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. 2023 Mar 28:14:1080666.
doi: 10.3389/fpls.2023.1080666. eCollection 2023.

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

Long Zhao  1   2   3 , Meiling Zou  3 , Ke Deng  1   2   3 , Chengcai Xia  3 , Sirong Jiang  3 , Chenji Zhang  4 , Yongzhen Ma  1   2 , Xiaorui Dong  3 , Miaohua He  3 , Tiancang Na  1   2   5   6   7 , Jian Wang  1   2   5   6   7 , Zhiqiang Xia  3 , Fang Wang  1   2   5   6   7
Affiliations

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

Long Zhao et al. Front Plant Sci. .

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.

Keywords: GWAS; eye depth; genetic diversity; population structure; tetraploid potato; tuber shape.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
SNP distributions on 48 chromosomes of potato. The horizontal axis displays the chromosome length, and the legend insert indicates SNP density. A1-A4 represents haplotype 1 - haplotype 4 respectively.
Figure 2
Figure 2
Population structure and genetic diversity analysis of the 370 studied tetraploid potatoes. (A) Principal component analysis of the 370 potato germplasm using high-quality SNPs and indels, where green, yellow and pink backgrounds represent Subgroup 1, Subgroup 2 and Subgroup 3, respectively. (B) Phylogenetic tree constructed for the 370 potato materials, where green, yellow and pink lines represent Subgroup 1, Subgroup 2 and Subgroup 3, respectively. (C) Population structure analysis with different cluster numbers (K=2, 3, 4 and 5) agrees with phylogenetic tree analysis. (D) Tajima’s D of the 370 studied tetraploid potatoes, indicating they lack rare alleles. (E) Nucleotide diversity (PI) and genetic differentiation coefficient (Fst) between any two of the three subgroups.
Figure 3
Figure 3
Manhattan plot and candidate regions associated with potato tuber shape. (A) Manhattan plot of potato tuber shapes. (B) Association regions on Chr01A1 and Chr02A1. (C, D) LD heatmaps of regions significantly associated with tuber shapes on Chr01A1 and Chr02A1, respectively. (E) Distribution of significant SNP markers on Chr01A1 of the round and elongated potatoes. From left to right are SNPs at Chr01A1:34451395, Chr01A1:34458899, Chr01A1:34466909, Chr01A1:34484034, Chr01A1:34484958 and Chr01A1:34503329 loci, where the upper half represents the round potatoes and lower half represents the very long potatoes, respectively. (F) The distribution and performance of significant SNP markers on Chr02A1 of the round and very long potatoes. From left to right are SNPs at Chr02A1:28359920, Chr02A1:28360022, Chr02A1:28360028, Chr02A1:28362877, Chr02A1:28381647 and Chr02A1:28381654, respectively.
Figure 4
Figure 4
Manhattan and candidate regions associated with potato tuber eye depth. (A) Manhattan plot of potato tuber eye depth. (B) Analysis of regions associated with tuber eye depth on Chr05A2 and Chr06A2. (C) and (D) LD heatmap of regions significantly associated with tuber eye depth on Chr05A2 and Chr05A2, respectively. (E) Distribution and performance of significant SNP markers on Chr05A2 of potatoes with shallow and deep tuber eyes. From left to right are SNPs at Chr05A2:50031597, Chr05A2:50087233, Chr05A2:50087238, Chr05A2:50087243, Chr05A2:50087245, Chr05A2:50087357, Chr05A2:50087467 Chr05A2:50143917, Chr05A2:50385093 and Chr05A2:50385385 loci, where the upper half represents potatoes with shallow tuber eyes and the lower half represents potatoes with deep tuber eyes.
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