A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome.
ABSTRACT Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly.
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ABSTRACT: BACKGROUND: Cotton fiber length is very important to the quality of textiles. Understanding the genetics and physiology of cotton fiber elongation can provide valuable tools to the cotton industry by targeting genes or other molecules responsible for fiber elongation. Ligon Lintless-1 (Li1) is a monogenic mutant in Upland cotton (Gossypium hirsutum) which exhibits an early cessation of fiber elongation resulting in very short fibers (< 6mm) at maturity. This presents an excellent model system for studying the underlying molecular and cellular processes involved with cotton fiber elongation. Previous reports have characterized Li1 at early cell wall elongation and during later secondary cell wall synthesis, however there has been very limited analysis of the transition period between these developmental time points. RESULTS: Physical and morphological measurements of the Li1 mutant fibers were conducted, including measurement of the cellulose content during development. Affymetrix microarrays were used to analyze transcript profiles at the critical developmental time points of 3 days post anthesis (DPA), the late elongation stage of 12 DPA and the early secondary cell wall synthesis stage of 16 DPA. The results indicated severe disruption to key hormonal and other pathways related to fiber development, especially pertaining to the transition stage from elongation to secondary cell wall synthesis. Gene Ontology enrichment analysis identified several key pathways at the transition stage that exhibited altered regulation. Genes involved in ethylene biosynthesis and primary cell wall rearrangement were affected, and a primary cell wall-related cellulose synthase was transcriptionally repressed. Linkage mapping using a population of 2,553 F2 individuals identified SSR markers associated with the Li1 genetic locus on chromosome 22. Linkage mapping in combination with utilizing the diploid G. raimondii genome sequences permitted additional analysis of the region containing the Li1 gene. CONCLUSIONS: The early termination of fiber elongation in the Li1 mutant is likely controlled by an early upstream regulatory factor resulting in the altered regulation of hundreds of downstream genes. Several elongation-related genes that exhibited altered expression profiles in the Li1 mutant were identified. Molecular markers closely associated with the Li1 locus were developed. Results presented here will lay the foundation for further investigation of the genetic and molecular mechanisms of fiber elongation.BMC Genomics 06/2013; 14(1):403. · 4.40 Impact Factor
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ABSTRACT: Molecular markers such as simple sequence repeats (SSR) are a useful tool for characterizing genetic diversity of Gossypium germplasm. Genetic profiles by DNA fingerprinting of cotton accessions can only be compared among different collections if a common set of molecular markers are used by different laboratories and/or research projects. Herein, we propose and report a core set of 105 SSR markers with wide genome coverage of at least four evenly distributed markers per chromosome for the 26 tetraploid cotton chromosomes. The core marker set represents the efforts of ten research groups involved in marker development, and have been systematically evaluated for DNA polymorphism on the 12 genotypes belonging to six Gossypium species [known collectively as the cotton marker database (CMD) panel]. A total of 35 marker bins in triplex sets were arranged from the 105 markers that were each labeled with one of the three fluorescent dyes (FAM, HEX, and NED). Results from this study indicated that the core marker set was robust in revealing DNA polymorphism either between and within species. Average value of polymorphism information content (PIC) among the CMD panel was 0.65, and that within the cultivated cotton species Gossypium hirsutum was 0.29. Based on the similarity matrix and phylogenetic analysis of the CMD panel, the core marker set appeared to be sufficient in characterizing the diversity within G. hirsutum and other Gossypium species. The portability of this core marker set would facilitate the systematic characterization and the simultaneous comparison among various research efforts involved in genetic diversity analysis and germplasm resource preservation.Euphytica 08/2012; 187(2):203-213. · 1.64 Impact Factor
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ABSTRACT: To better understand the genetic diversity of the cultivated Upland cotton (Gossypium hirsutum L.) and its structure at the molecular level, 193 Upland cotton cultivars collected from 26 countries were genotyped using 448 microsatellite markers. These markers were selected based on their mapping positions in the high density G. hirsutum TM-1 × G. barbadense 3-79 map, and they covered the whole genome. In addition, the physical locations of these markers were also partially identified based on the reference sequence of the diploid G. raimondii (D5) genome. The marker orders in the genetic map were largely in agreement with their orders in the physical map. These markers revealed 1,590 alleles belonging to 732 loci. Analysis of unique marker allele numbers indicated that the modern US Upland cotton had been losing its genetic diversity during the past century. Linkage disequilibrium (LD) between marker pairs was clearly un-even among chromosomes, and among regions within a chromosome. The average size of a LD block was 6.75 cM at r 2 = 0.10. A neighbor-joining phylogenic tree of these cultivars was generated using marker allele frequencies based on Nei’s genetic distance. The cultivars were grouped into 15 groups according to the phylogenic tree. Grouping results were largely congruent with the breeding history and pedigrees of the cultivars with a few exceptions.Euphytica 191(3). · 1.64 Impact Factor
A High-Density Simple Sequence Repeat and Single
Nucleotide Polymorphism Genetic Map of the
Tetraploid Cotton Genome
John Z. Yu,*,1Russell J. Kohel,* David D. Fang,†Jaemin Cho,* Allen Van Deynze,‡Mauricio Ulloa,§
Steven M. Hoffman,*,** Alan E. Pepper,** David M. Stelly,††Johnie N. Jenkins,‡‡Sukumar Saha,‡‡
Siva P. Kumpatla,§§Manali R. Shah,§§William V. Hugie,*** and Richard G. Percy*
*USDA–ARS, Southern Plains Agricultural Research Center, College Station, Texas 77845,†USDA–ARS, Cotton Fiber
Bioscience Research Unit, Southern Regional Research Center, New Orleans, Louisiana 70124,‡Seed Biotechnology
Center, University of California, Davis, California 95616,§USDA–ARS, WICSRU, Shafter Cotton Research Station, Shafter,
California 93263,**Department of Biology and††Department of Soil and Crop Sciences, Texas A&M University, College
Station, Texas 77843,‡‡USDA–ARS, Genetics and Precision Agriculture Research Unit, Starkville, Mississippi 39762,
§§Dow AgroSciences LLC, Indianapolis, Indiana 46268, and***Monsanto Company, St. Louis, Missouri 63167
ABSTRACT Genetic linkage maps play fundamental roles in understanding genome structure, explaining
genome formation events during evolution, and discovering the genetic bases of important traits. A high-
density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence
repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186
recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1)
and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered
3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The
allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At
and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM
(51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The
genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was
Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified
that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal
rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17
as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between
Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid
cottons, including germplasm characterization, gene discovery, and genome sequence assembly.
