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Abstract Background: Gossypium hirsutum L., or upland cotton, is an important renewable resource for textile fiber.
To enhance understanding of the genetic basis of cotton earliness, we constructed an intra-specific recombinant
inbred line population (RIL) containing 137 lines, and performed linkage map construction and quantitative trait
locus (QTL) mapping.
Results: Using restriction-site associated DNA sequencing, a genetic map composed of 6,434 loci, including 6,295
single nucleotide polymorphisms and 139 simple sequence repeat loci, was developed from RIL population. This map
spanned 4,071.98 cM, with an average distance of 0.63 cM between adjacent markers. A total of 247 QTLs for six
earliness-related traits were detected in 6 consecutive years. In addition, 55 QTL coincidence regions representing more
than 60 % of total QTLs were found on 22 chromosomes, which indicated that several earliness-related traits might be
simultaneously improved. Fine-mapping of a 2-Mb region on chromosome D3 associated with five stable QTLs
between Marker25958 and Marker25963 revealed that lines containing alleles derived from CCRI36 in this region
exhibited smaller phenotypes and earlier maturity. One candidate gene (EMF2) was predicted and validated by
quantitative real-time PCR in early-, medium- and late-maturing cultivars from 3- to 6-leaf stages, with highest
expression level in early-maturing cultivar, CCRI74, lowest expression level in late-maturing cultivar, Bomian1.
Conclusions: We developed an SNP-based genetic map, and this map is the first high-density genetic map for
short-season cotton and has the potential to provide deeper insights into earliness. Cotton earliness-related QTLs and
QTL coincidence regions will provide useful materials for QTL fine mapping, gene positional cloning and MAS. And the
gene, EMF2, is promising for further study.
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