Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip

Abstract

BackgroundThe increasing temperature associated with climate change impacts grapevine phenology and development with critical effects on grape yield and composition. Plant breeding has the potential to deliver new cultivars with stable yield and quality under warmer climate conditions, but this requires the identification of stable genetic determinants. This study tested the potentialities of the microvine to boost genetics in grapevine. A mapping population of 129 microvines derived from Picovine x Ugni Blanc flb, was genotyped with the Illumina® 18 K SNP (Single Nucleotide Polymorphism) chip. Forty-three vegetative and reproductive traits were phenotyped outdoors over four cropping cycles, and a subset of 22 traits over two cropping cycles in growth rooms with two contrasted temperatures, in order to map stable QTLs (Quantitative Trait Loci).ResultsTen stable QTLs for berry development and quality or leaf area were identified on the parental maps. A new major QTL explaining up to 44 % of total variance of berry weight was identified on chromosome 7 in Ugni Blanc flb, and co-localized with QTLs for seed number (up to 76 % total variance), major berry acids at green lag phase (up to 35 %), and other yield components (up to 25 %). In addition, a minor QTL for leaf area was found on chromosome 4 of the same parent. In contrast, only minor QTLs for berry acidity and leaf area could be found as moderately stable in Picovine. None of the transporters recently identified as mutated in low acidity apples or Cucurbits were included in the several hundreds of candidate genes underlying the above berry QTLs, which could be reduced to a few dozen candidate genes when a priori pertinent biological functions and organ specific expression were considered.ConclusionsThis study combining the use of microvine and a high throughput genotyping technology was innovative for grapevine genetics. It allowed the identification of 10 stable QTLs, including the first berry acidity QTLs reported so far in a Vitis vinifera intra-specific cross. Robustness of a set of QTLs was assessed with respect to temperature variation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0588-0) contains supplementary material, which is available to authorized users.

Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops

“…In addition to allowing for the rapid cycling of generations, microvines take up less space and could be a valuable tool for genomics studies and MAS (Chaïb et al, 2010). For example, recent work used microvines to aide in QTL identification for traits such as berry acidity (Houel et al, 2015). In apple, an early flowering transgenic line containing the BpMADS4 gene from silver birch ( Betula pendula ) was combined with MAS to pyramid resistance to apple scab, powdery mildew, and fire blight (Flachowsky et al, 2011).…”

Development and Use of Biotechnology Tools for Grape Functional Analysis

“…The study of the genetic control of major agronomic traits in grapevine using QTL analysis allowed the elucidation of traits such as seedlessness and berry weight [12,18,[21][22][23]; berry phenolic composition [24][25][26][27][28]; aroma [29,30]; berry firmness [31,32]; fertility [9,33]; flower hermaphroditism [34]; cluster architecture [35]; pathogen resistance [34,[36][37][38]; plant phenology [39,40]; and adaptation to abiotic stresses [41] and to climate change [42]. Despite several of the reports allowed the identification of candidate sequences, just few of them have finally characterized the genes responsible for a particular function or trait.…”

“…sylvestris, three V. cinerea, three V. berlandieri, three V. aestivalis, three V. labrusca, one V. lincecumii, and five Muscadinia rotundifolia genotypes using Illumina platforms. The use of this powerful tool in combination with the microvine model system [56] allowed an innovative study in grapevine genetics [9]. This work achieved the identification of 10 robust and stable QTLs for vegetative and reproductive traits as well as the first berry acidity QTLs reported so far in grapevine [9].…”

“…The use of this powerful tool in combination with the microvine model system [56] allowed an innovative study in grapevine genetics [9]. This work achieved the identification of 10 robust and stable QTLs for vegetative and reproductive traits as well as the first berry acidity QTLs reported so far in grapevine [9]. Additional initiatives like the recent development of large diversity panel including 279 cultivars from different uses (table and wine grapes) and geographical origin (eastern and western), and including most of the major founders of modern cultivars [10], will certainly increase the power and value of the 18K SNP chip for genome wide association studies and to gain more insight into the genetic control of many agronomic traits and their interaction with the environment.…”

“…Interval mapping based on DNA markers could be used to genetically localize QTLs in natural and experimental populations [7,8]. The development of new QTL mapping strategies and DNA research tools [9,10], as well as the successful identification of few genes responsible of simple Mendelian traits [11,12], have reinvigorated interest in grapevine QTL analysis. The present chapter summarizes the latest scientific advances in the field of grapevine functional analysis through the development and use of different biotechnological tools.…”