S. Caligari, Genetic Improvement of Tropical Crops,
Chapter 7
Bananas andPlantains (Musa spp.)
AllanBrown, RobooniTumuhimbise, DelphineAmah, BrigitteUwimana,
MosesNyine, HassanMduma, DavidTalengera, DeborahKaramura,
JeromeKuriba, andRonySwennen
7.1 Introduction
With a production of 145 million metric tons worldwide (worth 26.5 billion Euro),
banana (Musa spp.) is one of the world’s most important staple food crops and argu-
ably the world’s most popular fruit in terms of international trade (FAO 2014).
Banana and plantains (Musa spp.), collectively referred to here as bananas, are
grown in more than 135 countries and found in most tropical and subtropical regions
around the world. While industrialized nations view banana primarily as a dessert
A. Brown (*) • H. Mduma • R. Swennen
International Institute of Tropical Agriculture, Arusha, Tanzania
R. Tumuhimbise • J. Kuriba
National Agricultural Research Organization, Kampala, Uganda
D. Amah
International Institute of Tropical Agriculture, Ibadan, Nigeria
B. Uwimana • M. Nyine
International Institute of Tropical Agriculture, Kampala, Uganda
D. Talengera
National Agricultural Research Laboratories, Kampala, Uganda
D. Karamura
Bioversity International, Kampala, Uganda
item, many regions of the developing world consider cooking bananas and plantains
as essential staples that contribute signicantly to the caloric intake of low-income
subsistence farmers. Although sensitivity to photoperiod has been noted in certain
cultivars (Fortescue etal. 2011), banana is an almost nonseasonal crop that reliably
provides a carbohydrate source year-round which makes it vitally important to both
nutrition and food security. Propagation by farmers is commonly through suckers or
side shoots originating from lateral buds at the base of the main plant. Multiple
fungal and bacterial pathogens present serious constraints to production of bananas,
as does the occurrence of insects and nematodes (Jones 1999). Viral diseases caused
by banana streak virus (BSV), cucumber mosaic virus (CMV), banana bract mosaic
virus (BBMV), and the emerging banana bunchy top virus (BBTV) are also receiv-
ing increased attention (Kumar etal. 2015). The predominance of these biotic agents
differs from region to region, but most are found throughout the banana production
regions in Asia, Africa, and the Americas and represent common targets for plant
improvement worldwide. As with all crops, abiotic factors associated with climate
change such as drought and heat stress also present considerable challenges to pro-
duction (van Asten etal. 2011; Wairegi etal. 2010), but arguably the single greatest
constraint to genetic improvement is the narrow genetic basis of most cultivated
bananas (Hippolyte etal. 2012) and the physiological and reproductive barriers of
the plant itself (Ssesuliba etal. 2008; Fortescue and Turner 2004; Dumpe and Ortiz
1996). Reproductive barriers limit sexual recombination in banana and hinder plant
improvement. While all of the seed-bearing progenitors of modern banana cultivars
are diploid in nature, those that have been cultivated for consumption are primarily
seedless triploids. Female fertility of triploids has been described, but seed set is
generally extremely limited which complicates breeding efforts and intensives
resources and time required to develop superior varieties with enhanced resistance
to multiple biotic agents and abiotic agents. Banana improvement is further compli-
cated by parthenocarpy, reduced male fertility in some cultivars, low seed viability,
irregular meiotic behavior, long generation times, and diverse genomic congura-
tions (Ortiz 2013, 2015; Ortiz and Swennen 2014). To date, the limited progress that
has been achieved in banana breeding has occurred through crossbreeding
approaches that involve hybridization followed by phenotypic selection among half
sibs and/or full sib progenies.
7.2 Banana Classication
Banana is a monocotyledon herbaceous plant represented by three genera (Musa,
Ensete, and Musella) within the family Musaceae of the order Zingiberales (De
Langhe etal. 2009). The genus Ensete consists of monocarpic, unbranched herba-
ceous plants that rarely produce suckers and are used for food, ber, and ornamental
purposes. They resemble banana, but their oversized, edible corms and wide-
spreading and immensely long, paddle-shaped leaves with crimson midribs make
them very distinctive. Their fruits are similar in appearance to those of banana, but
A. Brown et al.
are dry, seedy, and inedible (Deckers etal. 2001). The most recognizable member of
this genus is perhaps the false or Abyssinian banana (E. ventricosum) that plays a
signicant role in Ethiopian agriculture and food security (Tsegaye and Struik
The genus Musa consists of cultivated triploid cultivars and clones propagated
through vegetative methods with limited genetic variation beyond what could be
expected through somaclonal variation (and perhaps epigenetics) and the diploid
wild progenitors of these cultivars that are capable of sexual recombination. More
than 60 species within four recognized sections of the genus Musa have been
described, but the taxonomy of Musa and the relationship between wild and culti-
vated bananas are far from settled (De Langhe et al. 2009; Janssens etal. 2016).
Almost all diploid species are native to Southeast Asia, from India and Thailand to
New Guinea and Queensland, Australia (Simmonds 1987). Edible bananas, with the
exception of the Fe’i group of the Australimusa section, are derived almost exclu-
sively from two species, Musa acuminata and Musa balbisiana of the section Musa
(Dodds 1945). M. acuminata and M. balbisiana are diploid (2n = 2x = 22) in their
base genomic complements and designated as AA and BB, respectively (Simmonds
and Shepherd 1955). In addition to monospecic cultivars (AA, BB), interspecic
diploid clones (AB) are also recognized. Higher-order combinations of the AA and
BB base genomes arose through chromosome restitution at meiosis, to produce dis-
tinct groupings at the triploid (AAA, AAB, ABB groups) and occasionally tetraploid
levels (Simmonds 1962). Triploids, due to their optimal vigor and seedless charac-
teristic, are the preferred conguration for most consumers throughout the world
(Simmonds 1987). The rare tetraploid cultivars tend to be physically larger but have
relatively small bunches, while most diploid cultivars tend to be weaker plants with
smaller bunches (De Langhe 1986). Edible parthenocarpic diploids are however cul-
tivated in certain regions such as Tanzania (Simmonds 1962) where the Mchare (or
Mshale) diploids are preferred for the unique texture characteristics of the fruit.
Generally, modern classication systems of banana tend to follow Simmonds
and others (Simmonds and Shepherd 1955; Stover and Simmonds 1987) and are
based on ploidy status and the relative contribution of the two genomes. Simmonds
(1962, 1966) suggested that the formal Latin nomenclature should be replaced by a
ploidy-based nomenclature in which the cultivar is referred to by the genus and a
genomic grouping (e.g., Musa, AAA Group, “Gros Michel”). Cultivars are placed
in higher-level groupings based on the number of chromosomes and the species
that contribute to their genetic makeup (AA, BB, AAA, AAB, and ABB) (Karamura
etal. 2012). Simmonds and Shepherd (1955) utilized 15 taxonomic characters spe-
cic to M. balbisiana and M. acuminata to assign cultivars to groups, and this clas-
sication scheme has been periodically updated (Stover and Simmonds 1987).
Below the level of group, cultivars are assigned to clusters of subgroups that
are characterized by a representative member. For example, “Cavendish” and
“Gros Michel” are considered separate subgroups under the AAA grouping along
with several mutants and variants derived from these economically important cul-
tivars. The grouping (AAA) also includes all of the economically important East
African Highland cooking bananas. While this classication system may be
7 Bananas andPlantains (Musa s pp.)
convenient, it appears to lack hierarchical, biological, or economic signicance,
for example, Mysore, Pome, and Plantain are all recognized subgroup clusters
within the AAB group, but they are utilized for different purposes, and subsequent
results of molecular and morphological diversity studies suggest that they are
genetically distinct and likely have arisen from dissimilar parentage (De Langhe
etal. 2010; Christelová etal. 2017).
Likely, cultivars within the AAA, AAB, and ABB groupings arose from multi-
ple hybridization events followed by subsequent backcrossing to various AA, BB,
and AB progenitors which results in an unequal chromosomal allocation at meiosis
(De Langhe etal. 2010). It has been suggested that this phenomenon could explain
the unequal and nonadditive chromosomal complementation which has been
observed among interspecic hybrids (d’Hont et al. 2000). If indeed cultivars
within groupings arose from multiple hybridization events, it suggests that classi-
cation may be more dependent on specic diploid progenitors than on traditional
groupings based on ploidy. Morphological characteristics and nuclear and cyto-
plasmic molecular markers have been used to differentiate the progenitor M. acu-
minata diploids into several subspecies that correspond to specic geographic
ranges from mainland Asia to the archipelagoes of Indonesia, New Guinea, and the
Philippines (Hippolyte et al. 2012; Carreel et al. 2002; Perrier et al. 2011).
Currently, there are eight recognized diploid AA subspecies that include roughly
from West to East: M. acuminata ssp. burmannica, M. acuminata ssp. siamea, M.
acuminata ssp. truncata, M. acuminata ssp. malaccensis, M. acuminata ssp. zeb-
rina, M. acuminata ssp. microcarpa, M. acuminata ssp. errans, and Musa acumi-
nata ssp. banksii. The subspecies have contributed important diploid parents to
modern breeding programs, but much work remains toward evaluating and pre-
serving germplasm that has not been readily accessed due to logistic or political
reasons in past collecting expeditions.
Considerable efforts have been made over the past few decades to preserve, char-
acterize, and provide access to genetic resources of Musa. Banana germplasm for
use in breeding is distributed through the Biodiversity International Musa
Germplasm Transit Centre which oversees more than 1500 accessions. The center
secures available banana germplasm for long-term conservation and holds the col-
lection in trust for the benet of future generations under the auspices of the Food
and Agriculture Organization of the United Nations. The conserved germplasm is
placed in the Multilateral System of Access and Benet Sharing of the International
Treaty on Plant Genetic Resources for Food and Agriculture. All accessions have
been indexed, conserved invitro (Van den houwe etal. 1995), and most stored under
cryopreservation (Panis etal. 2005). Characterization of germplasm occurs in both
eld trials and at the molecular level. Passport and characterization data is freely
available through the Musa Germplasm Information System (MGIS) (https://www.
A. Brown et al.
7.3 Banana Breeding Objectives
The primary objective of most banana breeding programs is the uniform production
of large bunches that meet the regional qualitative and quantitative demands of grow-
ers. These demands include superior fruit quality, high suckering ability, short stat-
ure, and enhanced root systems that provide effective soil anchorage and efcient
uptake of water and minerals. Other agronomic traits such as photosynthetic ef-
ciency and rapid cycling are also important breeding objectives for increased yield.
The relative importance of these objectives varies across geographic regions, among
subgroups of banana, and with the intended nal use of the product. In recent years,
the anticipated and realized threats of pests and diseases have resulted in increased
emphasis placed on identifying and utilizing improved sources of host- plant resis-
tance to pests and diseases, particularly in regard to the Sigatoka complex, multiple
races of Fusarium wilt, bacterial wilt, bunchy top, nematodes, and weevils.
In Uganda, banana breeding focuses largely on the improvement of East African
Highland (cooking) bananas (EAHBs) (AAA). The expected yield and plantation life
of these bananas has signicantly declined, in no small part due to pests (such as
banana weevils and nematodes) and diseases (including black Sigatoka and bacterial
wilt). Some of the key breeding objectives by the National Banana Research Program
of the Uganda National Agricultural Research Organization (NARO), in partnership
with the International Institute of Tropical Agriculture (IITA), have been to identify
and integrate host-plant resistance to the Sigatoka complex, weevils, and nematodes
from wild diploid progenitors into elite EAHB backgrounds. A generalized criterion
for selection of EAHB based on agronomic traits is presented in Table7.1.
