Detection of favorable alleles for yield and yield components by association mapping in upland cotton

  • Chengguang Dong
  • Juan Wang
  • Quanjia Chen
  • Yu Yu
  • Baocheng Li
Research Article
  • 13 Downloads

Abstract

Association mapping based on linkage disequilibrium provides a promising tool for dissecting the genetic basis underlying complex traits. To reveal the genetic variations of yield and yield components traits in upland cotton, 403 upland cotton accessions were collected and analyzed by 560 genome-wide simple sequence repeats (SSRs). A diverse panel consisting of 403 upland cotton accessions was grown in six different environments, and the yield and yield component traits were measured, and 560 SSR markers covering the whole genome were mapped. Association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Favorable alleles and typical accessions for yield traits were identified. A total of 201 markers were polymorphic, revealing 394 alleles. The average gene diversity and polymorphism information content were 0.556 and 0.483, respectively. Based on a population structure analysis, 403 accessions were divided into two subgroups. A mixed linear model analysis of the association mapping detected 43 marker loci according to the best linear unbiased prediction and in at least three of the six environments(− lgP > 1.30, P < 0.05). Among the 43 associated markers, five were associated with more than two traits simultaneously and nine were coincident with those identified previously. Based on phenotypic effects, favorable alleles and typical accessions that contained the elite allele loci related to yield traits were identified and are widely used in practical breeding. This study detected favorable quantitative trait loci’s alleles and typical accessions for yield traits, these are excellent genetic resources for future high-yield breeding by marker-assisted selection in upland cotton in China.

Keywords

Association analysis Molecular marker Upland cotton Yield traits 

Notes

Acknowledgements

This program was financially supported by National Natural Science Foundation of China (31260340; 31560410) and National Key R&D Program of China (2017YFD0101600). We thank Nie Xinhui from Shihezi University for help with the analysis.

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest. Chengguang Dong declares that he does not have conflict of interest. Juan Wang declares that he does not have conflict of interest. Quanjia Chen declares that she does not have conflict of interest. Yu Yu declares that he does not have conflict of interest. Baocheng Li declares that he does not have conflict of interest.

Research involving human and animal participants

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

13258_2018_678_MOESM1_ESM.docx (367 kb)
Supplementary material 1 (DOCX 366 KB)

