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During the Green Revolution, introducing the Semi-dwarf 1 (SD1) gene into tall rice varieties was crucial in improving yields. This resulted in the introduction of dwarf varieties with enhanced productivity in India. However, the molecular basis of the variation in the SD1 gene and the presence of additional genes responsible for reduced plant height in certain landraces remained unexplored. Our research aimed to fill this knowledge gap by resequencing a selection of rice landraces.
The study aimed to investigate the existing SD1 gene by resequencing selected rice landraces. The genetic variation within the SD1 gene across seven landraces (Ankalikyari, Dha, Gadyali, Lodiari, RatinDhan, Rodhni, and Thakurprasad) and two modified varieties (Improved Samba Masuri and Pusa 44) were analyzed. Plant height exhibited phenotypic diversity among these varieties. Through resequencing, Single Nucleotide Polymorphisms (SNPs) and Multi-Nucleotide Variations (MNVs) were identified within the SD1 gene and annotated in relation to the genic regions of the rice genome.
Analysis of SNP variations in the SD1 gene revealed interesting results. Ankalikyari and Dha exhibited no SNP variations and were identical to the reference SD1 gene (Nipponbare). In contrast, the other seven accessions shared a common SNP at position Chr1:38385057, resulting in an amino acid modification from Glutamine (GLN) to Arginine (ARG). This missense variant had a moderate impact on protein function.
Furthermore, the Improved Samba Masuri accession displayed three additional SNP variations. One particular SNP at position Chr1:38382764 (A to G) caused an amino acid modification from Tyrosine (TYR) to a stop codon. The truncated protein resulting from this SNP affected the folding of the SD1 protein, leading to defective function. Under controlled conditions, it was confirmed that Improved Samba Masuri had the shortest plant height among the tested varieties. Hence, this specific SNP variant may be responsible for the observed reduction in plant height in Improved Samba Masuri.
In conclusion, this study identified genetic variations within the SD1 gene, including a common SNP variant in seven accessions and a significant SNP variant in Improved Samba Masuri. These variations may influence plant height through alterations in protein function. The findings contribute to understanding the genetic factors underlying plant height variation in rice and have implications for adaptation and breeding efforts. Further research is needed to comprehensively understand the genetic factors involved in plant height variation and identify additional genes associated with this trait.
Keywords: rice landraces, resequencing, SNPs, SD-1 gene, allele mining.