Table 7.1 Characteristics of the ideotype of East African Highland cooking bananas
Trait Description
Yield potential >25t/ha/year
Bunch weight >15kg
Plant height <3m
Time of owering 210–270days
Time of bunch maturity 90–120days
Number of hands 8–12/bunch
Number of ngers 100–190/bunch
Fruit nger circumference 10–15cm
Fruit nger length 13–20cm
Suckering ability 75% follower sucker growth at harvest
Root system Vigorous (fast growing, deep, and branched)
Bunch orientation Pendent
Reaction to prevalent diseases Resistant to the black Sigatoka complex and bacterial
Reaction to prevalent pests Resistant to weevils and nematodes
Reaction to drought stress Resistant/tolerant
7 Bananas andPlantains (Musa s pp.)
7.4 Constraints toBanana Breeding
As previously discussed, the greatest constraint to banana genetic improvement is
the limited production of viable seeds due to polyploidy, female sterility, and
other factors affecting seed production in triploid and diploid banana. Female
sterility has been intensied as a consequence of human selection for partheno-
carpy in banana. Simmonds (1962) rst suggested that continuous clonal propaga-
tion of diploids has led to an accumulation of structural chromosomal changes
(translocations, inversions, and other events) that restrict normal meiosis and pol-
len fertility and reduce expected recombination. Specic abnormalities such as
translocations have been noted in the diploids “Pisang Lilin” and “Pisang Jari
Buaya,” but the extent to which this phenomenon occurs throughout Musa is still
not well understood. Adeleke etal. (2004) observed that in general, a higher
incidence of univalent formation was related to low pollen fertility in both diploids
and triploids. Sterility in plantains and EAHB triploid bananas has been associ-
ated with meiotic irregularities and uneven number of chromosomes, as well as to
environmental factors and to inuences of individual genotypes (Swennen and
Vuylsteke 1993; Ssebuliba etal. 2000). Seed yield is inuenced by time of polli-
nation, environmental conditions, genetic variation in female fertility, differences
observed among pollinations made between the basal and distal hand, and variation
associated with the relative contributions of the acuminata and balbisiana
genomes (Simmonds 1962). Sathiamoorthy and Rao (1980) observed increased
seed set with proportional contributions from the balbisiana genome and specu-
lated that the factors for seed sterility have accumulated preferentially in the M.
acuminata genome (Simmonds 1962). The use of embryo rescue has signicantly
improved seed germination with observations of up to 30% increases in viable
embryos (Swennen and Vuylsteke 1993).
A further complication associated with improvement of cultivated bananas is
that the highly heterozygous state of the parents results in extremely variable
progeny that makes predictions of progeny performance on the basis of parental
phenotypes unreliable (Ortiz 2000). The progeny from crosses can include mix-
tures of ploidy levels and sometimes aneuploids. Oselebe etal. (2006) reported
that while progeny of 2×–2× crosses were almost exclusively diploid (99.7%),
those of mixed ploidy crosses tended to include individuals that varied in their
chromosomal compliment. The same study observed that the direction of the
cross impacted results. When the diploid is used as the maternal parent in a 2×–4×
cross, over 96% of progeny are diploids, but when the tetraploid is used as the
maternal parent (4×–2×), the observed progeny is predominately triploid (94%)
with varying degrees of other ploidy levels between the diploid and the pentaploid
observed. While these mixed ploidy progenies provide a mechanism for enhanc-
ing genetic diversity and recombination, they also necessitate the use of early
screening of ploidy levels.
A. Brown et al.
7.5 Breeding Strategies
Plant breeding provides one of the highest returns of investment in agricultural
research, and while banana production has beneted from these investments, few
banana and plantain cultivars acceptable to farmers and consumers were produced
prior to the 1980s (Roux 2001). Triploid bananas are preferred by growers as they
commonly display the most advantageous combination of fruit and vegetative char-
acters (De Langhe 1986; Stover and Simmonds 1987), but it was generally assumed
that these triploid cultivars (such as “Cavendish”) were effectively sterile (Stover
and Buddenhagen 1986). Persistent efforts, however, from multiple breeding pro-
grams including IITA and the Honduran Foundation for Agricultural Research
(FHIA) have demonstrated that viable embryos could be produced from what were
previously considered recalcitrant triploids by making hybridizations with selected
pollen of diploid banana (Aguilar-Moran 2013). FHIA successfully produced 40
viable tetraploid embryos utilizing “Cavendish” as a female, although this effort
required an almost Herculean task that included the pollination of over 20,000
bunches. By the end of the twentieth century, efforts to improve banana focused
primarily on the use of improved diploid and synthesized tetraploid gene pools to
develop secondary triploids of bananas and plantains (Fig.7.1).
Under this breeding scheme, the identication of improved diploids that provide
donor traits of interest and cultivated triploids with superior quality characteristics
takes on a vital role in synthesizing superior secondary triploids. Conventionally, it
was assumed that when crosses were made between male diploids and female trip-
loids to obtain tetraploid progeny, all three sets of maternal chromosomes were trans-
mary hybrids)4x
Improved diploi
ry triploid) 3x
Fig. 7.1 The scheme of the banana breeding process whereby initial crosses are carried out
between triploid landrace (2n=3x) and diploid (2n=2x)
7 Bananas andPlantains (Musa s pp.)
ferred intact to the tetraploid offspring with recombination only occurring as a result
of the contribution of diploid male parent (Dodds 1943). Vuylsteke etal. (1993),
however, noted that tetraploid progeny from such crosses displayed variation in dis-
ease resistance, morphological traits, and growth and yield parameters that were
inconsistent with this hypothesis. It was further suggested that segregation and recom-
bination during modied megasporogenesis leading to the formation of 2n eggs in the
triploid parent perhaps better explained the observed results. With the advent of new
genomic resources and tools, this phenomenon needs to be further investigated in
order to better understand the extent of sexual recombination in banana breeding.
This breeding strategy has been adopted by multiple programs including FHIA
in Honduras which has produced a generation of acceptable tetraploids that are still
currently being used in breeding (Rowe and Rosales 1993). An example includes
FHIA 21, a tetraploid derived from AVP-67 French plantain that is still being uti-
lized in plantain improvement. IITA has also utilized this approach successfully to
introgress alleles for resistance/tolerance to key pest and diseases in high-yielding
hybrids derived from preferred plantain cultivars (Ortiz etal. 1995; Tenkouano and
Swennen 2004; Vuylsteke etal. 1993). Plantain hybrid releases include PITA 14 and
PITA 17 (primary tetraploids) and more recently PITA 21, PITA 23, and PITA 24
(secondary triploids) all derived from three seed-fertile triploid French plantains
Obino L’ewai, Bobby Tannap, and Mbi Egome. Their common attributes include
BLS resistance/tolerance and good bunch characteristics (Tenkouano etal. 2011)
and early suckering (Vuylsteke etal. 1993). These IITA hybrids have currently been
distributed to ten countries in Africa and three countries in Central and South
America for evaluation and adoption.
At NARO, tetraploids (AAAA) were synthesized from EAHBs (AAA) by cross-
ing to the wild-seeded, fertile male parent Calcutta 4 (AA) that is used by many
programs as a source of resistance to multiple pests and diseases. A number of these
tetraploids developed such as 365K-1, 1201K-1, 917K-2, 660K-1, 1438K-1, and
222K-1 25 were fundamental in the development of 27 NARITA triploid banana
hybrids by NARO and IITA (Tushemereirwe etal. 2015). These banana hybrids
were selected from early evaluation trials based largely on resistance to black
Sigatoka and bunch size and subsequently advanced to the preliminary yield trials
in Uganda. NARITAs are currently under evaluation for agronomic, sensory, pest,
and disease resistance traits in multi-environment trials in Uganda and Tanzania.
An alternative breeding scheme has been suggested by Vakili (1968) and involves
the polyploidization of diploid hybrids or cultivars through the use of colchicine or
oryzalin to obtain tetraploids for crossing with 2× lines to generate triploids. This
approach is currently being pursued by multiple breeding programs and shows con-
siderable promise (Bakry etal. 2009). According to Tenkouano etal. (2011), the two
schemes conform to differences in breeding philosophies. The former can be viewed
as evolutionary breeding as it attempts to mimic the developmental pathway of
Musa by crossing female triploid landraces to diploid accessions of M. acuminata
or M. balbisiana, while the latter can be considered reconstitutive breeding as it
utilizes the most likely diploid ancestors or relatives of triploid landraces for chro-
mosome doubling to create improved triploids.
A. Brown et al.
7.5.1 Development ofImproved Diploids
Regardless of the breeding scheme, the narrow genetic variability and limited
fertility among cultivated triploid bananas make diploid bananas vital to genetic
improvement. A number of fertile improved diploids with varying degrees of dis-
ease resistance have been released by IITA and FHIA (Tenkouano etal. 2003; Rowe
and Rosales 1993). Diploid improvement has almost exclusively been through the
use of M. acuminata cultivars such as “Calcutta 4” (M. acuminata), a source of
resistance to the Sigatoka complex, yellow Sigatoka, fusarium wilt, banana weevil,
and burrowing nematodes (Ortiz 2015). Decades of breeding utilizing this material
have resulted in the production of improved diploid lines which combine disease/
pest resistance, short stature, and interesting bunch characteristics (Tenkouano etal.
2003; Krishnamoorthy and Kumar 2005). Developing further improved diploids
that possess multiple sources of resistance, while preserving the quality characteris-
tics of preferred triploid would greatly increase the efciency of breeding efforts
that are hindered by the constraints previously described.
M. balbisiana diploid cultivars have made limited contributions to breeding due to
the presence of endogenous banana streak virus (eBSV) sequences originating from
the B genome that are activated under the appropriate conditions (Iskra- Caruana etal.
2014). Progenies of interspecic acuminata/balbisiana hybridizations have often
been associated with the occurrence of banana streak disease, and this has resulted in
the underutilization of the B genome which could be an important source of drought
tolerance and resistance alleles not found in M. acuminata (Bakry et al. 2009).
Recently, Noumbissie etal. (2016) reported segregation of the eBSV sequences in the
progeny of crosses between the tetraploid hybrid CRBP 39 (+eBSV) and the AA
male parent Pahang (eBSV), from which resulted triploid eBSV-free offspring.
Umber etal. (2016) also documented the successful creation of diploids free of eBSV
alleles from M. balbisiana diploids suggesting that recombination between M. acu-
minata and M. balbisiana can be accomplished for improvement of both cultivated
banana and plantain without concern of introducing banana leaf streak.
7.5.2 Breeding Methodology and Evaluation ofHybrids
Production of viable seed through hybridization is critical for the success of breed-
ing and is dependent on residual fertility of triploid cultivars. Practical aspects of
articial hybridization have been described by Tenkouano et al. (2011).
