Genome‐wide association mapping of distinctness, uniformity and stability traits and varietal identification in rice ( Oryza sativa L.)

BACKGROUND: Rice plays a key role in safeguarding food security as a result of its high nutritional value and adaptability to diverse climates. To release a new variety commercially, it is essential to register it, which largely relies on that variety's distinctness, uniformity, and stability (DUS) descriptors. Hence an effort was made to identify the genes associated with DUS descriptors employing a genome-wide association study (GWAS) for rice varieties using 23 DUS descriptors. METHODS AND RESULTS: The genome-wide association mapping using 57 429 single nucleotide polymorphism (SNP) markers detected a total of 57 stable MTAs (marker-trait associations) for 13 key DUS traits. A total of 136 genes were identified, of them 20 genes (eight characters) were prioritized in three databases. A total of five genes, namely, LOC_Os01g33300, LOC_Os01g33370, LOC_Os10g13700, LOC_Os11g17440 and LOC_Os11g17600 were prioritized for grain length. Decorticated grain length character was found to be associated with five genes, namely, LOC_Os03g11350, LOC_Os03g32590, LOC_Os07g17970, LOC_Os07g18120 and LOC_Os09g02790. Decorticated grain width was associated with two genes, that is, LOC_Os03g48810 and LOC_Os07g27480. For the characters' lemma anthocyanin colouration area below apex, panicle awns and decorticated grain shape each were found to be associated with one gene, that is, LOC_Os12g27102, LOC_Os07g11650 and LOC_Os01g33300 showing expression in three databases, respectively. A minimal set of 16 SNPs were identified for SNP fingerprinting that differentiated 96 genotypes. The present study demonstrates this potential with GWAS and use of SNPs and candidate genes associated with DUS traits for distinctiveness and uniformity. CONCLUSION: The major and novel MTAs identified in the present investigation for various DUS traits have been utilized to enhance accuracy and efficiency in determining distinctness, ensuring uniformity, and evaluating stability. The trait-associated SNPs and candidate genes identified for DUS characters distinguish morphologically distinct but genetically similar varieties and standardize DUS testing methods.