Genomic regions of Solanum tuberosum L. associated with the tuber eye depth

Abstract

Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber’s eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the “eye depth” trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1–48.9 Mb). The results of localization in the region 48.1–48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber’s eye depth were studied in the SolTub_3.0 potato genome assembly (https:// plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber’s eye depth.

MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms

“…Two SNPs, named as c1_8019 and c2_25471, were identified as significant by the polyploid packages GWASpoly and SHEsis (Figure 6b). Previous association studies also reported these SNPs where the SNP c1_8019 is associated with potato tuber shape and eye depth traits (Rosyara et al., 2016; Sharma et al., 2018), while the SNPs c2_45606 and c2_45611 are associated with eye depth (Totsky et al., 2020).…”

MultiGWAS: An integrative tool for Genome Wide Association Studies (GWAS) in tetraploid organisms

“…Two SNPs, named as c1_8019 and c2_25471, were identified as significant by the polyploid packages GWASpoly and SHEsis (Figure 6.b). Previous association studies also reported these SNP where the SNP c1_8019 is associated with potato tuber shape and eye depth traits [Rosyara et al, 2016, Sharma et al, 2018], while the SNPs c2_45606 and c2_45611 are associated to eye depth [Totsky et al, 2020].…”

Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato

“…Tuber eye depth is an important agronomic trait that affects the appearance and processing quality of tubers where potatoes with deep eyes contribute to significant peeling losses and are also not favoured by the consumers. To aid breeding potatoes with shallow eyes and uniform shape, several studies have been conducted in the past to identify genetic factors underlying this trait and identified a major locus controlling eye depth on chromosome 10 including minor effect QTLs on chromosomes 1, 2, 3, 4, 5, 6, 11, and 12 (Hara-Skrzypiec et al 2018 ; Li et al 2005 ; Lindqvist-Kreuze et al 2015 ; Pandey et al 2022 ; Prashar et al 2014 ; Rosyara et al 2016 ; Sharma et al 2018 ; Śliwka et al 2008 ; Totsky et al 2020 ; Zhang et al 2022 ; Zhao et al 2023 ). GWAS here detected the most significant QTL for tuber eye depth on chromosome 10 corroborating the findings from the previous studies, and additional significant QTL-MTAs were revealed on chromosomes 3, 4, 6, 7, 9, 10, 11 and 12 (Table 5 ; Figs.…”