Jean Michel Boursiquot

Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine

BackgroundStenospermocarpy is a mechanism through which certain genotypes of Vitis vinifera L. such as Sultanina produce berries with seeds reduced in size. Stenospermocarpy has not yet been characterized at the molecular level.ResultsGenetic and physical maps were integrated with the public genomic sequence of Vitis vinifera L. to improve QTL analysis for seedlessness and berry size in experimental progeny derived from a cross of two seedless genotypes. Major QTLs co-positioning for both traits on chromosome 18 defined a 92-kb confidence interval. Functional information from model species including Vitis suggested that VvAGL11, included in this confidence interval, might be the main positional candidate gene responsible for seed and berry development.Characterization of VvAGL11 at the sequence level in the experimental progeny identified several SNPs and INDELs in both regulatory and coding regions. In association analyses performed over three seasons, these SNPs and INDELs explained up to 78% and 44% of the phenotypic variation in seed and berry weight, respectively. Moreover, genetic experiments indicated that the regulatory region has a larger effect on the phenotype than the coding region. Transcriptional analysis lent additional support to the putative role of VvAGL11s regulatory region, as its expression is abolished in seedless genotypes at key stages of seed development. These results transform VvAGL11 into a functional candidate gene for further analyses based on genetic transformation.For breeding purposes, intragenic markers were tested individually for marker assisted selection, and the best markers were those closest to the transcription start site.ConclusionWe propose that VvAGL11 is the major functional candidate gene for seedlessness, and we provide experimental evidence suggesting that the seedless phenotype might be caused by variations in its promoter region. Current knowledge of the function of its orthologous genes, its expression profile in Vitis varieties and the strong association between its sequence variation and the degree of seedlessness together indicate that the D-lineage MADS-box gene VvAGL11 corresponds to the Seed Development Inhibitor locus described earlier as a major locus for seedlessness. These results provide new hypotheses for further investigations of the molecular mechanisms involved in seed and berry development.

Haplotype diversity of VvTFL1A gene and association with cluster traits in grapevine (V. vinifera)

BackgroundInteraction between TERMINAL FLOWER 1 (TFL1) and LEAFY(LFY) seem to determine the inflorescence architecture inArabidopsis. In a parallel way, overexpression of VvTFL1A, agrapevine TFL1 homolog, causes delayed flowering and production of aramose cluster in the reiterated reproductive meristem (RRM) somatic variant ofcultivar Carignan. To analyze the possible contribution of this gene to clusterphenotypic variation in a diversity panel of cultivated grapevine (Vitisvinifera L. subsp. vinifera) its nucleotide diversity wascharacterized and association analyses among detected sequence polymorphisms andphenology and cluster traits was carried out.ResultsA total of 3.6xa0kb of the VvTFL1A gene, including its promoter, wassequenced in a core collection of 140 individuals designed to maximize phenotypicvariation at agronomical relevant traits. Nucleotide variation forVvTFL1A within this collection was higher in the promoter and intronsequences than in the exon regions; where few polymorphisms were located inagreement with a high conservation of coding sequence. Characterization of theVvTFL1A haplotype network identified three major haplogroups,consistent with the geographic origins and the use of the cultivars that couldcorrespond to three major ancestral alleles or evolutionary branches, based on theexistence of mutations in linkage disequilibrium. Genetic association studies withcluster traits revealed the presence of major INDEL polymorphisms, explaining 16%,13% and 25% of flowering time, cluster width and berry weight, respectively, andalso structuring the three haplogroups.ConclusionsAt least three major VvTFL1A haplogroups are present in cultivatedgrapevines, which are defined by the presence of three main polymorphism LD blocksand associated to characteristic phenotypic values for flowering time, clusterwidth and berry size. Phenotypic differences between haplogroups are consistentwith differences observed between Eastern and Western grapevine cultivars andcould result from the use of different genetic pools in the domestication processas well as different selection pressures on the development of table and winecultivars, respectively. Altogether, these results are coherent with previousclassifications of grapevine phenotypic diversity mainly based on cluster andberry morphotypes as well as with recent results on the structure of geneticdiversity in cultivated grapevine.

Identification and characterization of an original grapevine cultivar (Vitis vinifera) found in Chile

Currently, many monovarietal vineyards present a minority of mixed cultivars. Some of these cultivars are unknown and could represent an opportunity to discover new and potentially useful genotypes both for research and production purposes. In a ‘Carmenere’ vineyard planted in 1994 in Palmilla (Colchagua Valley, Chile), a minority presence of other cultivars was found. The present work covers for the first time the identification and characterization of one of these cultivars, which presented a very poor fruit set. Through classic ampelography, it was not possible to associate the studied cultivar with any known cultivar in Chile. However, through a simple sequence repeats (SSR) comparison against the database of the INRA Germplasm Repository “Domaine de Vassal” in France, the cultivar was identified as a triploid accession named ‘Folle Blanche Faux’ ( Vitis vinifera L.) that was previously found in Chile during the season of 1950-1951. This cultivar presents earlier bud breaking than ‘Carmenere’, has morphologically complete flowers, and shows a physiological disorder around the fruit set, leading to partial or complete bunch necrosis under the environmental conditions of Palmilla. This cultivar contributes to the genotypic richness present in Chile and might be an interesting tool for physiological and molecular studies. It also could become productive under other environmental conditions (i.e., environmental conditions that favor a good fruit set) or by the application of adequate vineyard practices, such as cane girdling at bloom time. Actualmente, muchos vinedos monovarietales presentan mezclas de otros cultivares en proporciones menores. Algunos de estos cultivares son desconocidos y podrian representar una oportunidad para descubrir genotipos nuevos y potencialmente utiles en investigacion y/o produccion. En un vinedo cv. ‘Carmenere’, plantado en 1994 en la comuna de Palmilla (Valle de Colchagua, Chile), se determino la presencia minoritaria de otros cultivares. El presente trabajo cubre por primera vez la identificacion y caracterizacion de uno de estos cultivares, el cual presento una muy pobre fructificacion. A traves de ampelografia clasica, no fue posible asociar el cultivar en estudio a ningun cultivar conocido en Chile. Sin embargo, a traves de una comparacion de marcadores moleculares microsatelites con la base de datos del Repositorio de Germoplasma de Vid del INRA “Domaine de Vassal” en Francia, fue identificado como un acceso triploide llamado ‘Folle Blanche Faux’ ( Vitis vinifera L.), el cual habia sido descubierto en Chile previamente durante la temporada 1950-1951. Este cultivar presenta una brotacion mas precoz que la del cv. ‘Carmenere’, posee flores morfologicamente completas y muestra un notorio desorden fisiologico en su fructificacion, el cual se manifiesta a traves de una necrosis de racimo parcial o completa, bajo las condiciones ambientales de Palmilla. Este cultivar contribuye a la riqueza genotipica presente en Chile y eventualmente podria llegar a ser una herramienta interesante para estudios fisiologicos y moleculares. Adicionalmente, podria volverse productiva bajo otras condiciones ambientales ( i.e. condiciones ambientales que favorezcan una buena cuaja frutal) o por la aplicacion de practicas viticolas adecuadas, como el anillamiento de cargadores durante la floracion.