陆地棉D11染色体一个纤维长度主效位点的遗传解析

doi:10.3724/SP.J.1006.2025.44049

Abstract

Abstract:

Cotton fiber length is a crucial index of fiber quality, and analyzing its genetic basis is is significant for cultivating high-quality cotton varieties. To identify valuable loci related to cotton fiber quality, we utilized 40K SNP (single-nucleotide polymorphism) chips, were used to analyze fiber length-related QTLs in recombinant inbred lines (RIL) and SNP sites in natural populations of upland cotton. Four QTLs for fiber length were obtained from Q30-12 × 05SJ RIL, and located on chromosomes A05, D11 and D13, respectively. Twenty-four SNPs significantly associated fiber length were identified in natural populations, and located on chromosomes A01, A03, D05, D11, and D12, respectively. Based on the results of linkage analysis and association analysis, an overlapping region closely related to fiber length was found in the 23.99–24.01 Mb region of chromosome D11. Haplotype analysis revealed that the fiber length of germplasm carrying the Hap1 haplotype was significantly longer than that of the Hap2 haplotype. Approximately 95.3% of varieties from the Yellow River basin carried the Hap1 haplotype, whereas 45.5% of varieties from the northwest inland cotton region carried the Hap1 haplotype. More than half of the varieties from the northwest inland region with the Hap1 haplotype were related to the Yellow River basin cotton region. Three candidate genes, CML1, DTX51, and PCMP-E88, were discovered in the 28.4 kb region of Chr.D11 overlap interval by bioinformatics analysis, which may play an important role in cotton fiber elongation. In summary, the Hap1 haplotype identified in this study represents an excellent haplotype with significant application value for improving cotton fiber quality. Our results provide a reliable basis for analyzing fiber length-related loci and candidate genes on chromosome D11.

Key words: Gossypium hirsutum, fiber length, QTL mapping, genome-wide association analysis

GUO Shu-Hui, PAN Zhuan-Xia, ZHAO Zhan-Sheng, YANG Liu-Liu, HUANG-FU Zhang-Long, GUO Bao-Sheng, HU Xiao-Li, LU Ya-Dan, DING Xiao, WU Cui-Cui, LAN Gang, LYU Bei-Bei, TAN Feng-Ping, LI Peng-Bo. Genetic analysis of a major fiber length locus on chromosome D11 of upland cotton[J].Acta Agronomica Sinica, 2025, 51(2): 383-394.

References

[1] Fang L, Wang Q, Hu Y, Jia Y H, Chen J D, Liu B L, Zhang Z Y, Guan X Y, Chen S Q, Zhou B L, Mei G F, Sun J L, Pan Z E, He S P, Xiao S H, Shi W J, Gong W F, Liu J G, Ma J, Cai C P, Zhu X F, Guo W Z, Du X M, Zhang T Z. Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat Genet, 2017, 49: 1089–1098.

[2] 李付广. 全产业链布局推进中国棉花提质增效及提升国际竞争力. 农学学报, 2019, 9(3): 6–10.

Li F G. China’s cotton industry through construction of the whole industrial chain: Improving quality and performance and enhancing international competitiveness. J Agric, 2019, 9(3): 6–10 (in Chinese with English abstract).

[3] Su J J, Li L B, Pang C Y, Wei H L, Wang C X, Song M Z, Wang H T, Zhao S Q, Zhang C, Mao G Z, Huang L, Wang C S, Fan S L, Yu S X. Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection. Sci Rep, 2016, 6: 38496.

[4] Sohu R S, Singh P, Gill B S. Genetic analysis of fiber traits in upland cotton (Gossypium hirsutum L.). J Cotton Res Dev, 2016, 30: 22–28.

[5] Zhang C, Li L B, Liu Q B, Gu L J, Huang J Q, Wei H L, Wang H T, Yu S X. Identification of loci and candidate genes responsible for fiber length in upland cotton (Gossypium hirsutum L.) via association mapping and linkage analyses. Front Plant Sci, 2019, 10: 53.

[6] Said J I, Knapka J A, Song M Z, Zhang J F. Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum ´ G. barbadense populations. Mol Genet Genomics, 2015, 290: 1615–1625.

[7] Ijaz B, Zhao N, Kong J, Hua J P. Fiber quality improvement in upland cotton (Gossypium hirsutum L.): quantitative trait loci mapping and marker assisted selection application. Front Plant Sci, 2019, 10: 1585.