Hybridizations are made through manual pollinations in the early hours of the
morning when pollen availability is not a limiting factor. It can take up to several
months to obtain seeds from a desired cross, and production of seeds is generally
poor and has been reported in the range of 0.3–21.7 seeds per bunch (Swennen and
Vuylsteke 1993) (Fig.7.2). Seeds obtained from crosses also germinate poorly, and
it is standard practice by most programs to recover hybrids through invitro culture
(Bakry 2008) (Fig.7.3).
7 Bananas andPlantains (Musa s pp.)
Bunches are harvested prior to physiological maturity, generally when the rst
signs of yellow color are observed in the distal ngers. Bunches are left to ripen in
protected sheds, and seeds are extracted and surface-sterilized for embryo culture to
avoid seed/embryo desiccation. Embryos are extracted from dissected seeds under
aseptic conditions and cultured on articial culture media (Bakry etal. 2009; Uma
et al. 2011). Longitudinal excisions are made on the seed to expose the embryo
Fig. 7.2 Male banana owers open in the evening and are ready for pollination early in the
Fig. 7.3 Bract is pulled back and pollen applied directly to the receptive female owers
A. Brown et al.
beneath the micropyle. The embryo is placed on sterile culture medium and incubated
in the dark for germination. Embryos typically germinate between 5 and 20days after
which time they are transferred to an environment with appropriate light and dark
cycles for shoot and root development. Well-developed seedlings can then be cloned
to replicate one to four rooted plantlets or transferred to a screenhouse for condition-
ing prior to eld evaluations. More research on pollen production, pollen tube growth,
and embryo viability is required to better understand issues associated with poor seed
production and to optimize conditions that will lead to better seed yield (Uma etal.
2011). In particular, detailed knowledge of oral biology and seed development is
crucial for recovery of progeny from crosses (Fortescue and Turner 2011).
In the eld, new hybrids are subjected to early evaluation trials (EETs) with lim-
ited replication (one to ve plants). EETs are observed generally for two cycles
during which a few simply inherited traits such as bunch size and orientation,
Sigatoka resistance, seed production, and ploidy level are evaluated. Plants that
show promise in EETs are further evaluated in preliminary yield trials (PYTs)
where replicated clones of selected hybrids are evaluated over two cycles. PYTs
involve more detailed evaluation for additional, complex traits such as yield and
disease resistance. Finally, superior-performing plants from PYTs are cloned in sig-
nicant numbers to allow for multi-locational evaluation trials (MET) that often
include direct input from farmers (Tenkouano etal. 2011). In theory, this process
can take a minimum of 7years to produce a superior banana hybrid, although in
practice this time frame is often exceeded.
7.6 Applied Biotechnology
7.6.1 Molecular-Assisted Breeding
Due to the breeding constraints previously discussed, the use of molecular markers
holds considerable promise in improving the efciency of banana breeding but is
currently not routinely used in most breeding programs. Efforts toward the develop-
ment and use of molecular markers have been greatly facilitated by the recent
release and renement of the draft genomic sequence of the double haploid M.
acuminata cultivar “Pahang” (A genome) (D’Hont etal. 2012; Martin etal. 2016)
and a draft sequence of M. balbisiana “Pisang Klutuk Wulung” (B genome, Davey
etal. 2013). Multiple transcriptome data sets have also been published (Li etal.
2013; Wang etal. 2012), and of these publications, over 45,000 expressed sequence
tags, and 34,000 annotated genes associated with Musa are currently available
through NCBI-EST database. These genomic resources have contributed to the
availability of multiple classes of markers summarized in Tables 7.1 and 7.2.
Molecular markers provide genetic “landmarks” for tagging important traits in plant
breeding, conducting linkage analysis and estimates of genetic diversity, facilitating
gene introgression through marker-assisted studies, providing validation of taxon-
omy and cultivar identication, and estimating evolutionary and speciation events.
7 Bananas andPlantains (Musa s pp.)
Table 7.2 A summary of molecular markers utilized in banana research and their research applications
Marker application Marker type Reference
Molecular systematics Isozymes, SSR, DArTs, RFLP and ITS Perrier et al. (2011), Christelová et al. (2017), and Simmonds (1966)
Genetic diversity studies RAPD, SSR, AFLP and MSAP Karamura et al. (2016), Kitavi et al. (2016), Nyine and Pillay (2011), Opara
et al. (2010) Wang et al. (2007), Noyer et al. (2005), Creste et al. (2004), Ude
et al. (2003), Ude et al. (2002), Pillay et al. (2001), Crouch et al. (2000), and
Crouch et al. (1999)
Genome characterization RAPD, RFLP, ITS, dCAP and IRAP
Cultivar identication and
pedigree tracking
Isozymes, RFLP, SSR, RAPD,
Mbanjo et al. (2012), Hippolyte et al. (2012), and Raboin et al. (2005)
Linkage analysis Isozyme, RAPD, RFLP, AFLP, SSR
AS-PCR and DArTs
Mbanjo et al. (2012), Hippolyte et al. (2010) and Fauré et al. (1993)
Genome-wide association
studies and marker-assisted
Isozymes, dCAP and SNP Sardos et al. (2016), Umber et al. (2016), and Noumbissié et al. (2016)
A. Brown et al.
231 Association ofMolecular Marker withImportant Genes
The tagging of signicant genes contributing to traits of interest with genic or
linked markers allows for screening of plant germplasm at the earliest stages of
development. The association of these markers with important traits can come
through classical linkage or association studies or through candidate gene
approaches that leverage recently available genomic resources. An example of the
candidate gene approach is provided by Emediato et al. (2009) who amplied
homologues of black leaf streak disease resistance genes in Musa through the use
of degenerate primers based on genes from other crops. The study successfully
amplied sequence differences between the diploid M. acuminata cultivars
“Calcutta 4” (resistant) and “Pisang Berlin” (susceptible). This work followed the
earlier identication of 50 distinct tagged nucleotide binding site-leucine-rich
repeat (NBS-LRR) resistance gene analogs in cultivar “Calcutta 4” by Miller etal.
(2008). Wang et al. (2012) used pooled DNA from Fusarium oxysporum f.sp.
cubensis (Foc TR4)-resistant and susceptible cultivars to identify randomly ampli-
ed polymorphic DNA (RAPD) markers that could distinguish between resistant
and susceptible cultivars. Two RAPD markers were converted to sequence charac-
terized amplied region (SCAR) markers which could be amplied in Foc TR4-
resistant banana genotypes (“Williams 8818-1” and Goldnger), but not in ve
tested susceptible banana cultivars. Work on this continues at the national banana
program in Brazil (EMBRAPA) and shows great promise in providing an early
screen for resistance to Foc TR4 (Silva etal. 2016).
As previously discussed, endogenous banana streak virus (eBSV) limits the
extensive use of the B genome in banana breeding, but the tagging of this
sequence has opened possibilities of greater utilization in the future. Lheureux
etal. (2003) mapped the eBSV sequence using amplied fragment length poly-
morphism (AFLP) markers, and Noumbissié etal. (2016) used simple sequence
repeat (SSR) markers and eBSV-specic PCR markers to identify hybrids lack-
ing the eBSV sequence. Umber etal. (2016) successfully identied infectious
and noninfectious BSV alleles using derived cleaved amplied polymorphic
sequences (dCAPS). These studies suggest that these markers can be used early
in the breeding process as diagnostic markers for eBSV-free B genome hybrids
that will greatly enhance breeding efforts. While the progress shown by these
early efforts is promising, markers associated with traits of economic importance
need to be validated in broader germplasm pools over multiple years to ensure
that they will prove to be reliable and stable and that genotypic predictions at the
early stages of screening will be highly correlated with plant phenotypes at full
maturity under eld conditions.
7 Bananas andPlantains (Musa s pp.)
232 Linkage, Association Mapping, andGenomic Selection
Genetic linkage maps provide opportunities for gene identication and a mechanism
for understanding the inheritance pattern of both qualitative and quantitative traits.
Mapping requires appropriate plant populations of known structure derived from
parents that differ signicantly in traits of interest, a set of markers segregating in
the given population that provides substantial coverage of all chromosomes, and the
careful collection of phenotypic data from multiple years and preferably locations.
Linkage mapping has not gained signicant practical application in banana breed-
ing. This could be attributed in part to limitations inherent in marker technologies
and analysis (Foolad 2007; Pillay etal. 2012), to previously described chromosomal
abnormalities in banana that inhibit recombination and to contribute ambiguous
assignment of marker location. To date, principally F1 and F2 diploid populations
have been utilized due to difculties associated with developing double haploid or
recombinant inbred lines in banana.
The rst genetic mapping population in banana was reported in 1993 (Fauré
etal. 1993) and consisted of 92 F2 progeny (AA) derived from an F1 hybrid (SFB5)
of the cross “SF265” (CIRAD-IRFA II. × “banksii” (CIRAD-
IRFA II. Seventy-seven loci consisting of RAPDs, isozymes, and
restriction fragment length polymorphisms (RFLPs) were mapped onto 15 linkage
groups spanning 606cM. Segregation distortion was associated with 36% of the
mapped loci and was biased toward the “banksii” parent. Hippolyte etal. (2010)
published a more saturated map using an F1 diploid “AA” population created from
a cross between “Borneo” and “Pisang Lilin.” The map was constructed using 426
markers (SSR and DArT). Separate maps were constructed for markers that segre-
gated from each of the heterozygous parents, and a synthetic map was constructed
that spanned 11 linkage groups and represented 1197cM.Three regions of this
synthetic map were inconsistent between the two parents and were attributed by
the authors to structural rearrangements. Subsequent mapping projects have also
noted such incongruities, and while these suggestions are supported by cytogenetic
evidence such as multivalent pairing (Shepherd 1999), much work needs to be
done to verify this hypothesis and determine the extent that such phenomenon
occurs across Musa spp. Mbanjo etal. (2012) produced the most recent map utiliz-
ing an F1 population consisting of crosses between 6142-1 × 8075-7 and 6142-
1-S × 8075-7. Two maternal (6142-1 and 6142-1-S) and one paternal (8075-7)
maps were generated using diversity array technology (DArT), SSR, and allele-
specic PCR (AS-PCR) markers. As with other maps, considerable (41%)
segregation distortion was observed at marker loci.
Association mapping has been proposed as an alternative to conventional linkage
mapping. In this strategy, a panel of genotypes from unrelated population (or a
population with known genetic substructure) is utilized to identify associations
between molecular markers that are in linkage disequilibrium with genetic loci
affecting phenotypes. Molecular markers that are distributed throughout the genome
such as single nucleotide polymorphisms (SNP) are preferred for genome-wide
association studies (GWAS). Sardos et al. (2016) demonstrated the technique
by assembling a GWAS panel of 104 AA accessions using 5544 SNP markers
A. Brown et al.
derived from genotyping by sequencing (GBS) and publicly available phenotypic
data on parthenocarpy. The study identied 13 genomic regions associated with
parthenocarpy, and multiple candidate genes in these regions corresponded with
putative growth regulators and genes associated with gametophyte development and
female sterility in other plant species.
