Stable QTL Identification and KASP Marker Development for Grain Protein Content in Wheat Using a Linmai2/Zhong892 RIL Population

Grain protein content (GPC) is extremely important for common wheat (Triticum aestivum L.) end-use quality. Identifying genetic loci for GPC is helpful in creating new varieties with good processing quality. Linmai2 and Zhong892 are two elite wheat varieties with differences in GPC. In the present study, a recombinant inbred line (RIL) population derived from Linmai2 and Zhong892 was used to identify GPC loci. Linkage mapping was conducted by combining the wheat 90K single nucleotide polymorphisms (SNPs) chip data and GPC from four environments. Five QTLs on chromosomes 1B, 2B, 4A, 4B and 6B were identified, and designated as QGPC.lfnu-1BL, QGPC.lfnu-2BS, QGPC.lfnu-4AS, QGPC.lfnu-4B and QGPC.lfnu-6BS, respectively, explaining 5.21–11.38% of the phenotypic variances. The favorable alleles of QGPC.lfnu-1BL, QGPC.lfnu-4AS, QGPC.lfnu-4B and QGPC.lfnu-6BS originated from Zhong892, while the favorable allele of QGPC.lfnu-2BS came from Linmai2. Among these, QGPC.lfnu-1BL, QGPC.lfnu-2BS, QGPC.lfnu-4AS, and QGPC.lfnu-4B are potentially novel loci, whereas QGPC.lfnu-6BS likely represents the re-detection of Gpc-B1. Additionally, competitive allele-specific PCR (KASP) markers suitable for breeding were developed, and genetic effects were validated in a natural population. Four KASP markers, KASP-GPC-1BL, KASP-GPC-2BS, KASP-GPC-4B and KASP-GPC-6BS, were significantly associated with GPC in a diverse panel of 140 wheat varieties. A total of twelve potential genes involved in nitrogen assimilation, amino acid biosynthesis and transport, and NPF transporter and protein turnover were proposed as candidate genes within the intervals of five QTLs. These findings identified stable QTLs, available KASP markers and promising candidate genes for marker assisted selection to accelerate wheat GPC improvement.