Publications by Colleges and Departments (MSU - Bozeman)
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Item Improvement of Endosperm Hydration Counter the Negative Relationship Between Dormancy and Malt Quality in Barley (Hordeum vulgare)(Wiley, 2024-08) Jensen, Joseph; Uhlmann, Hannah; Lachowiec, Jennifer; Lutgen, Greg; Cook, Jason P.; Yin, Xiang S.; Kephart, Ken; Sherman, JamieDormancy in barley has been thoroughly studied and shown to negatively impact malt quality, resulting in selection against dormancy. However, reduced dormancy coincides with increased preharvest sprout (PHS) risk, thus sparking a new interest in integrating dormancy back into American barley lines if the negative effects of dormancy on malt quality can be overcome. We evaluated the dormancy and hydration index (HYI) in a biparental mapping population to determine the genotypes that would protect against PHS but have good malt quality. We found 4 HYI QTLs and 4 dormancy QTLs, one of which was near the well-described SD2 QTL. The HYI QTLs were pleiotropically related to seed size (1H), dormancy (5H) and malt quality (2H). Lines with dormancy (5H) and increased HYI (2H and 3H) had malt quality similar to nondormant lines while maintaining PHS resistance, suggesting improvements in HYI could be the key to overcoming the negative effects of dormancy in malting.Item QTL mapping reveals malt barley quality improvement in two dryland environments associated with extended grain fill and seminal root traits(Wiley, 2024-05) Williams, Jessica L.; Lamb, Peggy F.; Lutgen, Greg; Lachowiec, Jennifer; Cook, Jason P.; Jensen, Joseph; Bourgault, Maryse; Sherman, Jamie D.To achieve malt grade and receive full price, barley (Hordeum vulgare L.) crops must meet standards for certain quality traits including percent plump and protein. Terminal drought stress reduces quality and is projected to worsen in barley cultivation areas, underscoring the need for varieties that maintain good malt production with unreliable precipitation. The stay-green trait extends the grain fill phase between heading and maturity and has been linked to stable quality under dry conditions. However, this relationship can be inconsistent and is not well understood. To effectively leverage a longer grain fill phenotype for drought adaptation, a better grasp of its genetics and environmental interaction is needed. Stay-green root system differences have been observed and could be at play. We performed correlation and quantitative trait locus (QTL) analysis on grain fill duration, grain quality, and seminal root traits using a recombinant inbred line (RIL) population segregating for stay-green. Agronomic data were collected in four field trials at two distinct semiarid locations, and roots were measured in a greenhouse assay. Earlier heading and later maturity led to improved quality in both locations and more consistent quality between locations. Earlier heading had a greater influence on quality in the drier environment, while later maturity was more impactful in the less dry environment. We observed co-locations of seminal root trait QTLs with grain fill duration and grain quality. These QTLs lay the groundwork for further investigation into root phenotypes associated with stay-green and the deployment of these traits in breeding for drought adaptation.Item Dosage response to reduced height‐1 (Rht‐1) loss‐of‐function mutations and characterization of slender phenotype in hexaploid wheat(Wiley, 2023-10) Ugrin, Josey M.; Hogg, Andrew C.; Tracy, Emma M.; Tillet, Brandon J.; Cook, Jason P.; Martin, John M.; Giroux, Michael J.The reduced height (Rht-1) genes in wheat (Triticum aestivum L.) are integral in controlling plant height. Previous studies in other plant species have demonstrated that loss-of-function mutations in their orthologous Rht-1 genes results in plants with a slender phenotype illustrated by increased plant heights, sterility, and a constitutive gibberellic acid (GA3) response; however, this phenotype has not been described in wheat. In this study, nonsense alleles occurring in the GRAS domain of Rht-A1, B1, and D1 were combined to create single, double, and triple Rht-1 mutants. Homozygous lines possessing none, one, two, or three Rht-1 stop mutations were grown in replicated field trials in three environments to assess agronomic traits. Germination tests to measure GA3 responsiveness and gene expression analysis via RNA-seq were also performed. Rht-1 triple mutants exhibited a slender phenotype