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<p><i>Oryza sativa</i>, <i>L.,</i> and <i>Oryza glaberima</i>, Steud, are the two most-grown rice species, making rice the second most-produced crop globally. While <i>O. sativa</i> is widely cultivated due to its high yield and marketability, <i>O. glaberrima</i> possesses valuable genetic traits for stress tolerance, including resistance to drought, flooding, and salinity. Genome-wide association studies (GWAS) have gained more popularity in <i>O. sativa</i> than in <i>O. glaberrima</i>, providing information on biological mechanisms underlying key agronomic traits. The current study aimed to find the essential genes for salinity tolerance in <i>O. glaberrima</i> through marker-trait associations (MTAs) for traits related to salinity. Using the Yoshida nutrient solution, this study evaluated a previously developed association mapping panel of 335 <i>O. glaberrima</i> accessions under screen house conditions. The association mapping panel was genotyped using 9990 single nucleotide polymorphism (SNP) markers. Using 6103 polymorphic SNP markers, a GWAS was conducted to detect genomic regions associated with salinity tolerance. 34 MTAs were identified using the mixed linear model approach, representing 11 genomic regions on chromosomes 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12, except on chromosome 2, highlighting different significant loci contributing to salinity stress tolerance. Among the tested accessions, 21 genotypes were categorized as tolerant to moderately tolerant based on the standard evaluation system score, representing promising materials for breeding programs. The identified SNPs, genotypes, and genomic regions are valuable resources for understanding the potential genes and developing functional markers for salinity tolerance screening in African rice. This study underscores the potential of <i>O. glaberrima</i> as a genetic resource for improving rice productivity in salt-affected areas, thereby contributing to sustainable rice production.</p>

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Genome-wide association study for salinity tolerance in the African rice, Oryza glaberrima

  • 期刊论文

  • 发表日期：

    2025年5月20日

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  • Nafeti Titus Mheni,
  • Newton Kilasi,
  • Atugonza Bilaro,
  • Marie-Noelle Ndjiondjop,
  • Shalabh Dixit,
  • Abdelbagi M. Ismail,
  • Susan Nchimbi Msolla

摘要

Oryza sativa, L., and Oryza glaberima, Steud, are the two most-grown rice species, making rice the second most-produced crop globally. While O. sativa is widely cultivated due to its high yield and marketability, O. glaberrima possesses valuable genetic traits for stress tolerance, including resistance to drought, flooding, and salinity. Genome-wide association studies (GWAS) have gained more popularity in O. sativa than in O. glaberrima, providing information on biological mechanisms underlying key agronomic traits. The current study aimed to find the essential genes for salinity tolerance in O. glaberrima through marker-trait associations (MTAs) for traits related to salinity. Using the Yoshida nutrient solution, this study evaluated a previously developed association mapping panel of 335 O. glaberrima accessions under screen house conditions. The association mapping panel was genotyped using 9990 single nucleotide polymorphism (SNP) markers. Using 6103 polymorphic SNP markers, a GWAS was conducted to detect genomic regions associated with salinity tolerance. 34 MTAs were identified using the mixed linear model approach, representing 11 genomic regions on chromosomes 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12, except on chromosome 2, highlighting different significant loci contributing to salinity stress tolerance. Among the tested accessions, 21 genotypes were categorized as tolerant to moderately tolerant based on the standard evaluation system score, representing promising materials for breeding programs. The identified SNPs, genotypes, and genomic regions are valuable resources for understanding the potential genes and developing functional markers for salinity tolerance screening in African rice. This study underscores the potential of O. glaberrima as a genetic resource for improving rice productivity in salt-affected areas, thereby contributing to sustainable rice production.