Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between gossypium hirsutum and G. barbadense

<p>Abstract</p> <p>Background</p> <p>Cotton, with a large genome, is an important crop throughout the world. A high-density genetic linkage map is the prerequisite for cotton genetics and breeding. A genetic map based on simple polymerase chain reaction markers will be efficient for marker-assisted breeding in cotton, and markers from transcribed sequences have more chance to target genes related to traits. To construct a genome-wide, functional marker-based genetic linkage map in cotton, we isolated and mapped expressed sequence tag-simple sequence repeats (EST-SSRs) from cotton ESTs derived from the A₁, D₅, (AD)₁, and (AD)₂genome.</p> <p>Results</p> <p>A total of 3177 new EST-SSRs developed in our laboratory and other newly released SSRs were used to enrich our interspecific BC₁genetic linkage map. A total of 547 loci and 911 loci were obtained from our EST-SSRs and the newly released SSRs, respectively. The 1458 loci together with our previously published data were used to construct an updated genetic linkage map. The final map included 2316 loci on the 26 cotton chromosomes, 4418.9 cM in total length and 1.91 cM in average distance between adjacent markers. To our knowledge, this map is one of the three most dense linkage maps in cotton. Twenty-one segregation distortion regions (SDRs) were found in this map; three segregation distorted chromosomes, Chr02, Chr16, and Chr18, were identified with 99.9% of distorted markers segregating toward the heterozygous allele. Functional analysis of SSR sequences showed that 1633 loci of this map (70.6%) were transcribed loci and 1332 loci (57.5%) were translated loci.</p> <p>Conclusions</p> <p>This map lays groundwork for further genetic analyses of important quantitative traits, marker-assisted selection, and genome organization architecture in cotton as well as for comparative genomics between cotton and other species. The segregation distorted chromosomes can be a guide to identify segregation distortion loci in cotton. The annotation of SSR sequences identified frequent and rare gene ontology items on each chromosome, which is helpful to discover functions of cotton chromosomes.</p

BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton.

Acknowledgments “Dedicated to Dr. Ramesh Kantety, a mentor, colleague and friend”. We would like to acknowledge the support offered by Padmini Sripathi during data analysis and submissions. Author Contributions Conceived and designed the experiments: RVK JZY. Performed the experiments: RB ZX SM GBW. Analyzed the data: RB. Contributed reagents/materials/analysis tools: RVK RB JZY RJK BAR. Wrote the manuscript: RB. Revised the manuscript: RB RVK JZY RGP BAR GCS. Advised the research: RVK JZY RGP BAR GCS.Author Contributions Conceived and designed the experiments: RVK JZY. Performed the experiments: RB ZX SM GBW. Analyzed the data: RB. Contributed reagents/materials/analysis tools: RVK RB JZY RJK BAR. Wrote the manuscript: RB. Revised the manuscript: RB RVK JZY RGP BAR GCS. Advised the research: RVK JZY RGP BAR GCS.Although new and emerging next-generation sequencing (NGS) technologies have reduced sequencing costs significantly, much work remains to implement them for de novo sequencing of complex and highly repetitive genomes such as the tetraploid genome of Upland cotton (Gossypium hirsutum L.). Herein we report the results from implementing a novel, hybrid Sanger/454-based BAC-pool sequencing strategy using minimum tiling path (MTP) BACs from Ctg-3301 and Ctg-465, two large genomic segments in A12 and D12 homoeologous chromosomes (Ctg). To enable generation of longer contig sequences in assembly, we implemented a hybrid assembly method to process ~35x data from 454 technology and 2.8-3x data from Sanger method. Hybrid assemblies offered higher sequence coverage and better sequence assemblies. Homology studies revealed the presence of retrotransposon regions like Copia and Gypsy elements in these contigs and also helped in identifying new genomic SSRs. Unigenes were anchored to the sequences in Ctg-3301 and Ctg-465 to support the physical map. Gene density, gene structure and protein sequence information derived from protein prediction programs were used to obtain the functional annotation of these genes. Comparative analysis of both contigs with Arabidopsis genome exhibited synteny and microcollinearity with a conserved gene order in both genomes. This study provides insight about use of MTP-based BAC-pool sequencing approach for sequencing complex polyploid genomes with limited constraints in generating better sequence assemblies to build reference scaffold sequences. Combining the utilities of MTP-based BAC-pool sequencing with current longer and short read NGS technologies in multiplexed format would provide a new direction to cost-effectively and precisely sequence complex plant genomes.Yeshttp://www.plosone.org/static/editorial#pee