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Wheat (Triticum aestivum L.) wild relatives are rich genetic resources for genetic improvement of wheat. The short arm of rye (Secale cereale L.) chromosome 1 (1RS) contains many beneficial genes for resistance to drought, insects, and diseases, therefore the 1RS wheat translocations have been widely used in wheat breeding programs worldwide. To facilitate marker‐assisted identification of 1RS in wheat breeding, we designed a set of Kompetitive allele‐specific polymerase chain reaction (KASP) markers to detect the translocations of 1RS with long arm from wheat chromosome 1A (1RS.1AL) and 1RS with long arm from wheat chromosome 1B (1RS.1BL) based on the sequence flanking single nucleotide polymorphisms (SNPs) generated by genotyping‐by‐sequencing (GBS) between wheat and rye panels. We identified a set of three SNP markers for diagnosis and differentiation of the two 1RS translocations in wheat. Among the three KASP markers, 1AS‐05056 is 1RS specific, and clearly separated the genotypes with 1RS (1RS.1AL and 1RS.1BL) from those without the two 1RS translocations; whereas 1AS‐29875 clearly identified the 1RS.1AL translocation and 1BS‐16654 separated 1RS.1BL from 1RS.1AL. The three new KASP markers together accurately identified the presence of 1RS translocation on either 1A or 1B chromosome in a panel of 95 representative U.S. winter wheat accessions, which were further validated in two additional U.S. hard winter wheat panels. Therefore, they can be used for routine screening of 1RS.1BL and 1RS.1AL translocation lines in wheat breeding programs. Core Ideas: 1RS, 1AS, and 1BS specific SNPs were identified by analyzing GBS‐SNPs from both wheat and rye panels.Three chromosome‐arm‐specific KASPs clearly detected the 1RS.1AL and 1RS.1BL translocations in wheat.Three KASP markers were diagnostic for 1RS.1AL and 1RS.1BL in two U.S. hard winter wheat panels. [ABSTRACT FROM AUTHOR]

Key message: The recessive Hessian fly resistance gene h4 and flanking SNP markers were located to a 642 kb region in chromosome 1A of the wheat cultivar 'Java.' Hessian fly (HF), Mayetiola destructor, is one of the most destructive insect pests in wheat worldwide. The wheat cultivar 'Java' was reported to carry a recessive gene (h4) for HF resistance; however, its chromosome location has not been determined. To map the HF resistance gene in Java, two populations of recombinant inbred lines (RILs) were developed from 'Bobwhite' × Java and 'Overley' × Java, respectively, and were phenotyped for responses to infestation of HF Great Plains biotype. Analysis of phenotypic data from the F1 and the RIL populations confirmed that one recessive gene conditioned HF resistance in Java. Two linkage maps were constructed using single-nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). The h4 gene was mapped to the distal end of the short arm of chromosome 1A, which explained 60.4 to 70.5% of the phenotypic variation for HF resistance in the two populations. The GBS-SNPs in the h4 candidate interval were converted into Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) markers to eliminate the missing data points in GBS-SNPs. Using the revised maps with KASP markers, h4 was further located to a 642 kb interval (6,635,984–7,277,935 bp). The two flanking KASP markers, KASP3299 and KASP1871, as well as four other closely linked KASP markers, may be useful for pyramiding h4 with other HF resistance genes in breeding. [ABSTRACT FROM AUTHOR]

Hessian fly (HF, Mayetiola destructor Say), is a destructive insect pest in most wheat (Triticum aestivum L.) growing areas worldwide. Growing resistant cultivars can effectively reduce HF damage. The wheat cultivar 'Seneca' was reported to carry resistance genes H7 on chromosome 5D and H8 with unknown location. To further validate the resistance gene locations in Seneca, a recombinant inbred line (RIL) population from Bobwhite × Seneca was genotyped using 3,330 single nucleotide polymorphism (SNP) markers generated from genotyping‐by‐sequencing (GBS) and phenotyped for HF resistance in the greenhouse experiments. Phenotypic analyses showed at least two genes conditioning HF resistance in Seneca, but none of them was mapped on chromosome 5D, as previously reported. Instead, one major gene, designated as H7, was mapped to chromosome 6A and explained 60.7–78.3% of the phenotypic variation. The other gene with a minor effect, designated as H8, was found on chromosome 2B and explained 3.2–4.7% of the phenotypic variation. Based on the physical locations of flanking markers for H7 in the Chinese Spring reference genome, H7 was physically located in a 6‐Mb interval on 6AL. This study reassigned the major gene H7 to chromosome 6A and the minor gene H8 to 2B in Seneca using a high‐density SNP map. Seventeen GBS SNPs mapped in the H7 region were converted into Kompetitive allele specific polymerase chain reaction (KASP) markers for selecting this gene in breeding. [ABSTRACT FROM AUTHOR]