inbred line (RIL)
Cotton belongs to the Gossypium genus, which consists of approxi-
mately 45 diploid and 5 allotetraploid species of global distribution
(Beasley 1942; Endrizzi et al. 1985; Kohel et al. 2001; Stewart 1994;
Wendel and Cronn 2003). The gametic chromosome number of all
diploid species is 13, but significant differences among the genomes
in meiotic affinity and relative size led to the recognition of eight
genome groups: A through G and K (Beasley 1942; Endrizzi et al.
1985; Stewart 1994). Of the approximately 50 Gossypium species, four
have been domesticated independently: two diploid species, G. arbor-
eum L. and G. herbaceum L. (n = x = 13) with A1and A2genomes,
and two allotetraploid species, G. hirsutum L. and G. barbadense L.
(n = 2x = 26) with (AD)1and (AD)2genomes (Bowers et al. 2003; Lee
1984; Percival and Kohel 1990). The allotetraploid cotton species are
the products of a presumed single polyploidization event between
Copyright © 2012 Yu et al.
Manuscript received June 24, 2011; accepted for publication November 4, 2011
This is an open-access article distributed under the terms of the Creative
Commons Attribution Unported License (http://creativecommons.org/licenses/
by/3.0/), which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited.
Supporting information is available online at http://www.g3journal.org/lookup/
1Corresponding author: USDA–ARS, Southern Plains Agricultural Research Center,
2881 F&B Road, College Station, TX 77845.E-mail: email@example.com
Volume 2 |January 2012 |
ancient A-genome and D-genome diploids that occurred approxi-
mately 1-2 million years ago (Stelly et al. 2005; Wendel and Cronn
2003). Chromosome numbers assigned in allotetraploid cottons are
based on pairing relationships in diploid x tetraploid crosses, with
chromosomes 1213 corresponding to the At subgenome and chro-
mosomes 14226 to the Dt subgenome (Brown 1980).
Cotton species serve as a model system for polyploid plants and
plant cell elongation, cell wall and cellulose biosynthesis because they
are the only known plants that produce single-celled fibers (Jiang et al.
1998; Kim and Triplett 2001). The genes that make cotton valuable
function in unique ways, requiring long-term research into the de-
velopment of molecular tools such as DNA markers and genome
maps to translate genomic information into agronomic benefits and
to other biological systems.
Cotton researchers have explored genetic mapping with multiple
types of DNA markers, including restriction fragment-length poly-
morphism (RFLP) (Reinisch et al. 1994; Rong et al. 2004; Shappley
et al. 1998), amplified fragment-length polymorphism (Lacape et al.
2003), random-amplified polymorphic DNA (Kohel et al. 2001), and
simple sequence repeats (SSRs) (Guo et al. 2007; Lacape et al. 2009;
Park et al. 2005; Xiao et al. 2009; Yu et al. 2011). Although early
genetic mapping with hybridization-based markers such as RFLP
opened the door to important genomic studies (Jiang et al. 1998;
Shappley et al. 1998), recent genetic mapping with polymerase chain
reaction (PCR)-based markers such as SSR have facilitated portable
applications among different mapping populations and research pro-
grams (Abdurakhmonov et al. 2008; Zhang et al. 2003). As such, the
cotton research community has made efforts to develop many porta-
ble markers to overcome the problem of low DNA polymorphism
rates among various cultivated cotton breeding programs (http://
www.cottonmarker.org/; Blenda et al. 2006). To date, approximately
17,000 pairs of SSR primers have been developed from four cotton
species (G. arboreum, G. barbadense, G. hirsutum, and G. raimondii
Ulbrich) and a portion of this number have been surveyed for poly-
morphism against a 12-genotype panel of six Gossypium species
(Blenda et al. 2006; Yu 2004). As single nucleotide polymorphism
(SNP) markers are explored in other plant species (Ganal et al.
2009), new research has been initiated to examine nucleotide sequence
diversity in Gossypium genomes (An et al. 2008; Van Deynze et al.
2009). These findings are laying the groundwork for developing
large numbers of SNP markers in cotton. The growing collection of
portable markers in cotton provides a cost-effective tool for genome
mapping and gene discovery to understand and improve the cotton plant.
