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<p>We conducted a genome-wide association study (GWAS) on 63 genetically diverse walnut genotypes from Kashmir (Jammu and Kashmir), aiming to uncover marker-trait associations for seven key nut and kernel phenotypes such as nut length (NL), nut width (NWI), nut thickness (NT), shell thickness (ST), nut weight (NW), kernel percentage (KP), and kernel weight (KW). Phenotypic evaluation revealed highly significant variability across all traits (ANOVA, <i>p</i> &lt; 0.001). Using an initial set of 150 SSR markers, we identified 60 highly polymorphic loci (alleles per locus, 2–8; mean = 4.75; PIC range, 0.28–0.58; mean = 0.47), indicative of strong molecular diversity. Structure analysis (Δ<i>K</i>) revealed two sub-populations (<i>K</i> = 2). Association mapping uncovered 20 marker-trait associations via GLM and 18 via MLM (<i>K</i> + <i>Q</i>) models. Notably, markers WSSR-138, WSSR-107, and WSSR-150 each were associated with multiple traits, and individual SSRs explained 10.99–31.43% of phenotypic variance (<i>R</i><sup>2</sup>). Mapping these SSR loci onto the walnut reference genome identified 19 candidate genes across nine chromosomes, many involved in cell division, cell expansion, and seed development, consistent with their roles in nut size, kernel fill, and shell formation. These include gene models such as <i>PPR</i>, <i>SKP1</i>-like, <i>REF/SRPP</i>-like, and <i>auxin-binding protein</i>-like, found via SSR marker-trait overlaps. Our study significantly expands the genomic regions linked to economically important nut traits in walnut and provides new SSR-based markers and candidate genes for marker-assisted selection (MAS). This resource empowers breeders to more precisely shape nut quality traits, enhancing kernel yield, shell properties, and nut dimensions, thus contributing to accelerated improvement programs.</p>

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Microsatellite-Based Marker-Trait Associations and Identification of Genomic Regions Linked to Nut and Kernel Traits in Walnut (Juglans regia L.)

  • 期刊论文

  • 发表日期：

    2025年11月7日

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  • Rafiq A. Shah,
  • Misbah Hassan,
  • M. A. Mir,
  • Sheikh Khursheed,
  • Bilal A. Padder,
  • H. Itoo

摘要

We conducted a genome-wide association study (GWAS) on 63 genetically diverse walnut genotypes from Kashmir (Jammu and Kashmir), aiming to uncover marker-trait associations for seven key nut and kernel phenotypes such as nut length (NL), nut width (NWI), nut thickness (NT), shell thickness (ST), nut weight (NW), kernel percentage (KP), and kernel weight (KW). Phenotypic evaluation revealed highly significant variability across all traits (ANOVA, p < 0.001). Using an initial set of 150 SSR markers, we identified 60 highly polymorphic loci (alleles per locus, 2–8; mean = 4.75; PIC range, 0.28–0.58; mean = 0.47), indicative of strong molecular diversity. Structure analysis (ΔK) revealed two sub-populations (K = 2). Association mapping uncovered 20 marker-trait associations via GLM and 18 via MLM (K + Q) models. Notably, markers WSSR-138, WSSR-107, and WSSR-150 each were associated with multiple traits, and individual SSRs explained 10.99–31.43% of phenotypic variance (R2). Mapping these SSR loci onto the walnut reference genome identified 19 candidate genes across nine chromosomes, many involved in cell division, cell expansion, and seed development, consistent with their roles in nut size, kernel fill, and shell formation. These include gene models such as PPR, SKP1-like, REF/SRPP-like, and auxin-binding protein-like, found via SSR marker-trait overlaps. Our study significantly expands the genomic regions linked to economically important nut traits in walnut and provides new SSR-based markers and candidate genes for marker-assisted selection (MAS). This resource empowers breeders to more precisely shape nut quality traits, enhancing kernel yield, shell properties, and nut dimensions, thus contributing to accelerated improvement programs.