Solid Stems and Beyond: Challenges and Future Directions of Resistance to Wheat Stem Sawfly (Hymenoptera: Cephidae)

Peirce, Erika S; Cockrell, Darren M; Mason, Esten; Haley, Scott D.; Peairs, Frank B.; Nachappa, Punya

doi:10.1093/jipm/pmac023

Cited by 6 publications

(5 citation statements)

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“…The genetic architecture of stem solidness appears oligogenic, with large effect loci being the main contributors to solidness (Peirce, Cockrell, Mason, et al, 2022). One gene found responsible for solidness is Sst1 (Nilsen et al, 2017(Nilsen et al, , 2020, which was first identified in a quantitative trait locus (QTL) mapping study conducted by Cook et al (2004) on the long arm of wheat chromosome 3B (Qss.msub-3BL).…”

Section: Core Ideasmentioning

confidence: 99%

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HaploCatcher: An R package for prediction of haplotypes

Winn,

Hudson‐Arns,

Hammers

et al. 2023

The Plant Genome

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Wheat (Triticum aestivum L.) is crucial to global food security but is often threatened by diseases, pests, and environmental stresses. Wheat‐stem sawfly (Cephus cinctus Norton) poses a major threat to food security in the United States, and solid‐stem varieties, which carry the stem‐solidness locus (Sst1), are the main source of genetic resistance against sawfly. Marker‐assisted selection uses molecular markers to identify lines possessing beneficial haplotypes, like that of the Sst1 locus. In this study, an R package titled “HaploCatcher” was developed to predict specific haplotypes of interest in genome‐wide genotyped lines. A training population of 1056 lines genotyped for the Sst1 locus, known to confer stem solidness, and genome‐wide markers was curated to make predictions of the Sst1 haplotypes for 292 lines from the Colorado State University wheat breeding program. Predicted Sst1 haplotypes were compared to marker‐derived haplotypes. Our results indicated that the training set was substantially predictive, with kappa scores of 0.83 for k‐nearest neighbors and 0.88 for random forest models. Forward validation on newly developed breeding lines demonstrated that a random forest model, trained on the total available training data, had comparable accuracy between forward and cross‐validation. Estimated group means of lines classified by haplotypes from PCR‐derived markers and predictive modeling did not significantly differ. The HaploCatcher package is freely available and may be utilized by breeding programs, using their own training populations, to predict haplotypes for whole‐genome sequenced early generation material.

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Section: Core Ideasmentioning

confidence: 99%

“…Solid‐stem varieties of wheat have been available since the mid‐20th century (Peirce, Cockrell, Mason, et al., 2022; Weiss & Morrill, 1992). In solid‐stem varieties, undifferentiated parenchyma cells create a solid pith within the stem (Berzonsky et al., 2003).…”

Section: Introductionmentioning

confidence: 99%

HaploCatcher: An R package for prediction of haplotypes

Winn,

Hudson‐Arns,

Hammers

et al. 2023

The Plant Genome

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“…Wheat stem sawfly (WSS), Cephus cinctus (Hymenoptera: Cephidae) is a native, grass‐feeding insect and one of the most important insect pests of wheat in North America 1–3 . WSS has a univoltine life cycle, with adults that emerge in spring and lay eggs within host stems 4 .…”

Section: Introductionmentioning

confidence: 99%

Identifying novel sources of resistance to wheat stem sawfly in five wild wheat species