References

  1. Adams DC, Rohlf FJ (2000) Ecological character displacement in Plethodon: biomechanical differences found from a geometric morphometric study. Proc Natl Acad Sci USA 97:4106–4111CrossRefPubMedPubMedCentralGoogle Scholar
  2. Ai XT, Li XY, Qin WB, Sun GQ, Tuer XJ, Mo M (2005) The extend study on genetic composition of upland cotton breeding in Xinjiang. Mol Plant Breed 3:575–578Google Scholar
  3. 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 23:2633–2635CrossRefPubMedGoogle Scholar
  4. 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 56:51–62CrossRefPubMedGoogle Scholar
  5. Evanno G, Regnauts S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedGoogle Scholar
  6. Guo X, Guo YP, Ma J, Wang F, Sun MZ, Gui LJ, Zhou JJ, Song XL, Sun XZ, Zhang TZ (2013) Mapping heterotic loci for yield and agronomic traits using chromosome segment introgression lines in cotton. J Integr Plant Biol 55:759–774CrossRefPubMedGoogle Scholar
  7. Hou JF, Wang CL, Hong XJ, Zhao JM, Xue CC, Guo N, Gai JY, Xing H (2011) Association analysis of vegetable soybean quality traits with SSR markers. Plant Breed 130:444–449CrossRefGoogle Scholar
  8. Hu WJ, Zhang XY, Zhang TZ, Guo WZ (2008) Molecular tagging and source analysis of QTL for elite fiber quality in Upland cotton. Acta Agron Sin 34:578–586CrossRefGoogle Scholar
  9. Huang ZK (2007) The cultivars and their pedigree of cotton in China. China Agriculture Press, BeijingGoogle Scholar
  10. Iwata H, Ebana K, Uga Y, Hayashi T, Jannink JL (2010) Genome-wide association study of grain shape variation among Oryza sativa L. germplasms based on elliptic Fourier analysis. Mol Breed 25:203–215CrossRefGoogle Scholar
  11. Lacape JM, Gawrysiak G, Cao TV, Viot C, Llewellyn D, Liu SM, Jacobs J, Becker D, Vianna Barroso PA, Assunçãog JH et al (2013) Mapping QTLs for traits related to phenology, morphology and yield components in an inter-specific Gossypium hirsutum × G. barbadense cotton RIL population. Field Crop Res 144:256–267CrossRefGoogle Scholar
  12. Li XS, Chen ZZ (2010) Correctly using SPSS software for principal components analysis. Stat Res 27:105–108Google Scholar
  13. Li CQ, Ai NJ, Zhu YJ, Wang YQ, Chen XD, Li F, Hu QY, Wang QL (2016) Association mapping and favorable allele exploration for plant architecture traits in Upland cotton (Gossypium hirsutum L.) accessions. J Agr Sci Camb 154:567–583CrossRefGoogle Scholar
  14. Liu KJ, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129CrossRefPubMedGoogle Scholar
  15. Liu RZ, Ai NJ, Zhu XX, Liu FJ, Guo WZ, Zhang TZ (2014) Genetic analysis of plant height using two immortalized populations of “CRI12 × J8891” in Gossypium hirsutum L. Euphytica 196:51–61CrossRefGoogle Scholar
  16. Liu GZ, Mei HX, Wang S, Li XH, Zhu XF, Zhang TZ (2015) Association mapping of seed oil and protein contents in upland cotton. Euphytica 205:637–645CrossRefGoogle Scholar
  17. Ma XX, Ding YZ, Zhou BL, Guo WZ, Li YH, Zhang TZ (2008) QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium. J Genet Genom 35:751–762CrossRefGoogle Scholar
  18. Maccaferri M, Sanguineti MC, Natoli V, Ortega JLA, Salem MB, Bort J, Chenenaoui C, Ambrogio DE, Moral LGD, Montis AD et al (2006) A panel of elite accessions of durum wheat (Triticum durum Desf.) suitable for association mapping studies. Plant Genet Resour 4:79–85CrossRefGoogle Scholar
  19. Mei HX, Zhu XF, Zhang TZ (2013) Favorable QTL alleles for yield and its components identified by association mapping in Chinese upland cotton cultivars. PLoS ONE 8:e82193CrossRefPubMedPubMedCentralGoogle Scholar
  20. Mei HX, Ai NJ, Zhang X, Ning ZY, Zhang TZ (2014) QTLs conferring FOV7 resistance detected by linkage and association mapping in upland cotton. Euphytica 197:237–249CrossRefGoogle Scholar
  21. Nie XH, Huang C, You CY, Li W, Zhao WX, Shen C, Zhang BB, Wang HT, Yan ZH, Dai BS et al (2016) Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China. BMC Genom 17:352CrossRefGoogle Scholar
  22. Ning ZY, Zhao R, Chen H, Ai NJ, Zhang X, Zhao J, Mei HX, Wang P, Guo WZ, Zhang TZ (2013) Molecular tagging of a major quantitative trait locus for broad-spectrum resistance to verticillium wilt in upland cotton cultivar Prema. Crop Sci 53:2304–2312CrossRefGoogle Scholar
  23. Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Rep 11:122–127CrossRefGoogle Scholar
  24. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170–181CrossRefPubMedPubMedCentralGoogle Scholar
