SNP-Based molecular characterization of TAD1 , GS3 , and ABA8ox2 genes in Indonesian Rice for early marker discovery

Abstract

Abstract Improving rice ( Oryza sativa L.) breeding efficiency is essential to address challenges from climate change and population growth. Single-nucleotide polymorphisms (SNPs) serve as valuable markers for detecting genetic variation linked to agronomic traits. This study characterized SNP-based variation in three candidate genes ( TAD1 , GS3 , and ABA8ox2 genes) from Indonesian local and hybrid rice cultivars to identify early diagnostic markers. Primers were designed in silico using UGENE and Primer3Plus, targeting conserved regions and functional domains. Genomic DNA from three cultivars (Hawara Bunar, IPB 3S, and IPB 13S) was amplified using PCR, yielding 522 bp ( TAD1 ), 502 bp ( GS3 ), and 583 bp ( ABA8ox2 ) fragments. TAD1 gene showed the highest SNP count in Hawara Bunar (105 SNPs; 20.11%) and is associated with tall phenotypes, indicating potential as a negative selection marker in semi-dwarf breeding. ABA8ox2 gene displayed moderate variation (4.8%–9.6%) and may support as a positive selection marker. Due to sequencing failure in two cultivars, GS3 gene analysis was limited to IPB 3S, which showed low variation (0.59%), suggesting conservation in this grain size regulator. Despite the lack of phenotypic validation, SNP variations in TAD1, ABA8ox2 , and GS3 highlight their potential as early molecular markers for traits such as tiller number, drought tolerance, and grain size. Integrating phenotypic data in future studies will enable more precise selection in rice breeding programs.

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