Genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs

Abstract

SummaryTo cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennials, but requires to understand the genetic architecture of important traits. To go beyond QTL mapping in bi-parental crosses, we exploited a diverse panel of 279 Vitis vinifera L. cultivars. This panel planted in five blocks in the vineyard was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. Such an experimental design allowed us to reliably assess the genotypic values for most traits. The panel was genotyped for 60k SNPs by combining an 18K microarray and sequencing (GBS). Marker densification via GBS markedly increased the proportion of genetic variance explained by SNPs, and two multi-SNP models identified QTLs not found by a SNP-by-SNP model. This led to 489 reliable QTLs using the combined microarray-GBS SNPs for 41% more response variables than a SNP-by-SNP model applied to microarray-only SNPs, and many QTLs were new compared to the results from bi-parental crosses. Prediction accuracy ranging from 0.14 to 0.84 for 80% of the response variables was promising for genomic selection, and provided insights into the genetic architecture of each trait when put in perspective with the number of QTLs and heritability.

Biosynthesis and Cellular Functions of Tartaric Acid in Grapevines

“…cereal crops), due to the lower costs of high-throughput sequencing and phenotyping techniques. Recently, GWAS analyses of 472 Vitis accessions ( Liang et al, 2019 ) and 279 V. vinifera L. cultivars ( Flutre et al, 2020 ), were employed to identify loci associated with traits including TA accumulation, detailed further in Section 9.…”

“…Experimental evidence is required before we can further speculate on their potential functions in TA biosynthesis. In addition, another comprehensive GWAS analysis of 279 V. vinifera L. cultivars also identified loci associated with TA accumulation ( Flutre et al, 2020 ), although at this stage there is insufficient publicly available data to link this to a specific gene or set of genes.…”

Across-population genomic prediction in grapevine opens up promising prospects for breeding

“…The reported PA for mbw was 0.56, whereas in the present study, we obtained 0.35 in the Grenache x Syrah progeny (n=59). We further investigated such discrepancy, and found it related to a sampling bias due to the small VS size in Flutre et al 26 (data not shown).…”

“…Yet, Mendelian sampling PA was still quite high, considering that TS was essentially unrelated to VS, i.e., with no first-degree relationship with predicted progenies. The same diversity panel was previously used in Flutre et al 26 for predicting individual genotypic values of 23 additional Syrah x Grenache offspring. The reported PA for mbw was 0.56, whereas in the present study, we obtained 0.35 in the Grenache x Syrah progeny (n=59).…”

“…They applied GP and found little difference between PA values estimated within the panel or across populations. Finally, Flutre et al 26 studied 127 traits with GWAS and GP within a diversity panel; they also applied across-population GP, but with 23 test offspring and for one trait only. Before genomic selection can be deployed in grapevine, evaluating PA across populations is thus crucially needed.…”