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.