Abstract
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 ≈55.27 and ≈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 AT and A2 genomes and between the DT and D5 genomes,
although there were a few exchanges and introgressions among the chromosomes of
the A2 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.