Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton.
BACKGROUND
Improving fiber quality is a major challenge in cotton breeding, since the molecular basis of fiber quality traits is poorly understood. Fine mapping and candidate gene prediction of quantitative trait loci (QTL) controlling cotton fiber quality traits can help to elucidate the molecular basis of fiber quality. In our previous studies, one major QTL controlling multiple fiber quality traits was identified near the T1 locus on chromosome 6 in Upland cotton.


RESULTS
To finely map this major QTL, the F2 population with 6975 individuals was established from a cross between Yumian 1 and a recombinant inbred line (RIL118) selected from a recombinant inbred line population (T586 × Yumian 1). The QTL was mapped to a 0.28-cM interval between markers HAU2119 and SWU2302. The QTL explained 54.7 % (LOD = 222.3), 40.5 % (LOD = 145.0), 50.0 % (LOD = 194.3) and 30.1 % (LOD = 100.4) of phenotypic variation with additive effects of 2.78, -0.43, 2.92 and 1.90 units for fiber length, micronaire, strength and uniformity, respectively. The QTL region corresponded to a 2.7-Mb interval on chromosome 10 in the G. raimondii genome sequence and a 5.3-Mb interval on chromosome A06 in G. hirsutum. The fiber of Yumian 1 was much longer than that of RIL118 from 3 DPA to 7 DPA. RNA-Seq of ovules at 0 DPA and fibers at 5 DPA from Yumian 1 and RIL118 showed four genes in the QTL region of the G. raimondii genome to be extremely differentially expressed. RT-PCR analysis showed three genes in the QTL region of the G. hirsutum genome to behave similarly.


CONCLUSIONS
This study mapped a major QTL influencing four fiber quality traits to a 0.28-cM interval and identified three candidate genes by RNA-Seq and RT-PCR analysis. Integration of fine mapping and RNA-Seq is a powerful strategy to uncover candidates for QTL in large genomes.
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Dexin
D
Liu
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Jian
J
Zhang
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Xueying
X
Liu
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Wenwen
W
Wang
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Dajun
D
Liu
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Zhonghua
Z
Teng
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Xiaomei
X
Fang
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Zhaoyun
Z
Tan
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Shiyi
S
Tang
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Jinghong
J
Yang
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China.
Jianwei
J
Zhong
Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, 400716, Chongqing, People's Republic of China. zhangzs@swu.edu.cn.
Zhengsheng
Z
Zhang
D002874:Chromosome Mapping; D032561:Cotton Fiber; D003368:Gossypium / Q000235:genetics*; D010641:Phenotype; D040641:Quantitative Trait Loci; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D064201:Trichomes / Q000235:genetics
D018749:RNA, Plant
Fiber quality; Fine mapping; Gossypium hirsutum L.; Quantitative trait loci (QTL); RNA-Seq; Trichome