Evaluation of indica‐type DEP1 mutant allele for rice (Oryza sativa) yield improvement and development of allele‐specific co‐dominant marker

Abstract Erect panicles with enhanced grain numbers can rationally utilize solar energy for dry matter accumulation. Only in japonica cultivars an inactive natural nonsense mutant allele of DEP1 has been reported to pleiotropically improve panicle architecture, nitrogen use efficiency, nitrogen and dry matter translocation and strength of the stem. Genomic sequence comparison of DEP1 in indica , aus and aromatic genotypes of West Bengal led to the identification of four natural allelic variants based on three single nucleotide polymorphisms (SNPs) on intron 1, two SNPs on exon 5 and two deletions on intron 2. Among them, a yield favourable missense mutant allele of DEP1 with two amino acid substitutions from Patnai 23 has been identified, and an allele‐specific co‐dominant marker based on the SNP (A/G) at 333rd position of exon 5 was designed. Assessment of DEP1 Patnai 23 allele for yield improvement was examined in RILs and NILs developed from Patnai23 × N22 as N22 carries wild‐type allele. The relative abundance of DEP1 transcript in young panicles was twice as high in Patnai 23 than in N22. RIL‐ DEP1 Patnai 23 and NIL‐ DEP1 Patnai 23 showed enhanced grain number per panicle and total yield per plant compared to RIL‐ DEP1 N22 and NIL‐ DEP1 N22 allele. This newly identified DEP1 allele and marker will accelerate MAS to improve rice yield precisely.