Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome

Abstract

Potato is one of the world’s most important food crops, with a time-consuming breeding process. In this study, we performed a genome-wide association (GWAS) analysis of the two important traits of potato tuber shape and eye depth, using the tetraploid potato genome (2n=4x=48) as a reference. A total of 370 potatoes were divided into three subgroups based on the principal component analysis and evolutionary tree analysis. The genetic diversity within subgroups is low (5.18×10-5, 4.36×10-5 and 4.24×10-5). Genome-wide linkage disequilibrium (LD) analysis showed that their LD is about 60 Kb. GWAS analysis identified that 146 significant single nucleotide polymorphism (SNP) loci at Chr01A1:34.44−35.25 Mb and Chr02A1:28.35−28.54 Mb regions are significantly associated with potato tuber shape, and that three candidate genes that might be related to potato tuber traits, PLATZ transcription factor, UTP-glucose-1-phosphate uridylyltransferase and FAR1 DNA-binding domain, are in the association region of Chr02A1. GWAS analysis identified 53 significant SNP loci at Chr05A2: 49.644-50.146 Mb and Chr06A2: 25.866-26.384 Mb regions with robust associations with potato tuber eye depth. Hydrolase and methyltransferases are present in the association region of Chr05A2, and three CYPs are present in the association region of Chr06A2. Our findings suggested that these genes are closely associated with potato tuber shape and eye depth. Our study identified molecular markers and candidate genes for improving tetraploid potato tuber shape and eye depth and provided ideas and insights for tetraploid potato breeding.

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

“…The current study reports three QTL-MTAs on chromosome 4 (Table 5 ) and two (chr04_5763134 and chr04_10456693) of these support the chromosome 4 QTL reported by Hara-Skrzypiec et al ( 2018 ). Zhao et al ( 2023 ) found a QTL for eye depth on chromosome 6 (Chr06A2:25.9–26.4 Mb (Wang et al 2022 )) but the same chromosome QTLs (chr06_40734919 and chr06_40735030, Table 5 ) detected here were ~ 14 Mb distance apart. Hara-Skrzypiec et al ( 2018 ) identified another eye depth QTL towards the bottom part of chromosome 11 (44.8 cM; 34.2 Mb, DMv6.01; see above for cM-to-Mb conversion), however, all four QTL-MTAs detected in the current study were on the top part of the same chromosome (Table 5 ).…”

“…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.…”

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

“…As for other species, several studies have identified SNPs associated with agronomical and quality traits, such as tuber shape, eye depth, and fry color retention during low-temperature storage ( Sharma et al., 2018 ; Byrne et al., 2020 ; Zhang et al., 2022a ; Pandey et al., 2023 ; Zhao et al., 2023 ). Moreover, multiple genetic markers and candidate genes aimed at enhancing disease resistance to late blight have been identified by Wang et al.…”

“…As for other species, several studies have identified SNPs associated with agronomical and quality traits, such as tuber shape, eye depth, and fry color retention during low-temperature storage (Sharma et al, 2018;Byrne et al, 2020;Zhang et al, 2022a;Pandey et al, 2023;Zhao et al, 2023). Moreover, multiple genetic markers and candidate genes aimed at enhancing disease resistance to late blight have been identified by Wang et al (2021) and Sood et al (2023), while Dıáz et al (2021) and Alvarez-Morezuelas et al ( 2023) investigated plant's response to abiotic stressors, revealing genes and QTLs that may aid in developing varieties better suited to changing environmental conditions and drought seasons.…”