Genetic dissection and origin of pleiotropic loci underlying multi-level fiber quality traits in upland cotton (Gossypium hirsutum L.)

doi:10.1016/j.jia.2023.07.030

Journal of Integrative Agriculture

2024, Vol. 23

Issue (10): 3250-3263 DOI: 10.1016/j.jia.2023.07.030

Section 1: Cotton functional genomics

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Genetic dissection and origin of pleiotropic loci underlying multi-level fiber quality traits in upland cotton (Gossypium hirsutum L.)

Hongge Li^{1, 2*}, Shurong Tang^2*, Zhen Peng^{1, 2*}, Guoyong Fu², Yinhua Jia², Shoujun Wei², Baojun Chen², Muhammad Shahid Iqbal², Shoupu He^{1, 2#}, Xiongming Du^{1, 2#}

¹Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
² State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China

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摘要

棉花纤维品质决定着种植效益和棉纺织品的质量，因此受到人们的持续关注。然而，纤维品质检测仪器的局限性阻碍了对一些重要纤维特性（如纤维成熟度、细度和棉结）的准确评价，进而影响了对棉花纤维的遗传改良和工业化利用。本研究使用高级纤维信息系统仪(AFIS)对383个陆地棉 (Gossypium hirsutum L.) 品种的12个单纤维品质性状进行了检测。此外，还通过高容量仪器 (HVI) 检测了8种传统纤维品质性状。为了发掘纤维品质性状优异位点及其候选基因，我们相继开展了全基因组关联研究（GWAS）、连锁不平衡（LD）区块基因分型和功能鉴定。结果显示，控制纤维长度相关性状的多效性位点FL_D11在本研究中再次被鉴定到。更重要的是，基于AFIS性状我们鉴定到了调节纤维成熟度、细度和棉结的三个新的多效性位点（FM_A03、FF_A05、FN_A07）。联合 RNA-seq和qRT-PCR 分析，我们筛选出多个纤维品质候选基因，包括已经报道的纤维长度基因GhKRP6、新鉴定的成熟度候选基因GhMAP8 和细度候选基因GhDFR。多效性位点的起源和进化分析表明，随着育种时期的临近，FL_D11、FM_A03和FF_A05的选择压力将增大，而FM_A03和FF_A05可能来源于棉花地方品种。本文研究结果不仅揭示了纤维品质的遗传基础，而且为陆地棉纤维品质的遗传改良和纺织利用提供了新的视角。

Abstract

Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile products. However, the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity, fineness, and neps, which in turn has impeded the genetic improvement and industrial utilization of cotton fiber. Here, 12 single fiber quality traits were measured using Advanced Fiber Information System (AFIS) equipment among 383 accessions of upland cotton (Gossypium hirsutum L.). In addition, eight conventional fiber quality traits were assessed by the High Volume Instrument (HVI) System. Genome-wide association study (GWAS), linkage disequilibrium (LD) block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality traits. As a result, the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this study. More importantly, three novel pleiotropic loci (FM_A03, FF_A05, and FN_A07) regulating fiber maturity, fineness and neps, respectively, were detected based on AFIS traits. Numerous highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses, including the reported GhKRP6 for fiber length, the newly identified GhMAP8 for maturity and GhDFR for fineness. The origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11, FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton landraces. These findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in G. hirsutum.

Keywords: upland cotton single fiber quality pleiotropic loci candidate genes locus origin

Received: 06 May 2023 Accepted: 04 July 2023

Fund:

The authors appreciate the National Mid-term Gene Bank for Cotton at the Institute of Cotton Research, Chinese Academy of Agricultural Sciences for providing the cotton germplasm seeds. This work was supported by the National Key Research and Development Program of China (2022YFD1200300), the Central Plain Scholar Program, China (234000510004) and the National Supercomputing Center in Zhengzhou, China.

About author: Hongge Li, Tel: +86-372-2562252, E-mail: lihongge@caas.cn; #Correspondence Xiongming Du, Tel: +86-372-2562252, E-mail: dujeffrey8848@hotmail.com; Shoupu He, Tel: +86-372-2565353, E-mail: heshoupu@caas.cn * These authors contributed equally to this study. * These authors contributed equally to this work.

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	Hongge Li
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Cite this article:

Hongge Li, Shurong Tang, Zhen Peng, Guoyong Fu, Yinhua Jia, Shoujun Wei, Baojun Chen, Muhammad Shahid Iqbal, Shoupu He, Xiongming Du. 2024. Genetic dissection and origin of pleiotropic loci underlying multi-level fiber quality traits in upland cotton (Gossypium hirsutum L.). Journal of Integrative Agriculture, 23(10): 3250-3263.

Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23, 2633–2635.

Cai C, Ye W, Zhang T, Guo W. 2014. Association analysis of fiber quality traits and exploration of elite alleles in upland cotton cultivars/accessions (Gossypium hirsutum L.). Journal of Integrative Plant Biology, 56, 51–62.

Cheng Y, Huang C, Hu Y, Jin S, Zhang X, Si Z, Zhao T, Chen J, Fang L, Dai F, Yang W, Wang P, Mei G, Guan X, Zhang T. 2024. Gossypium purpurascens genome provides insight into the origin and domestication of upland cotton. Journal of Advanced Research, 56, 15–29.

Dai P, Miao Y, He S, Pan Z, Jia Y, Cai Y, Sun J, Wang L, Pang B, Wang M, Du X. 2019. Identifying favorable alleles for improving key agronomic traits in upland cotton. BMC Plant Biology, 19, 138.

Danecek P, Auton A, Abecasis G, Albers C A, Banks E, DePristo M A, Handsaker R E, Lunter G, Marth G T, Sherry S T, McVean G, Durbin R, Genomes Project Anal G. 2011. The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.

Feng H, Tian X, Liu Y, Li Y, Zhang X, Jones B J, Sun Y, Sun J. 2013. Analysis of flavonoids and the flavonoid structural genes in brown fiber of upland cotton. PLoS ONE, 8, e58820.

Feng H J, Sun J L, Wang J, Jia Y H, Zhang X Y, Pang B Y, Sun J, Du X M. 2011. Genetic effects and heterosis of the fibre colour and quality of brown cotton (Gossypium hirsutum). Plant Breeding, 130, 450–456.

Feng X, Zhang Y, Wang H, Tian Z, Xin S, Zhu P. 2021. The dihydroflavonol 4-reductase BoDFR1 drives anthocyanin accumulation in pink-leaved ornamental kale. Theoretical and Applied Genetics, 134, 159–169.

He S, Sun G, Geng X, Gong W, Dai P, Jia Y, Shi W, Pan Z, Wang J, Wang L, Xiao S, Chen B, Cui S, You C, Xie Z, Wang F, Sun J, Fu G, Peng Z, Hu D, et al. 2021. The genomic basis of geographic differentiation and fiber improvement in cultivated cotton. Nature Genetics, 53, 916–924.

Hequet E F. 2006. Creation of a set of reference material for cotton fiber maturity measurements. Textile Research Journal, 76, 576–586.

Hu Y, Chen J, Fang L, Zhang Z, Ma W, Niu Y, Ju L, Deng J, Zhao T, Lian J, Baruch K, Fang D, Liu X, Ruan Y L, Rahman M U, Han J, Wang K, Wang Q, Wu H, Mei G, et al. 2019. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nature Genetics, 51, 739–748.

Huang G, Huang J Q, Chen X Y, Zhu Y X. 2021. Recent advances and future perspectives in cotton research. Annual Review of Plant Biology, 72, 437–462.

Iqbal M S, Tang S, Sarfraz Z, Iqbal M S, Li H, He S, Jia Y, Sun G, Pan Z, Geng X, Mahmood A, Ahmad S, Nazir M F, Chen B, Wang L, Pang B, Wei S, Du X. 2021. Genetic factors underlying single fiber quality in A-genome donor Asian cotton (Gossypium arboreum). Frontiers in Genetics, 12, 758665.

Kang H M, Sul J H, Service S K, Zaitlen N A, Kong S Y, Freimer N B, Sabatti C, Eskin E. 2010. Variance component model to account for sample structure in genome-wide association studies. Nature Genetics, 42, 348–354.

Li H, Wang X, Qin N, Hu D, Jia Y, Sun G, He L, Zhang H, Dai P, Peng Z, Pang N, Pan Z, Zhang X, Dong Q, Chen B, Gui H, Pang B, Zhang X, He S, Song M, et al. 2024. Genomic loci associated with leaf abscission contribute to machine picking and environmental adaptability in upland cotton (Gossypium hirsutum L.). Journal of Advanced Research, 58, 31–43.

Li Z, Wang P, You C, Yu J, Zhang X, Yan F, Ye Z, Shen C, Li B, Guo K, Liu N, Thyssen G N, Fang D D, Lindsey K, Zhang X, Wang M, Tu L. 2020. Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton. The New Phytologist, 226, 1738–1752.

Liu W, Song C, Ren Z, Zhang Z, Pei X, Liu Y, He K, Zhang F, Zhao J, Zhang J, Wang X, Yang D, Li W. 2020. Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.). BMC Plant Biology, 20, 395.