High-resolution mapping in cotton has been conducted with
segregating populations that were derived from interspecific crosses
between Gossypium species because of limited DNA polymorphism
within a cotton species. The resulting segregating populations used in
major mapping projects often were either F2or BC1progeny (Guo
et al. 2007; Lacape et al. 2003; Rong et al. 2004; Yu et al. 2011). In
addition, these maps relied heavily on a single marker type such as
RFLP or SSR markers derived from limited sources. Rong et al. (2004)
reported the first high-density map in cotton using 57 F2plants de-
rived from an interspecific cross between G. hirsutum race “palmeri”
and G. barbadense acc. “K101.” The majority of markers used in this
map were RFLP markers. This map provided one of the first insights
into the allotetraploid cotton genome structure and evolution, al-
though the RFLP markers have proven to have limited portability
and utility for marker assisted breeding (Ulloa et al. 2005).
Guo et al. (2007) reported the first comprehensive SSR map by using
138 BC1plants derived from an interspecific cross of G. hirsutum TM-1/
G. barbadense Hai 7124//G. hirsutum TM-1. The majority of SSR
markers in this map were derived from cotton expressed sequence tag
(EST) sequences. Lacape et al. (2009) reported a genetic linkage map
that consisted of a total of approximately 800 (amplified fragment-
length polymorphism, RFLP, and SSR) marker loci via the use of 140
recombinant inbred lines (RILs); derived from an interspecific cross
between G. hirsutum Guazuncho 2 and G. barbadense VH8-4602. Re-
cently, Yu et al. (2011) used 141 BC1plants derived from an interspecific
cross of G. hirsutum Emian 22/G. barbadense 3-79//G. hirsutum Emian
22. As with Guo et al. (2007), this map also contained SSR markers, the
majority of which were derived from ESTs. In addition, a whole-genome
radiation hybrid population of 93 plants derived from an interspecific
cross of G. barbadense 3-79/G. hirsutum TM-1 was also explored for
mapping the cotton genome (Gao et al. 2004, 2006).
Here we report the development of a high-density cotton
(Gossypium spp.) genetic map by using representative sets of SSR
markers and the first public set of SNP markers to genotype 186 RILs
derived from an interspecific cross between G. hirsutum TM-1 and
G. barbadense 3-79. Both TM-1 and 3-79 are considered genetic stand-
ards for their respective species because of breeding and history of
genetic/genomic research conducted by the cotton community. These
two lines are highly homozygous, and extensive genetic and cytoge-
netic materials have been developed using them as reference parents,
including mutants and hypoaneuploids (Kohel et al. 1970; Stelly 1993;
Stelly et al. 2005). RILs possess several advantages over F2or BC1
populations for mapping genes and quantitative trait loci (QTL),
and high levels of homozygosity and recombination in the RILs enable
replicate studies across different environments by different research
groups. This immortal TM-1 · 3-79 RIL population is maintained at
USDA-ARS, College Station, Texas, USA, and it is used by the cotton
research community for genetic investigations, including QTL map-
ping studies. In addition, we selected SSR markers derived from dif-
ferent sequence sources (EST, genomic, and BAC clones). These
markers were developed by 16 research groups (all 16 sources available
to the public at Cotton Marker Database (http://www.cottonmarker.
org/). This combined high-density genetic map will facilitate the ad-
vancement of many basic and applied genomic studies in cotton.
MATERIALS AND METHODS
Plant materials and DNA extraction
The mapping population was an immortalized set of 186 RILs. At the
time of genomic DNA extraction for this study, the average generation
was F7. These lines were derived from selfing via single-seed descent
original individual F2plants from a cross between G. hirsutum TM-1
and G. barbadense 3-79, two highly homozygous parents (Kohel et al.
1970; Niles and Feaster 1984). Factors in selecting TM-1 and 3-79 as
parents in creation of a segregating population for genetic mapping
are the unique high-quality fiber characteristics of extra long staple
cotton 3-79 and the high productivity and modest environmental
sensitivity of Upland cotton TM-1 (Kohel et al. 2001). The parents
(TM-1 and 3-79) and their 186 RIL progeny are maintained as living
specimens to produce seed, fiber, and leaf tissue for this mapping
effort and other genetic studies.
Interspecific F1hypoaneuploid hybrids for specific chromosomes
were used for deficiency mapping by means of loss of heterozygosity.
All but one were derived previously by pollinating monosomic and
monotelodisomic aneuploids quasi-isogenic to TM-1 with pollen from
euploid 3-79,and recovering therespective deficiencyamongF1progeny.
The F1aneuploid monosomic for chromosome 26 was unusual in that
the deficiency arose de novo in 3-79 pollen, i.e. not via transmission from
the maternal TM-12like stock. The general procedures for mapping
| J. Z. Yu et al.
with cotton monosomic (2n = 51) and monotelodisomic stocks have
been described previously (Beasley 1942; Stelly 1993; Stelly et al. 2005).
Genomic DNA was extracted from fresh young leaf tissue of
individual cotton plants grown in the greenhouse in accordance with
the modified CTAB DNA extraction procedure as described by Kohel
et al. (2001).
