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Molecular Genetics and Genomics

, Volume 290, Issue 5, pp 1683–1700 | Cite as

Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.)

  • Dexin Liu
  • Fang Liu
  • Xiaoru Shan
  • Jian Zhang
  • Shiyi Tang
  • Xiaomei Fang
  • Xueying Liu
  • Wenwen Wang
  • Zhaoyun Tan
  • Zhonghua Teng
  • Zhengsheng Zhang
  • Dajun Liu
Original Paper

Abstract

Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5–62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.

Keywords

Genetic map Lint percentage Nutrient traits Quantitative trait loci (QTL) Upland cotton Gossypium hirsutum L. 

Notes

Acknowledgments

This study was financially supported by the Natural Science Foundation of China (31270037, 31271305, 30971827) and the “111” Project (B12006).

References

  1. An CF, Jenkins JN, Wu JX, Guo YF, Mccarty JC (2010) Use of fiber and fuzz mutants to detect QTL for yield components, seed, and fiber traits of upland cotton. Euphytica 172:21–34CrossRefGoogle Scholar
  2. Anderson OE, Worthington RE (1971) Boron and manganese effects on protein, oil content, and fatty acid composition of cottonseed. Agron J 63:566–569CrossRefGoogle Scholar
  3. Ashokkumar K, Ravikesavan R (2013) Genetic variation and heterotic effects for seed oil, seed protein and yield attributing traits in upland cotton (Gossypium hirsutum L.). Afr J Biotechnol 12:5183–5191Google Scholar
  4. Bechere E, Auld DL, Hequet E (2009) Development of ‘naked-tufted’ seed coat mutants for potential use in cotton production. Euphytica 167:333–339CrossRefGoogle Scholar
  5. Blenda A, Fang DD, Rami JF, Garsmeur O, Luo F, Lacape JM (2012) A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. PLoS One 7:e45739PubMedCentralCrossRefPubMedGoogle Scholar
  6. Chen ZJ, Scheffler BE, Dennis E, Triplett BA, Zhang TZ, Guo WZ, Chen XY, Stelly DM, Rabinowicz PD, Town CD, Arioli T, Brubaker C, Cantrell RG, Lacape JM, Ulloa M, Chee P, Gingle AR, Haigler CH, Percy R, Saha S, Wilkins T, Wright RJ, Deynze AV, Zhu YX, Yu SX, Abdurakhmonov I, Katageri I, Kumar PA, Rahman M, Zafar Y, Yu JZ, Kohel RJ, Wendel JF, Paterson AH (2007) Toward sequencing cotton (Gossypium) genomes. Plant Physiol 145:1303–1310PubMedCentralCrossRefPubMedGoogle Scholar
  7. Culp TW, Harrell W (1975) Influence of lint percentage, boll size, and seed size on lint yield of upland cotton with high fiber strength. Crop Sci 15:741–746CrossRefGoogle Scholar
  8. Dani RG, Pundarikakshudu R (1986) Cotton seed protein and oil with repeated harvests. Curr Sci India 55:795–796Google Scholar
  9. Dowd MK, Boykin DL, Meredith WR, Campbell BT, Bourland FM, Gannaway JR, Glass KM, Zhang JF (2010) Fatty acid profiles of cottonseed genotypes from the national cotton variety trials. J Cotton Sci 14:64–73Google Scholar
  10. Endrizzi JE, Turcotte EL, Kohel RJ (1984) Qualitative genetics, cytology, and cytogenetics. In: Kohel RJ, Lewis CF (eds) Cotton. Agronomy Society of America, Madison, pp p81–p119Google Scholar
  11. Guo WZ, Ma GJ, Zhu YC, Yi CX, Zhang TZ (2006) Molecular tagging and mapping of quantitative trait loci for lint percentage and morphological marker genes in upland cotton. J Integr Plant Biol 48:320–326CrossRefGoogle Scholar
  12. Hanny BW, Meredith WR, Bailey JC, Harvey AJ (1978) Genetic relationships among chemical constituents in seeds, flower buds, terminals, and mature leaves of cotton. Crop Sci 18:1071–1074CrossRefGoogle Scholar
  13. Kohel RJ (1985) Genetic analysis of fiber color variants in cotton. Crop Sci 25:793–797CrossRefGoogle Scholar
  14. Kohel RJ, Cherry JP (1983) Variation of cottonseed quality with stratified harvests. Crop Sci 23:1119–1124CrossRefGoogle Scholar
  15. Kohel RJ, Lewis CF, Richmond TR (1965) Linkage tests in upland cotton, Gossypium birsutum L. Crop Sci 5:582–585CrossRefGoogle Scholar
  16. Lacape JM, Dessauw D, Rajab M, Noyer JL, Hau B (2007) Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs. Mol Breed 19:45–58CrossRefGoogle Scholar
  17. Lander E, Kruglya kL (1995) Genetic dissection of complex traits-guidelines for interpreting and reporting linkage results. Nat Genet 11:241–247CrossRefPubMedGoogle Scholar
