Dataset Information

Sampling nucleotide diversity in cotton.

ABSTRACT:

Background

Cultivated cotton is an annual fiber crop derived mainly from two perennial species, Gossypium hirsutum L. or upland cotton, and G. barbadense L., extra long-staple fiber Pima or Egyptian cotton. These two cultivated species are among five allotetraploid species presumably derived monophyletically between G. arboreum and G. raimondii. Genomic-based approaches have been hindered by the limited variation within species. Yet, population-based methods are being used for genome-wide introgression of novel alleles from G. mustelinum and G. tomentosum into G. hirsutum using combinations of backcrossing, selfing, and inter-mating. Recombinant inbred line populations between genetics standards TM-1, (G. hirsutum) x 3-79 (G. barbadense) have been developed to allow high-density genetic mapping of traits.

Results

This paper describes a strategy to efficiently characterize genomic variation (SNPs and indels) within and among cotton species. Over 1000 SNPs from 270 loci and 279 indels from 92 loci segregating in G. hirsutum and G. barbadense were genotyped across a standard panel of 24 lines, 16 of which are elite cotton breeding lines and 8 mapping parents of populations from six cotton species. Over 200 loci were genetically mapped in a core mapping population derived from TM-1 and 3-79 and in G. hirsutum breeding germplasm.

Conclusion

In this research, SNP and indel diversity is characterized for 270 single-copy polymorphic loci in cotton. A strategy for SNP discovery is defined to pre-screen loci for copy number and polymorphism. Our data indicate that the A and D genomes in both diploid and tetraploid cotton remain distinct from each such that paralogs can be distinguished. This research provides mapped DNA markers for intra-specific crosses and introgression of exotic germplasm in cotton.

SUBMITTER: Van Deynze A

PROVIDER: S-EPMC2771027 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature

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Publications

Sampling nucleotide diversity in cotton.

Van Deynze Allen A Stoffel Kevin K Lee Mike M Wilkins Thea A TA Kozik Alexander A Cantrell Roy G RG Yu John Z JZ Kohel Russel J RJ Stelly David M DM

BMC plant biology 20091020

<h4>Background</h4>Cultivated cotton is an annual fiber crop derived mainly from two perennial species, Gossypium hirsutum L. or upland cotton, and G. barbadense L., extra long-staple fiber Pima or Egyptian cotton. These two cultivated species are among five allotetraploid species presumably derived monophyletically between G. arboreum and G. raimondii. Genomic-based approaches have been hindered by the limited variation within species. Yet, population-based methods are being used for genome-wid ...[more]

PMID: 19840401

Similar Datasets

Project description:BackgroundThe most widely cultivated cotton (Gossypium hirsutum L., AD-genome) is derived from tetraploidization between A- and D-genome species. G. arboreum L. (A-genome) and G. raimondii Ulbr. (D-genome) are two of closely-related extant progenitors. Gene expression studies in allotetraploid cotton are complicated by the homoeologous loci of A- and D-genome origins. To develop genomic resources for gene expression and cotton breeding, we sequenced and assembled expressed sequence tags (ESTs) derived from G. arboreum and G. raimondii.ResultsRoche/454 FLX sequencing technology was employed to sequence normalized cDNA libraries prepared from leaves, roots, bolls, ovules, and fibers in G. arboreum and G. raimondii, respectively. Sequencing reads from two independent libraries in each species were combined to assemble high-quality EST contigs. The combined sequencing reads included 1,699,776 from A-genome and 1,464,815 from D-genome, which were clustered into 89,588 contigs in the A-genome and 65,542 contigs in the D-genome. These contigs represented ~80% of EST collections in Cotton Gene Index 11 (CGI11, March 2011). Compared to the D-genome transcript database, 27,537 and 10,452 contigs were unique transcripts in A and D genomes, respectively. Further analysis using self-blastn reduced the unigene contig number by 52% in A-genome and 57% in D-genome, suggesting that 50% or more of contigs are paralogs or isoforms within each species. The majority of EST contigs (73-81%) were conserved between A- and D-genomes, whereas 27% and 19% contigs were specific to A- and D-genomes, respectively. Using these ESTs, we generated a total of 75,754 genome-specific single nucleotide polymorphism (SNP) (gSNPs or GNPs) or homoeologous-specific SNPs (hSNPs) of 10,885 contigs or genes between A and D genomes, indicating a possibility of separating allelic expression for those genes in allotetraploid cotton.ConclusionsExpressed genes are highly redundant within each diploid progenitor and between A and D progenitor species, suggesting that diploid progenitors in cotton are likely ancient tetraploids. This large set of A- and D-genome ESTs and GNPs will be valuable resources for genome annotation, gene expression, and crop improvement in allotetraploid cotton.

Dataset Information

Sampling nucleotide diversity in cotton.

Background

Results

Conclusion

Publications

Sampling nucleotide diversity in cotton.

Similar Datasets

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