Detection of Favorable QTL Alleles and Candidate Genes for Lint Percentage by GWAS in Chinese Upland Cotton.
Improving cotton yield is a major breeding goal for Chinese upland cotton. Lint percentage is an important yield component and a critical economic index for cotton cultivars, and raising the lint percentage has a close relationship to improving cotton lint yield. To investigate the genetic architecture of lint percentage, a diversity panel consisting of 355 upland cotton accessions was grown, and the lint percentage was measured in four different environments. Genotyping was performed with specific-locus amplified fragment sequencing (SLAF-seq). Twelve single-nucleotide polymorphisms (SNPs) associated with lint percentage were detected via a genome-wide association study (GWAS), in which five SNP loci distributed on chromosomes At3 (A02) and At4 (A08) and contained two major-effect QTLs, which were detected in the best linear unbiased predictions (BLUPs) and in more than three environments simultaneously. Furthermore, favorable haplotypes (FHs) of two major-effect QTLs and 47 putative candidate genes in the two linkage disequilibrium (LD) blocks of these associated loci were identified. The expression levels of these putative candidate genes were estimated using RNA-seq data from ten upland cotton tissues. We found thatGh_A02G1268was very highly expressed during the early fiber development stage, whereas the gene was poorly expressed in the seed. These results implied thatGh_A02G1268may determine the lint percentage by regulating seed and fiber development. The favorable QTL alleles and candidate genes for lint percentage identified in this study will have high potential for improving lint yield in future Chinese cotton breeding programs.
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China; Department of Plant Sciences, College of Agronomy, Northwest A&F UniversityYangling, China.
Junji
J
Su
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Shuli
S
Fan
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Libei
L
Li
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Hengling
H
Wei
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Caixiang
C
Wang
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Hantao
H
Wang
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Meizhen
M
Song
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Chi
C
Zhang
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Lijiao
L
Gu
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Shuqi
S
Zhao
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Guangzhi
G
Mao
Department of Plant Sciences, College of Agronomy, Northwest A&F University Yangling, China.
Chengshe
C
Wang
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS Anyang, China.
Chaoyou
C
Pang
State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China; Department of Plant Sciences, College of Agronomy, Northwest A&F UniversityYangling, China.
Shuxun
S
Yu
candidate genes; favorable haplotypes; genome-wide association study; lint percentage; upland cotton