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Refinement of the collection of wild peas (Pisum L.) and search for the area of pea domestication with a deletion in the plastidic psbA-trnH spacer

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Olga Zaytseva at Genos Ltd.
Olga Zaytseva
V. S. Bogdanova
V. S. Bogdanova
V. S. Bogdanova
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Anatoli Mglinets at Institute of Cytology and Genetics, Russian Academy of Sciences
Anatoli Mglinets
Oleg Kosterin at Institute of Cytology and Genetics, Russian Academy of Sciences
Oleg Kosterin
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Abstract and Figures

The plastidic psbA-trnH spacer was sequenced in 78 accessions representing the genus Pisum L. A nucleotide substitution C64T in the spacer was found to be specific for Pisum abyssinicum A. Br.; a substitution T75G occurred in five accessions of the wild pea [Pisum sativum L. subsp. elatius (Bieb.) Schmalh.], one from France, three from Greece and one from Turkey, and also in a primitive landrace from Afghanistan with signs of contamination. A 7-bp tandem duplication was found in two P. sativum subsp. elatius accessions, from Turkey and Georgia. All (except for the probably contaminated Afghan accession) of the cultivated subspecies P. sativum L. subsp. sativum had a deletion of one copy of a tandem 8-bp repeat. The same deletion was found in two wild pea (P. sativum subsp. elatius) accessions, from Bulgaria and Georgia, belonging to the same earlier defined lineage B as the cultivated pea. They are supposed to represent the ancestral evolutionary lineage of the cultivated pea. It is noteworthy that accessions from the proposed Core Area of the Near East founder crop domestication in south-eastern Turkey do not have the deletion. Most of wild representatives of lineage B have a scarcely pigmented flower with almost non-opening standard, but those from Transcaucasia have a normal flower. The revealed area of co-existence of the earlier defined wild pea lineages A and B (differing in alleles of three molecular markers from different cellular genomes) was extended from Turkey to include Georgia and probably North Africa. Accessions claimed to represent wild peas were tested for spontaneous pod dehiscing and 14 of them were disproved as such. They are enriched with ‘recombinant’ marker combinations and most probably resulted from hybridisation of wild and cultivated peas, either in nature or while reproducing in germplasm collections.
Alignment of the variants of the psbA-trnH plastidic spacer sequence found among the studied pea accessions (Table 1): predominating in wild peas (from VIR320), with substituton C → T in position 64 found in P. abyssinicum (from VIR1876), with substitution T → G in position 75 (from JI261), with an insertion in positions 165-171 (P013) and with a deletion in positions 142-149 (VIR1851). Positions are numerated from the beginning of the spacer
Alignment of the variants of the psbA-trnH plastidic spacer sequence found among the studied pea accessions (Table 1): predominating in wild peas (from VIR320), with substituton C → T in position 64 found in P. abyssinicum (from VIR1876), with substitution T → G in position 75 (from JI261), with an insertion in positions 165-171 (P013) and with a deletion in positions 142-149 (VIR1851). Positions are numerated from the beginning of the spacer
… 
Locations of accessions of Pisum sativum subsp. elatius s.l. (embracing all wild represenatives of P. sativum) with (filled signs) and without (empty signs) the 8 bp deletion in the psbA-trnH plastidic spacer and with different combitaions of alleles of the plastidic rbcL, mitochondrial cox1 and nuclear SCA genes: A (squares), C (triangles), D (inverted triangles), B (circles) and unusual combinations (diamonds). Insert shows provenances of the accessions from Israel. Numerals are the number of accessions from the same area the exact locations of which cannot be resolved in this map scale. Accessions with too general provenance (‘Palestine’, ‘Anatolia’ etc.) not shown
Locations of accessions of Pisum sativum subsp. elatius s.l. (embracing all wild represenatives of P. sativum) with (filled signs) and without (empty signs) the 8 bp deletion in the psbA-trnH plastidic spacer and with different combitaions of alleles of the plastidic rbcL, mitochondrial cox1 and nuclear SCA genes: A (squares), C (triangles), D (inverted triangles), B (circles) and unusual combinations (diamonds). Insert shows provenances of the accessions from Israel. Numerals are the number of accessions from the same area the exact locations of which cannot be resolved in this map scale. Accessions with too general provenance (‘Palestine’, ‘Anatolia’ etc.) not shown
… 
Flowers of some wild pea (Pisum sativum subsp. elatius s.l.) accessions studied; their provenances and combinations of alleles of three molecular markers (in parenthesis) are as follows: a 711, Israel (A); b 714, Israel (A); c VIR2521, Israel (A); d JI254, ?Ethiopia (C); e 723, Israel (A); f JI3557, Portugal (C); g WG26109, Georgia (A); h P017, Turkey (B); i P012, Turkey (B); j CE1, Crimea (B); k JI1794 Israel (B); l WG10925, Bulgaria (B); m P015, Turkey (B); n VIR2998, Georgia (B). Not to scale
Flowers of some wild pea (Pisum sativum subsp. elatius s.l.) accessions studied; their provenances and combinations of alleles of three molecular markers (in parenthesis) are as follows: a 711, Israel (A); b 714, Israel (A); c VIR2521, Israel (A); d JI254, ?Ethiopia (C); e 723, Israel (A); f JI3557, Portugal (C); g WG26109, Georgia (A); h P017, Turkey (B); i P012, Turkey (B); j CE1, Crimea (B); k JI1794 Israel (B); l WG10925, Bulgaria (B); m P015, Turkey (B); n VIR2998, Georgia (B). Not to scale
… 
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RESEARCH ARTICLE
Refinement of the collection of wild peas (Pisum L.)
