title: Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing.
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.
authors: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors: Hantao
authors: H
authors: Wang
authors: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors: Xin
authors: X
authors: Jin
authors: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors: Beibei
authors: B
authors: Zhang
authors: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
authors: Chao
authors: C
authors: Shen
authors: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China linzhongxu@mail.hzau.edu.cn.
authors: Zhongxu
authors: Z
authors: Lin
mesh_terms: D001483:Base Sequence; D003433:Crosses, Genetic; D020224:Expressed Sequence Tags; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics; D003368:Gossypium / Q000235:genetics*; D054643:INDEL Mutation; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D020161:Physical Chromosome Mapping / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers
keywords: Gossypium hirsutum, RAD sequencing; QTL mapping; comparative genomics; genetic map
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