[8] Ma Z Y, He S P, Wang X F, Sun J L, Zhang Y, Zhang G Y, Wu L Q, Li Z K, Liu Z H, Sun G F, Yan Y Y, Jia Y H, Yang J, Pan Z E, Gu Q S, Li X Y, Sun Z W, Dai P H, Liu Z W, Gong W F, Wu J H, Wang M, Liu H W, Feng K Y, Ke H F, Wang J D, Lan H Y, Wang G N, Peng J, Wang N, Wang L R, Pang B Y, Peng Z, Li R Q, Tian S L, Du X M. Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield. Nat Genet, 2018, 50: 803–813.

[9] Tang W X, Tu L L, Yang X Y, Tan J F, Deng F L, Hao J, Guo K, Lindsey K, Zhang X L. The calcium sensor GhCaM7 promotes cotton fiber elongation by modulating reactive oxygen species (ROS) production. New Phytol, 2014, 202: 509–520.

[10] 马艳明, 娄鸿耀, 王威, 孙娜, 颜国荣, 张胜军, 刘杰, 倪中福, 徐麟. 新疆冬小麦籽粒品质性状遗传差异与关联分析. 作物学报, 2024, 50: 1394–1405.

Ma Y M, Lou H Y, Wang W, Sun N, Yan G R, Zhang S J, Liu J, Ni Z F, Xu L. Genetic difference and genome association analysis of grain quality traits in Xinjiang winter wheat. Acta Agron Sin, 2024, 50: 1394–1405 (in Chinese with English abstract).

[11] 毕俊鸽, 曾占奎, 李琼, 洪壮壮, 颜群翔, 赵越, 王春平. 两个RIL群体中小麦籽粒品质相关性状QTL定位及KASP标记开发. 作物学报, 2024, 50 : 1669–1683.

Bi J G, Zeng Z K, Li Q, Hong Z Z, Yan Q X, Zhao Y, Wang C P. QTL mapping and KASP marker development of grain quality-relating traits in two wheat RIL populations. Acta Agron Sin, 2024, 50: 1669–1683 (in Chinese with English abstract).

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

[13] 柯会锋, 张震, 谷淇深, 赵艳, 李培育, 张冬梅, 崔彦茹, 王省芬, 吴立强, 张桂寅, 马峙英, 孙正文. 低磷胁迫下陆地棉苗期根生物量相关性状全基因组关联分析. 作物学报, 2022, 48: 2168–2179.

Ke H F, Zhang Z, Gu Q S, Zhao Y, Li P Y, Zhang D M, Cui Y R, Wang X F, Wu L Q, Zhang G Y, Ma Z Y, Sun Z W. Genome-wide association study of root biomass related traits at seeding stage under low phosphorus stress in cotton (Gossypium hirsutum L.). Acta Agron Sin, 2022, 48: 2168–2179 (in Chinese with English abstract).

[14] 姜洪真, 马伯军, 钱前, 高振宇. 全基因组关联分析(GWAS)在作物农艺性状研究中的应用. 农业生物技术学报, 2018, 26: 1244–1257.

Jiang H Z, Ma B J, Qian Q, Gao Z Y. The application of genome-wide association study (GWAS) in crop agronomic traits. J Agric Biotechnol, 2018, 26: 1244–1257 (in Chinese with English abstract).

[15] Li X Y, Wang P, Zhang K X, Liu S L, Qi Z Y, Fang Y L, Wang Y, Tian X C, Song J, Wang J J, Yang C, Sun X, Tian Z X, Li W X, Ning H L. Fine mapping QTL and mining genes for protein content in soybean by the combination of linkage and association analysis. Theor Appl Genet, 2021, 134: 1095–1122.

[16] Gong J W, Peng Y, Yu J W, Pei W F, Zhang Z, Fan D R, Liu L J, Xiao X H, Liu R X, Lu Q W, Li P T, Shang H H, Shi Y Z, Li J W, Ge Q, Liu A Y, Deng X Y, Fan S M, Pan J T, Chen Q J, Yuan Y L, Gong W K. Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton. Comput Struct Biotechnol J, 2022, 20: 1841–1859.