PCR primers and assays
The primer pairs used for PCR were developed by collaborators of the
cotton research community (Table 1). Approximately 10,000 pairs of
SSR primers from 16 different research projects (http://www.cotton-
marker.org/) were first analyzed to identify polymorphic markers be-
tween TM-1 and 3-79. Nine genomic DNA sources for SSR primer
pairs included BNL, CIR, CM, DOW, DPL, GH, JESPR, MUSB, and
TMB, and seven EST sources of SSR primer pairs included HAU,
MGHES, MUCS, MUSS, NAU, STV, and UCD. While EST SSR primer
pairs were developed from Gossypium cDNA clones that contain SSR,
genomic primer pairs were developed from Gossypium random
enriched small insert libraries except MUSB and TMB. MUSB was
developed from the end sequences of the bacterial artificial chromosome
(BAC) clones of G. hirsutum acc. Acala Maxxa (Frelichowski Jr. et al.
2006). TMB was developed from the BAC clones and/or physical con-
tigs of TM-1 (Guo et al. 2008). MUSB and TMB markers facilitate an
integration of genetic and physical maps of the allotetraploid cotton
genome (Xu et al. 2008). The first public SNP set (UC) also was in-
cluded in this mapping project (Van Deynze et al. 2009). SNP primer
pairs were largely derived from G. arboreum EST unigenes. The actual
sequence of the individual primer pairs and source clone for each SSR
or SNP marker set can be found at http://www.cottonmarker.org/.
PCR assays for amplifying SSR markers were performed in
a cocktail of 10 mL containing 20 ng of DNA, 0.25 mM forward
primer, 0.25 mM reverse primer, 0.25 mM dNTPs, 2.5 mM MgCl2,
and 0.65 unit DNA Taq polymerase. Thirty-five PCR cycles were used
to amplify SSR products, using a primer annealing temperature of 55?
or 60?. For nonlabeled SSR primers, amplified DNA products were
electrophoresed in a 20-cm-long horizontal agarose gel system (Owl
Separation Systems, Portsmouth, NH) with 1X TBE (45 mM tris-
borate, 1 mM EDTA, pH 8) running buffer and 3.5% Hi-Resolution
agarose (e.g. Metaphor agarose, Cambrex, East Rutherford, NJ; or SFR
agarose, Amresco, Solon, OH). PCR product sizes were estimated by
comparison with DNA size standard ladders (E and K Scientific, Santa
Clara, CA). For fluorescently labeled primers (forward primer only
with 6-FAM, HEX, or NED), amplified DNA products were separated
using 36-cm or 50-cm capillary electrophoresis of automated
ABI PRISM 3130xl or ABI PRISM 3730 Genetic Analyzer (Applied
Biosystems/Life Technology, Foster City, CA). In a separate project,
an array for Ilumina (San Diego, CA) Golden Gate assay was designed
to analyze 384 SNP markers between TM-1 and 3-79 (Van Deynze
et al. 2009). Polymorphic SNP markers based on the parental survey
were used to genotype the 186 RILs.
Marker data acquisition and linkage map construction
SSR data collection was performed either manually for gel-based
assays or with the GeneMapper 3.7. Among nearly 10,000 pairs of
primers that were surveyed, more than 2000 primer pairs that
detected the best resolution of polymorphisms between TM-1 and
3-79 were selected to genotype the 186 RILs. These primer pairs
included subsets (54 MUCS, 123 MUSB, and 93 MUSS) that were
previously used to genotype the same population (Park et al. 2005;
Frelichowski Jr. et al. 2006), and the genotyping data were incorpo-
rated into this mapping project.
Genotyping of the RIL population for SSR and SNPs was
performed as previously described (Park et al. 2005; Frelichowski Jr.
et al. 2006; Van Deynze et al. 2009). SSR markers were generally
codominant, but the calling or scoring of the tetraploid cotton alleles
at a specific locus required careful examination of gel images or elec-
trographs. Allotetraploid cottons likely had multiple copies of DNA
fragments or alleles amplified with a single primer-pair. To distinguish
dominant markers from codominant markers, any RIL missing one
pair of the parental polymorphic fragments/alleles indicated that
alleles were nonallelic or simply an existence of two dominant marker
loci after all pairing attempts had failed. A missing data point of a RIL
was determined if there was a lack of any signal attributable to failed
PCR amplification. Duplicate marker loci were designated by adding
a lower-case letter in alphabetical order after the primer name. The
raw scores were first inspected for any coding error and segregation
distortion before using the data as input for the JoinMap 4.0 program
(Van Ooijen 2006) for mapping analysis. Using the JoinMap’s func-
tion “identify identical loci,” we identified 47 identical or cosegregat-
ing loci (supporting information, Table S2) and removed them in
subsequent mapping. The Kosambi mapping function (Kosambi
1944) was selected to convert a recombination frequency to a genetic
distance (centiMorgan, or cM), and 40 cM was the threshold to de-
termine linkage between two markers. Linkage groups and marker
orders were determined on the basis of likelihood ratio statistic (or
LOD) 10 or greater (up to LOD 15). Chromosome assignment was
determined by the common markers that were located by authors in
previous publications (Frelichowski Jr. et al. 2006; Guo et al. 2007,
2008; Lacape et al. 2003; Liu et al. 2000; Park et al. 2005; Yu et al.
2011) and by use of the subsets of new SSR markers (GH, Table 3)
with the cotton hypoaneuploid stocks described previously. SSR loci
localized to one of the chromosomes (Chr.) 1 to 13 were assigned to
n Table 1 Primer sources of cotton molecular markers
Marker setNo. Mapped Marker Loci
EST, expressed sequence tag; SNP, single nucleotide polymorphism; SSR,
simple sequence repeat.
