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Article

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

1
Dipartimento di Agraria, Università degli Studi di Sassari, 07100 Sassari, Italy
2
Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale—CBV, Università degli Studi di Sassari, 07041 Alghero, Italy
3
Boyce Thompson Institute for Plant Research and U.S. Department of Agriculture—Agriculture Research Service, Ithaca, New York, NY 14853, USA
4
Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 0W9, Canada
5
Dipartimento di Scienze Agrarie, Alimentari e Ambientali—D3A, Università Politecnica delle Marche, 60131 Ancona, Italy
*
Author to whom correspondence should be addressed.
Genes 2020, 11(11), 1387; https://doi.org/10.3390/genes11111387
Received: 15 October 2020 / Revised: 19 November 2020 / Accepted: 20 November 2020 / Published: 23 November 2020
(This article belongs to the Special Issue Tomato Genetics)
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. View Full-Text
Keywords: Solanum lycopersicum L.; landraces; genomic diversity; digital phenotyping; RNA-Seq; genome-wide association study (GWAS) Solanum lycopersicum L.; landraces; genomic diversity; digital phenotyping; RNA-Seq; genome-wide association study (GWAS)
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MDPI and ACS Style

Rodriguez, M.; Scintu, A.; Posadinu, C.M.; Xu, Y.; Nguyen, C.V.; Sun, H.; Bitocchi, E.; Bellucci, E.; Papa, R.; Fei, Z.; Giovannoni, J.J.; Rau, D.; Attene, G. 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 2020, 11, 1387. https://doi.org/10.3390/genes11111387

AMA Style

Rodriguez M, Scintu A, Posadinu CM, Xu Y, Nguyen CV, Sun H, Bitocchi E, Bellucci E, Papa R, Fei Z, Giovannoni JJ, Rau D, Attene G. 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. 2020; 11(11):1387. https://doi.org/10.3390/genes11111387

Chicago/Turabian Style

Rodriguez, Monica, Alessandro Scintu, Chiara M. Posadinu, Yimin Xu, Cuong V. Nguyen, Honghe Sun, Elena Bitocchi, Elisa Bellucci, Roberto Papa, Zhangjun Fei, James J. Giovannoni, Domenico Rau, and Giovanna Attene. 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, no. 11: 1387. https://doi.org/10.3390/genes11111387

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