Abstract
BackgroundCotton, 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)2 genome.ResultsA total of 3177 new EST-SSRs developed in our laboratory and other newly released SSRs were used to enrich our interspecific BC1 genetic 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.ConclusionsThis 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.
Highlights
Cotton, with a large genome, is an important crop throughout the world
The early cotton genetic maps were comprised of only restriction fragment length polymorphisms (RFLPs) [2]; later, polymerase chain reaction (PCR)-based markers were widely adopted, including random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), sequence-related amplified polymorphism (SRAP), and target region amplification polymorphism (TRAP) [1]
Marker development A total of 1831 new expressed sequence tags (ESTs)-SSRs were developed from the assembled cotton ESTs in the the Institute for Genome Research (TIGR) database http://www. tigr.org based on the criteria of marker development: 346 from G. arboretum (HAU231-HAU576), 293 from G. raimondii (HAU577HAU869), and 1192 from G. hirsutum (HAU870HAU2061)
Summary
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. The early cotton genetic maps were comprised of only restriction fragment length polymorphisms (RFLPs) [2]; later, polymerase chain reaction (PCR)-based markers were widely adopted, including random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), sequence-related amplified polymorphism (SRAP), and target region amplification polymorphism (TRAP) [1]. SSRs, consisting of a variable number of tandem repeats, are mainly characterized by their high frequency, even distribution, co-dominance, reproducibility, and high polymorphism [14,15] Because of these characteristics, microsatellites have become the most favoured genetic markers for plant breeding and genetics such as genetic diversity assessment, genetic map construction, QTL mapping, and marker aided selection, etc [16]. Mining SSRs from ESTs is becoming popular for SSR development
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