  18. Lee JJ, Woodward AW, Chen ZJ (2007) Gene expression changes and early events in cotton fibre development. Ann Bot 100:1391–1401PubMedCentralCrossRefPubMedGoogle Scholar
  19. Li FG, Fan GY, Wang KB, Sun FM, Yuan YL, Song GL, Li Q, Ma ZY, Lu CR, Zou CS, Chen WB, Liang XM, Shang HH, Liu WQ, Shi CC, Xiao GH, Gou CY, Ye WW, Xu X, Zhang XY, Wei HL, Li ZF, Zhang GY, Wang JY, Liu K, Kohel RJ, Percy RG, Yu JZ, Zhu YX, Wang J, Yu SX (2014) Genome sequence of the cultivated cotton Gossypium arboretum. Nat Genet 46:567–572CrossRefPubMedGoogle Scholar
  20. Li L, Wang SF, Liu F, Tang SY, Tan ZY, Zhang J, Teng ZH, Liu DJ, Zhang ZS (2012) Chromosomal localization of transcription factors in Gossypium hirsutum. Acta Agron Sin 38:1361–1368 (in Chinese with English abstract)CrossRefGoogle Scholar
  21. Linos AA, Bebeli PJ, Kaltsikes PJ (2002) Cultivar identification Wcation in upland cotton using RAPD markers. Aust J Agric Res 53:637–642CrossRefGoogle Scholar
  22. Liu DJ, Zhang J, Zhang K, Wang W, Zhang ZS (2010) Mapping QTL for physical traits of seed in upland cotton (Gossypium hirsutum L.). Acta Agrono Sin 36:1–8Google Scholar
  23. Lukonge E, Labuschagne MT, Hugo A (2007) The evaluation of oil and fatty acid composition in seed of cotton accessions from various countries. J Sci Food Agric 87:340–347CrossRefGoogle Scholar
  24. Meredith WR (1984) Quantitative genetics. In: Kohel RJ, Lewis CF (eds) Cotton. Agronomy Society of America, Madison, pp p131–p150Google Scholar
  25. Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin DC, Llewellyn D, Showmaker KC, Shu SQ, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L, Grimwood J, Grover C, Grupp K, Hu GJ, Lee TH, Li JP, Lin LF, Liu T, Marler BS, Page JT, Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang HB, Xu CM, Wang JP, Wang ZN, Zhang D, Zhang L, Ashrafi H, Bedon F, Bowers JE, Brubaker CL, Chee PW, Das S, Gingle AR, Haigler CH, Harker D, Hoffmann LV, Hovav R, Jones DC, Lemke C, Mansoor S, Rahman MU, Rainville LN, Rambani A, Reddy UK, Rong JK, Saranga Y, Scheffler BE, Scheffler JA, Stelly DM, Triplett BA, Van Deynze A, Vaslin MFS, Waghmare VN, Walford SA, Wright RJ, Zaki EA, Zhang TZ, Dennis ES, Mayer KFX, Peterson DG, Rokhsar DS, Wang XY, Schmutz J (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492:423–428CrossRefPubMedGoogle Scholar
  26. 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
  27. Richmond TR (1943) Inheritance of green and brown lint in upland cotton. J Am Soc Agron 35:967–975CrossRefGoogle Scholar
  28. Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding X, Garza JJ, Marler BS, Park CH, Pierce GJ, Rainey KM, Rastogi VK, Schulze SR, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin TD, Wing RA, Wright RJ, Zhao X, Zhu L, Paterson AH (2004) A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166:389–417   PubMedCentralCrossRefPubMedGoogle Scholar
  29. Rong J, Pierce GJ, Waghmare VN, Rogers CJ, Desai A, Chee PW, May OL, Gannaway JR, Wendel JF, Wilkins TA, Paterson AH (2005) Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton. Theor Appl Genet 111(6):1137–1146CrossRefPubMedGoogle Scholar
  30. Said JI, Lin ZH, Zhang XL, Song MZ, Zhang JF (2013) A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton. BMC Genome 14:776CrossRefGoogle Scholar
  31. Said JI, Song MZ, Wang HT, Lin ZH, Zhang XL, Fang DD, Zhang JF (2014) A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations. Mol Genet Genomics. doi: 10.1007/s00438-014-0963-9 PubMedGoogle Scholar
  32. Shen XL, Guo WZ, Lu QX, Zhu XF, Yuan YL, Zhang TZ (2007) Genetic mapping of quantitative trait loci for fiber quality and yield trait by RIL approach in upland cotton. Euphytica 155:371–380CrossRefGoogle Scholar
  33. Simpson DM (1947) Fuzzy leaf in cotton and its association with short lint. J Hered 38:153–156Google Scholar
  34. Song XL, Zhang TZ (2007) Identification of quantitative trait loci controlling seed physical and nutrient traits in cotton. Seed Sci Res 17:243–251CrossRefGoogle Scholar
  35. Stephens SG (1955) Linkage in upland cotton. Genetics 40:903–917PubMedCentralPubMedGoogle Scholar
