The Hessian fly recessive resistance gene h4 mapped to chromosome 1A of the wheat cultivar 'Java' using genotyping-by-sequencing

Quantitative Trait Locus Analysis of Hessian Fly Resistance in Soft Red Winter Wheat

The Hessian fly (HF) is an invasive insect that has caused millions of dollars in yield losses to southeastern US wheat farms. Genetic resistance is the most sustainable solution to control HF. However, emerging biotypes are quickly overcoming resistance genes in the southeast; therefore, identifying novel sources of resistance is critical. The resistant line "UGA 111729" and susceptible variety "AGS 2038" were crossbred to generate a population of 225 recombinant inbred lines. This population was phenotyped in the growth chamber (GC) during 2019 and 2021 and in field (F) trials in Georgia during the 2021-2022 growing seasons. Visual scoring was utilized in GC studies. The percentage of infested tillers and number of pupae/larvae per tiller, and infested tiller per sample were measured in studies from 2021 to 2022. Averaging across all traits, a major QTL on chromosome 3D explained 42.27% (GC) and 10.43% (F) phenotypic variance within 9.86 centimorgans (cM). SNP marker IWB65911 was associated with the quantitative trait locus (QTL) peak with logarithm of odds (LOD) values of 14.98 (F) and 62.22 (GC). IWB65911 colocalized with resistance gene H32. KASP marker validation verified that UGA 111729 and KS89WGRC06 express H32. IWB65911 may be used for marker-assisted selection.

Molecular mechanisms, genetic mapping, and genome editing for insect pest resistance in field crops

Improving crop resistance against insect pests is crucial for ensuring future food security. Integrating genomics with modern breeding methods holds enormous potential in dissecting the genetic architecture of this complex trait and accelerating crop improvement. Insect resistance in crops has been a major research objective in several crop improvement programs. However, the use of conventional breeding methods to develop high-yielding cultivars with sustainable and durable insect pest resistance has been largely unsuccessful. The use of molecular markers for identification and deployment of insect resistance quantitative trait loci (QTLs) can fastrack traditional breeding methods. Till date, several QTLs for insect pest resistance have been identified in field-grown crops, and a few of them have been cloned by positional cloning approaches. Genome editing technologies, such as CRISPR/Cas9, are paving the way to tailor insect pest resistance loci for designing crops for the future. Here, we provide an overview of diverse defense mechanisms exerted by plants in response to insect pest attack, and review recent advances in genomics research and genetic improvements for insect pest resistance in major field crops. Finally, we discuss the scope for genomic breeding strategies to develop more durable insect pest resistant crops.

Precise mapping of QTL for Hessian fly resistance in the hard winter wheat cultivar 'Overland'

A major QTL for Hessian fly resistance was precisely mapped to a 2.32 Mb region on chromosome 3B of the US hard winter wheat cultivar 'Overland'. The Hessian fly (HF, Mayetiola destructor) is a destructive insect pest of wheat in the USA and worldwide. Deploying HF-resistant cultivars is the most effective and economical approach to control this insect pest. A population of 186 recombinant inbred lines (RILs) was developed from 'Overland' × 'Overley' and phenotyped for responses to HF attack using the HF biotype 'Great Plains'. A high-density genetic linkage map was constructed using 1,576 single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). Two quantitative trait loci (QTLs) with a significant epistatic effect on HF resistance were mapped to chromosomes 3B (QHf.hwwg-3B) and 7A (QHf.hwwg-7A) in Overland, which are located in similar chromosome regions as found for H35 and H36 in the cultivar 'SD06165', respectively. QHf.hwwg-3B showed a much larger effect on HF resistance than QHf.hwwg-7A. Five and four GBS-SNPs, respectively, in the QHf.hwwg-3B and QHf.hwwg-7A QTL intervals were converted into Kompetitive allele specific polymerase chain reaction (KASP) markers. QHf.hwwg-3B was precisely mapped to a 2.32 Mb interval (2,479,314-4,799,538 bp) using near-isogenic lines (NILs) and RILs that have recombination within the QTL interval. The US winter wheat accessions carrying contrasting alleles at KASP markers KASP-3B4525164, KASP-7A47772047 and KASP-7A65090410 showed significant difference in HF resistance. The combination of the two KASP markers KASP-3B3797431 and KASP-3B4525164 is near-diagnostic for the detection of QHf.hwwg-3B in a US winter wheat panel and can be potentially used for screening the QTL in breeding programs.

The Hessian fly recessive resistance gene h4 mapped to chromosome 1A of the wheat cultivar 'Java' using genotyping-by-sequencing

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.

The Hessian fly recessive resistance gene h4 mapped to chromosome 1A of the wheat cultivar 'Java' using genotyping-by-sequencing

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.

Identification of two novel Hessian fly resistance genes H35 and H36 in a hard winter wheat line SD06165

Two new Hessian fly resistance QTLs (H35 and H36) and tightly linked SNP markers were identified in a US hard winter wheat SD06165. Hessian fly (HF), Mayetiola destructor (Say), is one of the most destructive pests in wheat (Triticum aestivum L.) worldwide. Growing resistant cultivars is the most effective approach to minimize Hessian fly damage. To identify new quantitative trait loci (QTLs) for HF resistance, a recombinant inbred line population was developed by crossing HF resistant wheat line SD06165 to a susceptible line OK05312. The population was genotyped with 1709 single-nucleotide polymorphisms (SNPs) generated from genotyping-by-sequencing and phenotyped for HF resistance in greenhouses. Two novel QTLs for HF resistance were identified from SD06165. The major QTL, designated as H35, was closely linked to SNP marker SDOKSNP7679 on chromosome 3BS that explained 23.8% and 36.0% of the phenotypic variations; the minor QTL, designated as H36, was flanked by SNP markers SDOKSNP1618 and SDOKSNP8089 on chromosome 7AS and explained 8.5% and 13.1% of the phenotypic variation in the two experiments. Significant interaction was detected between the two QTLs. Seventeen SNPs that tightly link to H35 and eight SNPs that tightly link to H36 were converted to kompetitive allele specific polymerase chain reaction markers for selecting these QTLs in breeding programs.