and search for the area of pea domestication with a deletion
in the plastidic psbA-trnH spacer
O. O. Zaytseva .V. S. Bogdanova .A. V. Mglinets .O. E. Kosterin
Received: 19 May 2016 / Accepted: 29 August 2016 / Published online: 14 September 2016
ÓSpringer Science+Business Media Dordrecht 2016
Abstract The plastidic psbA-trnH spacer was
sequenced in 78 accessions representing the genus
Pisum L. A nucleotide substitution C64T in the spacer
was found to be specific for Pisum abyssinicum A. Br.;
a substitution T75G occurred in five accessions of the
wild pea [Pisum sativum L. subsp. elatius (Bieb.)
Schmalh.], one from France, three from Greece and
one from Turkey, and also in a primitive landrace from
Afghanistan with signs of contamination. A 7-bp
tandem duplication was found in two P. sativum
subsp. elatius accessions, from Turkey and Georgia.
All (except for the probably contaminated Afghan
accession) of the cultivated subspecies P. sativum L.
subsp. sativum had a deletion of one copy of a tandem
8-bp repeat. The same deletion was found in two wild
pea (P. sativum subsp. elatius) accessions, from
Bulgaria and Georgia, belonging to the same earlier
defined lineage B as the cultivated pea. They are
supposed to represent the ancestral evolutionary
lineage of the cultivated pea. It is noteworthy that
accessions from the proposed Core Area of the Near
East founder crop domestication in south-eastern
Turkey do not have the deletion. Most of wild
representatives of lineage B have a scarcely pigmented
flower with almost non-opening standard, but those
from Transcaucasia have a normal flower. The
revealed area of co-existence of the earlier defined
wild pea lineages A and B (differing in alleles of three
molecular markers from different cellular genomes)
was extended from Turkey to include Georgia and
probably North Africa. Accessions claimed to repre-
sent wild peas were tested for spontaneous pod
dehiscing and 14 of them were disproved as such.
They are enriched with ‘recombinant’ marker combi-
nations and most probably resulted from hybridisation
of wild and cultivated peas, either in nature or while
reproducing in germplasm collections.
Keywords Near East Pea crop wild relatives
Phylogeography Pisum sativum Plant
domestication Plastid genome Wild peas
Introduction
Pea (Pisum sativum L.) is one of the seven so-called
‘founder crops’ thought to be simultaneously domes-
ticated in the Near East on the transition from hunting
and gathering to farming, the so-called ‘Neolithic
Revolution’. This revolution took place independently
in a number of regions of the world and was among
most important events in the human prehistory leading
O. O. Zaytseva V. S. Bogdanova A. V. Mglinets
O. E. Kosterin (&)
Institute of Cytology and Genetics of the Siberian Branch
of Russian Academy of Sciences, Acad. Lavrentyev ave.
10, Novosibirsk, Russia 630090
e-mail: kosterin@bionet.nsc.ru
O. O. Zaytseva O. E. Kosterin
Novosibirsk State University, Pirogova str. 2,
Novosibirsk, Russia 630090
123
Genet Resour Crop Evol (2017) 64:1417–1430
DOI 10.1007/s10722-016-0446-4
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
... In recent decades, genetic diversity and phylogeny of peas were in the focus of extensive studies using different approaches (for reviews see Smýkal et al. 2011, Kosterin 2016a, most of which involved wild peas (e.g. Ellis et al. 1998;Vershinin et al. 2003;Jing et al. 2007;Schaefer et al. 2012;Zaytseva et al. 2012;Smýkal et al. 2018a;Bogdanova et al. 2018Bogdanova et al. , 2021Kreplak et al. 2019 and many more) and some regarded wild pea phylogeography (Kosterin et al. 2010;Zaytseva et al. 2017;Smýkal et al. 2017;Hellwig et al. 2021a;Bogdanova et al. 2021;Shatskaya et al. 2023). ...
... Some of them will also be referenced if adding some valuable information. Representation of main regions of wild pea range in germplasm collections will be outlined in brief, together with some results of our greenhouse testing (Zaytseva et al. 2017 1 ;Bogdanova et al. 2021 1 I have to indicate the following errors found in Zaytseva et al. (2017): in Table I, "P. sativum subsp. ...
... elatius at Chefchaouen Town in Er-Rif Mts, which gave rise to accession CE23. Older germplasm available in world collections proved to represent wild peas (Zaytseva et al. 2017) is so far limited to two accessions, IG64350 (Algeria, Blida), IG108291 (Tunisia, Silyanah); both from the ICARDA collection The former locates to the Atlas-Blida Range, the latter to the Dorsal Range, both belonging to the coastal Tell-Atlas Mountain System. These two accessions appeared to belong to distant evolutionary lineages and the Tunisian accession belongs to that mostly occurring in Tauro-Caucasian area and Asia Minor (Zaytseva et al. 2017), so germplasm confusion, quite common in the ICARDA collection (P. ...