Genomic selection (GS) is a form of marker-assisted selection that utilizes high-
density molecular markers such as SNPs to provide coverage of the whole genome,
ensuring that all quantitative trait loci (QTL) are in linkage disequilibrium with at
least one marker (Hayes and Goddard 2010). GS estimates the genomic breeding
value of individual genotypes in a large segregating population utilizing one of sev-
eral GS models (Meuwissen etal. 2001). GS is less concerned with the identica-
tion of individual QTL as it is with developing appropriate models to enhance
selection efciency. As the cost of generating marker data becomes increasingly
more affordable, GS has become an attractive alternative to many breeding pro-
grams (Lorenz etal. 2011; Crossa et al. 2010). Currently, efforts are underway to
evaluate GS as a strategy to improve banana by generating appropriate breeding
models for the improvement of EAHB (Nyine etal. 2016). Estimating Genetic Diversity andEvolutionary Events
Estimates of genetic diversity determine to a large extent the potential of plant
improvement that can be anticipated and can also provide guidance to breeders as to
the appropriate parents to use in breeding schemes. Estimates based on phenotypic or
morphological characters have long been used in banana (Karamura 1998), but often
these estimates can be biased by environmental inuences as well as the sometimes
complimentary and polygenic nature of underlying genetic factors. Molecular mark-
ers avoid these issues as they are highly heritable and have supplemented or replaced
the usage of such measurements in most plant species where they are available. In
banana, several classes of molecular markers have been used to estimate diversity
among populations of varying size representing regional collections and breeding
program germplasm. These include RFLPs (Jarret et al. 1993; Bhat et al. 1995),
RAPDs (Bhat etal. 1995; Crouch etal. 2000; Pillay et al. 2001; Ude et al. 2003;
Nyine and Pillay 2011), AFLPs (Ude etal. 2002, 2003; Noyer etal. 2005; Wang etal.
2007; Opara etal. 2010), SSRs (Kaemmer etal. 1997; Crouch etal. 1999; Tenkouano
etal. 1999; Noyer etal. 2005; Creste etal. 2004; Hippolyte etal. 2012; Kitavi etal.
2016; Karamura etal. 2016), sequence-related amplied polymorphisms (SRAPs)
(Wei etal. 2011; Valdez-Ojeda etal. 2014), DArT (Risterucci etal. 2009), and meth-
ylation-sensitive amplication polymorphism (MASP) (Noyer etal. 2005).
Estimates of genetic diversity generated from these studies vary with the class
and number of markers used and with the genotypes selected for inclusion in any
given study, but a few generalized observations can be made: (1) Diversity esti-
mates based on phenotypic measurements are often poorly correlated with molecu-
lar estimates (Crouch et al. 2000); (2) despite considerable phenotypic or
morphological variation among regional Musa landraces, they tend to have limited
genetic variation when assayed with molecular markers. For example, East African
7 Bananas andPlantains (Musa s pp.)
Highland bananas (EAHBs) have been classied into ve clades (clone sets) based
on their end use and morphological distinctiveness (Karamura 1998). Studies
focusing on EAHB using both RAPDs and SSR markers, however, found limited
evidence to support the signicant variation either within or between these clades
(Pillay etal. 2001; Kitavi etal. 2016; Karamura etal. 2016). This led to the sugges-
tion that EAHB arose from a single hybridization event that has subsequently been
acted on by a series of somatic mutations and inuenced by natural and directed
selection leading to many distinct cultivars. Presumably, the nite numbers of
markers used are unable to distinguish among the clades. Utilizing different classes
of molecular markers can sometimes reveal variation in populations where it has
not been previously noted. In plantain landraces of West Africa, RAPD, SSR, and
amplied fragment length polymorphism (AFLP) markers displayed few polymor-
phisms (Crouch etal. 2000). However, when HpaII and MspI methylation-sensitive
amplied markers were used, polymorphism (MSAP) proles revealed three clus-
ters (Noyer etal. 2005) and a genetically distinct subset of plantains from Cameroon
(Ude etal. 2003).
Molecular markers have played important roles in determining the evolutionary
history of cultivated banana and establishing links to diploid progenitors. Whether
the breeder utilizes an evolutionary or reconstitutive approach to banana improve-
ment (discussed in a previous section) plays a vital role in effectively combining
novel resistance traits with quality characteristics desired by growers. Perrier etal.
(2011) detail the available molecular, archaeology, genetic, and linguistic evidence
for this important aspect of breeding. Of particular interest to the dessert banana
industry has been the observation that East African diploid bananas appear to have
played an important evolutionary role in the development of “Cavendish” and “Gros
Michel,” the most widely used cultivars that have dominated the banana export
industry over the past century (Raboin etal. 2005; Risterucci etal. 2009).
7.7 Conclusions
While progress has been made toward genetic improvement since the rst formal
programs were established almost a hundred years ago, in some aspects the breed-
ing of banana is still in its infancy when compared to the improvement of other
important staple crops. In no small part, this is due to the physical and reproductive
constraints of the plant itself, but there is room for optimism as these constraints
appear to be neither absolute nor prohibitive. Molecular markers, the availability of
additional genomic resources, and ongoing studies elucidating the oral and repro-
ductive biology of banana hold great promise for the next hundred years of banana
Genetic engineering has not been discussed in this chapter, but the early work in
this arena also suggests that it also has the potential to make an important contribu-
tion to Musa improvement through the introduction of genetic factors not found
within cultivated or wild Musa germplasm (Tripathi etal. 2012).
A. Brown et al.
Further work is needed on predicting the performance and combining ability of
male and female parents in Musa improvement. Tenkouano etal. (2012) reported
the signicance of additive genetic effects on expression of bunch weight, fruit
lling time, fruit length, plant height, and number of leaves and nonadditive effects
for suckering behavior and fruit circumference in 3× hybrids obtained from plan-
tain derived 4×–2× crosses. They further suggested that maternal general combin-
ing ability (GCA) accounted for the additive genetic variation for plant height and
number of leaves, while paternal GCA effects accounted for fruit lling time,
bunch weight, and fruit length. On the other hand, specic combining ability
(SCA) effects were observed for all traits, except fruit lling time, suggesting that
additional genetic gain could be achieved through recombinative heterosis for such
traits. They concluded that increased bunch weight and faster cycling are inherited
from the 2× male parent, while plant height, number of leaves, and suckering
behavior are inherited from the 4× female parent which should guide parental
selection for 4×–2× crossbreeding. More of this information is needed to ef-
ciently guide the decision- making efforts of breeders and allow them to allocate
limited resources.
Finally, in the popular press, there has been considerable alarm in recent years as
to the future of banana in the face of an evolving pathogen (Foc TR4) that threatens
the production of much of the world’s dessert banana production. In some ways, the
economic damage that this pathogen will likely cause can be viewed as self-inicted
in nature. The export industry has demonstrated an overdependence on monoculture
and complacency in regard to breeding that has signicantly contributed to creating
an environment conducive to the selection and spread of novel pathogenic races.
This is a lesson that should have been learned more than a half century before when
a similar threat was encountered by a different race of the same pathogen. Banana
breeding efforts to improve the industry standard “Gros Michel” were curtailed or
sidelined when a suitable replacement (“Cavendish”) was selected from existing
stock. Hopefully, the current crises will provide an impetus and serve as a reminder
to all that proactive breeding programs are the most efcient and cost-effective
frontline defense against current and evolving threats to production.
Acknowledgments This research was undertaken with the support of the Belgium Government,
IITA, the Bill and Melinda Gates Foundation, the CGIAR Research Program on Roots, Tubers and
Banana (RTB), USAID and HarvestPlus, part of the CGIAR Research Program on Agriculture for
Nutrition and Health (A4NH).
Adeleke MT, Pillay M, Okoli BE (2004) The relationships between meiotic irregularities and fer-
tility in diploid and triploid Musa L.Cytologia 69:387–393
Aguilar Morán JF (2013) Improvement of Cavendish banana cultivars through conventional breed-
ing. Acta Hortic 986:205–208
van Asten PJA, Fermont AM, Taulya G (2011) Drought is a major yield loss factor for rainfed East
African highland banana. Agric Water Manag 98:541–552
7 Bananas andPlantains (Musa s pp.)
Bakry F (2008) Zygotic embryo rescue in bananas. Fruits 63:111–115
Bakry F, Carreel F, Jenny C, Horry JP (2009) Genetic improvement of banana. In: Jain SM,
Priyadarshan PM (eds) Breeding plantation tree crops: tropical species. Springer, NewYork,
Bhat KV, Jarret RL, Rana RS (1995) DNA proling of banana and plantain cultivars using random
amplied polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP)
markers. Electrophoresis 16:1736–1745
Carreel F, De Leon DG, Lagoda P etal (2002) Ascertaining maternal and paternal lineage within
Musa by chloroplast and mitochondrial DNA RFLP analyses. Genome 45:679–692
Christelová P, De Langhe E, Hřibová E et al (2017) Molecular and cytological characterization of
the global Musa germplasm collection provides insights into the treasure of banana diversity.
Biodivers Conserv 26:801–824
Creste S, Neto AT, Vencovsky R etal (2004) Genetic diversity of Musa diploid and triploid acces-
sions from the Brazilian banana breeding program estimated by microsatellite markers. Genet
Resour Crop Evol 51:723–733
Crossa J, de los Campos G, Pérez P etal (2010) Prediction of genetic values of quantitative traits
in plant breeding using pedigree and molecular markers. Genetics 186:713–724
Crouch JH, Crouch HK, Tenkouano A etal (1999) VNTR-based diversity analysis of 2x and 4x
full-sib Musa hybrids. Electron JBiotechnol 2:130–139
Crouch HK, Crouch JH, Madsen S etal (2000) Comparative analysis of phenotypic and genotypic
diversity among plantain landraces (Musa spp., AAB group). Theor Appl Genet 101:1056–1065
D’Hont A, Paget-Goy A, Escoute J et al (2000) The interspecic genome structure of culti-
vated banana, Musa spp. revealed by genomic DNA in situ hybridization. Theor Appl Genet
D’Hont A, Denoeud F, Aury JM etal (2012) The banana (Musa acuminata) genome and the evolu-
tion of monocotyledonous plants. Nature 488:213–217
Davey MW, Gudimella R, Harikrishna JA etal (2013) A draft Musa balbisiana genome sequence
for molecular genetics in polyploid, inter-and intra-specic Musa hybrids. BMC Genomics
De Langhe E (1986) Towards an international strategy for genetic improvement in the genus Musa.
In: Persley GJ, De Langhe EA (eds) Banana and plantain breeding strategies. Proceedings of an
International Workshop, Cairns, Australia. 1–17 October, 1986. INIBAP, Montpellier, p19–23
De Langhe E, Vrydaghs L, De Maret P etal (2009) Why bananas matter: an introduction to the
history of banana domestication. Ethnobot Res Appl 7:165–177
De Langhe E, Hribova E, Carpentier S etal (2010) Did backcrossing contribute to the origin of
hybrid edible bananas? Ann Bot 106:849–857
Deckers J, Tessera M, Alemu K, Abate T, Swennen R (2001) Ensete. In: Raemaekers RH (ed) Crop
production in tropical Africa. DGIC, Brussels, pp587–591
Dodds KS (1943) The genetic system of banana varieties in relation to banana breeding. Emp
JExp Agric 11:89–98
Dodds KS (1945) Genetical and cytological studies of Musa. VII.Certain aspects of polyploidy.
JGenet 46:161–179
Dumpe BB, Ortiz R (1996) Apparent male fertility in Musa germplasm. HortSci 31:1019–1022
Emediato FL, Nunes FA, Teixeira CC, Passos MA, Bertioli DJ, Pappas GJ, Miller RN (2009)
Characterization of resistance gene analogs in Musa acuminata cultivars contrasting in
resistance to biotic stresses. In: Shu QY (ed) Induced plant mutations in the genomics era.
