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Association mapping and favourable allele exploration for plant architecture traits in upland cotton (Gossypium hirsutum L.) accessions

Published online by Cambridge University Press:  22 May 2015

C. Q. LI
Affiliation:
Key Discipline Open Lab on Crop Molecular Breeding of Henan Institute of Higher Learning, Henan Institute of Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang 453003, Henan, China
N. J. AI
Affiliation:
Cotton Research Institute, Shihezi Agricultural Science and Technology Research Center, Shihezi 832000, China
Y. J. ZHU
Affiliation:
Zhumadian Academy of Agricultural Sciences, Zhumadian 463000, China
Y. Q. WANG
Affiliation:
Key Discipline Open Lab on Crop Molecular Breeding of Henan Institute of Higher Learning, Henan Institute of Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang 453003, Henan, China
X. D. CHEN
Affiliation:
Key Discipline Open Lab on Crop Molecular Breeding of Henan Institute of Higher Learning, Henan Institute of Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang 453003, Henan, China
F. LI
Affiliation:
Key Discipline Open Lab on Crop Molecular Breeding of Henan Institute of Higher Learning, Henan Institute of Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang 453003, Henan, China
Q. Y. HU
Affiliation:
Key Discipline Open Lab on Crop Molecular Breeding of Henan Institute of Higher Learning, Henan Institute of Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang 453003, Henan, China
Q. L. WANG*
Affiliation:
Key Discipline Open Lab on Crop Molecular Breeding of Henan Institute of Higher Learning, Henan Institute of Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang 453003, Henan, China
*
*To whom all correspondence should be addressed. Email: cottonmol@aliyun.com

Summary

Association mapping based on linkage disequilibrium (LD) is a promising tool to identify genes responsible for quantitative variations underlying complex traits. The present paper presents an association mapping panel consisting of 172 upland cotton (Gossypium hirsutum L.) accessions. The panel was phenotyped for five cotton plant architecture traits across multiple environments and genotyped using 386 simple sequence repeat (SSR) markers. Of these markers, 101 polymorphic SSR markers were used in the final analysis. There were abundant phenotypic variations within this germplasm panel and a total of 267 alleles ranging from two to seven per locus were identified in all collections. The threshold of LD decay was set to r2 = 0·1 and 0·2, and the genome-wide LD extended up to about 13–14 and 6–7 cM, respectively, providing the potential for association mapping of agronomically important traits in upland cotton. A total of 66 marker–trait associations were detected based on a mixed linear model, of which 35 were found in more than one environment. The favourable alleles from 35 marker loci can be used in marker-assisted selection of target traits. Both the synergistic alleles and the negative alleles for some traits, especially plant height and fruit branch angle, can be utilized in plant architecture breeding programmes according to specific breeding objectives.

Type
Crops and Soils Research Papers
Copyright
Copyright © Cambridge University Press 2015 