Natural range, habitats and populations of wild peas (Pisum L.)
Article
Full-text available
  • Feb 2023
  • GENET RESOUR CROP EV
The natural distributional ranges of pea crop wild relatives, confined to Pisum sativum L. subsp. elatius (M. Bieb.) Asch. & Graebn. sensu lato (alternatively Lathyrus oleraceus Lamarck subsp. biflorus (Rafin.) H. Schaefer, Coulot & Rabaute) and Pisum fulvum Sm. (alternatively Lathyrus fulvus (Sm.) Kosterin) are reconstructed as precise as possible from multiple regional floristic literature and internet resources. P. sativum subsp. elatius occupies the Mediterranean area in a broad sense and extends to Normandie and Moldova in the north, Kopet-Dagh Mts in the east and Djanet Oasis of Sahara in the south. P. fulvum is an East Mediterranean species ranging in Peloponnese, Crete, the East Aegean Islands, Cyprus, western and southern Anatolia, Lebanon, Syria, Jordan, Israel and Sinai Peninsula. Wild peas from North Africa, Greece and Iran are strongly underrepresented in germplasm collections. The ranges of both wild pea species were predicted to shrink in future because of the current climate change. P. sativum subsp. elatius in most of its range is confined to different versions of open oak or juniper forests or their derivatives in calcareous habitats but ecotypes confined to grassland and volcanic soils, as well as weedy ecotypes occurring in fields and plantations, are added in Levant and Turkey. P. fulvum prefers half-shaded woody, often stony habitats. Populations of P. sativum subsp. elatius are very small, dozens to hundreds of individuals, sparse to very rare, and occupy tiny areas. P. fulvum usually has larger populations and areas occupied by them. Both species exhibit seed dormancy, so that most individuals exist as seed bank in soil and litter. Because of their patchy nature, wild pea populations are quite homogeneous genetically, with scarce gene flow between them, making possible great inter-population diversity. At the same time, counter the common notion of the pea as a selfer, both wild pea taxa show high level of cross-pollination. Both species, but more P. sativum subsp. elatius, strongly suffer from ruminant grazing, and the latter taxon also from pea weevil. In situ protection of wild peas and investigation of their underestimated genetic diversity is of utmost importance. Special efforts are welcome to locate and investigate the enigmatic wild peas in Djanet Oasis in Sahara Desert (which could be the main reservoir of the genus still some 10,000 years ago), in subalpine communities of Georgia, and throughout Greece. Their search in the Asir Mts in Yemen would also be of some sense with respect to the problem of the origin of the cultivated taxon Pisum abyssinicum A. Braun (alternatively Lathyrus schaeferi Kosterin).
View
... In recent decades genetic diversity and phylogeny of peas were in the focus of extensive studies using different approaches (for reviews see Smýkal et al.2010, Kosterin 2015a, most of which involved wild peas (e.g. Ellis et al. 1998;Vershinin et al. 2003;Jing et al. 2007;Schaefer et al., 2012;Zaytseva et al. 2012;Smýkal et al. 2018a;Bogdanova et al. 2018Bogdanova et al. , 2021Kreplak et al. 2019 and many more) and some regarded wild pea phylogeography (Kosterin et al., 2010;Zaytseva et al., 2017;Smýkal et al. 2017;Hellwig et al. 2021a;Bogdanova et al., 2021). ...
... elatius at Chefchaouen Town in Er-Rif Mts, which gave rise to accession CE23. Older germplasm available in world collections proved to represent wild peas (Zaytseva et al., 2017) is so far limited to two accessions, IG64350 (Algeria, Blida), IG108291 (Tunisia, Silyanah); both from the ICARDA collection: the former locates to the Atlas-Blida Range, the latter to the Dorsal Range, both belonging to the coastal Tell-Atlas Mountain System. These two accessions appeared to belong to distant evolutionary lineages and the Tunisian accession belongs to that mostly occurring in Tauro-Caucasian area and Asia Minor (Zaytseva et al., 2017), so germplasm confusion in the ICARDA collection cannot be excluded (P. ...
... Older germplasm available in world collections proved to represent wild peas (Zaytseva et al., 2017) is so far limited to two accessions, IG64350 (Algeria, Blida), IG108291 (Tunisia, Silyanah); both from the ICARDA collection: the former locates to the Atlas-Blida Range, the latter to the Dorsal Range, both belonging to the coastal Tell-Atlas Mountain System. These two accessions appeared to belong to distant evolutionary lineages and the Tunisian accession belongs to that mostly occurring in Tauro-Caucasian area and Asia Minor (Zaytseva et al., 2017), so germplasm confusion in the ICARDA collection cannot be excluded (P. Smýkal, pers. ...
Natural range, habitats and populations of wild peas (Pisum L.)
