Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species
- 2.5k Downloads
Association mapping has been proposed as an efficient approach to assist in the identification of the molecular basis of agronomical traits in plants. For this purpose, we analyzed the phenotypic and genetic diversity of a large collection of tomato accessions including 44 heirloom and vintage cultivars (Solanum lycopersicum), 127 S. lycopersicum var. cerasiforme (cherry tomato) and 17 Solanum pimpinellifolium accessions. The accessions were genotyped using a SNPlex™ assay of 192 SNPs, among which 121 were informative for subsequent analysis. Linkage disequilibrium (LD) of pairwise loci and population structure were analyzed, and the association analysis between SNP genotypes and ten fruit quality traits was performed using a mixed linear model. High level of LD was found in the collection at the whole genome level. It was lower when considering only the 127 S. lycopersicum var. cerasiforme accessions. Genetic structure analysis showed that the population was structured into two main groups, corresponding to cultivated and wild types and many intermediates. The number of associations detected per trait varied, according to the way the structure was taken into account, with 0–41 associations detected per trait in the whole collection and a maximum of four associations in the S. lycopersicum var. cerasiforme accessions. A total of 40 associations (30 %) were co-localized with previously identified quantitative trait loci. This study thus showed the potential and limits of using association mapping in tomato populations.
KeywordsLinkage Disequilibrium Simple Sequence Repeat Marker Association Mapping Titratable Acidity Fruit Weight
The research was financed by INRA AIP Bioresources project. Jiaxin Xu was supported by China Scholarship Council. We thank Hélène Burck for characterizing and maintaining the INRA tomato Genetic Resources collection. We are grateful to Yolande Carretero, Esther Pelpoir and Laure David for their help with growing and phenotyping cherry tomato accessions.
- Aranzana MJ, Kim S, Zhao KY, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang CL, Toomajian C, Traw B, Zheng HG, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1:531–539CrossRefGoogle Scholar
- Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng DZ, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JDG, Michael T, Nemri A, Roux F, Salt DE, Tang CL, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631PubMedCrossRefGoogle 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 116:657–669PubMedCrossRefGoogle Scholar
- Miller JC, Tanksley SD (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80:437–448Google Scholar
- Moonsamy PV, Bonella PL, Williams TC, Holcomb CL, Turenchalk GS, Blake LA, Hoglund BN, Rastrou M, Daigle DA, Simen BB, Goodridge D, Hillman G, Hamilton A, May AP, Erlich HA (2011) Use of the fluidigm (R) access array (TM) system provides simplified amplicon library preparation in next generation sequencing for high throughput hla genotyping. Hum Immunol 72:S142–S142CrossRefGoogle Scholar
- Ranc N, Muños S, Xu J, Le Paslier MC, Chauveau A, Bounon R, Rolland S, Bouchet JP, Brunel D, Causse M (2012) Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. Genes Genomes Genet 2:853–864CrossRefGoogle Scholar
- Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Robin Buell C, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 7(7):e40563. doi: 10.1371/journal.pone.0040563 PubMedCrossRefGoogle Scholar
- Tobler AR, Short S, Andersen MR, Paner TM, Briggs JC, Lambert SM, Wu PP, Wang Y, Spoonde AY, Koehler RT, Peyret N, Chen C, Broomer AJ, Ridzon DA, Zhou H, Hoo BS, Hayashibara KC, Leong LN, Ma CN, Rosenblum BB, Day JP, Ziegle JS, De La Vega FM, Rhodes MD, Hennessy KM, Wenz HM (2005) The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. J Biomol Tech (JBT) 16:398–406Google Scholar