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

UMR AGAP - équipe DAAV - Diversité, adaptation et amélioration de la vigne[b]Background[/b] [br/]The 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). [br/][b]Results[/b] [br/]Ten 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. [br/][b]Conclusions[/b] [br/]This 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 variatio

Multiscale imaging of plants: current approaches and challenges

International audienceWe review a set of recent multiscale imaging techniques, producing high-resolution images of interest for plant sciences. These techniques are promising because they match the multiscale structure of plants. However, the use of such high-resolution images is challenging in the perspective of their application to high-throughput phenotyping on large populations of plants, because of the memory cost for their data storage and the computational cost for their processing to extract information. We discuss how this renews the interest for multiscale image processing tools such as wavelets, fractals and recent variants to analyse such high-resolution images

Service de phénotypage PHENOTIC : les sciences et technologies de l'information appliquées au phénotypage du végétal

à Angers (France) le 05/06/2012Journée Analyses et Végétal du Pôle de Compétitivité Végépoly

Isafruit - study of the genetic basis of prunus fruit quality in two peach and two apricot populations.

A European Integrated Project, untitled \u2018ISAFRUIT\u2019, has been engaged in January 2006. It deals with the improvement of fruit consumption by the consumers under both objectives: the optimization of the quality of the row products, and the optimization of the cultural practices. The project involves 40 Research Institutes and 20 Companies issued from 14 European countries and two associated countries. Within the whole project, a work package (6.1) is dedicated to the study of the genetics of fruit quality and health properties. It is subdivided in six main tasks, among them two concerning peach and apricot quality attributes have been already engaged: Task 1 \u2013 Identification and mapping of candidate genes for fruit quality in saturated maps of peach and apricot. Task 3 \u2013 QTLs analysis of fruit quality. Six research laboratories are involved in theses parts of the project based on the analysis of four Prunus progenies of 120 hybrid each, two apricot progenies cultivated in Avignon (Fr) and Bologna (It), and two peach progenies cultivated in Avignon and Bordeaux (Fr). Fruit quality characterization is based on (i) physical measurements (fruit weight, colour, firmness), (ii) biochemical measurements (refractometric index, titratable acidity) and (iii) on a fine metabolic profiling based on 1H RMN 1D, targeting the major metabolites, associated with a phenolic compounds characterization by HPLC. The related datasets will be joined with the genetic map under saturation for localising the associated QTLs. A particular attention will be paid to the co-linearity between species

A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine

Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220–244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis

The peach genome

The peach [Prunus persica (L.) Batsch] genome sequence has been recently made available to the scientific community. This represents the culmination of a long process that started less than two decades ago with the release of the first marker-based linkage maps. The process has advanced rapidly with the studies of molecular diversity, detection of genome positions of major genes and quantitative trait loci, development of large DNA sequence collections, transcriptome and proteome analyses, comparative genomic studies, construction of a physical map, and development of databases where researchers can access information. The growth of genomics knowledge has been partly due to the simplicity of the peach genome: short (230 Mbp), diploid, and distributed on eight pairs of chromosomes. Its unusually short intergeneration period (2–4 years) and selfing mating behavior, plus a dynamic peach scientific community that has often collaborated in the development of the necessary tools, have also facilitated in constructing a robust sequence of its complete genome. Peach is one of the best known species genetically among tree crops, with the promise of rapid advancement in the next few years. This paper reviews the resources available and the main results obtained, with emphasis placed on application to the development of improved varieties.The group of IRTA is a member of the CONSOLIDER Center for Basic Genomics and Agro-food Orientation (CSD2007-00036) and received additional funding for peach genomics research from a project of the Spanish Ministry of Education (AGL2009-07305).Peer reviewe