A perfect PCR based co-dominant marker for low grain-arsenic accumulation genotyping in rice

The development of low arsenic-accumulating varieties for the contaminated areas is one of the best options for reducing the dietary exposure of arsenic to human population through rice. In this study, grain-arsenic content in one hundred genotypes revealed a large variation ranging from 0.05 mg/kg to 0.49 mg/kg. Compared to high accumulating variety, Shatabdi, 6–8 times the transcript upregulation of Arsenic sequestering ATP binding cassette C1 type gene (ABCC1), was observed in first internode of low accumulating variety Gobindabhog when 5 mg/kg of arsenite was present in soil. A comparison of the genomic sequence of OsABCC1 identified 8 SNPs between the two genotypes; 5 in introns and 3 silent mutations in exons. We identified a PCR based co-dominant marker targeting an SNP (T/G) between the two genotypes, which clearly distinguished 100 genotypes into low (mean 0.14 mg/kg) and high (mean 0.35 mg/kg) accumulating groups. All aromatic genotypes, either long or small grain, carry the Gobindabhog-type ABCC1 allele and are low accumulators of arsenic. Gobindabhog allele carrying 62 RILs and NILs showed almost 40–50% less As-accumulation in grains relative to 84 RILs and NILs carrying Shatabdi type ABCC1-allele. The marker will be useful in introgression of low accumulating allele of OsABCC1 into high yielding photoperiod insensitive varietal backgrounds more easily and accurately. •6 times higher relative abundance of arsenic sequestering OsABCC1 gene transcripts observed in low As accumulating cv. Gobindabhog than high accumulating cv. Shatabdi.•A single nucleotide polymorphism (SNP) in ABCC1 sequence was confirmed in all the aromatic and low As accumulating genotypes.•A perfect PCR based co-dominant marker developed from the SNP for low grain-arsenic accumulation genotyping.•Identified Gobindabhog allele of ABCC1 reduces grain arsenic uploading in rice by more than 40 %.•The marker will be useful in introgression of low accumulating allele of OsABCC1 into multiple high yielding backgrounds.