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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.Item Identification of Candidate Genes Responsible for Stem Pith Production Using Expression Analysis in Solid-Stemmed Wheat(2017-07) Oiestad, Alanna J.; Martin, John M.; Cook, Jason P.; Varella, Andrea C.; Giroux, Michael J.The wheat stem sawfly (WSS) is an economically important pest of wheat in the Northern Great Plains. The primary means of WSS control is resistance associated with the single quantitative trait locus (QTL) Qss. msub. 3BL, which controls most stem solidness variation. The goal of this study was to identify stem solidness candidate genes via RNA-seq. This study made use of 28 single nucleotide polymorphism (SNP) makers derived from expressed sequence tags (ESTs) linked to Qss. msub. 3BL contained within a 5.13 cM region. Allele specific expression of EST markers was examined in stem tissue for solid and hollow-stemmed pairs of two spring wheat near isogenic lines (NILs) differing for the Qss. msub-3BL QTL. Of the 28 ESTs, 13 were located within annotated genes and 10 had detectable stem expression. Annotated genes corresponding to four of the ESTs were differentially expressed between solid and hollow-stemmed NILs and represent possible stem solidness gene candidates. Further examination of the 5.13 cM region containing the 28 EST markers identified 260 annotated genes. Twenty of the 260 Qss. msub. 3BL linked genes were up-regulated in hollow NIL stems, while only seven genes were up-regulated in solid NIL stems. An O-methyltransferase within the region of interest was identified as a candidate based on differential expression between solid and hollow-stemmed NILs and putative function. Further study of these candidate genes may lead to the identification of the gene(s) controlling stem solidness and an increased ability to select for wheat stem solidness and manage WSS.Item Characterization of resistance to the wheat stem sawfly in spring wheat landrace accessions from targeted geographic regions of the world(2017-07) Varella, Andrea C.; Weaver, David K.; Cook, Jason P.; Blake, Nancy K.; Hofland, Megan L.; Lamb, Peggy F.; Talbert, Luther E.Plant landraces have long been recognized as potential gene pools for biotic and abiotic stress-related genes. This research used spring wheat landrace accessions to identify new sources of resistance to the wheat stem sawfly (WSS) (Cephus cinctus Norton), an important insect pest of wheat in the northern Great Plains of North America. Screening efforts targeted 1409 accessions from six geographical areas of the world where other species of grain sawflies are endemic or where a high frequency of accessions possesses the resistance characteristic of solid stems. Resistance was observed in approximately 14% of accessions. Half of the lines displayed both antixenosis and antibiosis types of resistance. Among the resistant accessions, 41% had solid or semi-solid stems. Molecular genetic screening for haplotypes at the solid stem QTL, Qss.msub.3BL, showed that 15% of lines shared the haplotype derived from \'S-615\', the original donor of the solid stem trait to North American germplasm. Other haplotypes associated with solid stems were also observed. Haplotype diversity was greater in the center of origin of wheat. Evaluation of a representative set of resistant landrace accessions in replicated field trials at four locations over a three year period identified accessions with potential genes for reduced WSS infestation, increased WSS mortality, and increased indirect defense via parasitoids. Exploitation of distinct types of plant defense will expand the genetic diversity for WSS resistance currently present in elite breeding lines.