HaploCatcher: An R package for prediction of haplotypes DOI Creative Commons
Zachary J. Winn,

Emily E. Hudson‐Arns,

Mikayla Hammers

et al.

The Plant Genome, Journal Year: 2023, Volume and Issue: 17(1)

Published: Nov. 15, 2023

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

Language: Английский

Untargeted metabolomic and transcriptomic analysis in spring and durum wheat reveals potential mechanisms associated with the early stem solidness phenotype and resistance to wheat stem sawfly DOI Creative Commons
Megan Hager, Jason P. Cook, Brian Bothner

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 19, 2025

Wheat stem sawfly (WSS) causes devastating yield loss in both common bread wheat (Triticum aestivum L.) and durum turgidum L. var durum) the North American Great Plains. The early solidness phenotype confers solid stems plant development coinciding with flight period of WSS provides protection to plants during critical oviposition period. With this phenotype, pith is lost as develops, which may allow for enhanced biological control surviving larvae by braconid parasitoids Bracon cephi (Gahan) lissogaster Muesebeck, well having additional potential benefits from utilizing reabsorbed components. Here, we use an untargeted transcriptomics metabolomics approach explore mechanisms related three cultivars spring two addition near- isogenic pairs wheat. We identified effects growth stage allele on expression metabolites transcripts associated solidness, cell walls programmed death. A caffeic acid methylesterase pectin were upregulated hollow stemmed Reeder lines 3BLa allele, likely influences lignin subunit proportions production volatile semiochemicals that impact behavior adult WSS. TaVPE3cB, a gene death thickening walls, also had increased partially responsible observed. Growth affected involved phenylpropanoid pathway, carbohydrate glycoside biosynthesis lipid biosynthesis, implicating involvement these pathways resistance response infestation

Language: Английский

Citations

0
Adoption of Integrated Pest Management (IPM) for Sustainable Intensification in Wheat DOI

Deepika Sorahia,

A. Raj, Bimal Kumar Sahoo

et al.

IntechOpen eBooks, Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Wheat (Triticum aestivum L.), the most widely grown cereal, faces rising demand due to population growth and shifting consumption habits. However, its productivity is constrained by numerous abiotic biotic factors. Among constraints, insect pests are a major cause of yield loss. This chapter reviewed wheat their damage control methods. While chemical pesticides common, they harm environment as well human health. Existing pest management practices among growers lead economic losses, environmental degradation, operational inefficiencies that collectively undermine both short-term long-term sustainability in farming. To address these issues, Integrated Pest Management (IPM) favored. IPM combines cultural practices, biological control, host plant resistance for sustainable production. adoption limited factors like insufficient farmer knowledge, labor demands, complexity practices. Recent advancements technologies, including Artificial Intelligence (AI), Geographical Information System (GIS), Global Positioning (GPS), machine learning, improve data analysis, optimize management, predict outbreaks. These technologies accuracy, promote sustainability, reduce impact, increase crop yields.

Language: Английский

Citations

0
Identifying novel sources of resistance to wheat stem sawfly in five wild wheat species DOI Creative Commons
Erika Peirce, Byron Evers, Zachary J. Winn

et al.

Pest Management Science, Journal Year: 2024, Volume and Issue: 80(6), P. 2976 - 2990

Published: Feb. 7, 2024

The wheat stem sawfly (WSS, Cephus cinctus) is a major pest of (Triticum aestivum) and can cause significant yield losses. WSS damage results from boring and/or cutting, leading to the lodging plants. Although solid-stem genotypes effectively reduce larval survival, they may have lower yields than hollow-stem show inconsistent solidness expression. Because limited resistance sources WSS, evaluating diverse germplasm for novel genes crucial. We evaluated 91 accessions across five wild species monococcum, T. urartu, turgidum, timopheevii, Aegilops tauschii) common cultivars (T. antixenosis (host selection) antibiosis suitability) WSS. Host selection was measured as number eggs after adult oviposition, host suitability determined by examining presence or absence infestation within stem. plants were grown in greenhouse brought field infestation. In addition, phylogenetic analysis performed determine relationship between traits clustering.

Language: Английский

Citations

1
Host Plant Resistance to Insect Pests in Wheat DOI
Anamika Sharma, Venugopal Mendu, Gadi V. P. Reddy

et al.

Published: Jan. 1, 2024

Host plant resistance offers an excellent solution to pest problems, which reduces pesticide usage and environmental pollution. insect pests in wheat has enabled the management of major including Mayetiola destructor, Cephus cinctus, Diuraphis noxia, Schizaphis graminum, Rhopalosiphum padi. The sources genetic diversity for have been landraces cultivars wild relatives. Several genes identified are incorporated into cultivated (especially Triticum aestivum). Nevertheless, scanty information is available about other economically important such as Sitodiplosis mosellana Oulema melanopus. A coherent program incorporate resistant varieties integrated (IPM) needed better protect crop improve yields.

Language: Английский

Citations

1
Future Outlook of Dryland Crop Production Systems in the Semi-Arid High Plains Amid Climate Change DOI
Olivia E. Todd, Cody F. Creech, Vipan Kumar

et al.

Outlooks on Pest Management, Journal Year: 2024, Volume and Issue: 35(1), P. 4 - 10

Published: Feb. 1, 2024

Dryland agriculture or dry farming is a type of crop production that relies on stored soil moisture and occasional rainfall without providing supplemental irrigation. predominant system in the semi-arid High Plains United States where water resources are scarce, drought frequent, grain yields low. Producers struggling to balance their pest management needs with conservation practices such as no reduced tillage, well loss efficacy for some herbicide chemistries. The predicted increase dryland acreage due increasing underground resource limitations climate change, it prudent understand major issues develop research-lead solutions.

Language: Английский

Citations

0
Integrating solid stem and multiple disease resistance for developing climate-resilient wheat (Triticum aestivum L.) DOI

P. Shajitha,

Nisha Rani, M. Sivasamy

et al.

Cereal Research Communications, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 12, 2024

Language: Английский

Citations

0
HaploCatcher: An R package for prediction of haplotypes DOI Creative Commons
Zachary J. Winn,

Emily E. Hudson‐Arns,

Mikayla Hammers

et al.

The Plant Genome, Journal Year: 2023, Volume and Issue: 17(1)

Published: Nov. 15, 2023

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

Language: Английский

Citations

0