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<p>Buckwheat (<i>Fagopyrum</i> spp.) is an important pseudocereal with high nutritional value and strong adaptability to marginal environments; However, the genetic basis of key agronomic and physiological traits remain poorly understood. In the present study, genome-wide association analysis (GWAS) was conducted to identify genomic regions controlling morphological, physiological, and yield-related traits in buckwheat. A diverse panel of 102 accessions of <i>Fagopyrum esculentum</i> and <i>Fagopyrum tataricum</i> was phenotyped over two consecutive growing seasons (2024 and 2025) for ten traits and were genotyped using ApeKI-based genotyping-by-sequencing (GBS) on the Illumina HiSeq X10 platform (150-bp paired-end reads), followed by stringent quality filtering and SNP calling. A total of 31,045 high-quality Single nucleotide polymorphisms (SNPs) were obtained and used for population structure and association analysis. Population structure and principal component analyses revealed two distinct genetic subpopulations. Genome wide association analysis using three complementary models (Blink, FarmCPU, CMLM) identified 104 significant marker trait associations for the evaluated traits. Several stable loci were consistently detected across multiple models, including key regions on chromosomes 6 and 7, which were associated with petiole length, chlorophyll traits, and yield per plant. Notably, a major locus on chromosome 6 (Ft6:10161804) showed a strong association with yield per plant. Candidate gene analysis within ± 25 Kb of significant SNPs identified 88 candidate genes, including genes involved in starch binding and protein K63-linked deubiquitination, which are likely associated with carbohydrate metabolism and protein regulation underlying yield performance These findings provide valuable insights into the genetic architecture of complex traits in buckwheat and offer potential molecular targets for marker-assisted breeding and genetic improvement of this nutritionally important crop.</p>

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Dissecting the genetic architecture of agro-physiological traits in buckwheat through multi-model GWAS

  • 期刊论文

  • 发表日期：

    2026年8月4日

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  • Majid Rashid,
  • Manikandan Krishnan,
  • Mansoor Showkat,
  • Mahandiya Iqbal,
  • Bisma Majid,
  • Parvaze Ahmad Sofi,
  • Najeebul Rehman Sofi,
  • Ajaz Ahmad Malik,
  • Vandana Jaiswal,
  • Sajad Majeed Zargar

摘要

Buckwheat (Fagopyrum spp.) is an important pseudocereal with high nutritional value and strong adaptability to marginal environments; However, the genetic basis of key agronomic and physiological traits remain poorly understood. In the present study, genome-wide association analysis (GWAS) was conducted to identify genomic regions controlling morphological, physiological, and yield-related traits in buckwheat. A diverse panel of 102 accessions of Fagopyrum esculentum and Fagopyrum tataricum was phenotyped over two consecutive growing seasons (2024 and 2025) for ten traits and were genotyped using ApeKI-based genotyping-by-sequencing (GBS) on the Illumina HiSeq X10 platform (150-bp paired-end reads), followed by stringent quality filtering and SNP calling. A total of 31,045 high-quality Single nucleotide polymorphisms (SNPs) were obtained and used for population structure and association analysis. Population structure and principal component analyses revealed two distinct genetic subpopulations. Genome wide association analysis using three complementary models (Blink, FarmCPU, CMLM) identified 104 significant marker trait associations for the evaluated traits. Several stable loci were consistently detected across multiple models, including key regions on chromosomes 6 and 7, which were associated with petiole length, chlorophyll traits, and yield per plant. Notably, a major locus on chromosome 6 (Ft6:10161804) showed a strong association with yield per plant. Candidate gene analysis within ± 25 Kb of significant SNPs identified 88 candidate genes, including genes involved in starch binding and protein K63-linked deubiquitination, which are likely associated with carbohydrate metabolism and protein regulation underlying yield performance These findings provide valuable insights into the genetic architecture of complex traits in buckwheat and offer potential molecular targets for marker-assisted breeding and genetic improvement of this nutritionally important crop.