Journal
DNA RESEARCH
Volume 22, Issue 2, Pages 147-160Publisher
OXFORD UNIV PRESS
DOI: 10.1093/dnares/dsu047
Keywords
Gossypium hirsutum; RAD sequencing; genetic map; QTL mapping; comparative genomics
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Funding
- National Basic Research Program [2011CB109303]
- Fundamental Research Funds for the Central Universities [2014PY015]
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RAD sequencing was performed using DH962 and Jimian5 as upland cotton mapping parents. Sequencing data for DH962 and Jimian5 were assembled into the genome sequences of approximate to 55.27 and approximate to 57.06 Mb, respectively. Analysing genome sequences of the two parents, 1,323 SSR, 3,838 insertion/deletion (InDel), and 9,366 single-nucleotide polymorphism (SNP) primer pairs were developed. All of the SSRs, 121 InDels, 441 SNPs, and other 6,747 primer pairs were screened in the two parents, and a total of 535 new polymorphic loci were identified. A genetic map including 1,013 loci was constructed using these results and 506 loci previously published for this population. Twenty seven new QTLs for yield and fibre quality were identified, indicating that the efficiency of QTL detection was greatly improved by the increase in map density. Comparative genomics showed there to be considerable homology and collinearity between the A(T) and A(2) genomes and between the D-T and D-5 genomes, although there were a few exchanges and introgressions among the chromosomes of the A(2) genome. Here, the development of markers using parental RAD sequencing was effective, and a high-density intraspecific genetic map was constructed. This map can be used for molecular marker-assisted selection in cotton.
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