Multiple haplotype-based analyses provide genetic and evolutionary insights into tomato fruit weight and composition

To date, most marker-trait associations have been revealed using QTL and genome-wide association studies (GWAS), demonstrating both their successes and their limitations. Haplotypes are the particular combinations of alleles/markers observed on a chromosomal segment in a given population, and they make it possible to test multiple allelic interaction effects. Haplotypes can also increase the statistical power of GWAS by reducing the number of tests compared to using all SNPs. Alleles within the same haplotype block are more likely to be inherited together, while sharing a similar minor allele frequency (MAF). Haplotype-based analyses examine groups of SNPs simultaneously rather than individual SNPs, thereby increasing the statistical detection power for many aspects of both population and quantitative genetics, including identifying signals of recent positive selection and performing GWAS, respectively. Haplotype association mapping takes into account not only allelic heterogeneity but also possible statistical interactions among close markers, making it more powerful than single-marker and multiple-marker analysis.

Recently, scientists from the INRA Centre de Recherche PACA in France used an innovative approach to better understand the genetic architecture of tomato fruit quality traits and test the potential of haplotype-based approaches for association and genomic prediction studies. A core collection of tomato accessions was studied and genotyped with SNP markers. The haplotype architecture of the tomato genome was described and used to (1) deepen our understanding of its recent breeding history, (2) test the potential of haplotypes for the detection of new candidate QTL regions, and (3) predict phenotypes in the context of genomic selection. A number of haplotype-based analyses were performed to demonstrate the multiple benefits of using haplotypes in genetic analyses. This research was published in Horticulture Research.

“We demonstrated the benefits of haplotypes versus SNPs in many aspects, including identifying marker-trait associations, revealing the haplotype bifurcation patterns near the most significantly associated SNPs, explaining more missing heritability and increasing the genomic prediction accuracy”, Prof Causse said. These results will certainly be helpful for breeders and researchers focusing not only on tomatoes but also on other agronomic crops.

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Reference

Authors

Jiantao Zhao1,2, Christopher Sauvage1,3, Frédérique Bitton1 and Mathilde Causse1,*

Affiliations

1 INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, 67 Allée des Chênes CS 60094 – 84140, Montfavet Cedex, France

2 Boyce Thompson Institute for Plant Research, Cornell University, 533 T ower Road, Ithaca, NY 14853-1801, USA

3 Syngenta SAS France, 1228 Chemin de l’Hobit, Saint Sauveur 31790, France

About Professor Mathilde Causse

Dr. Mathilde Causse is an academician at the French Academy of Agricultural Sciences and a senior researcher in the field of plant genetics and breeding. Prof. Causse constructed the first genetic map of the rice genome in 1992. She served as the director of the Fruit and Vegetable Genetics and Breeding Department of the INRA Avignon Research Center for eight years and led a research team that studied the genetic and molecular basis of fruit quality. Her team located and identified several QTLs related to tomato fruit quality. At present, her group focuses on the impact of environmental stress on tomato fruit quality and yield and has made use of GWAS to perform tomato breeding. To date, Prof. Causse has published more than 120 papers in international journals.