Diploid genome assembly and annotation provide insights into allele-specific variants underlying fruit-quality QTLs

Abstract

Fruit-quality traits including berry aroma and bunch architecture are major targets for improvement in both the wine and table grape industry. However, our current understanding of their underlying genetic architecture is limited due to the complex polygenic nature of these fruit traits. To identify and characterise genetic variants related to berry aroma and bunch architecture, we utilised a biparental mapping population derived from a cross between the wine grape ‘Deckrot’ (‘Pinot gris’ x ‘Teinturier’) and a table grape selection, G1-7720 (‘Black Rose’ x ‘Muscat Seedless’). Diploid chromosome-scale genomes were assembled with PacBio HiFi reads for the parents of the population. Each diploid genome comprised of 19 pseudochromosomes for both haplophase (hap 1 and hap2) assemblies. Reference-based scaffolding generated assemblies with a length of 504.14 Mb for Deckrot hap 1, 490.18 Mb for Deckrot hap2, 496.07 Mb for G1-7720 hap1, and 489.16 Mb for G1-7720 hap2. Scaffold N50 value for all assemblies exceeded 25 Mb with a mean BUSCO score of 98.4%. Additionally, transcriptome-based gene annotation of Deckrot hap1, Deckrot hap2, G1-7720 hap1, and G1-7720 hap2 predicted 42215, 40766, 43207, and 40418 gene models, respectively. Comparative analysis of the annotated genomes identified structural variants, single nucleotide polymorphisms, and gene copy number variation potentially underlying QTLs for berry aromatic profiles and bunch phenotypes segregating in the population. Furthermore, the assembly of diploid genomes facilitated allele-specific expression (ASE) analysis with RNA-seq data generated from flower tissue of the progeny. Thus, allowing us to distinguish parental alleles, detect genes showing ASE, and provide insights into the regulatory mechanisms influencing candidate genes identified in the QTLs. Among the candidate genes interrogated in this analysis, the gene VvTPS29, found in a QTL associated with sesquiterpene biosynthesis, showed ASE in the population and a possible of loss-of-function allele in G1-7720. This study provides high-quality genome assemblies and annotations to dissect fruit-quality QTLs, identify putative candidate genes, and streamline genetic marker development. By implementing whole genome sequencing in this study, we demonstrated the utility of this approach in deciphering genetic variation and biological mechanisms underpinning key grapevine breeding targets.