, 215:35 | Cite as

Genome-wide association study reveals the genetic control underlying node of the first fruiting branch and its height in upland cotton (Gossypium hirsutum L.)

  • Yuanzhi Fu
  • Chengguang Dong
  • Juan Wang
  • Yuanyuan Wang
  • Chengqi LiEmail author


Improving early maturity in upland cotton (Gossypium hirsutum L.) is an important target in breeding. The node of the first fruiting branch (NFFB) and its height (HNFFB) are two important indexes to measure early maturity in cotton. To facilitate breeding for early maturity traits in upland cotton and reveal the genetic control underlying the two traits, a genome-wide association study was performed using 53,848 high-quality single nucleotide polymorphisms (SNPs) from 77,774 of a recently developed CottonSNP80K array. A total of 55 target trait-associated SNPs were detected, of which 12 SNPs were for NFFB and 43 were for HNFFB. Two SNPs for NFFB and 22 SNPs for HNFFB were repeatedly detected in at least two environments and/or by two models. These 24 SNPs also exhibited high phenotypic contributions of more than 10% and could be used for marker-assisted selection in future breeding programs. Furthermore, 89 candidate genes were identified in the genome sequence of upland cotton. These genes were categorized through Gene Ontology analysis. Gh_A05G1482 might be a potential candidate gene for improving the early maturation of cotton. These findings reveal the genetic control underlying NFFB and HNFFB and provide insight into genetic improvements for early maturity in upland cotton.


Upland cotton Genome-wide association study Node of the first fruiting branch Height of node of the first fruiting branch Single nucleotide polymorphism Candidate gene 



This work was supported by the Natural Science Foundation of China (31371677) and the Innovative Talent Support Program of Science and Technology of Henan Institute of Higher Learning (16HASTIT014).

Supplementary material

10681_2019_2361_MOESM1_ESM.xls (20 kb)
Supplementary material 1 (XLS 20 kb)
10681_2019_2361_MOESM2_ESM.xls (52 kb)
Supplementary material 2 (XLS 52 kb)
10681_2019_2361_MOESM3_ESM.xls (203 kb)
Supplementary material 3 (XLS 203 kb)
10681_2019_2361_MOESM4_ESM.xls (42 kb)
Supplementary material 4 (XLS 42 kb)