FAO, Rome, pp443–445
FAO (2014) Banana market review and banana statistics 2012–2013, Rep. I3627E/1/01.14. FAO,
Fauré S, Noyer JL, Horry JP et al (1993) A molecular marker-based linkage map of diploid
bananas (Musa acuminata). Theor Appl Genet 87:517–526
Foolad MR (2007) Genome mapping and molecular breeding of tomato. Int JPlant Genomics
A. Brown et al.
Fortescue JA, Turner DW (2004) Pollen fertility in Musa: viability in cultivars grown in southern
Australia. Aust JAgric Res 55:1085–1091
Fortescue JA, Turner DW (2011) Reproductive biology. In: Pillay M, Tenkouano A (eds) Banana
breeding: constraints and progress. CRC Press, Boca Raton, pp305–331
Fortescue JA, Turner DW, Romero R (2011) Romero evidence that banana (Musa spp.), a tropi-
cal monocotyledon, has a facultative long-day response to photoperiod. Funct Plant Biol
Hayes B, Goddard M (2010) Genome-wide association and genomic selection in animal breeding.
Genome 53:876–883
Hippolyte I, Bakry F, Seguin M etal (2010) A saturated SSR/DArT linkage map of Musa acumi-
nata addressing genome rearrangements among bananas. BMC Plant Biol 10:65
Hippolyte I, Jenny C, Gardes L etal (2012) Foundation characteristics of edible Musa triploids
revealed from allelic distribution of SSR markers. Ann Bot 109:937–951
Iskra-Caruana M, Chabannes M, Duroy PO etal (2014) A possible scenario for the evolution of
banana streak virus in banana. Virus Res 186:155–162
Janssens SB, Vandelook F, De Langhe E etal (2016) Evolutionary dynamics and biogeography of
Musaceae reveal a correlation between the diversication of the banana family and the geologi-
cal and climatic history of Southeast Asia. New Phytol 210:1453–1465
Jarret RL, Vuylsteke DR, Gawel NJ et al (1993) Detecting genetic diversity in diploid bananas
using PCR and primers from a highly repetitive DNA sequence. Euphytica 68:69–76
Jones DR (ed) (1999) Diseases of banana, abaca’ and enset. CABI, Wallingford
Kaemmer D, Fischer D, Jarret RL etal (1997) Molecular breeding in the genus Musa: a strong case
for STMS marker technology. Euphytica 96:49–63
Karamura DA (1998) Numerical taxonomic studies of the East African highland (Musa AAA East
Africa) in Uganda. Dissertation, University of Reading
Karamura DA, Karamura EB, Tinzaara W (2012) In: Karamura DA, Karamura EB, Tinzaara W
(eds) The current classication and naming of the East African highland bananas (Musa AAA)
based on Morphological Characteristics in book: Banana cultivar Names, Synonyms and their
Usage. Bioversity International, East Africa, pp 6–23
Karamura D, Kitavi M, Nyine M etal (2016) Genotyping the local banana landrace groups of East
Africa. Acta Hortic 1114:67–74
Kitavi M, Downing T, Lorenzen Jetal (2016) The triploid East African Highland Banana (EAHB)
genepool is genetically uniform arising from a single ancestral clone that underwent population
expansion by vegetative propagation. Theor Appl Genet 129:547–561
Krishnamoorthy V, Kumar N (2005) Preliminary evaluation of diploid banana hybrids for yield
potential, male fertility and reaction to Radopholus similis. Plant Gen Res Newsl 141:39–43
Kumar LP, Selvarajan R, Iskra-Caruana M, Chabannes M, Hanna R (2015) Biology, etiology, and
control of virus diseases of banana and plantain. In: Loebenstein G, Katis NI (eds) Advances in
virus research, vol 91. Academic, Burlington, pp229–269
Lheureux F, Carreel F, Jenny C et al (2003) Identication of genetic markers linked to banana
streak disease expression in inter-specic Musa hybrids. Theor Appl Genet 106:594–598
Li C, Shao J, Wang Y etal (2013) Analysis of banana transcriptome and global gene expression
proles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxy-
sporum f. sp. Cubense. BMC Genomics 14:851
Lorenz AJ, Chao S, Franco G etal (2011) Chap. 2: Genomic selection in plant breeding: knowl-
edge and prospects. Adv Agron 110:77–123
Martin G, Baurens FC, Droc G etal (2016) Improvement of the banana “Musa acuminata” refer-
ence sequence using NGS data and semi-automated bioinformatics methods. BMC Genomics
Mbanjo EGN, Tchoumbougnang F, Mouelle AS etal (2012) Development of expressed sequence
tags-simple sequence repeats (EST-SSRs) for Musa and their applicability in authentication of
a Musa breeding population. Afric JBiotechnol 11:13546–13559
Meuwissen TH, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-
wide dense marker maps. Genetics 157:1819–1829
7 Bananas andPlantains (Musa s pp.)
Miller RNG, Bertioli DJ, Baurens FC etal (2008) Analysis of non-TIR NBS-LRR resistance gene
analogs in Musa acuminata Colla: isolation, RFLP marker development, and physical map-
ping. BMC Plant Biol 8:15
Noumbissié GB, Chabannes M, Bakry F etal (2016) Chromosome segregation in an allotetraploid
banana hybrid (AAAB) suggests a translocation between the A and B genomes and results in
eBSV-free offsprings. Mol Breed 36:1–14
Noyer JL, Causse S, Tomekpe K etal (2005) A new image of plantain diversity assessed by SSR,
AFLP and MSAP markers. Genetica 124:61–69
Nyine M, Pillay M (2011) The effect of banana breeding on the diversity of East African Highland
banana (Musa, AAA). Acta Hortic 897:225–229
Nyine M, Uwimana B, Swennen R, Batte M, Brown A, Hřibová E, Doležel J(2016) Genomic
breeding approaches for East African Bananas. In: Abstracts of the plant and animal genome
conference XXIV January 08–13, San Diego, CA
Opara UL, Jacobson D, Al-Saady NA (2010) Analysis of genetic diversity in banana cultivars
(Musa cvs.) from the South of Oman using AFLP markers and classication by phylogenetic,
hierarchical clustering and principal component analyses. JZhejiang Univ Sci B 11:332–341
Ortiz R (2000) Understanding the Musa genome: an update. Acta Hortic 54:157–168
Ortiz R (2013) Conventional banana and plantain breeding. Acta Hortic 986:77–194
Ortiz R (2015) Plant breeding in the omics era. Springer, NewYork
Ortiz R, Swennen R (2014) From crossbreeding to biotechnology-facilitated improvement of
banana and plantain. Biotechnol Adv 32:158–169
Ortiz R, Ferris RSB, Vuylsteke DR (1995) Banana and plantain breeding. In: Gowen S (ed)
Bananas and plantains. Springer, NewYork, pp110–146
Oselebe HO, Tenkuoano A, Pillay M etal (2006) Ploidy and genome segregation in Musa breeding
populations assessed by ow cytometry and randomly amplied polymorphic DNA markers.
JAm Soc Hortic 131:780–786
Panis B, Piette B, Swennen R (2005) Droplet vitrication of apical meristems: a cryopreservation
protocol applicable to all Musaceae. Plant Sci 168:45–55
Perrier X, De Langhe E, Donohue M, Lentfer C, Vrydaghs L, Bakry F, Carreel F, Hippolyte I,
Horry J-P, Jenny C, Lebot V, Risterucci A-M, Tomekpe K, Doutrelepont H, Ball T, Manwaring
J, de Maret P, Denham T (2011) Multidisciplinary perspectives on banana (Musa spp.) domes-
tication. PNAS 108:11311–11318
Pillay M, Ogundiwin E, Nwakanma DC etal (2001) Analysis of genetic diversity and relationships
in East African banana germplasm. Theor Appl Genet 102:965–970
Pillay M, Ude G, Kole C (eds) (2012) Genetics, genomics and breeding of bananas. CRC, Boca
Raboin LM, Carreel F, Noyer JL etal (2005) Diploid ancestors of triploid export banana culti-
vars: molecular identication of 2n restitution gamete donors and n gamete donors. Mol Breed
Risterucci AM, Hippolyte I, Perrier X etal (2009) Development and assessment of diversity arrays
technology for high-throughput DNA analyses in Musa. Theor Appl Genet 119:1093–1103
Roux NS (2001) Mutation induction in Musa. In: Jain SM, Swennen R (eds) Banana improvement:
cellular, molecular biology, and induced mutations. Science, Eneld
Rowe P, Rosale F (1993) Diploid breeding at FHIA and the development of Goldnger (FHIA-01).
InfoMusa 2:9–11
Sardos J, Rouard M, Hueber Y etal (2016) A genome-wide association study on the seedless phe-
notype in banana (Musa spp.) reveals the potential of a selected panel to detect candidate genes
in a vegetatively propagated crop. PLoS One 11:5
Sathiamoorthy S, Rao VNM (1980) Pollen production in relation to genome and ploidy in banana
clones. Proc Nat Semi Banana Prod. Tech., TNAU, Coimbatore, pp65–66
Shepherd K (1999) Cytogenetics of the genus Musa. International Network for the Improvement
of Banana and Plantain, Montpellier
A. Brown et al.
Silva PRO, de Jesus ON, Bragança CAD etal (2016) Development of a thematic collection of
Musa spp accessions using SCAR markers for preventive breeding against Fusarium oxyspo-
rum f. sp cubense tropical race 4. Genet Mol Res 15:5017765
Simmonds NW (1962) The evolution of the bananas. Longmans, London
Simmonds NW (1966) Bananas, 2nd edn. Longmans, London
Simmonds NW (1987) Classication and breeding of bananas. In: Persley G, De Langhe E (eds)
Banana and plantain breeding strategies. Proceedings of an International Workshop held at
Cairns Australia, 13–17 October 1986. Austrailian Centre for International Agricultural
Research, Canberra
Simmonds NW, Shepherd K (1955) The taxonomy and origins of the cultivated bananas. JLinn
Soc Lond Bot 55:302–312
Ssebuliba R, Vuylsteke D, Hartman Jet al (2000) Towards improving highland bananas. Uganda
JAgric Sci 5:36–38
Ssesuliba RN, Tenkouano A, Pillay M (2008) Male fertility and occurrence of 2n gametes in East
African highland bananas (Musa spp.) Euphytica 164:153–162
Stover RH, Buddenhagen IW (1986) Banana breeding: polyploidy, disease resistance and produc-
tivity. Fruits 41:175–191
Stover RH, Simmonds NW (1987) Bananas, Tropical agricultural series, 3rd edn. Longmans,
Swennen R, Vuylsteke D (1993) Breeding black Sigatoka resistant plantain with a wild banana.
