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Discovery of Related Locus on Core Collection of Melon (Cucumis melo) Fruit Character Based on GWAS |
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Abstract Abstract The external characters of melon (Cucumis melo) fruit are the important agronomic characters which are closely related to the consumption habits. Discovery of the genes/loci affecting melon fruit character variation provides a basis for genetic improvement of exterior fruit quality. For this purpose, a total of 104 SSR markers distributed evenly across the melon chromosomes were used in the present study for identification the genotypes of a melon core collection, which was established using a stratified sampling method in our previous study. Five fruit characters of melon, fruit length (FL), fruit diameter (FD), fruit shape index (FS), flesh thickness (FT) and fruit fresh weight (FW) were determined during three years (from 2013 to 2015), and the genotype data of the core set was performed with genome-wide association study (GWAS). The results showed that a total of 456 alleles were detected in the melon core set, with polymorphism information index (PIC) of the markers ranged from 0.12~0.89 (mean=0.51). The core set had a high level of genetic diversity, all the Shannon's index of the five characters in the core set exceeded 2.0. Based on the Bayesian model, the melon core set could be separated into two subgroups, which were coincident with the subspecies classification of melon. This finding indicated that the melon core collection was suitable for association mapping. Totally, 42 loci (P<0.01) associated with the five characters were detected by GWAS within three successive years, of which four loci appeared repeatedly under three environmental conditions and 21 loci appeared repeatedly under two environmental conditions. Most of the stably expressed loci were in agreement with the previous results from linkage analysis. There were 10, 5, 9, 8 and 10 loci associated with FL, FD, FS, FT and FW, respectively, with the maximum explanation of phenotypic variation (R2) loci of HNM36, HNM16, CMCCA145, HNM31 and HNM31, respectively. Ten loci were found to associate with two or more characters, indicating the existence of trait correlation or pleiotropism. The results will lay a basis for fine mapping of melon fruit character QTL, candidate gene discovery and molecular marker development.
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Received: 15 February 2017
Published: 06 August 2017
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崔艳华, 邱丽娟, 常汝镇, 等. 2003. 植物核心种质研究进展[J]. 植物遗传资源学报, 4(3): 279-284. (Cui Y H, Qiu L J, Chang N Z, et al. 2003. Adances in research on core collection of plant germplasm resources[J]. Journal of Plant Genetic Resources, 4(3): 279-284.)胡建斌, 马双武, 王吉明, 等. 2013. 基于表型性状的甜瓜核心种质构建[J]. 果树学报, 30(3): 404-411. (Hu J B, Ma S W, Wang J M, et al. 2013. Establishment of a melon (Cucumis melo) core collection based on phenotypic characters[J]. Journal of Fruit Science, 30(3): 404-411.)林德佩. 2012. 甜瓜(Cucumis melo L.)种下分类专论[J]. 中国瓜菜, 25(5): 42-46. (Lin D P. 2012. Comments on intraspecific classification of melon[J]. China Cucurbit and Vegetables, 25(5): 42-46.)苏艳, 胡建斌, 黄松, 等. 2013. 甜瓜地方品种6个产量相关性状与SSR标记的关联分析[J]. 农业生物技术学报, 21(11): 1337-1344. (Su Y, Hu J B, Huang S, et al. 2013. Association analysis of six yield-related traits with SSR markers in melon (Cucumis melo L.) landraces[J]. Journal of Agricultural Biotechnology, 21(11): 1337-1344.)王盼乔, 周亚峰, 许彦宾, 等. 2016. 基于多序列比对的甜瓜SSR标记开发及应用[J]. 河南农业大学学报, 50(2): 189-197. (Wang P Q, Zhou Y F, Xu Y B, et al. 2016. Development of SSR markers based on multiple sequence alignment and their applications in melon[J]. Journal of Henan Agricultural University, 50(2): 189-197.)