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References

Abdurakhmonov, I. Y., Kohel, R. J., Yu, J. Z., Pepper, A. E., Abdullaev, A. A., Kushanov, F. N., Salakhutdinov, I. B., Buriev, Z. T., Saha, S., Scheffler, B. E., Jenkins, J. N. & Abdukarimov, A. (2008). Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics 92, 478487.Google Scholar
Abdurakhmonov, I. Y., Saha, S., Jenkins, J. N., Buriev, Z. T., Shermatov, S. E., Scheffler, B. E., Pepper, A. E., Yu, J. Z., Kohel, R. J. & Abdukarimov, A. (2009). Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica 136, 401417.CrossRefGoogle Scholar
Agrama, H. A., Eizenga, G. C. & Yan, W. (2007). Association mapping of yield and its components in rice cultivars. Molecular Breeding 19, 341356.Google Scholar
Barnaud, A. T., Lacombe, T. & Doligez, A. (2006). Linkage disequilibrium in cultivated grapevine, Vitis vinifera L. Theoretical and Applied Genetics 112, 708716.Google Scholar
Bowman, D. T. (2000). Attributes of public and private cotton breeding programs. The Journal of Cotton Science 4, 130136.Google Scholar
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, 26332635.Google Scholar
Brubaker, C. L., Paterson, A. H. & Wendel, J. F. (1999). Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42, 184203.Google Scholar
Buntjer, J. B., Sorensen, A. P. & Peleman, J. D. (2005). Haplotype diversity: the link between statistical and biological association. Trends in Plant Science 10, 466471.Google Scholar
Cai, C. P., Ye, W. X., Zhang, T. Z. & Guo, W. Z. (2014). Association analysis of fibre quality traits and exploration of elite alleles in Upland cotton cultivars/accessions (Gossypium hirsutum L.). Journal of Integrative Plant Biology 56, 5162.Google Scholar
Evanno, G., Regnaut, S. & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 26112620.CrossRefGoogle ScholarPubMed
Flint-Garcia, S. A., Thuillet, A. C., Yu, J., Pressoir, G., Romero, S. M., Mitchell, S. E., Doebley, J., Kresovich, S., Goodman, M. M. & Buckler, E. S. (2005). Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant Journal 44, 10541064.Google Scholar
Guo, W. Z., Zhang, T. Z., Ding, Y. Z., Zhu, Y. C., Shen, X. L. & Zhu, X. F. (2005). Molecular marker assisted selection and pyramiding of two QTLs for fibre strength in Upland cotton. Acta Genetica Sinica 32, 12751285.Google Scholar
Guo, W. Z., Cai, C. P., Wang, C. B., Han, Z. G., Song, X. L., Wang, K., Niu, X. W., Wang, C., Lu, K. Y., Shi, B. & Zhang, T. Z. (2007). A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics 176, 527541.Google Scholar
Gupta, P. K., Rustgi, S. & Kulwal, P. L. (2005). Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molecular Biology 57, 461485.Google Scholar
Hamblin, M. T., Mitchell, S. E., White, G. M., Gallego, J., Kukatla, R., Wing, R. A., Paterson, A. H. & Kresovich, S. (2004). Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. Genetics 167, 471483.CrossRefGoogle Scholar
Jannink, J. L., Bink, M. C. A. M. & Jansen, R. C. (2001). Using complex plant pedigrees to map valuable genes. Trends in Plant Science 6, 337342.Google Scholar
Joukhadar, R., El-Bouhssini, M., Jighly, A. & Ogbonnaya, F. C. (2013). Genome-wide association mapping for five major pest resistances in wheat. Molecular Breeding 32, 943960.Google Scholar
Kantartzi, S. K. & Stewart, J. McD. (2008). Association analysis of fibre traits in Gossypium arboreum accessions. Plant Breeding 127, 173179.Google Scholar
Kraakman, A. T. W., Niks, R. E., Van Den Berg, P. M. M. M., Stam, P. & Van Eeuwijk, F. A. (2004). Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168, 435446.Google Scholar
Kruglyak, L. (1999). Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genetics 22, 139144.Google Scholar
Kulwal, P. L., Roy, J. K., Balyan, H. S. & Gupta, P. K. (2003). QTL mapping for growth and leaf characters in bread wheat. Plant Science 164, 267277.Google Scholar
Li, C. Q., Wang, Q. L., Dong, N., Fu, Y. Z., Zhang, J. B. & Lian, X. D. (2010). Quantitative inheritance for main plant architecture traits of Upland cotton variety Baimian1. Cotton Science 22, 415421.Google Scholar
Li, C. Q., Liu, G. S., Zhao, H. H., Wang, L. J., Zhang, X. F., Liu, Y., Zhou, W. Y., Yang, L. L., Li, P. B. & Wang, Q. L. (2013). Marker-assisted selection of Verticillium wilt resistance in progeny populations of Upland cotton derived from mass selection-mass crossing. Euphytica 191, 469480.Google Scholar