  25. Qin HD, Guo WZ, Zhang YM, Zhang TZ (2008) QTL mapping of yield and fiber traits based on a four-way cross population in Gossypium hirsutum L. Theor Appl Genet 117:883–894CrossRefPubMedGoogle Scholar
  26. Qin YS, Liu RZ, Mei HX, Zhang TZ, Guo WZ (2009) QTL mapping for yield traits in upland cotton (Gossypium hirsutum L). Acta Agron Sin 35:1812–1821CrossRefGoogle Scholar
  27. Qin HD, Chen M, Yi XD, Bie S, Zhang C, Zhang YC, Lan JY, Meng YY, Yuan YL, Jiao CH (2015) Identification of associated SSR markers for yield component and fiber quality traits based on frame map and upland cotton collections. PLoS ONE 10:e0118073CrossRefPubMedPubMedCentralGoogle Scholar
  28. Schenkel FS, Schaeffer LR, Boettcher PJ (2002) Comparison between estimation of breeding values and fixed effects using Bayesian and empirical BLUP estimation under selection on parents and missing pedigree information. Genet Sel Evol 34:41–59CrossRefPubMedPubMedCentralGoogle Scholar
  29. Shao QS, Zhang FJ, Liu Y, Fang XM, Liu DJ, Zhang J, Teng ZH, Paterson AH, Zhang ZS (2014) Identifying QTL for fiber quality traits with three upland cotton (Gossypium hirsutum L.) populations. Euphytica 198:43–58CrossRefGoogle Scholar
  30. Shen XL, Guo WZ, Zhu XF, Yuan YL, Yu JZ, Kohel RJ, Zhang TZ (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in upland cotton using SSR markers. Mol Breed 15:169–181CrossRefGoogle Scholar
  31. Ulloa M, Meredith WR (2000) Genetic linkage map and QTL analysis of agronomic and fiber quality traits in an intraspecific population. J Cotton Sci 4:161–170Google Scholar
  32. Wang BH, Guo WZ, Zhu XF, Wu YT, Huang NT, Zhang TZ (2007) QTL mapping of yield and yield components for elite hybrid derived-RILs in upland cotton. Acta Genet Sin 34:35–45Google Scholar
  33. Wang FR, Gong YC, Zhang CY, Liu GD, Wang LM, Xu ZZ, Zhang J (2011) Genetic effects of introgression genomic components from Sea Island cotton (Gossypium barbadense L.) on fiber related traits in upland cotton (G. hirsutum L.). Euphytica 181:41–53CrossRefGoogle Scholar
  34. Yang XH, Yan JB, Shah T, Warburton ML, Li Q, Li L, Gao YF, Chai YC, Fu ZY, Zhou Y et al (2010) Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection. Theor Appl Genet 121:417–431CrossRefPubMedGoogle Scholar
  35. Yin JM, Wu YT, Zhang J, Zhang TZ, Guo WZ, Zhu XF (2002) Tagging and mapping of QTLs controlling lint yield and yield components in upland cotton (Gossypium hirsutum L.) using SSR and RAPD markers. Chin J Biotechnol 18:162–166Google Scholar
  36. Yu JW, Yu SX, Gore M, Wu M, Zhai HH, Li XL, Fan SL, Song MZ, Zhang JF (2013) Identification of quantitative trait loci across interspecific F2, F2:3 and testcross populations for agronomic and fiber traits in tetraploid cotton. Euphytica 191:375–389CrossRefGoogle Scholar
  37. Zeng L, Meredith WR Jr, Gutierrez OA, Boykin DL (2009) Identification of associations between SSR markers and fiber traits in an exotic germplasm derived from multiple cross among Gossypium tetraploid species. Theor Appl Genet 119:93–103CrossRefPubMedGoogle Scholar
  38. Zhang J, Guo WZ, Zhang TZ (2002) Molecular linkage map of allotetraploid cotton (Gossypium hirsutum L. × Gossypium barbadense L.) with a haploid population. Theor Appl Genet 105:1166–1174CrossRefPubMedGoogle Scholar
  39. Zhang K, Zhang J, Ma J, Tang SY, Liu DJ, Teng ZH, Liu DX, Zhang ZS (2012) Genetic mapping and quantitative traitlocus analysis of fiber quality traits using a three-parent composite population in upland cotton (Gossypium hirsutum L.). Mol Breed 29:335–348CrossRefGoogle Scholar
  40. Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P et al (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:e4CrossRefPubMedPubMedCentralGoogle Scholar
  41. Zhao L, Lv YD, Cai CP, Tong XC, Chen XD, Zhang W, Du H, Guo XH, Guo WZ (2012) Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information. BMC Genom 13:539CrossRefGoogle Scholar
  42. Zhao YL, Wang HM, Wei CW, Li YH (2014) Genetic structure, linkage disequilibrium and association mapping of verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PLoS ONE 9:e86308CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© The Genetics Society of Korea and Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Chengguang Dong
    • 1
    • 2
  • Juan Wang
    • 1
  • Quanjia Chen
    • 2
  • Yu Yu
    • 1
  • Baocheng Li
    • 1
  1. 1.Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Key Laboratory of China Northwesten Inland Region, Ministry of AgricultureShiheziChina
  2. 2.College of AgricultureXinjiang Agricultural UniversityÜrümqiChina

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