Volume 2 January 2012|An SSR and SNP Genetic Map of Cotton|
the A-subgenome (At), whereas loci localized to Chr. 14 to 26 were
assigned to the D-subgenome (Dt).
Parental polymorphisms and genotype frequencies of
the mapping population
Approximately 25% of the genomic SSR markers and approximately
15% of the cDNA SSR markers were polymorphic between TM-1 and
3-79. A total of 1601 pairs of polymorphic SSR primers were selected
and analyzed for genotyping 186 RILs. Of the 1601 SSR primer pairs
that revealed 1895 marker loci, 1344 primer pairs revealed one locus,
234 revealed two loci, and the remaining 23 revealed more than two
loci. Among the 1895 SSR marker loci, 1785 were codominant; 43
were dominant loci that received alleles from TM-1, and 67 were
dominant loci that received alleles from 3-79. Of these 1895 marker
loci, 1825 were mapped (Table 1). The remaining 70 loci were not
mapped because of highly skewed segregation (x2. 8.5) and high
levels of missing data. Fifty-five of the unmapped loci were dominant
loci. In addition, 247 of the 384 SNP primer pairs were polymorphic
between parents and used to genotype the 186 RILs. All 247 SNP
markers were codominant and revealed 247 loci (Table S1). Of these,
207 SNP loci were mapped in unique positions, and the remaining 40
SNP loci were identical to other mapped loci (Table S2). In summary,
a total of 1848 pairs of SSR and SNP primers were used to genotype
the 186 RILs, and 2142 marker loci were scored, of which 2072 marker
loci revealed by 1532 pairs of SSR and 247 pairs of SNP primers were
mapped (Table 1). Approximately 98% of 2072 total marker loci were
mapped in unique positions, with only 47 identical or cosegregating
markers including 40 SNP markers (Table S2).
This RIL population displayed a greater-than-expected level of
residual heterozygosity, i.e. 4.2% instead of the expected 1.6% for an F7
population derived by single-seed descent. Residual heterozygosity in
individual lines ranged from 0.8% to 19.9%. Among the 2032 codom-
inant SSR and SNP loci, the average residual heterozygosity for in-
dividual markers was 4.2%, ranging from 0% to 66.7% with SSR
marker STV129 demonstrating the greatest heterozygosity. Markers
that detected more than 20% residual heterozygosity of the RIL pop-
ulation were usually difficult to map because determining linkage of
these markers conflicted with more than one marker. Analysis of the
Figure 1 Distribution of the TM-1 and 3-79 allele frequencies in the RIL
mapping population (x2¼ 768 and P , 0.0001).
n Table 2 Distribution of 2072 SSR and SNP marker loci among the 26 allotetraploid cotton chromosomes
No. Marker LociRecombinational Size, cMAverage Marker Interval, cM No. Gaps .10 cM (Largest)
SNP, single nucleotide polymorphism; SSR, simple sequence repeat.
| J. Z. Yu et al.
Figure 2 Genetic linkage maps of 26 allotetraploid
cotton chromosomes that are presented in 13 At and
Dt subgenome homeologous pairs (in parentheses).
The names of DNA markers are shown on the right,
and the positions of the markers are shown in Kosambi
centiMorgan (cM) on the left. A line bar connects
duplicate marker loci between a pair of homeologous
chromosomes. Marker loci in bold are assigned to
cotton chromosomes by previously published studies
(Frelichowski Jr. et al. 2006; Guo et al. 2007, 2008;
Lacape et al. 2003; Liu et al. 2000; Park et al. 2005;
Yu et al. 2011) and marker loci in italic bold are
assigned to cotton chromosomes in this study (Table
3). Homeologous marker linkage relationships indicate
of reciprocal rearrangement between ancestral forms
of Chr. 02 and 03 and/or 14 and 17 relative to each
other; they also indicate that centromeric regions are
homeologous between Chr. 02 (A02) and Chr. 17
(D02), as well as between Chr. 03 (A03) and Chr. 14
(D03). Intrachromosomal duplications were noted
in Chr. 5, 11, and 21, the latter two in homeologous
Volume 2 January 2012|An SSR and SNP Genetic Map of Cotton|
Figure 2 Continued.
|J. Z. Yu et al.
Figure 2 Continued.
Volume 2January 2012|An SSR and SNP Genetic Map of Cotton|
Figure 2 Continued.
|J. Z. Yu et al.
Figure 2 Continued.
Volume 2January 2012|An SSR and SNP Genetic Map of Cotton|
Figure 2 Continued.
|J. Z. Yu et al.
Figure 2 Continued.
Volume 2 January 2012|An SSR and SNP Genetic Map of Cotton|
genotyping data revealed a statistically significant preference of TM-1
alleles to 3-79 alleles (x2= 768; Figure 1). Overall, the allele frequen-
cies of TM-1 and 3-79 were 52.3% and 47.7%, respectively.
Genetic linkage maps of the allotetraploid cotton
The genetic linkage map comprises 2072 SSR and SNP loci mapped
to the 26 linkage groups, corresponding to 26 chromosomes of
allotetraploid cotton, for a total map distance of 3380 cM (Table 2
and Figure 2). The average marker interval in this map is 1.63 cM.
