Scholarlink

<p>Rice (<i>Oryza sativa</i> L.), a thermophilic grain, is sensitive to cold stress. With climate change, rice production faces significant challenges, and cold stress is one of the primary factors restricting its yield and productivity. This study evaluated two hundred and forty-seven rice genotypes for cold tolerance at germination and seedling stages through two experiments. Using genotypic data from a 1502-SNP KASP array and phenotypic assessments—including GRI, REDCOL, PERCOL, seedling survival, and phenotypic scores—a high-resolution GWAS was conducted to elucidate the genetic architecture underlying cold tolerance in rice. GWAS identified seven marker–trait associations (MTAs) located on rice chromosomes1,7,11,4,5,8 and chromosome 10. Thereafter in silico search for mining of candidate genes was done on chromosome 1,7,11,4,5,8 and 10 by using RAPDB and a total of 47 transcripts were found having cold tolerance function. Out of 47, 12 genes were found in the vicinity of MTA “<i>qGRI.1</i>” on chromosome 1 on chromosomes 1, 4, 5, 7, 8, 10, and 11, explaining phenotypic variance ranging from 10.60% to 33.94%. An in-silico search identified 47 putative annotated candidate genes linked to cold tolerance in a 158 Kb region upstream and downstream of significant SNPs. The results enhance our understanding of the genetic basis of cold tolerance during germination and seedling stages and facilitate the development of molecular markers for breeding programs. Promising rice accessions identified for cold tolerance will serve as valuable resources in breeding efforts to develop resilient rice cultivars.</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

Genome-Wide Association Study Reveals Marker-Trait Associations and Genes Linked To Cold Tolerance during Developmental Stages in Rice

  • 期刊论文

  • 发表日期：

    2026年1月5日

查看全文
  • Humaira Jan,
  • Gazala H. Khan,
  • Mahandiya Iqbal,
  • Asif B. Shikari,
  • N. R. Sofi,
  • Raheel Shafeeq Khan,
  • Parvaiz. A. Sofi,
  • Zahida Rasheed,
  • Mohammad Saleem Dar,
  • Fehim Jeelani Wani,
  • Khairiah Mubarak Alwutayd,
  • Shabir Ahmad Ganai,
  • Sheikh Mansoor

摘要

Rice (Oryza sativa L.), a thermophilic grain, is sensitive to cold stress. With climate change, rice production faces significant challenges, and cold stress is one of the primary factors restricting its yield and productivity. This study evaluated two hundred and forty-seven rice genotypes for cold tolerance at germination and seedling stages through two experiments. Using genotypic data from a 1502-SNP KASP array and phenotypic assessments—including GRI, REDCOL, PERCOL, seedling survival, and phenotypic scores—a high-resolution GWAS was conducted to elucidate the genetic architecture underlying cold tolerance in rice. GWAS identified seven marker–trait associations (MTAs) located on rice chromosomes1,7,11,4,5,8 and chromosome 10. Thereafter in silico search for mining of candidate genes was done on chromosome 1,7,11,4,5,8 and 10 by using RAPDB and a total of 47 transcripts were found having cold tolerance function. Out of 47, 12 genes were found in the vicinity of MTA “qGRI.1” on chromosome 1 on chromosomes 1, 4, 5, 7, 8, 10, and 11, explaining phenotypic variance ranging from 10.60% to 33.94%. An in-silico search identified 47 putative annotated candidate genes linked to cold tolerance in a 158 Kb region upstream and downstream of significant SNPs. The results enhance our understanding of the genetic basis of cold tolerance during germination and seedling stages and facilitate the development of molecular markers for breeding programs. Promising rice accessions identified for cold tolerance will serve as valuable resources in breeding efforts to develop resilient rice cultivars.