王荣焕, 王天宇, 黎裕. 2007. 植物基因组中的连锁不平衡[J]. 遗传, 29(11): 1317-1323. (Wang R H, Wang T Y, Li Y. 2007. Linkage disequilibrium in plant genomes[J]. Hereditas, 29(11): 1317-1323.)于翠香, 韩忠才, 王占海, 等. 2016. 甜瓜果实性状遗传规律的研究进展[J]. 东北农业科学, (3): 91-94. (Yu C X, Han Z C, Wang Z H, et al. 2016. Advance of studies on genetic law of melon fruit characters[J]. Shandong Agricultural Science, (3): 91-94.)张宁, 张显, 张勇, 等. 2014, 甜瓜远缘群体果实性状遗传分析[J]. 西北农业学报, 23(5):121-128. (Zhang N, Zhang X, Zhang Y, et al. 2014. Genetic analysis of fruit traits in interspecific population of melon[J]. Acta Agriculturae Boreali-occidentalis Sinica, 23(5): 121-128.)张雪娇, 高鹏, 栾非时. 2013. 甜瓜果实相关性状QTL分析[J]. 中国蔬菜, (18): 35-41. (Zhang X J, Gao P, Luan F S. 2013. QTL analysis of fruits related traits in melon (Cucumis melo L.)[J]. China Vegetables, (18): 35-41.)Diaz A, Fergany M, Formisano G, et al. 2011. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)[J]. BMC Plant Biology. 2011, 11(1): e111.Eduardo I, Arus P, Monforte A J, et al. 2007. Estimating the genetic architecture of fruit quality traits in melon (Cucumis melo L.) using a genomic library of near-isogenic lines. Journal of the American Society for Horticultural Science[J]. 132(1): 1-10.Evanno G, Regnauts S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study[J]. Molecular Ecology, 14(8): 2611-2620.Fernandez-Silva I, Moreno E, Eduardo I, et al. 2009. On the genetic control of heterosis for fruit shape in melon (Cucumis melo L.). Journal of Heredity, 100(2): 229-235.Fukino N, Yoshioka Y, Kubo N, et al. 2008. Identification of QTLs for resistance to powdery mildew and SSR markers diagnostic for powdery mildew resistance genes in melon (Cucumis melo L.). Theoretical and Applied Genetics, 118(1): 165-175.Ingvarsson P K, Street N R. 2011. Association genetics of complex traits in plants[J]. New Phytologist, 189(4): 909-922.Jiang H, Huang L, Ren X, et al. 2014. Diversity characterization and association analysis of agronomic traits in a Chinese peanut (Arachis hypogaea L.) mini-core collection[J]. Journal of Integrative Plant Biology, 56(2): 159-169.Li X, Yan W, Agrama H, et al. 2011. Mapping QTLs for improving grain yield using the USDA rice mini-core collection[J]. Planta, 234(2): 347-361.Monforte A J, Oliver M, Gonzalo M J, et al. 2004. Identification of quantitative trait loci involved in fruit quality traits in melon (Cucumis melo L.)[J]. Theoretical and Applied Genetics, 108(1): 750-758.Obando J, Fernandez-Trujillo JP, Martinez JA, et al. 2008. Identification of melon fruit quality quantitative trait loci using near-isogenic lines[J]. Journal of the American Society for Horticultural Science, 133(1): 139-151.Paris M, Zalapa J E, McCreight J D, et al. 2008. Genetic dissection of fruit quality components in melon (Cucumis melo L.) using a RIL population derived from exotic×elite US Western Shipping germplasm[J]. Molecular Breeding, 22(3): 405-419.Perin C, Hagen L, Giovinazzo N, et al. 2002. Genetic control of fruit shape acts prior to anthesis in melon (Cucumis melo L.)[J]. Molecular Genetics and Genomics, 266(6): 933-941. Pitrat M. 2008. Melon (Cucumis melo L.)[M]. In: Prohens J, Nuez F (eds) Handbook of plant breeding, vol 1: vegetables. Springer, New York, pp. 283-315.Tomason Y, Nimmakayala P, Levi A, et al. 2013. Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon[J]. Molecular Breeding, 31(4): 829-841. Yan J, Warburton M, Crouch J. 2011. Association mapping for enhancing maize (Zea mays L.) genetic improvement[J]. Crop science, 51(2): 433-449.Zhao J, Artemyeva A, Del Carpio D P, et al. 2010. Design of a Brassica rapa core collection for association mapping studies[J]. Genome, 53(11): 884-898. |
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