Preprint
  • Oct 2022
The natural distributional ranges of pea crop wild relatives, confined to Pisum sativum subsp. elatius sensu lato (alternatively Lathyrus oleraceus subsp. biflorus) and Pisum fulvum (alternatively Lathyrus fulvus) are reconstructed as precise as possible from multiple regional floristic literature and internet resources. That of P. sativum subsp. elatius occupies the Mediterranean area in a broad sense and extends to Normandie and Moldova in the north, Kopet-Dagh Mts in the east and Djanet Oasis of Sahara in the south. P. fulvum is the East Mediterranean species ranging in Peloponnese, Crete, and the East Aegean Islands, Cyprus, western and southern Anatolia, Lebanon, Syria, Jordan, Israel and Sinai Peninsula. Wild peas from North Africa, Greece and Iran are strongly underrepresented in germplasm collections. The ranges of both wild pea taxa are predicted to shrink in future because of the current climate change. P. sativum subsp. elatius in most of its range is confined to different versions of open oak or juniper forests or their derivatives in calcareous habitats but ecotypes confined to grassland and volcanic soils, as well as weedy ecotypes occurring in fields and plantations, are added in Levant and Turkey. P. fulvum prefers half-shaded woody, often stony habitats. Populations of P. sativum subsp. elatius are very small, dozens to hundreds of individuals, sparse to very rare, and occupy tiny areas. P. fulvum usually has larger populations and areas occupied by them. Both species exhibit seed dormancy, so that most individuals exist as seed bank in soil and litter. Because of their patchy nature, wild pea populations are quite homogeneous genetically, with scarce gene flow between them, making possible great inter-population diversity. At the same time, counter the common notion of the pea as a selfer, both wild pea taxa show high level of cross-pollination. Both species, but more P. sativum subsp. elatius, strongly suffer from ruminant grazing, and the latter taxon also from pea weevil. In situ protection of wild peas and investigation of their underestimated genetic diversity is of utmost importance. Special efforts are welcome to locate and investigate the enigmatic wild peas in Djanet Oasis of Sahara (which could be the main reservoir of the genus still some ten thousand years ago), in subalpine communities of Georgia, and throughout Greece; their search in the Asir Mts in Yemen would also be of some sense with respect to the problem of the origin of the cultivated taxon Pisum abyssinicum (alternatively Lathyrus schaeferi).
View
... In addition, wild peas are a good model for studying microevolution, being annual plants with very small populations. However, wild peas are insufficiently studied, and their diversity is obscured by a number of circumstances: (i) taxonomic instability of the genus (Maxted and Ambrose, 2001;Rabaute, 2016, 2017), (ii) confusion of genuine wild plants with 'primitive', traditionally cultivated local landraces or feral cultivated peas, (iii) spontaneous crossing during reproduction in germplasm collections, (iv) confusion of labels and physical contamination of seeds in germplasm collections, (v) explicit or hidden duplication of accessions in different collections (Kosterin, 2016;Zaytseva et al., 2017), and (vi) depletion and extinction of wild pea populations due to deterioration of natural habitats (Maxted and Kell, 2009). These complications, especially (i) and (ii), hindered interpretation of the results of repeated phylogenetic and diversity analyses (Ellis et al., 1998;Vershinin et al., 2003;Jing et al., 2005Jing et al., , 2007Jing et al., , 2010Tar'an et al., 2005;Smýkal et al., 2017). ...
... The key feature of wild peas is dehiscing pods, which provide ballistic seed dispersal (Weeden, 2007;Ambrose and Ellis, 2008;Zaytseva et al., 2017). Plants with non-dehiscing pods cannot persist in nature, while plants with dehiscing pods cannot be harvested. ...
... These combinations were denoted A (rbcL with the restriction site for Hsp AI, cox1 with the restriction site for Psi I, and the fast SCA electromorph), C (differing from A by the absence of the Psi I recognition site in cox1) and B (the mentioned restriction sites missing both from rbcL and cox1, the slow SCA electromorph) (Kosterin and Bogdanova, 2008;Kosterin et al., 2010). From this point of view, we attempted a reconstruction of the phylogeography of wild peas (Kosterin et al., 2010;Zaytseva et al., 2017). Then we performed phylogenetic reconstruction based on the genes His5 and His7 of histone H1 subtypes 5 and 7, respectively, of which the former appeared to be a good phylogenetic marker (Zaytseva et al., 2012. ...
Discordant evolution of organellar genomes in peas (Pisum L.)
Article
  • Mar 2021
Plastids and mitochondria have their own small genomes, which do not undergo meiotic recombination and may have evolutionary fates different from each other and that of the nuclear genome. For the first time, we sequenced mitochondrial genomes of pea (Pisum L.) from 42 accessions mostly representing diverse wild germplasm from throughout the pea geographical range. Six structural types of the pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant, implying not less than six events of hybridisation between diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles could have been driven by plastid-nuclear incompatibility, which is known to be widespread in crosses involving wild peas and affects organellar inheritance. The topology of the phylogenetic tree based on nucleotide sequences of a nuclear gene, His5, encoding a histone H1 subtype, corresponded to the current taxonomy and resembled that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin, resulting from crosses of peas related to those presently inhabiting the southeastern and northeastern Mediterranean in a broad sense. These results highlight the roles of hybridisation and cytonuclear conflict in shaping plant microevolution.
