Development of AS-PCR marker based on a key mutation confirmed by resequencing of Wx-mp in Milky Princess and its application in japonica soft rice (Oryza sativa L.) breeding

Soft rice with low amylose content (AC) ranging by 5-15% is a unique type with special eating and appearance quality and has become popular in the rice market. We resequenced the Wx-mp, a key allele from Milky Princess, a Japanese low AC variety, and found that the +473 mutation in exon 4 is the key mutation in both Wx-mp and its ancestor allele, Wx-mq from Milky Queen. Based on this functional mutation, an allele-specific PCR (AS-PCR) marker was developed and proven in a breeding population derived from a cross between a Chinese late variety Nan Keng 46 (Wx-mp/Wx-mp) and an early line Ning 63121(Wx-b/Wx-b). Based on the marker-aided selection by our newly developed AS-PCR marker for Wx-mp and the known ST10 marker for Stvb-i, a total of 12 Wx-mp homozygotes were selected from 198 F-2 progenies, and four of them were immune to rice stripe virus (RSV) with averagely 11.3 days earlier heading than Nan Keng 46 without significant change in grain yield.