High-Throughput Genotyping of Resilient Tomato Landraces to Detect Candidate Genes Involved in the Response to High Temperatures.

Genes
Fabrizio OlivieriAmalia Barone

Abstract

The selection of tolerant varieties is a powerful strategy to ensure highly stable yield under elevated temperatures. In this paper, we report the phenotypic and genotypic characterization of 10 tomato landraces to identify the best performing under high temperatures. The phenotyping of five yield-related traits allowed us to select one genotype that exhibits highly stable yield performances in different environmental conditions. Moreover, a Genotyping-by-Sequencing approach allowed us to explore the genetic variability of the tested genotypes. The high and stable yielding landrace E42 was the most polymorphic one, with ~49% and ~47% private SNPs and InDels, respectively. The effect of 26,113 mutations on proteins' structure was investigated and it was discovered that 37 had a high impact on the structure of 34 proteins of which some are putatively involved in responses to high temperatures. Additionally, 129 polymorphic sequences aligned against tomato wild species genomes revealed the presence in the genotype E42 of several introgressed regions deriving from S. pimpinellifolium. The position on the tomato map of genes affected by moderate and high impact mutations was also compared with that of known markers/QTLs (Quantitativ...Continue Reading

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Methods Mentioned

BETA
protein folding
genotyping
RAD-seq
Whole Genome Sequencing
two hybrid
two hybrids

Software Mentioned

CircosVCF
Stacks
MEM
BLAST
SNPeff
Blast Genome Workbench
DOCET
PLINK
BWA
SPSS

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