Fusarium head blight (FHB), mainly caused by Fusarium graminearum, is one of the most devastating diseases of wheat worldwide. Identification and validation of major quantitative trait loci (QTLs) for FHB resistance without negative effects on agronomic traits is critical to success in breeding FHB-resistant cultivars. In this study, a stable major QTL on chromosome arm 2DL was identified by evaluating a recombinant inbred line (RIL) population derived from Shi4185×Shijiazhuang 8 in both field and greenhouse experiments. QTL mapping and pedigree analyses indicated that the 2DL QTL is the same as QFhb-2DL previously identified in Ji5265; therefore, it was designated Fhb9. Four kompetitive amplicon sequence polymorphism (KASP) markers were developed based on exome capture sequencing data to enhance marker density in the Fhb9 region, and it was delimited to an interval between single nucleotide polymorphism (SNP) markers KASP-12056 (533.8 Mb) and KASP-525 (525.9 Mb) explained 26.0–30.1% of the phenotypic variation. Analysis of the geographic distribution of the Fhb9 resistance allele suggests that it originated from the Huang-Huai winter wheat region in China. The very low frequency of Fhb9 in modern Chinese cultivars reveals that it has not been widely deployed in breeding programs. Field and greenhouse evaluations of yield-related traits in near-isogenic lines (NILs) contrasting in Fhb9 alleles reveal that the Fhb9 resistance allele have no adverse effects on these traits. Fhb9 showed an additive effect on enhancing FHB resistance with Fhb1. Therefore, Fhb9 is a valuable major QTL for improving FHB resistance in wheat, and the near-diagnostic markers developed in this study will facilitate its deployment in wheat breeding programs.

The Hessian fly (HF, Mayetiola destructor) is one of the destructive pests of wheat (Triticum aestivum L.) worldwide. Resistant cultivars can effectively minimize wheat damage due to this insect pest. To identify new quantitative trait loci (QTL) for HF resistance, a population of recombinant inbred lines (RILs) was developed from a cross between the HF-resistant wheat cultivar ‘Chokwang’ and susceptible wheat ‘Ning 7840’, and phenotyped for responses to HF attack. A linkage map was constructed using 1147 single nucleotide polymorphism (SNP) markers generated from genotyping-by-sequencing (GBS). One major QTL, QHf.hwwg-6BS, for HF-resistance was identified on chromosome arm 6BS, which explained up to 84.0% of the phenotypic variation and was contributed by Chokwang. Two RILs showed recombination in the candidate interval of QHf.hwwg-6BS, which delimited QHf.hwwg-6BS to a 4.75 Mb physical interval between 6,028,601 bp and 10,779,424 bp on chromosome arm 6BS of IWGSC Chinese Spring reference genome RefSeq v2.0. Seven GBS-SNPs in the candidate interval were converted into Kompetitive allele specific polymerase chain reaction (KASP) markers. Two of them, KASP-6B112698 and KASP-6B7901215, were validated in a U.S. winter wheat panel. KASP-6B112698 was nearly diagnostic, thus can be used to screen QHf.hwwg-6BS and pyramid it with other resistance genes in breeding programs.

Wheat leaf rust is a prevalent foliar disease in wheat worldwide. Growing resistant cultivars is an effective strategy to minimize the impact of leaf rust on yield and grain quality. Lr42 is a leaf rust resistance gene identified from Aegilops tauschii and is still effective against current predominant leaf rust races in the United States and many other countries. In this study, we developed diagnostic DNA markers for Lr42 using the sequence polymorphisms of a differentially expressed gene (TaRPM1) encoding a putative NB-ARC protein in the Lr42 candidate region identified by RNA-sequencing of two near-isogenic lines contrasting in Lr42 alleles. Markers were designed based on a deletion mutation and a single nucleotide polymorphism (SNP) in the gene. Haplotype analyses of the newly developed markers in the three diversity panels demonstrated that they are diagnostic for Lr42, and superior to previously used markers in selection accuracy. These markers have the advantages of low cost and easy assay, and they are suitable for marker-assisted selection in breeding programs with either high- or low-throughput marker screening facilities.

Fusarium head blight (FHB) is one of the prevalent fungal diseases of wheat worldwide. Exploring new FHB resistance quantitative trait loci (QTL) in adapted wheat cultivars is a critical step for breeding new FHB-resistant cultivars. In this study, we developed a population of 236 F_5:7 recombinant inbred lines (RILs) using two popular Chinese wheat cultivars, Yangmai 158 and Zhengmai 9023, with moderate FHB resistance to identify the QTL for FHB type Ⅱ resistance. This population was evaluated for percentage of symptomatic spikelets per spike (PSS) using single floret injection in repeated greenhouse experiments. Mean PSSs were 33.2% for Yangmai 158 and 30.3% for Zhengmai 9023. A genetic linkage map of 1002 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) was constructed for the RIL population. Six QTL were identified for FHB resistance, and three of them were repeatable in the both experiments. Zhengmai 9023 contributed the resistance allele at one repeatable QTL, designated as Qfhb.7D, whereas Yangmai 158 contributed the resistance alleles at the other two repeatable QTL, Qfhb.3AL and Qfhb.2DS. The additional QTL, Qfhb.4AS was significant in the mean PSS, and Qfhb.2DL and Qfhb.7AS were significant in only one experiment. Replacement of each allele individually at the three repeatable QTL significantly changed PSSs. Qfhb.3AL, Qfhb.2DS, and Qfhb.7D explained 8.35% to 9.89%, 5.13% to 7.43%, and 6.15% to 9.32% of the phenotypic variations, respectively. The three repeatable QTL contributed by the two parents were additive and stacking the resistance alleles from all the three repeatable QTL showed the highest level of resistance in the current RIL population. Ten SNPs in the QTL regions of Qfhb.3AL, Qfhb.2DS, and Qfhb.7D were converted into KBioscience competitive allele-specific PCR (KASP) assays. One KASP marker for Qfhb.3AL was validated in a panel of wheat cultivars from China. Some of these KASP markers could be useful for marker-assisted selection to stack these QTL.