Ma Z, He S, Wang X, Sun J, Zhang Y, Zhang G, Wu L, Li Z, Liu Z, Sun G, Yan Y, Jia Y, Yang J, Pan Z, Gu Q, Li X, Sun Z, Dai P, Liu Z, Gong W, et al. 2018. Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield. Nature Genetics, 50, 803–813.

Merk H L, Yarnes S C, Van Deynze A, Tong N, Menda N, Mueller L A, Mutschler M A, Loewen S A, Myers J R, Francis D M. 2012. Trait diversity and potential for selection indices based on variation among regionally adapted processing tomato germplasm. Journal of the American Society for Horticultural Science, 137, 427–437.

Nie X, Huang C, You C, Li W, Zhao W, Shen C, Zhang B, Wang H, Yan Z, Dai B, Wang M, Zhang X, Lin Z. 2016. Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China. BMC Genomics, 17, 352.

Paudel D R, Hequet E F, Abidi N. 2013. Evaluation of cotton fiber maturity measurements. Industrial Crops and Products, 45, 435–441.

Said J I, Knapka J A, Song M, Zhang J. 2015. Cotton QTLdb: A cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum × G. barbadense populations. Molecular Genetics and Genomics, 290, 1615–1625.

Su J, Ma Q, Li M, Hao F, Wang C. 2018. Multi-locus genome-wide association studies of fiber-quality related traits in Chinese early-maturity upland cotton. Frontiers in Plant Science, 9, 1169.

Sun Z, Wang X, Liu Z, Gu Q, Zhang Y, Li Z, Ke H, Yang J, Wu J, Wu L, Zhang G, Zhang C, Ma Z. 2017. Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L. Plant Biotechnology Journal, 15, 982–996.

Thyssen G N, Fang D D, Zeng L, Song X, Delhom C D, Condon T L, Li, Kim H J. 2016. The immature fiber mutant phenotype of cotton (Gossypium hirsutum) is linked to a 22-bp frame-shift deletion in a mitochondria targeted pentatricopeptide repeat gene. Genes Genomes Genetics, 6, 1627–1633.

Thyssen G N, Jenkins J N, McCarty J C, Zeng L, Campbell B T, Delhom C D, Islam M S, Li P, Jones D C, Condon B D, Fang D D. 2019. Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics, 132, 989–999.

Turner S D. 2014. qqman: An R package for visualizing GWAS results using QQ and manhattan plots. bioRxiv: 005165.

Wang K, Li M, Hakonarson H. 2010. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38, e164.

Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L, Zhou X, Nie X, Li Z, Guo K, Ma Y, Huang C, Jin S, Zhu L, Yang X, Min L, et al. 2017. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nature Genetics, 49, 579–587.

Wang P, Dong N, Wang M, Sun G, Jia Y, Geng X, Liu M, Wang W, Pan Z, Yang Q, Li H, Wei C, Wang L, Zheng H, He S, Zhang X, Wang Q, Du X. 2022. Introgression from Gossypium hirsutum is a driver for population divergence and genetic diversity in Gossypium barbadense. The Plant Journal, 110, 764–780.

Wen T, Wu M, Shen C, Gao B, Zhu D, Zhang X L, You C Y, Lin Z X. 2018. Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum). Plant Biotechnology Journal, 16, 1654–1666.

Wen Y, He P, Bai X, Zhang H, Zhang Y, Yu J.2024. Strigolactones modulate cotton fiber elongation and secondary cell wall thickening. Journal of Integrative Agriculture, 23, 1850–1863.

Yang Z, Ge X, Yang Z, Qin W, Sun G, Wang Z, Li Z, Liu J, Wu J, Wang Y, Lu L, Wang P, Mo H, Zhang X, Li F. 2019. Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nature Communications, 10, 2989.

Yang Z, Qanmber G, Wang Z, Yang Z, Li F. 2020. Gossypium genomics: Trends, scope, and utilization for cotton improvement. Trends in Plant Science, 25, 488–500.

Zeng J, Xi J, Li B, Yan X, Dai Y, Wu Y, Xiao Y, Pei Y, Zhang M. 2022. Microtubules play a crucial role in regulating actin organization and cell initiation in cotton fibers. Plant Cell Reports, 41, 1059–1073.

Zhu S H, Xue F, Li Y J, Liu F, Zhang X Y, Zhao L J, Sun Y Q, Zhu Q H, Sun J. 2018. Identification and functional characterization of a microtubule-associated protein, GhCLASP2, from upland cotton (Gossypium hirsutum L.). Frontiers in Plant Science, 9, 882.

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