Li, C. Q., Song, L., Zhao, H. H., Xia, Z., Jia, Z. F., Wang, X. Y., Dong, N. & Wang, Q. L. (2014). Quantitative trait loci mapping for plant architecture traits across two Upland cotton populations using SSR markers. Journal of Agricultural Science, Cambridge 152, 275287.Google Scholar
Liu, K. J. & Muse, S. V. (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 21282129.Google Scholar
Liu, R. Z., Ai, N. J., Zhu, X. X., Liu, F. J., Guo, W. Z. & Zhang, T. Z. (2014). Genetic analysis of plant height using two immortalized populations of “CRI12×8891” in Gossypium hirsutum L. Euphytica 196, 5161.Google Scholar
Maccaferri, M., Sanguineti, M. C., Noli, E. & Tuberosa, R. (2005). Population structure and long-range linkage disequilibrium in a drum wheat elite collection. Molecular Breeding 15, 271289.Google Scholar
Malysheva-Otto, L. V., Ganal, M. W. & Roder, M. S. (2006). Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genetics 7, 6. doi:10.1186/1471-2156-7-6.Google Scholar
Massman, J., Cooper, B., Horsley, R., Neate, S., Dill-Macky, R., Chao, S., Dong, Y., Schwarz, P., Muehlbauer, G. J. & Smith, K. P. (2011). Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm. Molecular Breeding 27, 439454.Google Scholar
Mei, H. X., Zhu, X. F. & Zhang, T. Z. (2013). Favourable QTL alleles for yield and its components identified by association mapping in Chinese Upland cotton cultivars. PLoS ONE 12, e82193. DOI: 10.1371/journal.pone.0082193.Google Scholar
Mei, M., Syed, N. H., Gao, W., Thaxton, P. M., Smith, C. W., Stelly, D. M. & Chen, Z. J. (2004). Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theoretical and Applied Genetics 108, 280291.Google Scholar
Multani, D. S. & Lyon, B. R. (1995). Genetic fingerprinting of Australian cotton cultivars with RAPD markers. Genome 38, 10051008.Google Scholar
Myles, S., Peiffer, J., Brown, P. J., Ersoz, E. S., Zhang, Z. W., Costich, D. E. & Buckler, E. S. (2009). Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21, 21942202.Google Scholar
Neumann, K., Kobiljski, B., Denčić, S., Varshney, R. K. & Börner, A. (2011). Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Molecular Breeding 27, 3758.CrossRefGoogle Scholar
Nguyen, T. B., Giband, M., Brottier, P., Risterucci, A. M. & Lacape, J. M. (2004). Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theoretical and Applied Genetics 109, 167175.CrossRefGoogle ScholarPubMed
Niu, Y., Xu, Y., Liu, X. F., Yang, S. X., Wei, S. P., Xie, F. T. & Zhang, Y. M. (2013). Association mapping for seed size and shape traits in soybean cultivars. Molecular Breeding 31, 785794.Google Scholar
Paterson, A. H., Brubaker, C. L. & Wendel, J. F. (1993). A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Molecular Biology Reporter 11, 122127.Google Scholar
Peng, J., Richards, D. E., Hartley, N. M., Murphy, G. P., Devos, K. M., Flintham, J. E., Beales, J., Fish, L. J., Worland, A. J., Pelica, F., Sudhakar, D., Christou, P., Snape, J. W., Gale, M. D. & Harberd, N. P. (1999). ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400, 256261.Google Scholar
Perreira, M. G. & Lee, M. (1995). Identification of genomic regions affecting plant height in sorghum and maize. Theoretical and Applied Genetics 90, 380388.Google Scholar
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A. & Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 38, 904909.CrossRefGoogle ScholarPubMed
Pritchard, J. K., Stephens, M. & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945959.Google Scholar
Qin, H. D., Guo, W. Z., Zhang, Y. M. & Zhang, T. Z. (2008). QTL mapping of yield and fiber traits based on a four-way cross population in Gossypium hirsutum L. Theoretical and Applied Genetics 117, 883894.Google Scholar
Reinhard, T. D. & Kuhlemeier, C. (2002). Plant architecture. EMBO Reports 3, 846851.Google Scholar
Remington, D. L., Thornsberry, J. M., Matsuoka, Y., Wilson, L. M., Whitt, S. R., Doebley, J., Kresovich, S., Goodman, M. M. & Buckler, E. S. (2001). Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proceedings of the National Academy of Sciences of the United States of America 98, 1147911484.CrossRefGoogle ScholarPubMed
Shen, X. L., Guo, W. Z., Zhu, X. F., Yuan, Y. L., Yu, J. Z., Kohel, R. J. & Zhang, T. Z. (2005). Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers. Molecular Breeding 15, 169181.Google Scholar
