GWAS Based on RNA-Seq SNPs and High-Throughput Phenotyping Combined with Climatic Data Highlights the Reservoir of Valuable Genetic Diversity in Regional Tomato Landraces

Abstract

Tomato (Solanum lycopersicum L.) is a widely used model plant species for dissecting out the genomic bases of complex traits to thus provide an optimal platform for modern "-omics" studies and genome-guided breeding. Genome-wide association studies (GWAS) have become a preferred approach for screening large diverse populations and many traits. Here, we present GWAS analysis of a collection of 115 landraces and 11 vintage and modern cultivars. A total of 26 conventional descriptors, 40 traits obtained by digital phenotyping, the fruit content of six carotenoids recorded at the early ripening (breaker) and red-ripe stages and 21 climate-related variables were analyzed in the context of genetic diversity monitored in the 126 accessions. The data obtained from thorough phenotyping and the SNP diversity revealed by sequencing of ripe fruit transcripts of 120 of the tomato accessions were jointly analyzed to determine which genomic regions are implicated in the expressed phenotypic variation. This study reveals that the use of fruit RNA-Seq SNP diversity is effective not only for identification of genomic regions that underlie variation in fruit traits, but also of variation related to additional plant traits and adaptive responses to climate variation. These results allowed validation of our approach because different marker-trait associations mapped on chromosomal regions where other candidate genes for the same traits were previously reported. In addition, previously uncharacterized chromosomal regions were targeted as potentially involved in the expression of variable phenotypes, thus demonstrating that our tomato collection is a precious reservoir of diversity and an excellent tool for gene discovery.

Keywords: RNA-Seq; Solanum lycopersicum L.; digital phenotyping; genome-wide association study (GWAS); genomic diversity; landraces.

Figure 1

Principal component analysis performed on all of the morphophenological and fruit quality traits. ELR, exotic landraces; SLR, Sardinian landraces; CV, modern and vintage cultivars. Accessions are attributed to three phenotypic groups (yellow, green, red), based on the hierarchical clustering obtained with the same data.

Figure 2

Population structure analysis as obtained from STRUCTURE (A) and DAPC (B) methods. (A) Accessions attributed to three genetic groups (yellow, green, red). (B) Accessions attributed to four genetic groups (yellow, green, orange, red). In both cases shown, each vertical bar indicates a single accession, which is colored according to the genetic group to which it was assigned. Accessions not assigned to a single group are colored according to the estimated proportion of membership to each genetic group and are defined as admixed. ELR, exotic landraces; SLR, Sardinian landraces; CV, modern and vintage cultivars.

Figure 3

Linkage disequilibrium decay levels over all chromosomes calculated using the standard r² coefficient and the r² measure corrected for population structure (r_s²), kinship (r_v²) and both population structure and kinship (r_vs²).