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 F2 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.