Trop Agric 70:74–77
Tenkouano A, Swennen R (2004) Progress in breeding and delivering improved plantain and
banana to African farmers. Chron Hortic 44:9–15
Tenkouano A, Crouch JH, Crouch HK et al (1999) Comparison of DNA marker and pedigree-
based methods of genetic analysis of plantain and banana (Musa spp.) clones. I.Estimation of
genetic relationships. Theor Appl Genet 98:62–68
Tenkouano A, Vuylsteke D, Okoro Jetal (2003) Registration of TMB2x5105-1 and TMB2x9128-3
diploid banana hybrids with good combining ability, partial resistance to black Sigatoka and
resistance to nematodes. Hortscience 38:468–472
Tenkouano A, Pillay M, Ortiz R (2011) Breeding techniques. In: Pillay M, Tenkouano A (eds)
Banana breeding: constraints and progress. CRC Press, Boca Raton, pp181–202
Tenkouano A, Ortiz R, Vuylsteke D (2012) Estimating genetic effects in maternal and paternal
half-sibs from tetraploid-diploid crosses in Musa spp. Euphytica 185:295–301
Tripathi JN, Muwonge A, Tripathi L (2012) Efcient regeneration and transformation of plantain
cv. ‘Gonja manjaya’ (Musa spp. AAB) using embryogenic cell suspensions. In Vitro Cell Dev
Biol 48:216–224
Tsegaye A, Struik PC (2002) Analysis of enset (Ensete ventricosum) indigenous production meth-
ods and farm-based biodiversity in major enset-growing regions of southern Ethiopia. Explor
Agric 38:291–315
Tushemereirwe W, Batte M, Nyine M, Tumuhimbise R, Barekye A, Tendo S, Talengera D, Kubiriba
J, Lorenzen J, Swennen R, Uwimana B (2015) Performance of NARITA banana hybrids in the
preliminary yield trial for three cycles in Uganda. Banana Technical Report, 35p. www.musalit.
Ude G, Pillay M, Nwakanma D etal (2002) Genetic diversity in Musa acuminata Colla and Musa
balbisiana Colla and some of their natural hybrids using AFLP markers. Theor Appl Genet
Ude G, Pillay M, Ogundiwin E etal (2003) Genetic diversity in an African plantain core collection
using AFLP and RAPD markers. Theor Appl Genet 107:248–255
Uma S, Lakshmi S, Saraswathi MS etal (2011) Embryo rescue and plant regeneration in banana
(Musa spp.) plant cell. Tissue Organ Cult 105:105–111
Umber M, Pichaut JP, Farinas B etal (2016) Marker-assisted breeding of Musa balbisiana genitors
devoid of infectious endogenous banana streak virus sequences. Mol Breed 36:1–11
Vakili NG (1968) Responses of Musa acuminata species and edible cultivars to infection by
Mycosphaerella musicola. Trop Agric 45:13–22
7 Bananas andPlantains (Musa s pp.)
Valdez-Ojeda R, James-Kay A, Ku-Cauich JR etal (2014) Genetic relationships among a collec-
tion of Musa germplasm by uorescent-labeled SRAP.Tree Genet Genomic 10:465–476
Van den Houwe I, De Smet K, Tezenas de Montcel H etal (1995) Variability in storage potential
of banana shoot cultures under medium term storage conditions. Plant Cell Tissue Organ Cult
Vuylsteke D, Swennen R, Ortiz R (1993) Development and performance of Black Sigatoka-
resistant tetraploid hybrids of plantain (Musa spp., AAB group). Euphytica 65:33–42
Wairegi LWI, van Asten PJA, Tenywa MM etal (2010) Abiotic constraints override biotic con-
straints in East African highland banana systems. Field Crop Res 117:146–153
Wang XL, Chiang TY, Roux N et al (2007) Genetic diversity of wild banana (Musa balbisiana
Colla) in China as revealed by AFLP markers. Genet Resour Crop Evol 54:11251132
Wang W, Hu Y, Sun D etal (2012) Identication and evaluation of two diagnostic markers linked
to Fusarium wilt resistance (race 4) in banana (Musa spp.) Mol Biol Rep 39:451–459
Wei JY, Liu DB, Wei SX etal (2011) Analysis of genetic diversity in banana cultivars (Musa spp.)
using sequence-related amplied polymorphism markers. Acta Hortic 897:263–265
A. Brown et al.
... Banana weevils have been cited as one of the major factors that have caused production decline and disappearance of East African highland bananas (AAAh) in Central Uganda Gold et al., 1999) and in some littoral regions of Kagera in Tanzania (Mbwana and Rukazambuga, 1998). Therefore resistance to banana weevils is one of the breeding goals for the improvement of these two groups of bananas (Brown et al., 2017). ...
... This is a three-step process, first focusing on the improvement of the 2x parents from the wild genotypes to get rid of the non-domestication traits. Second, the improved 2x are crossed with triploid (3x) landraces to generate primary tetraploids (4x), and third, the primary 4x are further crossed with the improved 2x to generate secondary 3x hybrids which should combine parthenocarpy with high yield, resistance to pests and diseases, and fruit qualities comparable with those of the original landraces (Lorenzen et al., 2010;Ortiz and Swennen, 2014;Brown et al., 2017). Improved varieties have been developed through this method by a handful number of breeding programs (Tushemereirwe et al., 2015;Tumuhimbise et al., 2016;Dépigny et al., 2018;Tenkouano et al., 2019). ...
... However, the 4x "Monyet" plants in the collection at IITA Sendusu reveal no morphological features of the enlarged pseudostem and drooping leaves typical for 4x bananas. As a result of the 4x of "Monyet, " the progeny of "Monyet" × "Kokopo" was 96% 3x, as expected from a cross between 4x and 2x bananas (Brown et al., 2017). ...
Full-text available
The first step toward marker-assisted selection is linking the phenotypes to molecular markers through quantitative trait loci (QTL) analysis. While the process is straightforward in self-pollinating diploid (2x) species, QTL analysis in polyploids requires unconventional methods. In this study, we have identified markers associated with weevil Cosmopolites sordidus (Germar) resistance in bananas using 138 triploid (2n = 3x) hybrids derived from a cross between a tetraploid “Monyet” (2n = 4x) and a 2x “Kokopo” (2n = 2x) banana genotypes. The population was genotyped by Diversity Arrays Technology Sequencing (DArTSeq), resulting in 18,009 polymorphic single nucleotide polymorphisms (SNPs) between the two parents. Marker–trait association was carried out by continuous mapping where the adjusted trait means for the corm peripheral damage (PD) and total cross-section damage (TXD), both on the logit scale, were regressed on the marker allele frequencies. Forty-four SNPs that were associated with corm PD were identified on the chromosomes 5, 6, and 8, with 41 of them located on chromosome 6 and segregated in “Kokopo.” Eleven SNPs associated with corm total TXD were identified on chromosome 6 and segregated in “Monyet.” The additive effect of replacing one reference allele with the alternative allele was determined at each marker position. The PD QTL was confirmed using conventional QTL linkage analysis in the simplex markers segregating in “Kokopo” (AAAA × RA). We also identified 43 putative genes in the vicinity of the markers significantly associated with the two traits. The identified loci associated with resistance to weevil damage will be used in the efforts of developing molecular tools for marker-assisted breeding in bananas.
... The overall objective of breeding programs is to select, produce and deploy the best available genetically improved materials as efficiently, extensively and effectively as possible. Conventional breeding in Musa is mainly conducted through sexual hybridization by hand pollination; a laborious, often stressful, costly and time consuming process in which individual female and or male flowers are covered shortly before anthesis to prevent contamination by unwanted pollen [1]. At anthesis, pollen grains from male flowers are collected and brushed against female flowers (whose flowering duration is often less than a week) usually between 0700 and 1030 hours [2]. ...
... It is important therefore to examine if open pollination in Musa could also result in loss of productivity and inbreeding depression compared to hand pollination. According to Brown et al. [1] the limited progress that has been achieved in Musa breeding has occurred through crossbreeding approaches that involve hybridization followed by phenotypic selection among half sibs and/or full sib progenies. In order to effectively assess the true effects of hand and open pollination methods on Musa, this experiment set out to investigate how diploid and tetraploid progenies obtained from both pollination methods compared to each other and to their parental clones. ...
... Although nematicides, fungicides, pesticides, and other chemicals have been extensively used to manage diseases in bananas, they are potentially harmful to humans and toxic to non-target organisms, with detrimental effects on ecosystems (Rani et al. 2021;Wesseling et al. 2010). Concurrently, the breeding of disease-resistant and high-yielding banana varieties is highly restricted because of the parthenocarpic nature of banana plants, as well as differences in ploidy levels and relatively low fertility (Brown et al. 2017). Thus, a systematic, interdisciplinary, and holistic approach is necessary to improve the disease resistance of high-yielding banana varieties without affecting the existing ecosystems. ...
Bananas are the most produced and exported fresh fruit globally; but their sustainable production is always under threat owing to their vegetative reproduction method, in which plants are generated with nearly identical genetic compositions, making them vulnerable to multiple pathogens. To counteract such pathogens, bananas produce phenyl-phenalenones (PPs) as phytoalexins. PPs are cyclic diarylheptanoids with a tricyclic phenalene-1H-one nucleus attached to a phenyl ring that is produced specifically against multiple pathogens and insect pests in bananas. Since there are no comprehensive studies on banana PPs, the aim of this review was to provide a complete and exhaustive summary with multifaceted biological insights on them. The review begins with a brief description of the significance of banana production, the importance of PPs in banana improvement, and the general background of PPs. Further, we emphasize on the identification of PPs in different banana cultivars against various pathogens, elicitors, and tissues, followed by the antimicrobial activities of PPs against phytopathogens, PPs associated with human health promotion, and the putative biosynthesis pathway of PPs in bananas. PPs could be a potential target for improving the natural defense systems of bananas against multiple pathogens; however , the genes of the underlying biosynthesis pathway remain elusive. We therefore believe that this review will be insightful and potentially assist future studies to discover the genes contributing to PP biosynthesis in bananas and explore their applications in various fields. Keywords Phenylphenalenones Á Phytoalexins Á Banana Á Musaceae Abbreviations AKR Aldo-keto reductase A549 Human lung cell line BGH Banana genome hub CURS Curcumin synthase DAC Diels-alder cyclase DCS Diketidyl-CoA synthase Supplementary Information The online version contains supplementary material available at https://doi.().,-volV) (01234567 89().,-volV) Content courtesy of Springer Nature, terms of use apply. Rights reserved.
... Although nematicides, fungicides, pesticides, and other chemicals have been extensively used to manage diseases in bananas, they are potentially harmful to humans and toxic to non-target organisms, with detrimental effects on ecosystems (Rani et al. 2021;Wesseling et al. 2010). Concurrently, the breeding of disease-resistant and high-yielding banana varieties is highly restricted because of the parthenocarpic nature of banana plants, as well as differences in ploidy levels and relatively low fertility (Brown et al. 2017). Thus, a systematic, interdisciplinary, and holistic approach is necessary to improve the disease resistance of high-yielding banana varieties without affecting the existing ecosystems. ...
Full-text available
Bananas are the most produced and exported fresh fruit globally; but their sustainable production is always under threat owing to their vegetative reproduction method, in which plants are generated with nearly identical genetic compositions, making them vulnerable to multiple pathogens. To counteract such pathogens, bananas produce phenylphenalenones (PPs) as phytoalexins. PPs are cyclic diarylheptanoids with a tricyclic phenalene-1H-one nucleus attached to a phenyl ring that is produced specifically against multiple pathogens and insect pests in bananas. Since there are no comprehensive studies on banana PPs, the aim of this review was to provide a complete and exhaustive summary with multifaceted biological insights on them. The review begins with a brief description of the significance of banana production, the importance of PPs in banana improvement, and the general background of PPs. Further, we emphasize on the identification of PPs in different banana cultivars against various pathogens, elicitors, and tissues, followed by the antimicrobial activities of PPs against phytopathogens, PPs associated with human health promotion, and the putative biosynthesis pathway of PPs in bananas. PPs could be a potential target for improving the natural defense systems of bananas against multiple pathogens; however, the genes of the underlying biosynthesis pathway remain elusive. We therefore believe that this review will be insightful and potentially assist future studies to discover the genes contributing to PP biosynthesis in bananas and explore their applications in various fields.