View
... sativum) was among the founder crops domesticated in the Near East at the onset of the Neolithic revolution (Zohary and Hopf 2000) and continues to be an important crop of moderate latitudes, rich in protein and used as vegetable, grain, fodder and natural soil fertiliser. Importantly, there exist genuine wild populations of the same species, the natural range of which in Mediterranean and Anterior Asia extends from Portugal to Turkmenistan and from North Africa to Normandy and Hungary (Zaytseva et al. 2017;Coulot and Rabaute 2016;Kosterin 2017a). A number of names of different taxonomic rank were proposed for different wild peas, variably adopted as valid in different taxonomical systems. ...
... Importantly, wild representatives of P. sativum exhibit a great genetic diversity and belong to a number of evolutionary lineages, only one of which was involved into the Near East domestication to give rise to P. sativum subsp. sativum (Ellis et al. 1998;Vershinin et al. 2003;Jing et al. 2007Jing et al. , 2010; Kosterin and Bogdanova 2008;Kosterin et al. 2010;Zaytseva et al. 2012Zaytseva et al. , 2015Zaytseva et al. , 2017Bogdanova et al. 2018;Kreplak et al. 2019). This makes the 'wild subspecies' P. sativum subsp. ...
... Allele combinations A and B of three molecular markers from different cellular genomes, rbcL, cox1 and SCA, according to Kosterin and Bogdanova (2008) are indicated. Accessions with combination A represent the evolutionary 'lineage AC' in P. sativum, those with combination B represent the 'lineage B' in the sense of Zaytseva et al. (2015Zaytseva et al. ( , 2017. Some of their quantitative characteristics are provided in Table 2 along with those of F 1 hybrids. ...
Reciprocal compatibility within the genus Pisum L. as studied in F1 hybrids: 4. Crosses within P. sativum L. subsp. elatius (Bieb.) Aschers. et Graebn.
Article
Full-text available
  • Aug 2021
  • GENET RESOUR CROP EV
Five accessions representing divergent lineages of wild peas (Pisum sativum subsp. elatius) were crossed with each other in both directions and also artificially pollinated with own pollen, to evaluate reproductive barriers inside Pisum sativum which may be important for pea pre-breeding. The outcome of hybrid seeds was evaluated for each combination of crosses. Reciprocal classes of F1 hybrids were compared for pollen and seed fertility and quantitative traits including seed productivity, total biomass etc. Pollination of accession VIR320 with two accessions resulted in hybrids with drastically reduced leaves and pigmentation, resembling known cases of conflict of the nucleus and plastids. Four pairs of reciprocal F1 hybrids showed strong differences in male and female fertility, supposedly a milder manifestation of cytonuclear conflict. Male and female fertility of hybrids correlated with each other, the former appearing more convenient for evaluating genetic disturbance of gametogenesis. Only two hybrid classes showed fully fertile pollen. Some of the accessions studied have been previously reported to differ in a reciprocal translocation and their hybrids were expected to have half-sterile pollen. However accession VIR320 seems to ‘bridge’ both karyological classes showing relatively high pollen fertility in some crosses with representatives of both of them, the reasons for which is discussed. Generally, strong and usually asymmetric cases of incompatibility manifested in the drop of fertility were revealed and their pattern did not correlate with phylogenetic relatedness of the accessions. Hence, wild representatives of P. sativum can hardly be subdivided into natural biological taxa below species rank and their involvement in pea pre-breeding can be complicated by unexpected crossing barriers.
View
... The characteristic feature of wild peas is dehiscing pods, providing quick and distant seed dispersal (Zaytseva et al., 2017). It is hard for plants with nondehiscent pods to survive in the wild, and plants with dehiscing pods are hard to be harvested. ...
Unraveling Origin, History, Genetics, and Strategies for Accelerated Domestication and Diversification of Food Legumes
Article
Full-text available
  • Jul 2022
Domestication is a dynamic and ongoing process of transforming wild species into cultivated species by selecting desirable agricultural plant features to meet human needs such as taste, yield, storage, and cultivation practices. Human plant domestication began in the Fertile Crescent around 12,000 years ago and spread throughout the world, including China, Mesoamerica, the Andes and Near Oceania, Sub-Saharan Africa, and eastern North America. Indus valley civilizations have played a great role in the domestication of grain legumes. Crops, such as pigeon pea, black gram, green gram, lablab bean, moth bean, and horse gram, originated in the Indian subcontinent, and Neolithic archaeological records indicate that these crops were first domesticated by early civilizations in the region. The domestication and evolution of wild ancestors into today’s elite cultivars are important contributors to global food supply and agricultural crop improvement. In addition, food legumes contribute to food security by protecting human health and minimize climate change impacts. During the domestication process, legume crop species have undergone a severe genetic diversity loss, and only a very narrow range of variability is retained in the cultivars. Further reduction in genetic diversity occurred during seed dispersal and movement across the continents. In general, only a few traits, such as shattering resistance, seed dormancy loss, stem growth behavior, flowering–maturity period, and yield traits, have prominence in the domestication process across the species. Thus, identification and knowledge of domestication responsive loci were often useful in accelerating new species’ domestication. The genes and metabolic pathways responsible for the significant alterations that occurred as an outcome of domestication might aid in the quick domestication of novel crops. Further, recent advances in “omics” sciences, gene-editing technologies, and functional analysis will accelerate the domestication and crop improvement of new crop species without losing much genetic diversity. In this review, we have discussed about the origin, center of diversity, and seed movement of major food legumes, which will be useful in the exploration and utilization of genetic diversity in crop improvement. Further, we have discussed about the major genes/QTLs associated with the domestication syndrome in pulse crops and the future strategies to improve the food legume crops.
