Association analysis of grapevine bunch traits using a comprehensive approach

Abstract

Bunch compactness plays an important role in the sanitary status and perceived quality of table and wine grapes, being influenced by cultural practices and by environmental and genetic factors, which are mostly unknown. In this work, we took advantage of genetic, genomic and bioinformatic advances to analyze part of its molecular basis through a combination of transcriptomic and association analyses. Results from different transcriptomic comparisons between loose and compact grapevine clones were analyzed to select a set of candidate genes likely involved in the observed variation for bunch compactness. Up to 183 genes were sequenced in a grapevine collection, and 7032 single nucleotide polymorphisms (SNPs) were detected in more than 100 varieties with a frequency of the minor allele over 5%. They were used to test their association in three consecutive seasons with bunch compactness and two of its most influencing factors: total berry number and length of the first ramification of the rachis. Only one SNP was associated with berry number in two seasons, suggesting the high sensitiveness of this trait to seasonal environmental changes. On the other hand, we found a set of SNPs associated with both the first ramification length and bunch compactness in various seasons, in several genes which had not previously related to bunch compactness or bunch compactness-related traits. They are proposed as interesting candidates for further functional analyses aimed to verify the results obtained in this work, as a previous step to their inclusion in marker-assisted selection strategies.

The Major Origin of Seedless Grapes Is Associated with a Missense Mutation in the MADS-Box Gene VviAGL11

“…The gene VviAGL11 (VIT_18s0041g01880) plus a 2-kb upstream sequence (9,849 bp in total, corresponding to positions chr18:26,888,672-chr26,898,521 in the PN40024 12X.0 grapevine reference genome) were sequenced in a collection of 110 accessions (Supplemental Table S7) by BGI, as described by Tello et al (2016). Briefly, Agilent SureSelect was used to target the VviAGL11 locus that was then sequenced in 90-nucleotide paired-end reads using Illumina HiSeq 2000.…”

Differences in Flower Transcriptome between Grapevine Clones Are Related to Their Cluster Compactness, Fruitfulness, and Berry Size

“…In this work we performed transcriptomic analyses of Garnacha Tinta clones, with stable differences in specific compactness-related parameters (berry number, berry size), to identify genes and gene networks involved in cluster compactness characteristics. From this transcriptomics study, 183 candidate genes were selected for an association analysis in a collection of grapevine varieties (Tello et al, 2016). …”

What do we know about grapevine bunch compactness? A state-of-the-art review

“…Little is known about the genetic basis and molecular mechanisms of bunch compactness. Recent linkage mapping (Correa et al ) and association mapping (Tello et al ) studies have suggested the likely involvement of some genes on the determination of bunch architecture, but they need further research to test their functionality and phenotypic effect by means of specific gene‐directed studies. Although these genes are interesting candidates, they might be single pieces of a highly complex puzzle.…”

“…There is also a wide range of diversity for berry number between grapevine cultivars (Dry et al , Tello et al ). Flower number and fruitset rate are under the control of complex genetic networks and are also affected by the environment, which hinders the genetic analysis of grape berry number (Fanizza et al , Tello et al ). Recently, it has been suggested that fruitset differences between three cultivars, Shiraz, Merlot and Cabernet Sauvignon, are attributable to differences in pollen viability and in the concentration of diverse amines (e.g.…”