Shen, X. L., Guo, W. Z., Lu, Q. X., Zhu, X. F., Yuan, Y. L. & Zhang, T. Z. (2007). Genetic mapping of quantitative trait loci fibre quality and yield trait by RIL approach in Upland cotton. Euphytica 155, 371380.Google Scholar
Song, X. L. & Zhang, T. Z. (2009). Quantitative trait loci controlling plant architectural traits in cotton. Plant Science 177, 317323.Google Scholar
Stich, B., Melchinger, A. E., Frisch, M., Maurer, H. P., Heckenberger, M. & Reif, J. C. (2005). Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theoretical and Applied Genetics 111, 723730.Google Scholar
Stich, B., Maurer, H. P., Melchinger, A. E., Frisch, M., Heckenberger, M., Rouppe Van Der Voort, J., Peleman, J., Sørensen, A. P. & Reif, J. C. (2006). Comparison of linkage disequilibriumin elite European maize inbred lines using AFLP and SSR markers. Molecular Breeding 17, 217226.Google Scholar
Sun, F. D., Zhang, J. H., Wang, S. F., Gong, W. K., Shi, Y. Z., Liu, A. Y., Li, J. W., Gong, J. W., Shang, H. H. & Yuan, Y. L. (2012). QTL mapping for fiber quality traits across multiple generations and environments in Upland cotton. Molecular Breeding 30, 569582.Google Scholar
Ulloa, M., Meredith, W. R., Shappley, Z. W. & Kahler, A. L. (2002). RFLP genetic linkage maps from four F2:3 populations and a joinmap of Gossypium hirsutum L. Theoretical and Applied Genetics 104, 200208.Google Scholar
Wang, B. H., Wu, Y. T., Huang, N. T., Zhu, X. F., Guo, W. Z. & Zhang, Z. T. (2006). QTL mapping for plant architecture traits in Upland cotton using RILs and SSR markers. Acta Genetica Sinica 33, 161170.Google Scholar
Xu, Y. & Crouch, J. (2008). Marker-assisted selection in plant breeding: from publications to practice. Crop Science 48, 391407.Google Scholar
Yan, J., Warburton, M. & Crouch, J. (2011). Association mapping for enhancing maize (Zea mays L.) genetic improvement. Crop Science 51, 433449.Google Scholar
Yang, X. C. & Hwa, C. M. (2008). Genetic modification of plant architecture and variety improvement in rice. Heredity 101, 396404.Google Scholar
Yang, X. H., Yan, J. B., Shah, T., Warburton, M. L., Li, Q., Li, L., Gao, Y. F., Chai, Y. C., Fu, Z. Y., Zhou, Y., Xu, S., Bai, Gd., Meng, Y. J., Zheng, Y. P. & Li, J. S. (2010). Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection. Theoretical and Applied Genetics 121, 417431.Google Scholar
Yu, J., Pressoir, G., Briggs, W. H., Vroh, B. I., Yamasaki, M., Doebley, J. F., McMullen, M. D., Gaut, B. S., Nielsen, D. M., Holland, J. B., Kresovich, S. & Buckler, E. S. (2005). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38, 203208.Google Scholar
Yu, J., Holland, J. B., McMullen, M. D. & Buckler, E. S. (2008). Genetic design and statistical power of nested association mapping in maize. Genetics 178, 539551.Google Scholar
Yu, S. X. (2007). Short-season Cotton Breeding in China. Beijing: Science Press.Google Scholar
Zhang, J., Guo, W. Z. & Zhang, T. Z. (2002). Molecular linkage map of allotetraploid cotton (Gossypium hirsutum L. × Gossypium barbadense L.) with a haploid population. Theoretical and Applied Genetics 105, 11661174.Google Scholar
Zhang, P. T., Zhu, X. F., Guo, W. Z., Yu, J. Z. & Zhang, T. Z. (2006). Inheritance and QTLs tagging for ideal plant architecture of Simian 3 using molecular markers. Cotton Science 18, 1318.Google Scholar
Zhang, T. Z., Yuan, Y. L., Yu, J., Guo, W. Z. & Kohel, R. J. (2003). Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theoretical and Applied Genetics 106, 262268.Google Scholar
Zhang, T. Z., Qian, N., Zhu, X. F., Chen, H., Wang, S., Mei, H. X. & Zhang, Y. M. (2013). Variations and transmission of QTL alleles for yield and fiber qualities in Upland cotton cultivars developed in China. PLoS ONE 8, e57220. DOI: 10.1371/journal.pone.0057220.Google Scholar
Zhao, K., Aranzana, M. J., Kim, S., Lister, C., Shindo, C., Tang, C., Toomajian, C., Zheng, H., Dean, C., Marjoram, P. & Nordborg, M. (2007). An arabidopsis example of association mapping in structured samples. PLoS Genetics 31, e4. DOI: 10.1371/journal.pgen.0030004.Google Scholar
Zhao, Y. L., Wang, H. M., Chen, W. & Li, Y. H. (2014). Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PLoS ONE 1, e86308. DOI: 10.1371/journal.pone.0086308.Google Scholar
Zhuang, J. Y., Lin, H. X., Lu, J., Qian, H. R., Hittalmani, S., Huang, N. & Zheng, K. L. (1997). Analysis of QTL × environment interaction for yield components and plant height in rice. Theoretical and Applied Genetics 95, 799808.Google Scholar