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

Authors: RODIGUEZ, MONICA - University Of Sassari; SCIUNTI, ALESSANDRO - University Of Sassari; POSADINU, CHIARA - University Of Sassari; XU, YIMIN - Boyce Thompson Institute; NGUYEN, CUONG - University Of Saskatchewan; SUN, HONGHE - Boyce Thompson Institute; BITOCCHI, ELENA - Polytechnic University Of Marche; BELLUCCI, ELISA - Polytechnic University Of Marche; PAPA, ROBERTO - Polytechnic University Of Marche; FEI, ZHANGJUN - Boyce Thompson Institute; Giovannoni, James; RAU, DOMENICO - University Of Sassari; ATTENE, GIOVANNA - University Of Sassari

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/19/2020
Publication Date: 11/20/2020
Citation: Rodiguez, M., Sciunti, A., Posadinu, C., Xu, Y., Nguyen, C., Sun, H., Bitocchi, E., Bellucci, E., Papa, R., Fei, Z., Giovannoni, J.J., Rau, D., Attene, G. 2020. 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. Genes. 11:1387. https://doi.org/10.3390/genes11111387.
DOI: https://doi.org/10.3390/genes11111387

Interpretive Summary: Tomato is a major vegetable crop worldwide and a widely used model species in genomic studies and breeding. The rapidly increasing availability of genomic data has allowed researchers to bypass the limitations of a single reference genome and has facilitated development of a pan-genome that represents the genetic diversity of cultivated and wild tomato species. Recent groundbreaking studies have shown how the integration of widely variable tomato collections and genomics tools can contribute to advances in population genomics, domestication and plant evolution studies. Here we used three different GWAS approaches that provided an output of 536 significant associations related to plant and fruit traits including those related to fruit quality and response to climate. We demonstrate the value of this unique and diverse tomato collection for future gene-function, genome-editing and crop-breeding applications.

Technical Abstract: Tomato is a widely used model plant species for dissecting out the genomic bases of complex traits t. 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. 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.