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Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS

ABSTRACT: Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain between 12.6% and 44.1% of the phenotypic variance. A set of 6 QTL were found to be associated with more than one variable. Marker WDP-9.21 was found associated with tuber fresh weigh under WD and gene annotation analysis revealed co-localization with the Glucan/water dikinase (GWD) gene. Of the nine QTL detected from DTI on chromosomes 2,3,5,8,10 and 12, three candidate genes with a feasible role in water deficit response were identified. The findings of this study can be used in marker-assisted selection (MAS) for water- deficit tolerance breeding in potato.

SUBMITTER: Diaz P

PROVIDER: S-EPMC8575265 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Tuber tissue discolorations caused by impact (blackspot bruising) and enzymatic discoloration (ED) after tuber cutting are crucial quality traits of the cultivated potato. To understand the complex genetics of the traits, quantitative trait locus (QTL) analysis using diploid mapping population and diversity array technology (DArT) markers was performed. The phenotypic assessment included the complex evaluation of blackspot bruising susceptibility through two methods: rotating drum (B RD) and falling bolt (B FB) in combination with the evaluation of enzymatic discoloration. Because of observed in-practice relationship between bruising susceptibility and tuber starch content (TSC), analysis of starch content-corrected bruising susceptibility (SCB) was performed. QTLs for bruising were detected on chromosomes I, V with both test methods. The rotating drum method enabled the detection of additional QTLs on chromosomes VIII and XII. Analysis of SCB enabled the identification of the major QTL on chromosome V and two weaker QTLs on chromosomes VIII and XII, independently of starch content. The QTL for bruising detected on chromosome I overlapped with the most significant QTL for tuber starch content. This QTL was not significant for starch content-corrected bruising susceptibility, and the effect of the QTL on chromosome V was enhanced for this trait. The QTL analysis of ED revealed the contribution of seven QTLs for the trait, located on six chromosomes, including these detected for the first time: a major locus on chromosome V and minor QTLs on chromosomes VII and X, which were specific for the trait. The QTL for ED on chromosome VIII was co-localized with the marker for polyphenol oxidase (POT32). The phenotypic correlation between bruising and ED was confirmed in QTL analyses of both traits, and the QTLs detected for these traits overlapped on chromosomes I, V, and VIII. Our results should provide a basis for further studies on candidate genes affecting blackspot bruise susceptibility and enzymatic discoloration.

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Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS

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