Scholarlink

<p>Pigeonpea is a popular grain legume due to its high protein content and superior nutritious values in the Indian subcontinent. The yield in pigeonpea is a complex trait determined by multiple factors, including background genotypic variations and their environmental interactions as it is grown under different agro-climatic conditions. Understanding the genetic basis of yield component traits, such as number of seeds per pod, is essential to boost pigeonpea production. To understand the genetic basis of number of seed number per pod (SNPP) in pigeonpea, we focused on identifying the genome wide variants using the whole genome resequencing (WGRS) data of eight contrasting genotypes. Our analysis revealed that genotypes with low SNPP exhibit 782,805 to 1,082,329 SNPs, while those with high SNPP show a range from 772,795 to 1,136,487 SNPs. Similarly, InDels varied from 49,756 to 72,319 in low SNPP genotypes and from 45,897 to 71,878 in high SNPP genotypes. We identified unique set of 247,611 SNPs, and 9205 InDels in the promoter, coding and non-coding region of genes of the genotypes with high SNPP. Similarly, 257,603 SNPs, 15,494 MNPs and 9722 Indels unique to low SNPP genotypes were identified. We shortlisted putative candidate genes bearing high impact variants including SIRP1, Heading date 3A, Sepallata 1 and ABC transporter in genotypes with high SNPP while STY46, PPR protein, Maintenance of meristem, Dead box helicase in genotypes with low SNPP based on the annotation analysis. Further, candidate gene based association resulted in identification 5 MTAs in RNA-directed DNA methylation 3 and zinc finger BED domain-containing protein RICESLEEPER 2 which were consistent across the year in multi-model approach. The expression of the selected key genes were also supporting their involvement in regulation of seed and pod development. The variants and markers identified in the current study could be a potential candidate for validation and application for the pigeonpea breeders to develop varieties with high SNPP.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Genomics data reveals DNA polymorphism associated with seed number per pod (SNPP) in pigeonpea, Cajanus cajan (L.) Millsp.

  • 期刊论文

  • 发表日期：

    2025年8月7日

查看全文
  • Akash Paul,
  • Kuldeep Kumar,
  • Machindra Nirgude,
  • Antara Das,
  • Sandhya Sharma,
  • Kishor Gaikwad

摘要

Pigeonpea is a popular grain legume due to its high protein content and superior nutritious values in the Indian subcontinent. The yield in pigeonpea is a complex trait determined by multiple factors, including background genotypic variations and their environmental interactions as it is grown under different agro-climatic conditions. Understanding the genetic basis of yield component traits, such as number of seeds per pod, is essential to boost pigeonpea production. To understand the genetic basis of number of seed number per pod (SNPP) in pigeonpea, we focused on identifying the genome wide variants using the whole genome resequencing (WGRS) data of eight contrasting genotypes. Our analysis revealed that genotypes with low SNPP exhibit 782,805 to 1,082,329 SNPs, while those with high SNPP show a range from 772,795 to 1,136,487 SNPs. Similarly, InDels varied from 49,756 to 72,319 in low SNPP genotypes and from 45,897 to 71,878 in high SNPP genotypes. We identified unique set of 247,611 SNPs, and 9205 InDels in the promoter, coding and non-coding region of genes of the genotypes with high SNPP. Similarly, 257,603 SNPs, 15,494 MNPs and 9722 Indels unique to low SNPP genotypes were identified. We shortlisted putative candidate genes bearing high impact variants including SIRP1, Heading date 3A, Sepallata 1 and ABC transporter in genotypes with high SNPP while STY46, PPR protein, Maintenance of meristem, Dead box helicase in genotypes with low SNPP based on the annotation analysis. Further, candidate gene based association resulted in identification 5 MTAs in RNA-directed DNA methylation 3 and zinc finger BED domain-containing protein RICESLEEPER 2 which were consistent across the year in multi-model approach. The expression of the selected key genes were also supporting their involvement in regulation of seed and pod development. The variants and markers identified in the current study could be a potential candidate for validation and application for the pigeonpea breeders to develop varieties with high SNPP.