  1. Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664PubMedPubMedCentralCrossRefGoogle Scholar
  2. Basbag S, Ekinci R, Gencer O (2007) Combining ability and heterosis for earliness characters in line x tester population of Gossypium hirsutum L. Hereditas 144:185–190PubMedCrossRefGoogle Scholar
  3. Bates D, Maechler M, Bolker B (2011) Lme4: linear mixed effects models using S4 classes. Accessed 1 Sept 2011
  4. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635CrossRefGoogle Scholar
  5. Cai X, Huang A, Xu S (2011) Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping. BMC Bioinform 12:1–13CrossRefGoogle Scholar
  6. Cai CP, Ye WX, Zhang TZ, Guo WZ (2014) Association analysis of fiber quality traits and exploration of elite alleles in upland cotton cultivars/accessions (Gossypium hirsutum L.). J Integr Plant Biol 56:51–62PubMedCrossRefGoogle Scholar
  7. Cai CP, Zhu GZ, Zhang TZ, Guo WZ (2017) High-density 80 K snp array is a powerful tool for genotyping G. hirsutum, accessions and genome analysis. BMC Genom 18:654CrossRefGoogle Scholar
  8. Chen ZJ, Scheffler BE, Dennis E (2007) Toward sequencing cotton (Gossypium) Genomes. Plant Physiol 145:1303–1310PubMedPubMedCentralCrossRefGoogle Scholar
  9. Cheng HL, Yu SX (1994) Studies on the earliness inheritance of upland cottons (G. hirsutum L.). Cotton Sci 6:9–15Google Scholar
  10. Fan SL, Yu SX, Zhang CJ, Yuan RH, Song MZ (2004) Study on heredity and combining ability of earliness of short season cotton. Cotton Sci 16:211–215Google Scholar
  11. Fan SL, Yu SX, Song MZ, Yuan RH (2006) Construction of molecular linkage map and QTL mapping for earliness in short-season cotton. Cotton Sci 18:135–139Google Scholar
  12. Fang L, Gong H, Hu Y, Liu C, Zhou B, Huang T, Wang Y, Chen S, Fang DD, Du X, Chen H, Chen J, Wang S, Wang Q, Wan Q, Liu B, Pan M, Chang L, Wu H, Mei G, Xiang D, Li X, Cai C, Zhu X, Chen ZJ, Han B, Chen X, Guo W, Zhang T, Huang X (2017) Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Genome Biol 18:33PubMedPubMedCentralCrossRefGoogle Scholar
  13. Feng JY, Wen YJ, Zhang J, Zhang YM (2016) Advances on methodologies for genome-wide association studies in plants. Acta Agron Sin 42:945–956CrossRefGoogle Scholar
  14. Gapare W, Conaty W, Zhu QH, Liu S, Stiller W, Llewellyn D, Wilson L (2017) Genome-wide association study of yield components and fiber quality traits in a cotton germplasm diversity panel. Euphytica 213:66CrossRefGoogle Scholar
  15. Ginestet C (2011) Ggplot2: elegant graphics for data analysis. J R Stat Soc A 174:245–246CrossRefGoogle Scholar
  16. Guo YF, McCarty JC, Jenkins JN, Saha S (2008) QTLs for node of first fruiting branch in a cross of an upland cotton, Gossypium hirsutum L., cultivar with primitive accession Texas 701. Euphytica 163:113–122CrossRefGoogle Scholar
  17. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485PubMedCrossRefGoogle Scholar
  18. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620CrossRefGoogle Scholar
  19. Huang C, Nie XH, Shen C, You CY, Li W, Zhao WX, Zhang XL, Lin ZX (2017) Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs. Plant Biotechnol J 15:1374PubMedPubMedCentralCrossRefGoogle Scholar
  20. Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM (2015) Development of a 63 K SNP Array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. G3 Genes Genom Genet 5:1187–1209Google Scholar
  21. Islam MS, Thyssen GN, Jenkins JN, Zeng L, Delhom CD, McCarty JC, Deng DD, Hinchliffe DJ, Jones DC, Fang DD (2016) A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC Genom 17:903CrossRefGoogle Scholar
  22. Li C, Wang C, Dong N, Wang X, Zhao H, Converse R, Xia Z, Wang R, Wang Q (2012) QTL detection for node of first fruiting branch and its height in upland cotton (Gossypium hirsutum L.). Euphytica 188:441–451CrossRefGoogle Scholar
  23. Li H, Peng Z, Yang X, Wang W, Fu J, Wang J, Han Y, Chai Y, Guo T, Yang N, Liu J, Warburton ML, Cheng Y, Hao X, Zhang P, Zhao J, Liu Y, Wang G, Li J, Yan J (2013a) Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet 45:43–50PubMedCrossRefGoogle Scholar
  24. Li J, Fan SL, Song MZ, Pang CY, Wei HL, Li W, Ma JH, Wei JH, Jing JG, Yu SX (2013b) Cloning and characterization of a FLO/LFY ortholog in Gossypium hirsutum L. Plant Cell Rep 32:1675–1686PubMedCrossRefGoogle Scholar
  25. Li C, Zhang J, Hu G, Fu Y, Wang Q (2016) Association mapping and favorable allele mining for node of first fruiting/sympodial branch and its height in upland cotton (Gossypium hirsutum L.). Euphytica 210:57–68CrossRefGoogle Scholar
  26. Li C, Fu Y, Sun R, Wang Y, Wang QL (2018) Single-locus and multi-locus genome-wide association studies in the genetic dissection of fiber quality traits in upland cotton (Gossypium hirsutum L.). Front Plant Sci 9:1083PubMedPubMedCentralCrossRefGoogle Scholar
  27. Low A, Hesketh J, Muramoto H (1969) Some environmental effects on the varietal node number of the first fruiting branch. Cotton Grow Rev 40:181–188Google Scholar
  28. Mackay TFC, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10:565–577PubMedCrossRefGoogle Scholar
  29. Magwa RA, Zhao H, Xing Y, Xing Y (2016) Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.). BMC Genet 17:28PubMedPubMedCentralCrossRefGoogle Scholar
