Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content

Abstract

Valorisation of tuber protein is relevant for the potato starch industry to create added-value and reduce impact on the environment. Hence, protein content has emerged as a key quality trait for innovative potato breeders. In this study, we estimated trait heritability, explored the relationship between protein content and tuber under-water weight (UWW), inferred haplotypes underlying quantitative trait loci (QTLs) and pinpointed candidate genes. We used a panel of varieties (N = 277) that was genotyped using the SolSTW 20 K Infinium single-nucleotide polymorphism (SNP) marker array. Protein content data were collected from multiple environments and years. Our genome-wide association study (GWAS) identified QTLs on chromosomes 3, 5, 7 and 12. Alleles of StCDF1 (maturity) were associated with QTLs found on chromosome 5. The QTLs on chromosomes 7 and 12 are presented here for the first time, whereas those on chromosomes 3 and 5 co-localized with loci reported in earlier studies. The candidate genes underlying the QTLs proposed here are relevant for functional studies. This study provides resources for genomics-enabled breeding for protein content in potato.

Genome‐wide association analysis of agronomical and physiological traits linked to drought tolerance in a diverse potatoes (Solanum tuberosum) panel

“…The GWAS analysis in traits with low heritability should consider the population structure, the SNP bias as well as the loss of statistical power in order to recognise QTL with minor effect and avoid false positives (Vos, 2016). As was described for the starch content (Klaassen et al., 2019), increases in the statistical power with a larger potatoes panel should be included in future related GWAS studies.…”

“…The SNP allele frequency (%) in the potatoes panel was performed using the SNP dosage score as described by Klaassen et al. (2019): …”

Overview on domestication, breeding, genetic gain and improvement of tuber quality traits of potato using fast forwarding technique (GWAS): A review

“…Several studies used Infinium SolCAP 8k, 12k and 20k potato array for GWAS in potato to detect genomic regions associated with tuber quality traits (Berdugo‐Cely et al., 2017; Klaassen et al., 2019; Schönhals et al., 2017; Sharma et al., 2018; Zia et al., 2020). QTL mapping was performed using SolCAP 8K SNP array by Massa et al.…”

“…Higher delta K is an indication of genetic diversity or unrelatedness of individuals in an association panel. The variable number "clusters/subpopulations" or "Kinship groups" were identified in the literature for GWAS in potato, such as K = 6 (Rosyara et al., 2016), K = 3 (Vos et al., 2017), K = 10 (Sharma et al., 2018), K = 3 (Klaassen et al., 2019) and K = 4 (Zia et al., 2020).…”

“…Moreover, molecular studies showed that intracellular glucose is used by plants to synthesize both starch and protein. Hence, concluded that the genes that affect starch content may also regulate protein content in potato (Klaassen et al., 2019).…”