  36. Sun SK, Chen JH, Xian SK, Wei SJ (1987) Study on the nutritional quality of cotton seeds. Sci Agric Sinica 5:12–16Google Scholar
  37. Suo J, Liang X, Pu L, Zhang Y, Xue Y (2003) Identification of GhMYB109 encoding a R2R3MYB transcription factor that expressed specifically in 37 fibre initials and elongating fibers of cotton (Gossypium hirsutum L.). Biochim Biophys Acta 1630:25–34CrossRefPubMedGoogle Scholar
  38. Tang SY, Teng ZH, Zhai TF, Fang XM, Liu F, Liu DJ, Zhang J, Liu DX, Wang SF, Zhang K, Shao QS, Tan ZY, Paterson AH, Zhang ZS (2015) Construction of genetic map and QTL analysis of fiber quality traits for upland cotton (Gossypium hirsutum L.). Euphytica 201:195–213CrossRefGoogle Scholar
  39. Turner JH, Ramey HH, Worley S (1976) Relationship of yield, seed quality, and fiber properties in Upland cotton. Crop Sci 16:578–580CrossRefGoogle Scholar
  40. Van Ooijen JW (2006) JoinMap® 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenGoogle Scholar
  41. Van Ooijen JW (2009) MapQTL 6: Software for the mapping of quantitative trait loci in experimental populations of diploid species. Plant Research International, WageningenGoogle Scholar
  42. Wan Q, Zhang Z, Hu M, Chen L, Liu D, Chen X, Wang W, Zheng J (2007) T1 locus in cotton is the candidate gene affecting lint percentage, fiber quality and spiny bollworm (Earias spp.) resistance. Euphytica 158:241–247CrossRefGoogle Scholar
  43. 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. J Genet Genomics 34:34–45Google Scholar
  44. Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, Gou C, Zheng Z, Yin Y, Zhang X, Liu K, Wang B, Song C, Shi N, Kohel RJ, Percy RG, Yu JZ, Zhu Y-X, Wang J, Yu SX (2012) The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 44:1098–1103CrossRefPubMedGoogle Scholar
  45. Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. Adv Agron 78:139–186CrossRefGoogle Scholar
  46. Wu JX, Gutierrez OA, Jenkins JN, McCarty JC, Zhu J (2009) Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton. Euphytica 165:231–245CrossRefGoogle Scholar
  47. Ye ZH, Lu ZZ, Zhu J (2003) Genetic analysis for developmental behavior of some seed quality traits in upland cotton (Gossypum hirsutum L.). Euphytica 129:183–191CrossRefGoogle Scholar
  48. Yi CX, Zhang TZ, Guo WZ (2001) Morphological and molecular tagging of lint percent QTL in upland cotton. Acta Agron Sin 27:781–786Google Scholar
  49. Yu Y, Yuan D, Liang S, Li X, Wang X et al (2011) Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. BMC Genom 12:15CrossRefGoogle Scholar
  50. Yu JW, Yu SX, Fan SL, Song MZ, Zhai HH, Li XL, Zhang JF (2012) Mapping quantitative trait loci for cottonseed oil, protein and gossypol content in a Gossypium hirsutum × Gossypium barbadense backcross inbred line population. Euphytica 187:191–201CrossRefGoogle Scholar
  51. 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
  52. Zeng L, Meredith WR (2009) Associations among Lint yield, yield components, and fiber properties in an introgressed population of cotton. Crop Sci 49:1647–1654CrossRefGoogle Scholar
  53. Zhang ZS, Xiao YH, Luo M, Li XB, Luo XY, Hou L, Li DM, Pei Y (2005) Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.). Euphytica 144:91–99CrossRefGoogle Scholar
  54. Zhang ZS, Hu MC, Zhang J, Liu DJ, Zhang K, Wang W, Wan Q (2009) Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.). Mol Breed 24:49–61CrossRefGoogle Scholar
  55. 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
  56. Zhe X, Zhang X, Liu YY, Zhao HH, Li CQ (2014) Major gene identification and quantitative trait locus mapping for yield-related traits in upland cotton (Gossypium hirsutum L.). J Integr Agr 13:299–309CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Dexin Liu
    • 1
  • Fang Liu
    • 1
  • Xiaoru Shan
    • 1
  • Jian Zhang
    • 1
  • Shiyi Tang
    • 1
  • Xiaomei Fang
    • 1
  • Xueying Liu
    • 1
  • Wenwen Wang
    • 1
  • Zhaoyun Tan
    • 1
  • Zhonghua Teng
    • 1
  • Zhengsheng Zhang
    • 1
  • Dajun Liu
    • 1
  1. 1.Engineering Research Center of South Upland Agriculture, Ministry of EducationSouthwest UniversityChongqingPeople’s Republic of China

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