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.

Yield-enhancing SPIKE allele from the aus-subtype indica rice and its allele specific codominant marker.

Improving spikelet number without limiting panicle number is an important strategy to increase rice productivity. In this study, a spikelet number enhancing SPIKE-allele was identified from the aus subtype indica rice, cv. Bhutmuri, which has an identical japonica like corresponding sequence including a retrotransposon sequence, usually absent in indica genotypes, like IR64. An allele-specific singletube PCR-based codominant marker targeting an A/G single-nucleotide polymorphism (SNP) at the 3'UTR was identified for easier genotyping. The yield enhancing ability of the Bhutmuri-SPIKE allele carrying RILs and NILs over IR64-SPIKE allele carrying alleles was due to increased number of filled grains/panicle. More than three times higher abundance of SPIKE transcripts was observed in Bhutmuri and NILs carrying this allele compared with IR64 and its allele carrying NILs. Higher rate of photosynthesis at more than 900 µmolm-2s-1 light intensity and more than six small vascular bundles between the two large vascular bundles in the flag leaves of Bhutmuri and its allele carrying NILs were also observed. The identified SPIKE allele and the marker associated with it will be useful for increasing the productivity of rice by marker-assisted breeding.