AUTHOR=Jiang Xiao , Gong Juwu , Zhang Jianhong , Zhang Zhen , Shi Yuzhen , Li Junwen , Liu Aiying , Gong Wankui , Ge Qun , Deng Xiaoying , Fan Senmiao , Chen Haodong , Kuang Zhengcheng , Pan Jingtao , Che Jincan , Zhang Shuya , Jia Tingting , Wei Renhui , Chen Quanjia , Wei Shoujun , Shang Haihong , Yuan Youlu 

TITLE=Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 12 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.753755

DOI=10.3389/fpls.2021.753755

ISSN=1664-462X

ABSTRACT=Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties( sGK156 and 901-001) and used here to investigate the source of high-quality related alleles. Base on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable QTLs, we found 289 QTLs and 1476 promising: 36 of them were stable QTLs, of which 18 were novel. Based on the transcriptome analysis for two parents and two RILs, 24941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength QTLs, 320 DEGs were identified, suggesting  that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence fiber strength, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits.