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<p>Potato, a crucial food crop feeding over a billion people worldwide, remains relatively underexplored in terms of the genetic factors that control its yield and nutritional quality. To bridge this gap, a comprehensive study was conducted, integrating genome-wide association study (GWAS) with genotyping-by-sequencing (GBS) analysis on a diverse panel of 357 potato accessions. These genotypes were cultivated over two consecutive winter seasons (2021-22 and 2022-23) in the sub-tropical Himalayan region of India. Detailed phenotypic data were systematically recorded for average tuber yield per plant, along with 23 agro-morphological and biochemical traits. Correlation analysis revealed a significant positive association between tuber yield per plant and several morphological and yield-related traits, including number of stems per plant, leaflet length, leaflet width, leaf length, leaf width, leaf area, number of tubers per plant, tuber length, tuber width, and average tuber weight. Using genotyping by sequencing (GBS), a set of high quality 5470 SNPs were identified for downstream analysis. Hierarchical cluster analysis based on phenotype data classified the accessions into two major clusters, with 4 sub-clusters. Marker trait analysis revealed 8 significant SNPs detected through additive and simplex dominance models. Notably, one SNP (chr04_3551782) was found to influence plant height, while two SNPs (chr05_17842252 and chr08_14450306) showed consistent association with the number of leaves per plant across multiple years. Interestingly, these trait-linked SNPs were distributed across different chromosomes, with chromosomes 1, 6, and 10 emerging as potential hotspots for yield-related genes. Furthermore, candidate genes were identified for several important traits, including plant height (on chromosomes 4 and 12), number of compound leaves per plant (chromosomes 5 and 8), tuber width (chromosome 9), tuber dry matter content (chromosomes 9 and 12), and non-reducing sugars (chromosome 6). These genes encode proteins that play crucial roles in tuber growth and development, such as hydroxyproline-rich glycoprotein family protein (Chr04), MATH domain-containing protein (Chr05), GTP-binding protein (Chr08), and serine/threonine-protein kinase BRI1 (Chr12). Collectively, the findings of this study provide valuable insights into SNP markers associated with yield-related traits and help unravel the complex genetic architecture governing key agronomic characteristics in potato.</p>

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Genomic Insights into Tuber Yield and Associated Morphological and Biochemical Traits in Potato (Solanum tuberosum L.) Through GWAS

  • 期刊论文

  • 发表日期：

    2025年10月28日

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  • Jagmeet Singh,
  • Kritika Singh,
  • Vinay Bhardwaj,
  • Vikas Mangal,
  • Ramesh Kumar,
  • Dharminder Kumar,
  • Salej Sood

摘要

Potato, a crucial food crop feeding over a billion people worldwide, remains relatively underexplored in terms of the genetic factors that control its yield and nutritional quality. To bridge this gap, a comprehensive study was conducted, integrating genome-wide association study (GWAS) with genotyping-by-sequencing (GBS) analysis on a diverse panel of 357 potato accessions. These genotypes were cultivated over two consecutive winter seasons (2021-22 and 2022-23) in the sub-tropical Himalayan region of India. Detailed phenotypic data were systematically recorded for average tuber yield per plant, along with 23 agro-morphological and biochemical traits. Correlation analysis revealed a significant positive association between tuber yield per plant and several morphological and yield-related traits, including number of stems per plant, leaflet length, leaflet width, leaf length, leaf width, leaf area, number of tubers per plant, tuber length, tuber width, and average tuber weight. Using genotyping by sequencing (GBS), a set of high quality 5470 SNPs were identified for downstream analysis. Hierarchical cluster analysis based on phenotype data classified the accessions into two major clusters, with 4 sub-clusters. Marker trait analysis revealed 8 significant SNPs detected through additive and simplex dominance models. Notably, one SNP (chr04_3551782) was found to influence plant height, while two SNPs (chr05_17842252 and chr08_14450306) showed consistent association with the number of leaves per plant across multiple years. Interestingly, these trait-linked SNPs were distributed across different chromosomes, with chromosomes 1, 6, and 10 emerging as potential hotspots for yield-related genes. Furthermore, candidate genes were identified for several important traits, including plant height (on chromosomes 4 and 12), number of compound leaves per plant (chromosomes 5 and 8), tuber width (chromosome 9), tuber dry matter content (chromosomes 9 and 12), and non-reducing sugars (chromosome 6). These genes encode proteins that play crucial roles in tuber growth and development, such as hydroxyproline-rich glycoprotein family protein (Chr04), MATH domain-containing protein (Chr05), GTP-binding protein (Chr08), and serine/threonine-protein kinase BRI1 (Chr12). Collectively, the findings of this study provide valuable insights into SNP markers associated with yield-related traits and help unravel the complex genetic architecture governing key agronomic characteristics in potato.