... Next to in vitro collections, many institutes hold banana seed collections, such as the Plant Resources Center in Vietnam and the Millennium Seed Bank in Great Britain (Kallow et al. 2022). Banana seed storage can be a cost-efficient complementary method for the long-term conservation and distribution of banana genetic resources (Li and Pritchard 2009), but many issues remain unresolved regarding their collection, seed banking, and germination (Brown et al. 2017;Kallow et al. 2020b, a;Panis et al. 2020). ...
Full-text available
Collection and storage of crop wild relative (CWR) germplasm is crucial for preserving species genetic diversity and crop improvement. Nevertheless, much of the genetic variation of CWRs is absent in ex situ collections and detailed passport data are often lacking. Here, we focussed on Musa balbisiana, one of the two main progenitor species of many banana cultivars. We investigated the genetic structure of M. balbisiana across its distribution range using microsatellite markers. Accessions stored at the International Musa Germplasm Transit Centre (ITC) ex situ collection were compared with plant material collected from multiple countries and home gardens from Vietnam. Genetic structure analyses revealed that accessions could be divided into three main clusters. Vietnamese and Chinese populations were assigned to a first and second cluster respectively. A third cluster consisted of ITC and home garden accessions. Samples from Papua New Guinea were allocated to the cluster with Chinese populations but were assigned to a separate fourth cluster if the number of allowed clusters was set higher. Only one ITC accession grouped with native M. balbisiana populations and one group of ITC accessions was nearly genetically identical to home garden samples. This questioned their wild status, including accessions used as reference for wild M. balbisiana. Moreover, most ITC accessions and home garden samples were genetically distinct from wild populations. Our results highlight that additional germplasm should be collected from the native distribution range, especially from Northeast India, Myanmar, China, and the Philippines and stored for ex situ conservation at the ITC. The lack of passport data for many M. balbisiana accessions also complicates the interpretation of genetic information in relation to cultivation and historical dispersal routes.
... Next to in vitro collections, many institutes hold banana seed collections, such as the Plant Resources Center in Vietnam and the Millennium Seed Bank in Great Britain (Kallow et al. 2022). Banana seed storage can be a cost-efficient complementary method for the long-term conservation and distribution of banana genetic resources (Li and Pritchard 2009), but many issues remain unresolved regarding their collection, seed banking, and germination (Brown et al. 2017;Kallow et al. 2020b, a;Panis et al. 2020). ...
Full-text available
Collection and storage of crop wild relative (CWR) germplasm is crucial for preserving species genetic diversity and crop improvement. Nevertheless, much of the genetic variation of CWRs is absent in ex situ collections and detailed passport data are often lacking. Here, we focussed on Musa balbisiana, one of the two main progenitor species of many banana cultivars. We investigated the genetic structure of M. balbisiana across its distribution range using microsatellite markers. Accessions stored at the International Musa Germplasm Transit Centre (ITC) ex situ collection were compared with plant material collected from multiple countries and home gardens from Vietnam. Genetic structure analyses revealed that accessions could be divided into three main clusters. Vietnamese and Chinese populations were assigned to a first and second cluster respectively. A third cluster consisted of ITC and home garden accessions. Samples from Papua New Guinea were allocated to the cluster with Chinese populations but were assigned to a separate fourth cluster if the number of allowed clusters was set higher. Only one ITC accession grouped with native M. balbisiana populations and one group of ITC accessions was nearly genetically identical to home garden samples. This questioned their wild status, including accessions used as reference for wild M. balbisiana. Moreover, most ITC accessions and home garden samples were genetically distinct from wild populations. Our results highlight that additional germplasm should be collected from the native distribution range, especially from Northeast India, Myanmar, China, and the Philippines and stored for ex situ conservation at the ITC. The lack of passport data for many M. balbisiana accessions also complicates the interpretation of genetic information in relation to cultivation and historical dispersal routes. Supplementary information: The online version contains supplementary material available at 10.1007/s10722-022-01389-4.
... Bananas (Musa spp.) are important staple foods for people living in tropical and sub-tropical regions of the world (Brown et al., 2017); and have been part of the human diet since the start of history (Nelson et al., 2006), contributing significantly to food security (Oyeyinka and Afolayan, 2019). However, the prevalence of various cultivar names and synonyms in their different languages and dialects of a country or region is a common problem faced by banana taxonomists and horticulturists (Karamura et al., 2012;Valmayor et al., 2000). ...
The potential of unripe banana flour multi-elemental fingerprints for classifying banana genomic and sub-genomic groups was assessed using chemometrics. The elemental concentration of N, P, K, Mg, Ca, Zn, Cu, Mn, Fe, and B in unripe banana flour from 33 banana varieties belonging to four genome groups and 11 sub-genome groups were determined using Flame-atomic Absorption spectrometry and colorimetry. Principal component analysis (PCA) combined with linear discriminant analysis (LDA), support vector machine (SVM), and artificial neural network (ANN) was applied for classification with an 80:20 split between the calibration and verification sets (157 and 39 samples, respectively). The elements K, N, and Mg presented the highest mean concentrations of 1273 mg/100 g, 424 mg/100 g, and 132 mg/100 g, respectively. The classification model verification set samples were successfully classified based on their genome groups (100% accuracy) and sub-genome groups (78.95 to 100% accuracy) for PCA-LDA, PCA-ANN, and PCA-SVM models. The results demonstrate that multi-elemental fingerprinting combined with chemometrics can be employed as an effective and feasible method for classification of Musa genomic and sub-genomic groups.
... The banana is a herbaceous plant with three genera (Musa, Musella, and Ensete) that belong to the Musaceae family (Probojati et al., 2021). Musa acuminata and M. balbisiana are the main species that produce edible bananas (Brown et al., 2017). According to their ploidy, bananas are classified as diploid (AA and AB), triploid (AAA, AAB, and ABB), or tetraploid (AAAA, AAAB, and AABB; Amah et al., 2019). ...
Bananas (Musaceae) are one of the world's most common fruit crops and the oldest medicinal plants that are used to treat a variety of infections. There has been recent interest in elucidating the efficiency of the naturally active ingredients, particularly the antimicrobials, in this plant. This review begins with a short background of the banana plant and its cultivars as well as a brief description of its parts. Different experimental tests of the antimicrobial effects and the responsible bioactive compounds of the banana part extracts are then elaborated. A variety of recent and evolving applications of banana parts in the development of functional bakery, dairy, beverage, and meat products as a wheat substitute, fiber/prebiotic source, fat/sucrose substitute, and natural antioxidant are also discussed. Finally, the recent challenges and opportunities presented by different banana parts in creating bio‐packaging materials and bactericidal nanoparticles are addressed. This plant contains a variety of antimicrobial substances, including dopamine, gentisic acid, ferulic acid, lupeol, and 3‐carene. However, few studies have been conducted on its use as a bio‐preservative in food products; it should also be seen as a natural source of both antimicrobial and antioxidant agents. It offers a potentially simple eco‐friendly alternative to antibacterial and fungicidal agents rather than chemicals. Low cost, reliable methods for purifying these compounds from banana waste could be useful for food storage and creating more value‐added bio‐packaging products for perishable food goods.
Full-text available
East African banana ( Musa sp.) breeding efforts have focused mainly on enhancing ‘Matooke’ productivity through the development of high-yielding, pathogen-resistant cultivars with adequate stability to contribute to regional food security. Before a breeding program can recommend promising cultivars for release, they must pass the sensory screens; be evaluated in the target population environments; and the data analyzed for yield, adaptability, and stability. Twenty-four primary and secondary triploid hybrids [NARITA (N)] derived from ‘Matooke’ bananas, six triploid local ‘Matooke’ cultivars, and one exotic cultivar were evaluated for their yield, adaptability, and stability across the East African region at three highland sites in Uganda’s western and central regions, as well as at three sites in Tanzania’s northeastern and southern highlands regions, from 2016–19. A randomized complete block design with four replicates was used for multisite trials. The mixed-model restricted maximum likelihood/best linear unbiased prediction approach, along with additive main effect multiplicative interaction model biplots, were used to dissect and visualize genotype-by-environment patterns. Following the likelihood ratio test, both genotype and interaction effects were highly significant, confirming the influence of genotype and site heterogeneity for selecting specific and broadly adapted cultivars. N23 had the greatest yield across all sites associated with adaptability and stability, outperforming the overall mean yield of all genotypes by 34.2%. In Tanzania, N27 (second), N7 (third), N18 (fourth), N4 (fifth), N12 (sixth), and N13 (seventh); and in Uganda, N17 (second), N18 (third), N2 (fourth), N8 (fifth), N13 (sixth), N12 (seventh), N4 (eighth), and N24 (ninth) demonstrated good adaptability and stability, as well as high yield. Furthermore, the fungal pathogen Pseudocercospora fijiensis had no significant effect ( P > 0.05) on yield, stability, and adaptability of the hybrids. As a result, they can be introduced into areas where black leaf streak constrains banana production significantly and threatens farmers’ livelihoods. The average site yield potential ranged from 9.7 to 24.3 t⋅ha –1 per year. The best discriminating sites for testing breeding clones were Lyamungo in Tanzania and Sendusu in Uganda. Hence, these testing sites are recommended as ideal examples of locations for selecting superior genotypes.
Full-text available
Crop wild relatives (CWR) are an indispensable source of alleles to improve desired traits in related crops. While knowledge on the genetic diversity of CWR can facilitate breeding and conservation strategies, it has poorly been assessed. Cultivated bananas are a major part of the diet and income of hundreds of millions of people and can be considered as one of the most important fruits worldwide. Here, we assessed the genetic diversity and structure of Musa balbisiana , an important CWR of plantains, dessert and cooking bananas. Musa balbisiana has its origin in subtropical and tropical broadleaf forests of northern Indo-Burma. This includes a large part of northern Vietnam where until now, no populations have been sampled. We screened the genetic variation and structure present within and between 17 Vietnamese populations and six from China using 18 polymorphic SSR markers. Relatively high variation was found in populations from China and central Vietnam. Populations from northern Vietnam showed varying levels of genetic variation, with low variation in populations near the Red River. Low genetic variation was found in populations of southern Vietnam. Analyses of population structure revealed that populations of northern Vietnam formed a distinct genetic cluster from populations sampled in China. Together with populations of central Vietnam, populations from northern Vietnam could be subdivided into five clusters, likely caused by mountain ranges and connected river systems. We propose that populations sampled in central Vietnam and on the western side of the Hoang Lien Son mountain range in northern Vietnam belong to the native distribution area and should be prioritised for conservation. Southern range edge populations in central Vietnam had especially high genetic diversity, with a high number of unique alleles and might be connected with core populations in northern Laos and southwest China. Southern Vietnamese populations are considered imported and not native.
