Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches

Abstract

Background: Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds. Results: Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotypephenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed. Conclusions: We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.

QTL Mapping for Leaf Area of Tea Plants (Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing

“…The average SNP density was 9.6/Kb, which is much higher than that previously reported ( An et al, 2020 ). Similar to other crops ( Shen et al, 2017 ; Thakur and Randhawa, 2018 ; Muñoz-Espinoza et al, 2020 ), transitions had an absolute advantage in SNPs, and the ts/tv value was approximately 2.51, which was higher than Cucurbita ( Xanthopoulou et al, 2019 ) but lower than lotus ( Huang et al, 2018 ). Moreover, 242,044 and 185,799 SNPs were annotated as non-synonymous mutations and synonymous mutations, respectively.…”

The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes

“…The phenotypic traits that were subject to selection during domestication 31 were presumably related to flower sex determination, with nearby mutations within a sex locus in the upper arm of chromosome 2 involved in the transition from dioecious plants in sylvestris to hermaphrodites in sativa 32 , and to berry morphology, with an increase in berry size and flesh-to-seed ratio going from sylvestris to sativa that made the grapes more attractive to human consumption and more amenable to wine making, with their genetic determinants still unknown. Quantitative trait loci (QTLs) controlling a series of berry traits in wine as well as in table grapes have been found overlapping with the sweep region on chromosome 17 33 , 34 .

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Optimization of an In Vitro Embryo Rescue Protocol for Breeding Seedless Table Grapes (Vitis vinifera L.) in Italy

“…Quantitative trait loci linked to seedlessness were firstly identified on chromosome 18 [52][53][54], and later, Mejía et al [55] developed an intragenic simple sequence repeats (SSR) marker mapped on the regulatory region of the VviAGL11 candidate gene (p3_VvAGL11). More recently, discovery and exploitation of new DNA-based markers associated with seedlessness were carried out by Karaagac et al [56], Akkurt et al [10], Li et al [15], Zhu et al [3], and Muñoz-Espinoza et al [57].…”