Genome Resequencing, Improvement of Variant Calling, and Population Genomic Analyses Provide Insights into the Seedlessness in the GenusVitis

Abstract

The seedlessness of grape derived from stenospermocarpy is one of the most prized traits of table or raisin grapes. It is controlled by a complex genetic system containing one dominant gene and multiple recessive genes. Here, we collected dense variation data from high-depth resequencing data of seeded, seedless, and wild relative grape genomes sequenced to > 37x mean depth. Variant calls were made using a modified variant calling pipeline that was suitable for highly diverse interspecific grape accessions. The modified pipeline enabled us to call several million more variants than the commonly recommended pipeline. The quality was validated by Sanger sequencing data and subsequently supported by the genetic population structure and the phylogenetic tree constructed using the obtained variation data, results of which were generally consistent with known pedigree and taxonomic classifications. Variation data enabled us to confirm a dominant gene and identify recessive loci for seedlessness. Incidentally, we found that grape cultivar Rizamat contains an ancestral chromosomal region of the dominant gene in Sultanina, a predominant seedlessness donor cultivar. Furthermore, we predicted new candidate causal genes including Vitvi01g00455, Vitvi08g01528, and Vitvi18g01237 associated with the recessive seedless-regulating loci, which showed high homology with genes that regulate seed development in Arabidopsis. This study provides fundamental insights relevant to variant calling from genome resequencing data of diverse interspecific hybrid germplasms such as grape and will accelerate future efforts aimed at crop improvement.

Functional conservation of the grapevine candidate gene INNER NO OUTER for ovule development and seed formation

“…Moreover, more recently QTLs studies have revealed the contribution of a region located on top of chromosome 1 including VviINO gene to the total seeds fresh weight (TSFW) per berry trait 44 , further supporting VviINO as a candidate for grapevine seedlessness. An association to seedlessness in this genomic part of Chr1 was also confirmed by resequencing of seedless and seeded varieties, even though no associated SNP located in this gene were found in the studied panel 10 .…”

“… 4 , 5 for a summary). The Sultanine (or Thomson seedless) cultivar contributes to the SEED DEVELOPMENT INHIBITOR ( SDI ) locus, the major source of seedlessness exploited for breeding purposes and in commercial grapevine cultivars 6 – 10 . A recent study has elucidated the molecular basis of this trait demonstrating this is associated with a missense mutation in the MADS-Box gene VviAGL11 controlling seed coat development and lignification 11 .…”

Complex of Glycyrrhizic and Salicylic Acids: A New Root Length Growing Means for Grapes to Grow from the Apical Meristem

“…It is one of the most used varieties to develop new genotypes 28 . As a seeded grape variety, it contains recessive loci for seedlessness 29 . Alternate drip irrigation of the Rizamat variety was shown to keep the same photosynthesis level but a lower transpiration rate 30 .…”

De novoassembling a high-quality genome sequence of Amur grape (Vitis amurensisRupr.) gives insight intoVitisdivergence and sex determination

“…We explored the Vv SDR syntenic region between 5055465 and 5198824 on Amur grape chromosome 2, showing good synteny between two species. To determine whether the Amur grape putative SDR region is related to sex, we adopted the selective sweep method, which allows analysis of fewer samples than GWAS (Kim et al ., 2020).…”