Full-text available
Bananas (Musa spp.) are an indispensable part of life in Eastern Africa providing up to one fifth of total calorie consumption per capita. Unlike many staple crops, bananas deliver food throughout the year, making them an ideal crop for household incomes, food and nutrition security. However, banana yields are low due to several factors amongst others pests and diseases: weevils and nematodes, Fusarium wilt, bacterial wilt and black Sigatoka. There are many potential technology-based interventions for increasing banana yields but host plant resistance is the most appropriate and cost effective intervention given the current stage of development of banana systems in the region. Host-plant resistance also offers significant spill over benefits for human health and positive environmental impacts. Therefore, the Ugandan National Agricultural Research Organization (NARO) and the International Institute of Tropical Agriculture (IITA) jointly breed bananas largely for host-plant resistance to improve banana yields. One of the most important current products of their joint banana breeding efforts is secondary triploid hybrids for food and juice herein referred to as NARITA hybrids. This name specifies the contribution of NARO and IITA. An earlier report (NARITA report 1) presented the results of 25 NARITA hybrids for cycles 1 and 2 combined. The current report presents and discusses the results of the same 25 NARITA hybrids (18 for food and seven for juice) evaluated for three crop cycles at Sendusu in central Uganda and analyzed in combined and separate forms. Results of individual NARITA hybrids within cycles showed high degree of variation for the traits assessed, implying a high potential for selection among the NARITA hybrids evaluated. For example, the bunch weight (BWT) of the individual NARITA hybrids ranged from as low as 5 kg for NARITA 19 to as high as 45 kg for NARITA 24 with a mean of 17.8 kg. Averaged across three cycles, BWT ranged from as low as 8.7 kg for NARITA 19 to as a high as 30.4 kg for NARITA 24. Ninety six per cent of the hybrids had a mean BWT greater than the mean of the local check (Mbwazirume) (11.0 kg). Similarly, NARITA hybrids were better than Mbwazirume for most of the other traits assessed. Eighty four per cent of the NARITA hybrids evaluated were better than the best founder parent (NFUUKA) for bunch yield (t ha-1), indicative of the significant breeding progress made by NARO and IITA in this breeding program. This could be confirmed by the positive better founder parent heterosis for BWT recorded by all NARITA hybrids, with NARITA 17, NARITA 18, NARITA 7 (M9), NARITA 21 and NARITA 14 (all food type) exhibiting highest heterosis. Results of combined analysis of variance (ANOVA) showed significant differences among the NARITA hybrids for all the 14 traits assessed including BWT. This indicated the potential for further selection and improvement of the NARITA hybrids for all the 14 traits. Additionally, results of combined ANOVA showed significant differences among three crop cycles for all the traits assessed except days to bunch maturity (DTM) and number of functional leaves at flowering (NFLF), indicating that the selection of banana hybrids could best be done at certain cycle numbers. The performance of NARITA hybrids for most traits was much higher at cycles 2 and 3 than at cycle 1 with the highest performance observed at cycle 3. However, the difference between cycle 2 and cycle 3 was not significantly different for most traits including BWT. The clear implication of this is that selection for banana hybrids should be done at cycle 2 to reduce costs involved in the management of trials since banana trials are always huge considering the size of bananas as well as spacing of 3 x 3 m or 2 x 3 m commonly used. Also, banana performance data analysis should not be based on a combined evaluation of cycle 1 and 2, as was previously done for NARITA report 1, but on an analysis of individual cycles, preferably cycle 2. The limitation of single site and single line plots is acknowledged. Hence, NARITA hybrids will be evaluated in larger and replicated multi-location trials to ascertain their actual performance, adaptability and stability in comparison with the local EAHB cultivars. Nevertheless, based on these preliminary results, potential high yielding banana hybrids combining resistance to black Sigatoka and farmer-preferred quality traits exist within this NARITA population.
Full-text available
Bananas (Musa spp.) are one of the main fruit crops grown worldwide. With the annual production reaching 144 million tons, their production represents an important contribution to the economies of many countries in Asia, Africa, Latin-America and Pacific Islands. Most importantly, bananas are a staple food for millions of people living in the tropics. Unfortunately, sustainable banana production is endangered by various diseases and pests, and the breeding for resistant cultivars relies on a far too small base of genetic variation. Greater diversity needs to be incorporated in breeding, especially of wild species. Such work requires a large and thoroughly characterized germplasm collection, which also is a safe depository of genetic diversity. The largest ex situ Musa germplasm collection is kept at the International Transit Centre (ITC) in Leuven (Belgium) and currently comprisesover 1500 accessions. This report summarizes the results of systematic cytological and molecular characterization of the Musa ITC collection. By December 2015, 630 accessions have been genotyped. The SSR markers confirmed the previous morphological based classification for 84% of ITC accessions analyzed. The remaining 16% of the genotyped entries may need field verification by taxonomist to decide if the unexpected classification by SSR genotyping was correct. The ploidy level estimation complements the molecular data. The genotyping continues for the entire ITC collection, including newly introduced accessions, to assure that the genotype of each accession is known in the largest global Musa gene bank.
Full-text available
Breeding new interspecific banana hybrid varieties relies on the use of Musa acuminata and M. balbisiana parents. Unfortunately, infectious alleles of endogenous Banana streak virus (eBSV) sequences are present in the genome of Musa balbisiana genitors. Upon activation by biotic and abiotic stresses, these infectious eBSVs lead to spontaneous infections by several species of Banana streak virus in interspecific hybrids harboring both Musa acuminata and M. balbisiana genomes. Here we provide evidence that seedy M. balbisiana diploids display diverse eBSV allelic combinations and that some eBSVs differ structurally from those previously reported. We also show that segregation of infectious and non-infectious eBSV alleles can be achieved in seedy M. balbisiana diploids through self-pollination or chromosome doubling of haploid lines. We report on the successful breeding of M. balbisiana diploid genitors devoid of all infectious eBSV alleles following self-pollination and on the potential of breeding additional M. balbisiana diploid genitors free of infectious eBSVs by crossing parents displaying complementary eBSV patterns. Our work paves the way to the safe use of M. balbisiana genitors for breeding banana interspecific hybrid varieties with no risk of activation of infectious eBSVs.
Full-text available
Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.
Full-text available
Crop landraces (largely resulting from adaptation and continuous selection by farmers) are more diverse within field populations than modern cultivars (produced by deliberate crossing), yet their distribution has continued to shrink in the past decades. The temporal dynamics of this shrinking is little known. The analysis of genetic variation within and between landraces is essential for making efficient breeding and conservation decisions with the available variability. Seven diploid landraces originally from Tanzania, 37 triploid landraces (24 East African highland bananas (EAHB); 5 'Ilalyi' (AAA genome), and 8 ill-defined types from Tanzania), 6 exotic triploids, and 3 exotic diploids originally from the International Transit Center were genotyped with simple sequence repeat (SSR) markers. This study sought to understand the genetic relationship between the EAHB and the diploid landraces and other banana groups (local triploid landraces, and introduced (exotic) cultivars) so as to decide whether to include the diploids in the breeding scheme of EAHB. Results showed the highest average genetic distance (degree of genomic difference by proportion) within the diploids (0.5666), followed by the hybrid triploids (0.4568) and the lowest within the 'Ilalyi' (0.0748) and the EAHB (0.0827) landraces. The variation within each clone set of EAHB was higher in 'Nakitembe' (0.0948) and 'Musakala' (0.1052). These two are commercial clone sets whose variation may be due to high and long-term selection pressure. In contrast, between the banana groups, the diploid landraces were more distant (highest average genetic distance) from the triploid landraces (0.4351-0.4430) and could thus provide useful breeding traits. On the other side, the triploid landraces had a narrow genetic base which should be broadened. Results did not identify those local east African diploids closest to the EAHB or other local triploids, although local diploids show breeding potential. This could widen the genetic base and probably improve performance of the triploid
Full-text available
Many banana cultivars (including the Plantain type) are triploid interspecific hybrids between Musa acuminata (A genome) and Musa balbisiana (B genome). M. balbisiana contains endogeneous Banana streak virus sequences (eBSVs) that can, in interspecific genome context, spontaneously release infectious viral genomes. We analyzed, a triploid progeny of 184 individuals from a cross between a tetraploid AAAB breeding accession (CRBP39) and the diploid AA accession (Pahang) with 38 SSR and eBSV-specific PCR markers. The results showed that (1) most of the alleles are found/transmitted in the expected frequency to the progeny with only 10 % biased; (2) 70 % of the loci displayed a tetrasomic allele segregation and (3) interspecific intrachromosomal recombinations occurred for all the chromosome segments surveyed. However, half of the offspring obtained resulted from maternal unbalanced gametes transmission. Analysis of gamete composition and marker association suggested the presence of a large translocation between A and B genome involving chromosome 1 and 3. The two infectious eBSVs present in the maternal parent CRBP39 are located on chromosome 1B and appeared in a higher proportion than expected in the progeny. Interestingly, we showed that both eBSVs were absent from 24 offspring that represent promising material for breeding.
Full-text available
Background Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata). Results We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of Musa acuminata. Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total Musa scaffold number from 7513 to 1532 (i.e. by 80 %), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5 % of the assembly was anchored to the 11 Musa chromosomes compared to the previous 70 %. Unknown sites (N) were reduced from 17.3 to 10.0 %. Conclusion The release of the Musa acuminata reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in other species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2579-4) contains supplementary material, which is available to authorized users.
Full-text available
Bananas are one of the most consumed fruits worldwide, but are affected by many pests and diseases. One of the most devastating diseases is Fusarium wilt, caused by Fusarium oxysporum f. sp cubense (Foc). Recently, Fusarium tropical race 4 (Foc TR4) has been causing irreparable damage, especially in Asia and Africa where it has devastated entire plantations, including areas with Cavendish, which is known to be resistant to Foc race 1. Although this race is not yet present in Brazil, results obtained by Embrapa in partnership with the University of Wageningen, The Netherlands, indicate that 100% of the cultivars used by Brazilian growers are susceptible to Foc TR 4. In our study, 276 banana accessions were screened with sequence characterized amplified region (SCAR) markers that have been linked to the resistance of Foc TR 4. Two SCAR primers were tested and the results revealed that SCAR ScaU1001 was efficient at discriminating accessions with possible resistance in 36.6% of the evaluated accessions. This is the first attempt to develop a thematic collection of possible Foc TR 4 resistant banana accessions in Brazil, which could be tested in Asian or African countries to validate marker-assisted selection (MAS), and for use in the preventive breeding of the crop to safeguard our banana plantations against Foc TR 4. We believe that this is an important step towards the prevention of this devastating disease, especially considering that our banana plantations are at risk.
The triploid plantain landrace Obino l’Ewai (Musa spp., AAB genome) has been crossed with a wild diploid banana (M. acuminata subsp. burmannica var. ‘Calcutta 4’, AA genome) to generate full-sib diploid and tetraploid hybrids combining good agronomic performance and disease resistance. Microsatellite marker analysis of the parental genotypes confirmed the highly heterozygous nature of both parental genotypes. Comparative analysis of 2x and 4x full-sib hybrids with their parental genotypes indicated that tetraploid hybrids are generally more closely related to Obino l’Ewai than their diploid full-sibs. Based on VNTR analysis it is possible to identify those hybrids, which may be most useful in subsequent breeding of secondary triploid hybrids. There was a significant (P