[17] Zhang Z P, Li Z, He F, Lyu J J, Xie B, Yi X Y, Li J M, Li J, Song J H, Pu Z E, Ma J, Peng Y Y, Chen G Y, Wei Y M, Zhang Y L, Li W. Genome-wide association and linkage mapping strategies reveal the genetic loci and candidate genes of important agronomic traits in Sichuan wheat. J Integr Agric, 2023, 22: 3380–3393.

[18] Wang H, Xu S T, Fan Y M, Liu N N, Zhan W, Liu H J, Xiao Y J, Li K, Pan Q C, Li W Q, Deng M, Liu J, Jin M, Yang X H, Li J S, Li Q, Yan J B. Beyond pathways: genetic dissection of tocopherol content in maize kernels by combining linkage and association analyses. Plant Biotechnol J, 2018, 16: 1464–1475.

[19] 霍强, 杨鸿, 陈志友, 荐红举, 曲存民, 卢坤, 李加纳. 基于QTL定位和全基因组关联分析筛选甘蓝型油菜株高和一次有效分枝高度的候选基因. 作物学报, 2020, 46: 214–227.

Huo Q, Yang H, Chen Z Y, Jian H J, Qu C M, Lu K, Li J N. Candidate genes screening for plant height and the first branch height based on QTL mapping and genome-wide association study in rapeseed (Brassica napus L.). Acta Agron Sin, 2020, 46: 214–227 (in Chinese with English abstract).

[20] Liu R X, Gong J W, Xiao X H, Zhang Z, Li J W, Liu A Y, Lu Q W, Shang H H, Shi Y Z, Ge Q, Iqbal Muhammad S, Deng X Y, Li S Q, Pan J T, Duan L, Zhang Q, Jiang X, Zou X Y, Hafeez A, Chen Q J, Geng H W, Gong W K, Yuan Y L. GWAS analysis and QTL identification of fiber quality traits and yield components in upland cotton using enriched high-density SNP markers. Front Plant Sci, 2018, 9: 1067.

[21] 温天旺. 连锁和关联作图解析棕色棉重要农艺性状的遗传基础. 华中农业大学博士学位论文, 湖北武汉, 2019.

Wen T W. Genetic Basis of the Agronomic Traits of Brown Fiber Cotton Revealed by Linkage and Association Mapping. PhD Dissertation of Huazhong Agricultural University, Wuhan, Hubei, China, 2019 (in Chinese with English abstract).

[22] Wang M J, Tu L L, Lin M, Lin Z X, Wang P C, Yang Q Y, Ye Z X, Shen C, Li J Y, Zhang L, Zhou X L, Nie X H, Li Z H, Guo K, Ma Y Z, Huang C, Jin S X, Zhu L F, Yang X Y, Min L, Yuan D J, Zhang Q H, Lindsey K, Zhang X L. Asymmetric sub genome selection and cis-regulatory divergence during cotton domestication. Nat Genet, 2017, 49: 579–587.

[23] 宋国立, 崔荣霞, 王坤波, 郭立平, 黎绍惠, 王春英, 张香娣. 改良CTAB法快速提取棉花DNA. 棉花学报, 1998, 10(5): 50–52.

Song G L, Cui R X, Wang K B, Guo L P, Li S H, Wang C Y, Zhang X D. A rapid improved CTAB method for extraction of cotton genomic DNA. Cotton Sci, 1998, 10(5): 50–52 (in Chinese with English abstract).

[24] 徐云碧, 杨泉女, 郑洪建, 许彦芬, 桑志勤, 郭子锋, 彭海, 张丛, 蓝昊发, 王蕴波, 吴坤生, 陶家军, 张嘉楠. 靶向测序基因型检测(GBTS)技术及其应用. 中国农业科学, 2020, 53: 2983–3004.

Xu Y B, Yang Q N , Zheng H J, Xu Y F, Sang Z Q, Guo Z F, Peng H, Zhang C, Lan H F, Wang Y B, Wu K S, Tao J J, Zhang J N. Genotyping by target sequencing (GBTS) and its applications. Sci Agric Sin, 2020, 53: 2983–3004 (in Chinese with English abstract).

[25] Si Z F, Jin S K, Li J Y, Han Z G, Li Y Q, Wu X N, Ge Y X, Fang L, Zhang T Z, Hu Y. The design, validation, and utility of the “ZJU CottonSNP40K” liquid chip through genotyping by target sequencing. Ind Crops Prod, 2022, 188: 115629.