Forty-seven pairs of marker loci were found to be either identical or
cosegregated (Table S2), and therefore only one locus from each pair is
shown on the map. For example, BNL3545b is identical to or cosegre-
gated with BNL3545a, so only BNL3545a is shown on Chr. 14 (D03).
The At subgenome consisted of 1138 marker loci (927 SSR and
211 SNP), and the total genetic distance was 1726.8 cM with an
average marker interval of 1.52 cM. The largest chromosome in terms
of recombination frequency was Chr. 05 (A05), which spans 199.2 cM
with 139 marker loci. The second largest was Chr. 11 (A11), which
spans 166.5 cM with 140 loci. The shortest was Chr. 04 (A04), which
spans 101.6 cM with 56 loci (Table 2 and Figure 2). In the At sub-
genome, there were 11 gaps greater than 10 cM, and the largest gap
between two loci was 16.52 cM on Chr. 08 (A08).
The Dt subgenome consisted of 934 marker loci (898 SSR and 36
SNP), and the total genetic distance was 1653.1 cM, with an average
marker interval of 1.77 cM. The largest chromosome with respect to
recombination frequency was Chr. 19 (D05), which spans 227.2 cM
with 132 loci, and the shortest chromosome was Chr. 22 (D04), which
spans 77.9 cM with 45 loci (Table 2 and Figure 2). There were 10 gaps
greater than 10 cM, and the largest gap between two loci was 22.01 cM
on Chr. 17 (D02). Although SNP marker loci were largely mapped in
the At subgenome because of the A-genome origin of SNP primers
(Van Deynze et al. 2009), the At subgenome and Dt subgenome had
virtually similar numbers of SSR marker loci and total genetic dis-
tances. Furthermore, there were similar amounts of recombination
between each of 13 pairs of cotton homeologous chromosomes.
Complete assignment of linkage groups to
A complete set of 26 cotton chromosomes (13 At subgenome and 13
Dt subgenome) were identified that correspond to 26 respective
linkage groups (Figure 2). Assignment of SSR markers and linkage
groups to the cotton chromosomes was achieved in part by compar-
ison of the common markers (bold font in Figure 2) with the previous
SSR mapping reports (Frelichowski Jr. et al. 2006; Guo et al. 2007;
n Table 3 Assignment of 37 GH SSR markers to specific allotetraploid cotton chromosomes
Marker NameFragment Size, bp HypoaneuploidMapped Chromosome
SSR, simple sequence repeat.
| J. Z. Yu et al.
Lacape et al. 2003; Park et al. 2005; Yu et al. 2011) and with the three
aneuploid studies for TMB markers (Guo et al. 2008) and BNL
markers (Gutiérrez et al. 2009; Liu et al. 2000), respectively. In addi-
tion, hypoaneuploid cottons were also analyzed to identify TM-1 de-
ficiency with 37 newly developed GH markers (bold italic in Figure 2)
from G. hirsutum and other SSR markers of interest in the mapping
study (Table 3 and Figure 3) (Hoffman et al. 2007). Although most
SSR markers generally agreed with published reports, a few incongru-
ities, such as GH034 and GH526, between various data types were
encountered when cotton hypoaneuploid stocks were used along with
individual mapping populations. Additional mapping analyses in the
present research confirmed or reassigned such SSR markers to the
corresponding cotton chromosomes (Table 3).
Genomic duplication and chromosomal translocation of
Among 1601 SSR primer pairs that amplified 1895 loci in TM-1 and
3-79, 257 SSR primer pairs amplified two or more loci, resulting in
a total of 551 duplicate loci. Excluding dominant loci amplified by
these SSRs, there were 494 codominant loci that were duplicated,
resulting in 247 pairs (Table S3). Most of the duplicate loci were
mapped on the homeologous chromosome pairs (Table 4 and Figure
2). The relative orders of most duplicate loci on the homeologous
chromosomes were similar (Figure 2). The duplicate loci identified
by these SSR markers demonstrated the complex but linear features
of the allotetraploid cotton genomes. A few duplicate loci also were
present between nonhomeologous chromosomes and/or within the
same subgenome, which indicated likely genome rearrangements
(Table 4 and Table S3). For example, an intrasubgenome duplication
was revealed by the marker BNL1044 between Chr. 04 (A04) and Chr.
05 (A05). Distinct intrachromosome duplications were indicated by
one SSR duplication in Chr. 11 (A11) and three SSRs in Chr. 21 (D11)
(Figure 2). In chromosome 11 (A11), TMB0426 revealed two loci that
were mapped 8.1 cM apart. In chromosome 21 (D11), three markers
(i.e. CM0160, JESPR211, and JESPR244) each revealed two loci. In the
latter, the recombination rates remained similar (~8-9 cM) but the
relative orders among duplicated loci were altered.
A postpolyploidization reciprocal translocation of chromosomes
02 (A02) and 03 (A03) was suggested by 10 pairs of duplicate loci
(Figure 2 and Table 4). Five pairs of duplicate loci were identified
between chromosomes 02 (A02) and 14 (D03) and 5 pairs between
chromosomes 03 (A03) and 17 (D02). The marker TMB1025 revealed
duplicate loci between chromosomes 02 (A02) and 03 (A03), which
inferred a possible breakpoint for the reciprocal translocation in these
two At subgenome chromosomes. Additional mapping data in the
vicinity of TMB1025 will be necessary to confirm this conclusion.