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... Based on this, different combinations (A, B and C) of alleles of the three mentioned dimorphic marker genes SCA, rbcL and cox1 from different cellular genomes, respectively nuclear, plastid and mitochon drial, were proposed for a simple classification of evolutionary lineages of the wild pea subspecies P. sativum subsp. elatius (Kosterin, Bogdanova, 2008;Kosterin et al., 2010), which was then used repeatedly (Zaytseva et al., 2012(Zaytseva et al., , 2015(Zaytseva et al., , 2017Bogdanova et al., 2021). So, the electromorphs of SCA appeared to be useful in the studies of genetic diversity of the pea crop wild relatives, which are important for the involvement of their potentially useful ge netic resources into breeding (Ali et al., 1994;Maxted, Kell, 2009;Coyne et al., 2011;Ford-Lloyd et al., 2011;Maxted et al., 2012). ...
Identification of the gene coding for seed cotyledon albumin SCA in the pea (Pisum L.) genome
Article
Full-text available
  • Jul 2022
Albumins SCA and SAA are short, highly hydrophilic proteins accumulated in large quantities in the cotyledons and seed axes, respectively, of a dry pea ( Pisum sativum L.) seed. SCA was earlier shown to have two allelic variants differing in mobility in polyacrylamide gel electrophoresis in acid medium. Using them, the corresponding gene SCA was mapped on Linkage Group V. This protein was used as a useful genetic and phylogeographical marker, which still required electrophoretic analysis of the protein while the DNA sequence of the corresponding SCA gene remained unknown. Based on the length, the positive charge under acidic conditions and the number of lysine residues of SCA and SAA albumins, estimated earlier electrophoretically, the data available in public databases were searched for candidates for the SCA gene among coding sequences residing in the region of the pea genome which, taking into account the synteny of the pea and Medicago truncatula genomes, corresponds to the map position of SCA . Then we sequenced them in a number of pea accessions. Concordance of the earlier electrophoretic data and sequence variation indicated the sequence Psat0s797g0160 of the reference pea genome to be the SCA gene. The sequence Psat0s797g0240 could encode a minor related albumin SA-a2, while a candidate gene for albumin SAA is still missing (as well as electrophoretic variation of both latter albumins). DNA amplification using original primers SCA1_3f and SCA1_3r from genomic DNA and restriction by endonuclease Hind II made it possible to distinguish the SCA alleles coding for protein products with different charges without sequencing the gene. Thus, the gene encoding the highly hydrophilic albumin SCA accumulated in pea seeds, the alleles of which are useful for classification of pea wild relatives, has now been identified in the pea genome and a convenient CAPS marker has been developed on its basis.
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Multiple Origin of Organellar Genomes of Cultivated Pea (Pisum Sativum L. Subsp. Sativum)
Preprint
  • Apr 2024
Plant domestication is a matter of hot debates. Earlier we found that pea cultivar Cameor had plastid and mitochondrial genomes related to wild peas of different provenance. We sequenced complete plastid and mitochondrial genomes from 27 accessions to compile a sample of 91 peas including 26 landraces of traditional cultivation. The vast majority of plastid genomes of cultivated peas tightly clustered and was most closely related to wild peas from Ponto-Caspian area. However, two accessions from Central Asia showed affinity to a different wild pea lineage. Mitochondrial genomes of most cultivated peas were found in three clusters. Accessions most related to wild peas from the domestication ‘Core Area’ originated from periphery of traditional pea cultivation: Africa, Central Asia and Himalaya. Another cluster was present in Central Asia and Greece. Accessions most related to the European cultivar Cameor were found throughout the pea cultivation range. We hypothesise that the pea cultivation area, initially occupied by peas domesticated in the ‘Core Area’, underwent two subsequent waves of invasion of cultivated peas with mitochondria introgressed from wild peas: the first from South-East Europe and/or West Asia and the second from Europe. Mitochondrial genomes were supposed to introgress readily from wild to cultivated peas.
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New Insights into Plastid and Mitochondria Evolution in Wild Peas (Pisum L.)
Article
Full-text available
  • Feb 2023
  • Diversity
Plastids and mitochondria are organelles of plant cells with small genomes, which may exhibit discordant microevolution as we earlier revealed in pea crop wild relatives. We sequenced 22 plastid and mitochondrial genomes of Pisum sativum subsp. elatius and Pisum fulvum using Illumina platform, so that the updated sample comprised 64 accessions. Most wild peas from continental southern Europe and a single specimen from Morocco were found to share the same organellar genome constitution; four others, presumably hybrid constitutions, were revealed in Mediterranean islands and Athos Peninsula. A mitochondrial genome closely related to that of Pisum abyssinicum, from Yemen and Ethiopia, was unexpectedly found in an accession of P. sativum subsp. elatius from Israel, their plastid genomes being unrelated. Phylogenetic reconstructions based on plastid and mitochondrial genomes revealed different sets of wild peas to be most related to cultivated P. sativum subsp. sativum, making its wild progenitor and its origin area enigmatic. An accession of P. fulvum representing ‘fulvum-b’ branch, according to a nuclear marker, appeared in the same branch as other fulvum accessions in organellar trees. The results stress the complicated evolution and structure of genetic diversity of pea crop wild relatives.
