Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

Abstract

BackgroundCotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton.ResultsIn this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium.ConclusionThis study will serve as a valuable genomic resource for tetraploid cotton genome assembly, for cloning genes related to superior agronomic traits, and for further comparative genomic analyses in Gossypium.

Genome-wide identification of mitogen-activated protein kinase gene family in Gossypium raimondii and the function of their corresponding orthologs in tetraploid cultivated cotton

“…The chromosome numbers are indicated at the top of each bar. The chromosome numbers from D1 to D5, and D7 to D12 were consistent with our newly-updated interspecific genetic map in allotetraploid cultivated cotton species reported recently (Zhao et al [32]), and the scaffolds name from G. raimindii genome was showed in the bracket. Lines were drawn to connect duplicated genes.…”

Mapping QTL for cotton fiber quality traits using simple sequence repeat markers, conserved intron-scanning primers, and transcript-derived fragments

“…Chromosome nomenclatures adhered to an earlier system (Wang et al 2006). To confirm positioning of linkage groups, we used 215 SSR markers that had been previously anchored on chromosomes (e.g., Han et al 2004;Yu et al 2007;2011;Guo et al 2008;Zhao et al 2013).…”

Recent Developments in Fiber Genomics of Tetraploid Cotton Species

“…With the advance on molecular marker development in cotton, three new marker types, indel (insertion-deletion), SNP, and retrotransposon-microsatellite amplified polymorphism (REMAP) were used to increase map density in allotetraploid cotton cultivars [33]. SNP markers in cotton can be used to associate genes with the respective fiber traits.…”

“…New marker loci and linkage groups were applied in different cotton species using informative sequence-based markers and DNA sequence information. Some of the ESTs and BACs were physically anchored and clustered into the high-density genetic map, and functionally annotated and classified into different Gossypium species [33].…”