Peirce,

Evers,

Winn

et al. 2024

Pest Management Science

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BACKGROUNDThe wheat stem sawfly (WSS, Cephus cinctus) is a major pest of wheat (Triticum aestivum) and can cause significant yield losses. WSS damage results from stem boring and/or cutting, leading to the lodging of wheat plants. While solid‐stem wheat genotypes can effectively reduce larval survival, they may have lower yields than hollow‐stem genotypes and show inconsistent solidness expression. Due to limited resistance sources to WSS, evaluating diverse wheat germplasm for novel resistance genes is crucial. We evaluated 91 accessions across five wild wheat species (Triticum monococcum, T. urartu, T. turgidum, T. timopheevii, and Aegilops tauschii) and common wheat cultivars (T. aestivum) for antixenosis (host selection) and antibiosis (host suitability) to WSS. Host selection was measured as the number of eggs after adult oviposition, and host suitability was determined by examining the presence or absence of larval infestation within the stem. The plants were grown in the greenhouse and brought to the field for WSS infestation. In addition, a phylogenetic analysis was performed to determine the relationship between the WSS traits and phylogenetic clustering.RESULTSOverall, Ae. tauschii, T. turgidum, and T. urartu had lower egg counts and larval infestation than T. monococcum, and T. timopheevii. T. monococcum, T. timopheevii, T. turgidum, and T. urartu had lower larval weights compared to T. aestivum.CONCLUSIONThis study shows that wild relatives of wheat could be a valuable source of alleles for enhancing resistance to WSS and identifies specific germplasm resources that may be useful for breeding.

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“…Solid-stem varieties of wheat have been available since the mid-twentieth century (Peirce, Cockrell, Mason, et al, 2022;Weiss & Morrill, 1992). In solid-stem varieties, undifferentiated parenchyma cells create a solid pith within the stem (Berzonsky et al, 2003) and this lessens the severity of yield losses in wheat plants (Beres et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

“…In solid-stem varieties, undifferentiated parenchyma cells create a solid pith within the stem (Berzonsky et al, 2003) and this lessens the severity of yield losses in wheat plants (Beres et al, 2007). The genetic architecture of stem solidness appears oligogenic, with large effect loci being the main contributors to solidness (Peirce, Cockrell, Mason, et al, 2022). One gene found responsible for solidness is Sst1 (Nilsen et al, 2020(Nilsen et al, , 2017, which was first identified in a QTL study conducted by Cook et al (2004) on the long arm of wheat chromosome 3B (Qss.msub-3BL).…”

Section: Introductionmentioning

confidence: 99%

HaploCatcher: An R Package for Prediction of Haplotypes

Winn,

Hudson-Arns,

Hammers

et al. 2023

Preprint

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Wheat (Triticum aestivum L.) is crucial to global food security, but is often threatened by diseases, pests, and environmental stresses. Wheat stem sawfly (Cephus cinctus Norton) poeses a major threat to food security in the United States, and solid-stem varieties, which carry the stem-solidness locus (Sst1), are the main source of genetic resistance against sawfly. Marker-assisted selection uses molecular markers to identify lines possessing beneficial haplotypes, like that of the Sst1 locus. In this study, an R package titled "HaploCatcher" was developed to predict specific haplotypes of interest in genome-wide genotyped lines. A training population of 1,056 lines genotyped for the Sst1 locus, known to confer stem solidness, and genome-wide markers was curated to make predictions of the Sst1 haplotypes for 292 lines from the Colorado State University wheat breeding program. Predicted Sst1 haplotypes were compared to marker derived haplotypes. Our results indicated that the training set was substantially predictive, with kappa scores of 0.83 for k-nearest neighbors and 0.88 for random forest models. Forward validation on newly developed breeding lines demonstrated that a random forest model, trained on the total available training data, had comparable accuracy between forward and cross-validation. Estimated group means of lines classified by haplotypes from PCR-derived markers and predictive modeling did not significantly differ. The HaploCatcher package is freely available and may be utilized by breeding programs, using their own training populations, to predict haplotypes for whole genome sequenced early generation material.

show abstract

Solid Stems and Beyond: Challenges and Future Directions of Resistance to Wheat Stem Sawfly (Hymenoptera: Cephidae)

Cited by 6 publications

References 105 publications

HaploCatcher: An R package for prediction of haplotypes

HaploCatcher: An R package for prediction of haplotypes

Identifying novel sources of resistance to wheat stem sawfly in five wild wheat species

HaploCatcher: An R Package for Prediction of Haplotypes

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