  30. Munro JM (1971) An analysis of earliness in cotton. Cotton Grow Rev 48:28–41Google Scholar
  31. Müssig C, Kauschmann A, Clouse SD, Altmann T (2000) The Arabidopsis PHD-finger protein SHL is required for proper development and fertility. Mol Gen Genet 264:363–370PubMedCrossRefGoogle Scholar
  32. Narayanan S, Vara Prasad PV, Shroyer K, Gill BS, Fritz A (2014) Characterization of a spring wheat association mapping panel for root traits. Agron J 106:1593–1604CrossRefGoogle Scholar
  33. Reinisch AJ, Dong JM, Brubaker CL, Stelly DM, Wendel JF, Paterson AH (1994) A detailed RFLP map of cotton, Gossypium hirsutum × Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829–847PubMedPubMedCentralGoogle Scholar
  34. Su CF, Lu WG, Zhao TJ, Gai JY (2010) Verification and fine-mapping of QTLs conferring days to flowering in soybean using residual heterozygous lines. Chin Sci Bull 55:499–508CrossRefGoogle Scholar
  35. Su J, Fan S, Li L, Wei H, Wang C, Wang H, Song M, Zhang C, Gu L, Zhao S, Mao G, Wang C, Pang C, Yu S (2016a) Detection of favorable QTL alleles and candidate genes for lint percentage by GWAS in Chinese upland cotton. Front Plant Sci 7:1576PubMedPubMedCentralGoogle Scholar
  36. Su J, Li L, Pang C, Wei H, Wang C, Song M, Wang H, Zhao S, Zhang C, Mao G, Huang L, Wang C, Fan S, Yu S (2016b) Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection. Sci Rep 6:38496PubMedPubMedCentralCrossRefGoogle Scholar
  37. Su J, Pang C, Wei H, Li L, Liang B, Wang C, Song M, Wang H, Zhao S, Jia X, Mao G, Huang L, Geng D, Wang C, Fan S, Yu S (2016c) Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton. BMC Genom 17:687CrossRefGoogle Scholar
  38. Su J, Li L, Zhang C, Wang C, Gu L, Wang H, Wei H, Liu Q, Huang L, Yu S (2018) Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton. Theor Appl Genet 131:1299–1314PubMedCrossRefGoogle Scholar
  39. Sun FD, Zhang JH, Wang SF, Gong WK, Shi YZ, Liu AY, Li JW, Gong JW, Shang HH, Yuan YL (2012) QTL mapping for fiber quality traits across multiple generations and environments in upland cotton. Mol Breed 30:569–582CrossRefGoogle Scholar
  40. 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 Biotechnol J 15:982–996PubMedPubMedCentralCrossRefGoogle Scholar
  41. Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2015) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162CrossRefGoogle Scholar
  42. Turner SD (2014) qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. Biorxiv. CrossRefGoogle Scholar
  43. Wang JK, Li HH, Zhang LY, Meng L (2012) Users’ manual of QTL IciMapping version 3.2, 50–81. The Quantitative Genetics Group, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, ChinaGoogle Scholar
  44. Wang X, Fan S, Song M, Pang C, Wei H, Yu J, Ma Q, Yu S (2014) Upland cotton gene GhFPF1 confers promotion of flowering time and shade-avoidance responses in Arabidopsis thaliana. PLoS ONE 9:e91869PubMedPubMedCentralCrossRefGoogle Scholar
  45. Wen Z, Tan R, Yuan J, Bales C, Du W, Zhang S, Chilvers M, Schmidt C, Song Q, Cregan P, Wang D (2014) Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean. BMC Genom 15:809CrossRefGoogle Scholar
  46. Yang N, Lu YL, Yang XH, Huang J, Zhou Y, Ali F, Wen W, Liu J, Li J, Yan J (2014) Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS ONE 9:e1004573Google Scholar
  47. Yu SX, Huang ZM (1990) Short season cotton varieties precocious constitute factors of genetic analysis. Sci Agri-cultura Sin 23:48–54Google Scholar
  48. Yu SX, Wang HT, Wei HL, Su JJ (2017) Research progress and application of early maturity in upland cotton. Cotton Sci 29(supplement):1–10Google Scholar
  49. Zhang XL, Wang KB, Song GL, Liu F, Li SH, Wang CY, Zhang XD, Wang YH (2008) Primary QTL mapping of upland cotton RIL CRI-G6 by SSR marker. Cotton Sci 20:192–197Google Scholar
  50. Zhang F, Zhu Z, Tong X, Zhu Z, Qi T, Zhu J (2015a) Mixed linear model approaches of association mapping for complex traits based on omics variants. Sci Rep 5:10298PubMedPubMedCentralCrossRefGoogle Scholar
  51. Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Saski CA, Scheffler BE, Stelly DM, Hulse-Kemp AM, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L, Zhang W, Song Q, Kirkbride RC, Chen X, Dennis E, Llewellyn DJ, Peterson DG, Thaxton P, Jones DC, Wang Q, Xu X, Zhang H, Wu H, Zhou L, Mei G, Chen S, Tian Y, Xiang D, Li X, Ding J, Zuo Q, Tao L, Liu Y, Li J, Lin Y, Hui Y, Cao Z, Cai CP, Zhu X, Jiang Z, Zhou B, Guo W, Li R, Chen Z (2015b) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 33:531–537PubMedCrossRefGoogle Scholar
  52. Zhao LY, Chen SW, Xu SA (1974) An estimation of heritability of the indicative characters of earliness in Upland cotton. Acta Genet Sin 1:107–115Google Scholar
  53. Zhou Q, Zhou C, Zheng W, Mason AS, Fan S, Wu C, Fu D, Huang Y (2017) Genome-wide SNP markers based on SLAF-Seq uncover breeding traces in Rapeseed (Brassica napus L.). Front Plant Sci 8:648PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.School of Life Science and TechnologyHenan Institute of Science and Technology/Collaborative Innovation Center of Modern Biological Breeding, Henan ProvinceXinxiangChina
  2. 2.Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Key Laboratory of China Northwestern Inland RegionMinistry of AgricultureShiheziChina

Personalised recommendations