[26] Su J J, Wang C X, Yang D L, Shi C H, Zhang A, Ma Q, Liu J J, Zhang X L, Huang L, Ma X F. Decryption of favorable haplotypes and potential candidate genes for five fiber quality properties using a relatively novel genome-wide association study procedure in upland cotton. Ind Crops Prod, 2020, 158: 113004.

[27] Meng L, Li H H, Zhang L Y, Wang J K. QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J, 2015, 3: 269–283.

[28] Su J J, Ma Q, Li M, Hao F S, Wang C X. Multi-locus genome-wide association studies of fiber-quality related traits in Chinese early-maturity upland cotton. Front Plant Sci, 2018, 9: 1169.

[29] Liu S, Fan C C, Li J N, Cai G Q, Yang Q Y, Wu J, Yi X Q, Zhang C Y, Zhou Y M. A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus. Theor Appl Genet, 2016, 129: 1203–1215.

[30] Chang C C, Chow C C, Tellier L C, Vattikuti S, Purcell S M, Lee J J. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience, 2015, 4: 7.

[31] Zhang T Z, Hu Y, Jiang W K, Fang L, Guan X Y, Chen J D, Zhang J B, Saski C A, Scheffler B E, Stelly D M, Hulse-Kemp A M, Wan Q, Liu B L, Liu C X, Wang S, Pan M Q, Wang Y K, Wang D W, Ye W X, Chang L J, Zhang W P, Song Q X, Kirkbride R C, Chen X Y, Dennis E, Llewellyn D J, Peterson D G, Thaxton P, Jones D C, Wang Q, Xu X Y, Zhang H, Wu H T, Zhou L, Mei G F, Chen S Q, Tian Y, Xiang D, Li X H, Ding J, Zuo Q Y, Tao L N, Liu Y C, Li J, Lin Y, Hui Y Y, Cao Z S, Cai C P, Zhu X F, Jiang Z, Zhou B L, Guo W Z, Li R Q, Chen Z J. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM–1) provides a resource for fiber improvement. Nature Biotechnol, 2015, 33: 531–537.

[32] Zhu T, Liang C Z, Meng Z G, Sun G Q, Meng Z H, Guo S D, Zhang R. CottonFGD: an integrated functional genomics database for cotton. BMC Plant Biol, 2017, 17: 101.

[33] Naoumkina M, Thyssen G N, Fang D D, Jenkins J N, McCarty J C, Florane C B. Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population. BMC Genomics, 2019, 20: 112.

[34] Chen H, Han Z G, Ma Q, Dong C G, Ning X Z, Li J L, Lin H, Xu S Z, Li Y Q, Hu Y, Si Z F, Song Q P. Identification of elite fiber quality loci in upland cotton based on the genotyping-by-target-sequencing technology. Front Plant Sci, 2022, 13: 1027806.

[35] 赵芊, 赵雪萌, 宋聪, 黄媛媛, 贾振华, 宋水山.植物CaMs/CMLs家族研究进展. 植物生理学报, 2024, 60: 1357–1366.

Zhao Q, Zhao X M, Song C, Huang Y Y, Jia Z H, Song S S. Research progress of CaMs/CMLs family in plant. Plant Physiol J, 2024, 60: 1357–1366 (in Chinese with English abstract).

[36] 何永辉. 棉花钙调素与类钙调素基因家族表达分析及棉花纤维离子组测定. 华中农业大学硕士学位论文, 湖北武汉, 2015.

He Y H. Expression Analysis of Calmodulin and Calmodulin-like Gene Family and Ionome Analysis of Cotton Fiber. MS Thesis of Huazhong Agricultural University, Wuhan, Hubei, China, 2015 (in Chinese with English abstract).

[37] Wang R, Liu X Y, Liang S, Ge Q, Li Y F, Shao J X, Qi Y F, An L J, Yu F. A subgroup of MATE transporter genes regulates hypocotyl cell elongation in Arabidopsis. J Exp Bot, 2015, 66: 6327–6343.

[38] Zhao N, Wang Y M, Hua J P. Genomewide identification of PPR gene family and prediction analysis on restorer gene in Gossypium. J Genet, 2018, 97: 1083–1095.

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Genetic analysis of a major fiber length locus on chromosome D11 of upland cotton

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