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<p><i>Allium cepa</i> is a major vegetable crops in Asia but rapid seed viability loss severely constrains seed chain continuity between successive planting seasons. To identify markers associated with Allium seed longevity a panel of storage induced aged seeds of 96 <i>Allium cepa</i> genotypes, was used for genome-wide association studies (GWAS) using 10 NAC-transcription factor-derived simple sequence repeats, mined from <i>Allium cepa</i> and <i>Allium sativum,</i> 10 previously reported <i>Allium cepa</i> intron-length polymorphic (AcILP) markers, and 7,734 GBS based SNP markers. The NAC-derived SSR markers had a prevalence of hexanucleotide repeats (81.8%) and showed strong cross-transferability between Alliums, with a mean polymorphism information content of 0.34 and a heterozygosity index of 0.45. AcILP markers demonstrated high cross-transferability (86%), with a mean heterozygosity index of 0.47 and a polymorphism information content of 0.35. Descriptive statistics for germination percentage and vigour index I (germination % × seedling length) and vigour index II (germination % × seedling dry weight) revealed a wide variability in these seed longevity traits. A significant association of SNP SCAJJJL010033730.1_40317 with both germination percentage and vigour index I, suggested a strong association between germination and early seedling growth. Furthermore, SNPs SCAJJJL010043805.1_135933, SCAJJJL010063632.1_30460, and SCAJJJL010052679.1_514690 were significantly associated with vigour index II. Genes flanking the associated SNPs encoded putative gag-pol protein, putative reverse transcriptase and hypothetical proteins, suggesting their role in stress adaptation. This study for the first time identifies SNPs linked to seed longevity in Alliums and provides molecular markers for breeding onion varieties with improved seed longevity.</p>

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Identification and Characterization of NAC Transcription Factor-Based Simple Sequence Repeat Markers and Genome-Wide Association Studies for Seed Longevity in Alliums

  • 期刊论文

  • 发表日期：

    2026年3月12日

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  • Deepanshu Jayaswal,
  • Deepesh Kumar,
  • Nandita Banerjee,
  • Ankit Badesra,
  • Himanshu Sharma,
  • Garima Yadav,
  • Sanjay Kumar,
  • Rajiv Baliram Kale,
  • Kuldip Jayaswall

摘要

Allium cepa is a major vegetable crops in Asia but rapid seed viability loss severely constrains seed chain continuity between successive planting seasons. To identify markers associated with Allium seed longevity a panel of storage induced aged seeds of 96 Allium cepa genotypes, was used for genome-wide association studies (GWAS) using 10 NAC-transcription factor-derived simple sequence repeats, mined from Allium cepa and Allium sativum, 10 previously reported Allium cepa intron-length polymorphic (AcILP) markers, and 7,734 GBS based SNP markers. The NAC-derived SSR markers had a prevalence of hexanucleotide repeats (81.8%) and showed strong cross-transferability between Alliums, with a mean polymorphism information content of 0.34 and a heterozygosity index of 0.45. AcILP markers demonstrated high cross-transferability (86%), with a mean heterozygosity index of 0.47 and a polymorphism information content of 0.35. Descriptive statistics for germination percentage and vigour index I (germination % × seedling length) and vigour index II (germination % × seedling dry weight) revealed a wide variability in these seed longevity traits. A significant association of SNP SCAJJJL010033730.1_40317 with both germination percentage and vigour index I, suggested a strong association between germination and early seedling growth. Furthermore, SNPs SCAJJJL010043805.1_135933, SCAJJJL010063632.1_30460, and SCAJJJL010052679.1_514690 were significantly associated with vigour index II. Genes flanking the associated SNPs encoded putative gag-pol protein, putative reverse transcriptase and hypothetical proteins, suggesting their role in stress adaptation. This study for the first time identifies SNPs linked to seed longevity in Alliums and provides molecular markers for breeding onion varieties with improved seed longevity.