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Main conclusion <p>Additive effects of three candidate genes—<i>SAMBA</i>, <i>NAC TF25</i>, and <i>ARF18</i>—significantly influenced seed weight in <i>Brassica juncea</i>, collectively accounting for 35.79% of the trait variation.</p> Abstract <p>Seed weight is a major determinant of seed yield in <i>Brassica juncea</i>, yet its inheritance and underlying genes remain insufficiently understood. To address this, generation mean analysis (GMA) was conducted using populations derived from two contrasting parents, DRMRIJ-31 (bold seeded) and RLC-3 (small seeded), for thousand-seed weight (TSW). In addition, a GWAS was conducted employing SNP genotyping of 142 diverse genotypes of <i>B. juncea</i> targeting TSW across 2 <i>rabi</i> seasons (2020–2021 and 2021–2022). GMA suggested the predominance of <i>d</i>, <i>h</i> and <i>i</i> components influencing the seed weight, along with a significant maternal influence. GWAS identified two stable SNPs, Bj-B3-p17726495 (PVE: 17.77%; chromosome B03) and Bj-B4-p10707039 (PVE: 18.05%; chromosome B04), associated with candidate genes <i>SAMBA</i> and <i>NAC TF25</i>, respectively. Cloning and sequencing of these genes from both parents uncovered multiple SNPs and In/Dels, highlighting their potential role in trait variation. Molecular markers developed from these MTAs were validated in F<sub>2</sub> population of DRMRIJ-31 and RLC-3. Furthermore, comparative analysis with major seed weight QTLs on chromosome A09 of <i>B. napus</i> identified <i>ARF18</i> as an additional candidate gene. Sequencing of <i>ARF18</i> across bold- and small-seeded <i>B. juncea</i> genotypes revealed several SNPs and In/Dels. Targeting the In/Del, a gene-based marker was designed and validated in germplasm panel with PVE 10.79%. Collectively, the three loci (<i>Bj-</i>B3-p17726495, Bj-B4-p10707039, and <i>ARF18</i>) demonstrated additive effects with PVE 35.79%. This initial study on seed weight candidate genes and molecular markers in <i>Brassica juncea</i> will aid future efforts to improve seed weight either through marker-assisted breeding or genome-editing mediated mutagenesis.</p>

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Unlocking the genetic and molecular secrets of thousand-seed weight in Indian mustard [Brassica juncea (L.) Czern. & Coss.] employing generation mean and candidate gene analysis

  • 期刊论文

  • 发表日期：

    2026年1月14日

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  • Manoj Kumar Patel,
  • Masochon Zimik,
  • Sneha Adhikari,
  • Yashpal Taak,
  • Navin C. Gupta,
  • Joghee Nanjundan,
  • K. K. Vinod,
  • Sujata Vasudev,
  • Devendra Kumar Yadava,
  • Navinder Saini

摘要

Main conclusion

Additive effects of three candidate genes—SAMBA, NAC TF25, and ARF18—significantly influenced seed weight in Brassica juncea, collectively accounting for 35.79% of the trait variation.

Abstract

Seed weight is a major determinant of seed yield in Brassica juncea, yet its inheritance and underlying genes remain insufficiently understood. To address this, generation mean analysis (GMA) was conducted using populations derived from two contrasting parents, DRMRIJ-31 (bold seeded) and RLC-3 (small seeded), for thousand-seed weight (TSW). In addition, a GWAS was conducted employing SNP genotyping of 142 diverse genotypes of B. juncea targeting TSW across 2 rabi seasons (2020–2021 and 2021–2022). GMA suggested the predominance of d, h and i components influencing the seed weight, along with a significant maternal influence. GWAS identified two stable SNPs, Bj-B3-p17726495 (PVE: 17.77%; chromosome B03) and Bj-B4-p10707039 (PVE: 18.05%; chromosome B04), associated with candidate genes SAMBA and NAC TF25, respectively. Cloning and sequencing of these genes from both parents uncovered multiple SNPs and In/Dels, highlighting their potential role in trait variation. Molecular markers developed from these MTAs were validated in F2 population of DRMRIJ-31 and RLC-3. Furthermore, comparative analysis with major seed weight QTLs on chromosome A09 of B. napus identified ARF18 as an additional candidate gene. Sequencing of ARF18 across bold- and small-seeded B. juncea genotypes revealed several SNPs and In/Dels. Targeting the In/Del, a gene-based marker was designed and validated in germplasm panel with PVE 10.79%. Collectively, the three loci (Bj-B3-p17726495, Bj-B4-p10707039, and ARF18) demonstrated additive effects with PVE 35.79%. This initial study on seed weight candidate genes and molecular markers in Brassica juncea will aid future efforts to improve seed weight either through marker-assisted breeding or genome-editing mediated mutagenesis.