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Archaeoentomological assessment of weevil (Coleoptera, Bruchidae) infestation level of pea (Pisum sativum) at the Late Bronze Age settlement Hissar
Article
Full-text available
  • Jan 2021
A find of 2572 charred seeds of pea (Pisum sativum L.) was detected at the Late Bronze Age tell settlement Hissar near Leskovac, in Serbia, belonging to the Brnjica cultural group, 14-10 cent. BC. Two types of pea seeds were observed: apparently healthy seeds and seeds damaged by the activity of a weevil (Coleoptera, Bruchidae). At least two-fifths of all finds have apparently been infested most probably by pea weevil (Bruchus pisorum L.), one of the most important pea pests worldwide, especially in medium-moist and dry climates, such as Southern Europe and Australia. A large amount of infested pea seeds indicates a developed pea production on small plots, strongly indicating that cultivating this ancient pulse crop must have been well-rooted in field conditions. Previous DNA analyses of charred pea placed the ancient Hissar pea at an intermediate position between extantly cultivated pea (P. sativum L. subsp. sativum var. sativum) and a wild, winter hardy, 'tall' pea (P. sativum subsp. elatius (Steven ex M. Bieb.) Asch. et Graebn.). Based on an assumption of its late harvest time and combined with pea weevil life cycle stage in charred seeds, it was possible to estimate the season during which the seeds were carbonized, namely, the second half of July or the first days of August at the latest. Older, final weevil instars were predominant before seed carbonization. The pea infestation rate at Hissar is one of the highest noted among pulses in the Old World and the highest among peas, so far.
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Characterization of variability of the intergenic spacers cpDNA trnH–psbA, trnY–trnT AND rpoB–trnC in representatives of Pisum L. (Tribe Fabeae)
Article
  • Jan 2021
Background. Plant chloroplast genome have conservative structure, but its nucleotide sequence is polymorphous due to which cpDNA fragments are often used in taxonomic and phylogenetic studies. Despite the widespread distribution and use of Fabeae species, mainly peas (Pisum), data on the intraspecific diversity of cpDNA fragments are almost absent. The aim of the work was to analyze the intraspecific variability of three cpDNA spacers in Pisum. Materials and methods. As a result of the work, intergenic spacers trnYtrnT, trnHpsbA and rpoBtrnC in 38 accessions of the Pisum and related Fabeae species were sequenced. Despite the fact that the selected chloroplast fragments are generally considered to be sufficiently variable in plants and are often used for phylogenetic studies, Pisum accessions have been found to have no intraspecific differences in two of the three spacers sequences analyzed. Results and conclusion. A total 97 SNPs were detected in Pisum accessions, seven of them distinguished P. sativum from P. fulvum. The most variable of the analyzed fragments was the intergenic spacer rpoBtrnC. Based on rpoBtrnC sequence 17 haplotypes in P. sativum and four haplotypes in P. fulvum were revealed. The cpDNA sequencing data were used for a phylogenetic analysis. On the obtained tree Vavilovia formosa accession formed a separate branch from pea accessions. All Pisum accessions fall in one cluster, split into distinct P. sativum and P. fulvum subclusters (BI = 99%).
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The "when", the "where" and the "why" of the Neolithic revolution in the Levant
Article
Full-text available
  • Dec 2001
An accumulation of data concerning the domestication of plants and the refinement of research questions in the last decade have enabled us a new look at the Neolithic Revolution and Neolithization processes in the Levant. This paper raises some points concerning the “When” and “Where” of plant domestication and suggests that the origins of plant domestication were in a welldefined region in southeast Turkey and north Syria. It presents a view on the process of Neolithization in the Levant and offers some comments concerning the background and motivations behind the Neolithic Revolution.
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Nuclear-Cytoplasmic Conflict in Pea (Pisum sativum L.) Is Associated with Nuclear and Plastidic Candidate Genes Encoding Acetyl-CoA Carboxylase Subunits
Article
Full-text available
In crosses of wild and cultivated peas (Pisum sativum L.), nuclear-cytoplasmic incompatibility frequently occurs manifested as decreased pollen fertility, male gametophyte lethality, sporophyte lethality. High-throughput sequencing of plastid genomes of one cultivated and four wild pea accessions differing in cross-compatibility was performed. Candidate genes for involvement in the nuclear-plastid conflict were searched in the reconstructed plastid genomes. In the annotated Medicago truncatula genome, nuclear candidate genes were searched in the portion syntenic to the pea chromosome region known to harbor a locus involved in the conflict. In the plastid genomes, a substantial variability of the accD locus represented by nucleotide substitutions and indels was found to correspond to the pattern of cross-compatibility among the accessions analyzed. Amino acid substitutions in the polypeptides encoded by the alleles of a nuclear locus, designated as Bccp3, with a complementary function to accD, fitted the compatibility pattern. The accD locus in the plastid genome encoding beta subunit of the carboxyltransferase of acetyl-coA carboxylase and the nuclear locus Bccp3 encoding biotin carboxyl carrier protein of the same multi-subunit enzyme were nominated as candidate genes for main contribution to nuclear-cytoplasmic incompatibility in peas. Existence of another nuclear locus involved in the accD-mediated conflict is hypothesized.
