GSE107014
Analysis of the origin of stenospermocarpy under the control of the major seedlessness locus in grapevine
Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpy determined by the Seed Development Inhibitor (SDI) locus is the usual source of seedlessness in commercial grapevine cultivars, the sdi mutation underlying this locus remained unknown and we undertook an integrative approach to identify it. Quantitative genetics and fine mapping studies in two Crimson Seedless (CS)-derived F1 populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a region of 323 kb on chromosome 18. Transcriptomics comparing gene expression between seeds and seed traces in RG (Red Globe) × CS progeny identified processes triggered during sdi-determined seed abortion, including the activation of salicylic acid (SA)-dependent defenses. RNA-seq and NimbleGen microarray datasets were investigated for candidate genes and, while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide sequence changes in the seedless haplotype were predicted in two genes within the sdi fine mapping interval, VviPPAT2 and VviAGL11. Targeted re-sequencing of the two genes in a collection of 126 cultivars showed that only the point variation causing the Arg197Leu substitution in the seed morphogenesis regulator gene VviAGL11 was fully linked with seedlessness. Remarkably, this missense mutation was not detected in seeded clonal variants of Sultanina cultivar, the original donor of the sdi mutation, providing genetic evidence that this is the major cause of seedlessness in cultivated grapevines. The identification of the dominant effects of this amino acid substitution in seed abortion can be exploited to boost seedless grape breeding. Overall design: A total of 6 independent cDNA libraries were sequenced. RNA from stenospermocarpic seed traces of three seedless (669-60, 670-17, 675-17) and from seeds of three seeded (665-17, 671-19, 677-06) Red Globe×Crimson Seedless F1 Vitis vinifera table grape hybrids was compared. Every sample was collected simultaneously and three replicates were analyzed for the two genotypically and phenotypically constrasting offspring classes.