Another translocation between At subgenome chromosomes 04
(A04) and 05 (A05), as previously suggested by Guo et al. (2007),
was observed by the marker BNL1044 loci (BNL1044a at 33.6 cM of
A05) and (BNL1044c at 48.1 cM of A04) (Figure 2 and Table S3).
Furthermore, the marker GH252 loci showed a translocation between
non-homeologous chromosomes 05 (A05) with GH252a at 136.4 cM
and 22 (D04) with GH252b at 18.3 cM.
The high-density genetic linkage map created in this research is
composed of 2072 SSR and SNP loci representing many individual
groups of the cotton research community, and it provides a transfer-
able platform that is essential for a broad spectrum of basic and
applied studies aimed at understanding and manipulating complex
cotton genomes. Among the 17 sets of SSR and SNP marker loci,
BAC-derived SSRs (310 TMB Table S1 and 155 MUSB) facilitate an
integration of genetic and physical maps of the cotton chromosomes
(Frelichowski Jr. et al. 2006; Xu et al. 2008). The markers linked to the
novel genes can be used to screen cotton BAC clones or physical
contigs from which the SSR markers were developed (Yin et al.
2006). The 357 EST-derived SSR markers mapped herein offer an
opportunity to study functional genes and gene islands for fiber de-
velopment and other important traits of interest. In addition, the
Figure 3 Deletion analysis of cotton SSR markers. GH584 amplified
(from L to R) cotton hemizygous F1hypoaneuploids as well as homo-
zygous TM-1 and 3-79. TM-1 allele (140 bp) was missing in both lanes
(see arrow) with the H09 template, suggesting the location of GH584
locus on chromosome 09 (A09).
n Table 4 Pairs of duplicate marker loci between homeologous and nonhomeologous chromosomes in cotton
No. Pairs of
No. Pairs of
Volume 2January 2012|An SSR and SNP Genetic Map of Cotton|
genetic mapping of the 247 SNP markers is the first major public
effort to use nucleotide sequence diversity in cotton species by map-
ping SNP loci (Table S1). Localization of these SNP markers to the 26
individual cotton chromosomes and their integration with large num-
bers of SSR markers will facilitate other studies in cotton genomics.
We believe that the high-density genetic map reported herein is a sat-
urated one for the allotetraploid cotton, as evidenced by a separate
mapping analysis (data not shown). Further increase in the map
density may not significantly change the total genetic length of this
map but will facilitate whole-genome physical alignment, sequencing,
and mapping of genes for cotton improvement.
Deviation from a Mendelian segregation ratio is common in intra-
and interspecific crosses (Causse et al. 1994; Lacape et al. 2009; Rong
et al. 2004; Ulloa et al. 2002; Yu et al. 2011). An extremely severe
distortion (99%) toward G. hirsutum was observed by Lacape et al.
(2009) when 140 RILs were used to produce a low-density map of
approximately 800 loci. Only 15 of the 140 RILs exhibited 50% or
more G. barbadense parental alleles. In this research, TM-1 was less
environmentally sensitive than 3-79, as reflected by the allele trans-
mission preference in the advancement of generations of the RIL
population (Figure 1). Of the 2072 mapped marker loci, 1391
(67.1%) fit an expected 1:1 segregation ratio, and 681 (32.9%) deviated
significantly (x2. 3.8) from expectations among 186 RILs. The 681
segregation-distorted loci (SDL) were mapped in all 26 groups with
349 mapped in At subgenome, and 332 in Dt subgenome chromo-
somes. Four chromosomes, i.e. Chr. 15 (D01), Chr. 05 (A05), Chr. 07
(A07), and Chr. 08 (A08), had the most SDL, with 68, 60, 57, and 42
loci, respectively. However, Chr. 26 (D12) has the greatest percentage
of SDL, 75%, followed by Chr. 15 (D01) with 73.9%, Chr. 07 (A07)
with 68.7% and Chr. 05 (A05) with 45.1%. In most cases, the SDL
were mapped at centromeric regions.
Our mapping studies indicate that the two subgenomes of
allotetraploid cottons are equivalent in recombination frequencies
despite the extra repetitive DNA in the At subgenome (Zhao et al.
1998). This result is consistent with other independent mapping stud-
ies in which the authors used different allotetraploid cotton popula-
tions (F2or BC1) where variation between At and Dt map sizes
supports the ratio of our genetic distances between the two subge-
nomes. Rong et al. (2004) mapped a total of 2584 STS loci that span
4447 cM, with the A subgenome being 9.5% larger genetically than the
D subgenome. To the contrary, Guo et al. (2007) mapped a total of
1790 SSR loci that span 3426 cM, with the D subgenome being 4.5%
larger genetically than the A subgenome. Yu et al. (2011) mapped
a total of 2316 SSR loci that span 4419 cM with the A subgenome
being 3.9% larger genetically than the D subgenome. In this study, the
tetraploid cotton were mapped with 1106 loci (54.5%) on 13 At chro-
mosomes at 1726.8 cM (51.1%) and 922 loci (45.5%) on 13 Dt chro-
mosomes at 1653.1 cM (48.9%). Variation in the ratio of subgenome
map distances is likely the result of differences in mapping population
sizes, as well as in the numbers and sources of DNA markers.
