ArticleFunctional & integrative genomics2024
Genome-wide association study reveals effect of nsSNPs on candidate genes in rice during iron deficiency.
Article in Functional & integrative genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Aus rice: a source of promising donor genotypes for low N tolerance under field conditions.Scientific reports · 2026Article
- Article
- Genomic insights into sheath blight resistance: leveraging natural variation in the Bengal-Assam-Aus rice panel for multi-season association mapping.Frontiers in plant science · 2026Article
- Comparative transcriptomic insights into iron deficiency response in contrasting rice varieties at the seedling stage reveal distinct response strategies and identify novel candidate genes.Frontiers in plant science · 2026Article
- GWAS and haplotype analysis reveal the intricate interplay of hormones in rice seed germination under hypoxic conditions.3 Biotech · 2025Article
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Authors and funding
10 authors.
Funding
Abstract
Resource-poor areas with moisture deficit lands following aerobic and direct seeded rice (DSR) methods of cultivation face severe problems of iron deficiency. In this study, Bengal and Assam Aus rice panel was phenotyped at the seedling stage using an iron-deprived hydroponic medium for various shoot and root traits. A novel iron deficiency scoring scale was used to classify the tolerance reaction and could range anywhere between 0 and 9, indicating the most tolerant and susceptible, respectively. The GWAS results identified four putative candidate genes; OsFLA for number of leaves and shoot length, OsBIDK1 for root traits; average diameter, volume, biomass, projected area, and surface area, OsHPL3 for chlorophyll index of the third leaf and AKR2B (XBOS252) was for Fe score, (which was earlier reported in relation to Xa21). The nsSNP (nsSNPs) variations in these gene sequences were used to group the panel and identify superior haplotypes and donors. BR16 was identified as a superior donor, with higher chlorophyll index and shoot length than RA23, also higher values for root traits like root average diameter, root volume, root projected area and root surface area followed by Shete Bhado. The impact of identified nsSNPs on protein structure and stability was investigated. The conserved domains detected in the mutated proteins of the superior haplotypes are very informative, highlighting that natural selection favors abiotic stress tolerant variants in resource poor areas. Thus, justifying our choice of Aus landraces for association mapping of Fe deficiency tolerant genes in rice.
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