Identification of genomic regions associated with low phosphorus tolerance in japonica rice (Oryza sativa L.) by QTL-Seq

Phosphorus (P) is a major nutrient supporting rice productivity. Improving low-P tolerance of rice is expected to reduce dependence on P fertilizer, thereby reducing rice production costs and environmental impacts. This report describes the mapping of quantitative trait loci (QTL) associated with P deficiency tolerance in japonica rice. An F5 population derived from a cross of the low-P tolerant cultivar Akamai (Yamagata) and the sensitive cultivar Koshihikari was evaluated for shoot growth under low-P conditions. Then single nucleotide polymorphism (SNP) profiles of the low-P tolerant and sensitive bulks were compared on a genome-wide scale by QTL-Seq, a rapid QTL mapping method using next-generation sequencing technology. Results show a major QTL associated with low-P tolerance located on the long arm of chromosome 12. It has been named QTL for low-P tolerance 1 or qLPT1. SNPs were detected in 45 genes of qLPT1 region and the 5 genes were harboring synonymous SNPs, although none of them had been reported as involved in low-P tolerance. This result implies that the novel gene responsible for low-P tolerance exists in qLPT1. This study will contribute to the elucidation of mechanisms underlying low-P tolerance of Akamai and will facilitate the breeding of rice with low-P tolerance.