As evidenced in our mapping data, two reciprocal translocations
(between Chr. 02 and 03 and between Chr. 04 and 05) are inferred
during or after the polyploidization process of two ancestral diploid
genomes (A and D). The translocation breakpoint between Chr. 02
and Chr. 03 may be at or near homeologous SSR marker TMB1025.
Further investigation is needed to identify additional markers in the
vicinity of TMB1025. On the basis of homeologous markers of the two
chromosome pairs (A02-D02 and A03-D03), the majority of duplicate
loci were mapped to individual pairs of Chr. 02 vs. Chr. 17 and Chr.
03 vs. Chr. 14. The centromeric cores of these chromosomes seem to
show the homeologous relationship, either reciprocal insertional
translocations or two temporally separate traditional reciprocal trans-
locations. Thus, we propose to name Chr. 17 as D02 and Chr. 14 as
D03, whereas Chr. 02 and Chr. 03 remain as A02 and A03, respec-
tively, which is a revision to Wang et al. (2006b) and Guo et al. (2007).
Duplication of marker loci revealed genome rearrangements within
the same individual chromosomes and/or between nonhomeologous
chromosomes (Table S3). We recognize that nomenclature revision of
cotton chromosomes and linkage groups would be needed in the
future, but this could be accomplished by an international committee
of experts in the subject matter.
Genetic mapping coupled with physical alignment of genomic
regions into chromosomal maps will expedite the discovery of
resistance (R) or pathogen-induced R genes underlying QTL involved
in resistance to nematode and Fusarium wilt (Ulloa et al. 2011).
Chromosomes 11 (A11) and 21 (D11) are homologs that harbor
important genes for cotton improvement because these chromosomes
contain genes for resistance to reniform (Dighe et al. 2009) and root-
knot nematodes (Wang et al. 2006a), race 1 of Fusarium (Ulloa et al.
2010) and other traits affecting fiber yield and quality. The high-
density genetic map will facilitate and expedite the analysis of plant
defense genes against nematodes and other biotrophic pathogens.
This high-density cotton map was constructed with an immortal
RIL mapping population. A high level of homozygosity in this RIL
population (currently in F8-F9) was achieved with less than 5% ge-
nome-wide residual heterozygosity. The RILs are maintained as living
stocks to produce seed sources for multilocation research on fiber
among other traits and to extract fresh DNA samples for a broad
spectrum of genomic studies. Our mapping population of 186 RILs
is the largest population ever used in high-density cotton genetic
mapping. The accuracy of mapping results can be improved substan-
tially as the proportion of recombination between the two linked
markers in an inbred population is about twice that of a single meiotic
event F2or BC1population when linkage distances are small (,12.5
cM) and increase nonlinearly to 50% for unlinked markers (Burr et al.
1988; Haldane and Waddington 1931). This population provides the
greatest mapping power currently known in cotton to detect addi-
tional loci between closely linked markers by members of the cotton
research community who are interested in SSR and SNP augmenta-
tion. The advantages of this immortal RIL population and its parental
lines make it practical for high-resolution consensus mapping with
additional sequence-based portable markers, enabling better under-
standing and exploitation of complex Gossypium genomes (Mace et al.
2009). This information will complement other work because of the
use of the same parents in developing genetic resources, such as
hypoaneuploid cytogenetic stocks, chromosome substitution lines,
chromosome specific RILs, and QTL mapping populations in other
research programs (Jenkins et al. 2006, 2007; Saha et al. 2006, 2010,
2011; Stelly et al. 2005).
The International Cotton Genome Initiative (http://icgi.tamu.edu/)
has proposed to map and sequence the Gossypium genomes (Brubaker
et al. 2000; Chen et al. 2007; Paterson 2008; Wilkins 2008; Yu et al.
2008), but large amounts of dispersed repetitive elements and dupli-
cate loci between and within the allotetraploid cotton chromosomes
present great challenges to properly assemble a complex Gossypium
genome. Development of additional numbers of SSR and SNP
markers from the fingerprinted and sequenced BAC clones or physical
contigs, such as the 310 TMB and 155 MUSB markers on the present
map, would provide a unique opportunity to facilitate the mapping
the gaps (5215 cM) of genomic regions (Lin et al. 2010; Xu et al.
2008; Yin et al. 2006). A high-density genetic map is essential in the
reconciliation with a whole-genome physical map to facilitate genome
|J. Z. Yu et al.
sequencing, sequence assembly, gene mapping, and the design of
targeted genetic markers for better understanding and improvement
of the cotton plant.
We offer our appreciation to many technical staff residing in the
various laboratories who contributed in the development and
mapping of SSRs and SNPs on the RIL population. Special thanks
go to Ping Cui, Jianmin Dong, Nicole Steele, and Jewel Stroupe for
their technical assistance in surveying parental DNA polymorphism
and in genotyping the RIL mapping population, and special thanks to
Jared Harris for his assistance in maintaining the immortal RIL
population. We also would like to thank Cotton Incorporated, Cary,
NC, for facilitating the dye-labeled SSR primers, and Dr. Roy Cantrell
for his contribution and valuable discussion on this research project.
Mention of trade names or commercial products in this article is
solely for the purpose of providing specific information and does not
imply recommendation or endorsement by the U.S. Department
of Agriculture. The U.S. Department of Agriculture is an equal
opportunity provider and employer.
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Volume 2 January 2012|An SSR and SNP Genetic Map of Cotton |