Genome-wide association-mapping for fruit quality traits in tomato
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A diverse collection of 174 tomato plants was selected, including 123 accessions of cherry tomato (So lanum lycopersicum var. cerasiforme) and 51 accessions of heirloom cultivars (So lanum lycopersicum). Association-mapping for fruit nutritional and quality traits was conducted with 182 SSR using the mixed linear models. A total of 111 marker-trait associations (MTAs) (P < 0.005) were detected for ten measured traits. Most association loci were detected for fruit equatorial diameter, ascorbic acid and fruit weight, with 22, 22, 17 marker-trait associations, respectively. Co-localised quantitative trait loci (QTLs) and significant associations are compared, such as fw2.2, fw11.1, ED2a, brx2.1, PD3a, and PD9a, which validate this study. Moreover, we also compared previous genome-wide association studies and confirmed certain identified MTAs (e.g. CON30D-472, Z1707-10D) or genes, such as Solyc11g071840.1.1. Our results confirm some QTLs and highlight some new candidate chromosome regions with potential for further tomato fruit quality breeding.
KeywordsTomato Fruit-quality traits Association-mapping Quantitative trait loci
Thanks are due to Drs. Xu Shutu, Qingmei Guan and Yanxu Yi for technical support. We gratefully acknowledge the help provided by Xinli Huang who supplied the fruits used in the study. This work was supported by the National Agricultural Science Foundation [201203002 to Zou Z].
- Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300Google Scholar
- Ersoz ES, Yu J, Buckler ES (2007) Application of linkage mapping in crop plants. Genomics Approaches Platforms 1:97–119Google Scholar
- Food and Agriculture Organization of the United Nations (2015) Statistical pocketbook world food and agricultureGoogle Scholar
- Hatzig SV, Frisch M, Breuer F, Nesi N, Ducournau S, Wagner M, Leckband G, Abbadi A, Snowdon RJ (2015) Genome-wide association mapping unravels the genetic control of seed germination and vigor in Brassica napus. Front Plant Sci 6Google Scholar
- Kumar S, Rowan D, Hunt M, Chagné D, Whitworth C, Souleyre E (2015) Genome-wide scans reveal genetic architecture of apple flavour volatiles. Mol Breed 35Google Scholar
- Mazzucato A, Papa R, Bitocchi E, Mosconi P, Nanni L, Negri V, Picarella ME, Siligato F, Soressi GP, Tiranti B, Veronesi F (2008) Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces. Theor Appl Genet 116:57–669CrossRefGoogle Scholar
- Pers TH, Karjalainen JM, Chan Y, Westra H, Wood AR, Yang J, Lui JC, Vedantam S, Gustafsson S, Esko T, Frayling T, Speliotes EK, Boehnke M, Raychaudhuri S, Fehrmann RSN, Hirschhorn JN, Franke L (2015) Biological interpretation of genome-wide association studies using predicted gene functions. Nat Commun 6:5890CrossRefGoogle Scholar
- Rick CM (1976) Tomato, Lycopersicon e sculentum (Solanaceae). In: Simmonds NW (ed) Evolution of crop plants. Longman Group, London, pp 268–273Google Scholar