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MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
Article
Full-text available
  • Oct 2013
  • MOL BIOL EVOL
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements our RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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Plant Domestication and Crop Evolution in the Near East: On Events and Processes
Article
Full-text available
  • May 2012
Reconstructing the evolutionary history of crop plants is fundamental for understanding their adaptation profile and the genetic basis of yield-limiting factors, which in turn are critical for future crop improvement. A major topic in this field is the recent claim for a millennia-long ‘protracted’ domestication process. Here we evaluate the evidence for the protracted domestication model in light of published archaeobotanical data, experimental evidence and the biology of the Near Eastern crops and their wild progenitors. The crux of our discussion is the differentiation between events or ‘domestication episodes’ and the later following crop evolutionary processes under domestication (frequently termed ‘crop improvement stage’), which are by definition, still ongoing. We argue that by assuming a protracted millennia-long domestication process, one needlessly opts to operate within an intellectual framework that does not allow differentiating between the decisive (critical) domestication traits and their respective loci, and those that have evolved later during the crop dissemination and improvement following the episodic domestication event. Therefore, in our view, apart from the lack of experimental evidence to support it, the protracted domestication assumption undermines the resolution power of the study of both plant domestication and crop evolution, from the cultural as well as from the biological perspectives.
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Peas (Pisum L.)
Chapter
  • Jan 2001
The garden or field pea is cultivated worldwide in temperate climates, but Pisum sativum L. is naturally found in Europe, north-west Asia and extending south to temperate east Africa, while P. fulvum Sibth. and Sm. is restricted to the Middle East. The pea has been cultivated for millennia, possibly because of the low levels of toxins in the seed (Liener, 1982) and the relatively high protein content of 25% (Monti 1983). Peas remain today one of the most important temperate pulse, fodder and vegetable crops. Garden peas (P. sativum var. sativum) are produced primarily for human consumption, field peas (P. sativum var. arvense (L.) Poiret) for livestock and traditionally as green manure. The pods are also eaten immature as a vegetable (e.g. mangetout, sugar snap peas or snow peas). In a number of developed countries, a significant proportion of the crop is now harvested in an immature state and frozen to make a convenience food.
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The Biosystematics and Domestication of Peas (Pisum L.)
Article
  • Nov 1975
Morphological, archaeological, cytogenetic and phytochemical data pertaining to species differentiation and the selection of cultivated varieties in the genus Pisum are discussed. The albumin and globulin electrophoretic patterns of 7 wild genotypes, including material of P. elatius Bieb., P. humile Boiss & Noë, and P. fulvum Sibth. & Sm., and of 32 primitive and modern cultivars of P. sativum L. indicate little phytochemical differentiation between and among taxa at the seed-protein level. This is consistent with the interpretation that Pisum consists of two biological species, the orange-yellow flowered P. fulvum and an aggregate P. sativum which includes wild genotypes of P. elatius and P. humile as well as cultivars. Artificial selection for smooth testa, for pod indehiscence, or for genotypes homozygous for the alleles af; af, tl; or tl, did not appear to alter the albumin and globulin protein patterns.
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Cultivation and domestication had multiple origins: Arguments against the core area hypothesis for the origins of agriculture in the Near East
Article
  • Dec 2011
  • World Archaeol
This paper debates claims that plant domestication occurred rapidly in a single restricted sub-section of the Near Eastern Fertile Crescent. Instead we argue for numerous parallel processes of domestication across the region in the Early Holocene. While a previous generation of genetic results seemed to support a single ‘core area’, the accumulation of genetic evidence and refinements in methods undermine this, pointing increasingly towards multiple geographical origins. We stress that it is important to recognize that modern germplasm collections are an imperfect sample of the diversity of wild and cultivated populations of the past, which included some extinct lineages. We briefly synthesize the accumulated data from archaeobotany, defending the reliability of archaeological science to inform us about the past plant populations used by people. These data indicate an extended period of pre-domestication cultivation of at least a millennium and the slow evolution of morphological domestication adaptations in crop plants. The appearance of early cultivars and domesticates was spread piecemeal around the Near East, and a whole crop package is not evident. The ‘core area’ claimed by some authors has no better claim for primacy or completeness in comparison to other parts of the Near East. Evidence from zooarchaeology similarly points towards a diffuse appearance of various domesticated animals. The ‘non-centric’ appearance of domesticates from the Near East is therefore similar to the emerging evidence from many other regions of the world where plants were domesticated. We develop a hypothesis of why this should be expected given that anatomically modern human ancestors shared practices of vegetation management and planting, the necessary background knowledge for cultivation. Cultivation then was not a rare discovery but was a strategic and systematic shift in economies. The question then becomes why it was developed in the particular regions and periods where it appeared.
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