characterized by rapid growth, elongated coleoptiles and internodes, elongated spikes, decreased tiller and spikelet number, and sterile heads. The presence of a single functional Rht-1 gene resulted in a normal phenotype. Differences in plant height among the Rht-1 double mutants, Rht-1 single mutants, and Rht-1 all wild-type dosages trended toward increased plant height with increased Rht-1 stop mutation dosage. Differences in Rht-1 homeolog gene expression did not equate to differences in plant height between the different Rht-1 stop mutations.Item Evaluation of wheat stem sawfly‐resistant solid stem Qss.msub‐3BL alleles in hard red winter wheat(Wiley, 2023-01) Wong, Mei Ling; Bruckner, Philip L.; Berg, Jim E.; Lamb, Peggy F.; Hofland, Megan L.; Caron, Christopher G.; Heo, Hwa‐Young; Blake, Nancy K.; Weaver, David K.; Cook, Jason P.Host plant resistance provided by solid stems has been the most effective means for mitigating wheat stem sawfly (WSS) (Cephus cinctus Norton) damage in spring and winter wheat (Triticum aestivum L.). The solid stem trait originates from the spring wheat cultivar “Rescue” and is associated with a quantitative trait locus allele Qss.msub-3BL.b that explains the majority of the variation for stem solidness. Recently, a new Qss.msub-3BL solid stem allele, designated Qss.msub-3BL.c, was identified in the spring wheat cultivar “Conan”. It produces a solid stem phenotype early in plant development but dissipates during plant growth. The Qss.msub-3BL.c allele provides effective WSS resistance in spring wheat but has not been tested in winter wheat. To examine if the Qss.msub-3BL.c allele provides adequate WSS resistance in winter wheat, near-isogenic lines (NILs) were developed using marker-assisted backcrossing. This enabled comparisons between the hollow stem Qss.msub-3BL.a, solid stem Qss.msub-3BL.b and solid stem Qss.msub-3BL.c alleles for stem solidness, WSS resistance, and agronomic traits in Montana growing environments. Compared to the hollow stem allele, the NILs with the Qss.msub-3BL.c allele increased stem solidness and reduced WSS stem cutting. However, the Qss.msub-3BL.c allele resulted in lower solid stem scores and greater WSS stem cutting compared to the Qss.msub-3BL.b allele. Overall, these findings indicate that the Qss.msub-3BL.c allele failed to provide sufficient WSS resistance in the winter wheat backgrounds tested in this study.Item Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize(2020-05) Ramstein, Guillaume P.; Larsson, Sara J.; Cook, Jason P.; Edwards, Jode W.; Ersoz, Elhan S.; Flint-Garcia, Sherry; Gardner, Candice A.; Holland, James B.; Lorenz, Aaron J.; McMullen, Michael D.; Millard, Mark J.; Rocheford, Torbert R.; Tuinstra, Mitchell R.; Bradbury, Peter J.; Buckler, Edward S.; Romay, M. CintaSingle-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.Item Registration of ‘StandClear CLP’ hard red winter wheat(2020-06) Berg, Jim E.; Kephart, Ken D.; Lamb, Peggy F.; Davis, Edward S.; Eberly, Jed O.; Miller, John H.; Chen, Chengci; Pradhan, G. P.; Torrion, Jessica A.; Ramsfield, Ron; Smith, Vincent H.; Nash, Deanna L.; Holen, Doug L.; Cook, Jason P.; Gale, Sam; Jin, Yue; Chen, X.; Bruckner, Phil L.‘StandClear CLP’ (Reg. no. CV-1162, PI 693236) hard red winter (HRW) wheat (Triticum aestivum L.) was developed and released by the Montana Agricultural Experiment Station and exclusively licensed to Loveland Products, Inc., in 2020. StandClear CLP is a two-gene Clearfield, semisolid-stem wheat intended for use with the selective imidazolinone (IMI) herbicide imazamox. StandClear CLP resulted from a cross of MTS0531 to an IMI herbicide tolerant F1 plant from a population segregating for two acetohydroxyacid synthase (AHAS) genes [TaAHAS1D and TaAHAS1B]. Original herbicide tolerance donors were IMI ‘Fidel’ (TX12588*4/FS2, BASF) for allele TaAHAS1D via descended experimental lines MTCL0309 and MTCL0510, and proprietary hard red spring wheat line CDC Teal 11A (BASF Corporation) for allele TaAHAS1B. StandClear CLP was selected as a F6:7 headrow in 2014 following multiple cycles of phenotypic mass selection for IMI herbicide tolerance and stem solidness. StandClear CLP was tested under the experimental number MTCS1601 from 2016 to 2019 in Montana for field performance, herbicide tolerance, and end-use quality. StandClear CLP is a high-yielding, Clearfield HRW wheat cultivar with intermediate stem solidness, moderate host plant resistance to wheat stem sawfly, and acceptable milling and baking quality.