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

Abstract

Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpic seed abortion determined by the () locus is the usual source of seedlessness in commercial grapevine () cultivars, the underlying mutation remains unknown. Here, we undertook an integrative approach to identify the causal mutation. Quantitative genetics and fine-mapping in two 'Crimson Seedless'-derived F1 mapping populations confirmed the major effect of the locus and delimited the mutation to a 323-kb region on chromosome 18. RNA-sequencing comparing seed traces of seedless and seeds of seeded F1 individuals identified processes triggered during-determined seed abortion, including the activation of salicylic acid-dependent autoimmunity. The RNA-sequencing data set was investigated for candidate genes, and while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide changes in coding sequences of the seedless haplotype were predicted in two genes within the fine-mapping interval. Targeted resequencing of the two genes in a collection of 124 grapevine cultivars showed that only the point variation causing the arginine-197-to-leucine substitution in the seed morphogenesis regulator gene () was fully linked with stenospermocarpy. The concurrent postzygotic variation identified for this missense polymorphism and seedlessness phenotype in seeded somatic variants of the original stenospermocarpic cultivar supports a causal effect. We postulate that seed abortion caused by this amino acid substitution in VviAGL11 is the major cause of seedlessness in cultivated grapevine. This information can be exploited to boost seedless grape breeding.

Somatic Variation and Cultivar Innovation in Grapevine

“…More recently, long-read sequencing technologies such as PacBio are facilitating the release of haplotype-resolved assemblies, which are already available for the heterozygous grapevine cultivars Cabernet Sauvignon and Chardonnay [23,24]. By the time being, the availability of reference genomes combined with the development of next-generation sequencing (NGS) technologies enable genome-wide analysis of the grapevine germplasm at affordable costs, which is extremely useful in genetic diversity studies as well as to search for mutations causing phenotypic variation [15,[24][25][26]. Although the use of these approaches to characterize somatic variation in grapevine is still scarce, an increasing number of publications are shedding light on the magnitude and type of variation that accumulates at the genome level within given cultivars.…”

Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

“…In the past ten years, a number of grape genetic maps have been constructed based on different mapping populations [20,[22][23][24][25][26][27][28][29][30][31][32][33]. Numerous QTLs for important economic traits, including resistance to downy mildew [10,16,22,[34][35][36][37][38], powdery mildew [34,36,[39][40][41], anthracnose [24], root-knot nematodes [42], and grape phylloxera [43,44], as well as flower sex [45,46], berry color [46,47], seedlessness [48], berry weight [18,32], soluble solid content [32], acidity [20], and muscat flavor [49], have been identified.…”

QTL-seq Analysis of Seed Size Trait in Grape Provides New Molecular Insight on Seedlessness

“…Among nine selected genes, G2,was down-regulated during all ovule developmental stages in the seedless progeny. Whereas, the expression of the other eight candidate genes was up-regulated at least during one ovule developmental stage in seedless progeny compared to the seeded ones.It is notablethat the arginine-197-to-leucine substitution on Chromosome 18 in VviAGL11 [18] was also identified in our results,however, compared with other genes, this gene did not perform well in our SNP-index analysis, so not listed as a key candidate genefor further analysis.According to our transcriptomic analysis, VviAGL11is not identified as DEGs, and our results are consistent with the previous findings, so we have not considered this gene for further research. Motif analysis of the mutation region was carried out, and results showed that mutation in G1 happened in 'ML domain',G2…”

“…Recently, the major origin of seedless grapes was found to be associated with a missense mutation in the MADS-box gene VviAGL11 with two F1 mapping populations [18]. In general, despite all the progress made in molecular biology underlying grape seedlessness, the grape ovule identity gene and corresponding regulation mechanism was still not clear enough.…”