{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T03:03:56Z","timestamp":1793502236789,"version":"4.5.0"},"reference-count":59,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T00:00:00Z","timestamp":1788307200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100011929","name":"Foundation for Food and Agriculture Research","doi-asserted-by":"publisher","award":["CA19-SS-0000000146"],"award-info":[{"award-number":["CA19-SS-0000000146"]}],"id":[{"id":"10.13039\/100011929","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2020-68012-31934"],"award-info":[{"award-number":["2020-68012-31934"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004952","name":"Minnesota Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004952","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    The University of Minnesota has been domesticating the perennial forage intermediate wheatgrass (IWG) since 2011 using a combination of conventional methods and modern breeding tools such as genomic selection. Globally, most IWG selection nurseries are spaced-planted individuals of several hundred genotypes whereas commercial fields established for grain production are row-planted panmictic populations. This study evaluated genomic prediction models and estimated genetic gain in yield and agronomic performance of row-planted IWG half-sib families assessed over 3 years and 2 locations, Lamberton and St. Paul, MN, USA. The strongest trait correlation was negative (r\u2009=\u2009\u22120.49) between 2023 St. Paul height and 2022 St. Paul seed size. The three St. Paul environments were more similar for plant height and seed size and so were the Lamberton environments yet no specific trend was observed for grain yield. Evaluation of different univariate and multivariate genomic prediction models showed that multivariate models outperformed the best univariate models by 23 percentage points, yet no single multivariate model was the best predictor of all traits. Cross-environment predictions were the best among St. Paul environments and no single environment was the best predictor of the remaining environments. Genetic gain estimates indicated a 20 kg ha\n                    <jats:sup>-1<\/jats:sup>\n                    increase in grain yield and 3 cm reduction in plant height per breeding cycle. While no single model predicted all traits with high accuracy, results obtained in this study suggest that evaluating IWG sibs in row plots followed by genomic trait predictions could lead to desired breeding progress for desired traits.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0357452","type":"journal-article","created":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T17:27:18Z","timestamp":1788370038000},"page":"e0357452","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Assessment of genomic prediction and genetic gain in multi\u2011population half-sib families in the perennial grass crop intermediate wheatgrass"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3093-5582","authenticated-orcid":true,"given":"Prabin","family":"Bajgain","sequence":"first","affiliation":[{"name":"USDA-ARS United States Dairy Forage Research Center","place":["Madison, Wisconsin, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob M.","family":"Jungers","sequence":"additional","affiliation":[{"name":"University of Minnesota","place":["St. Paul, Minnesota, United States of America"],"department":["Department of Agronomy and Plant Genetics"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James A.","family":"Anderson","sequence":"additional","affiliation":[{"name":"University of Minnesota","place":["St. Paul, Minnesota, United States of America"],"department":["Department of Agronomy and Plant Genetics"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,2]]},"reference":[{"key":"pone.0357452.ref001","volume-title":"Grasses of the Soviet Union (Russian Translations Series, 8) Hardcover","author":"NN 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Assessing the potential of genomic selection to improve yield and persistence in white clover. Massey University. 2020. http:\/\/hdl.handle.net\/10179\/16246"},{"key":"pone.0357452.ref024","doi-asserted-by":"crossref","first-page":"108856","DOI":"10.1016\/j.agee.2023.108856","article-title":"Is interannual grain yield decline of intermediate wheatgrass influenced by management and climate in the Upper Midwest?","volume":"362","author":"X Zhen","year":"2024","journal-title":"Agriculture, Ecosystems & Environment"},{"issue":"4","key":"pone.0357452.ref025","doi-asserted-by":"crossref","DOI":"10.1002\/csc2.70126","article-title":"Genetic characterization of trait architecture in multi\u2011population half\u2010sib families of the perennial crop intermediate wheatgrass","volume":"65","author":"P Bajgain","year":"2025","journal-title":"Crop Science"},{"issue":"7","key":"pone.0357452.ref026","doi-asserted-by":"crossref","first-page":"667","DOI":"10.3390\/agriculture11070667","article-title":"Multi-Allelic Haplotype-Based Association Analysis Identifies Genomic Regions Controlling Domestication Traits in Intermediate Wheatgrass","volume":"11","author":"P Bajgain","year":"2021","journal-title":"Agriculture"},{"issue":"2","key":"pone.0357452.ref027","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0032253","article-title":"Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach","volume":"7","author":"JA Poland","year":"2012","journal-title":"PLoS One"},{"key":"pone.0357452.ref028","unstructured":"Thinopyrum intermedium Genome Sequencing Consortium. Thinopyrum intermedium v3.1. https:\/\/phytozome-next.jgi.doe.gov\/info\/Tintermedium_v3_1. 2025."},{"issue":"14","key":"pone.0357452.ref029","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"16","key":"pone.0357452.ref030","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"19","key":"pone.0357452.ref031","doi-asserted-by":"crossref","first-page":"2633","DOI":"10.1093\/bioinformatics\/btm308","article-title":"TASSEL: software for association mapping of complex traits in diverse samples","volume":"23","author":"PJ Bradbury","year":"2007","journal-title":"Bioinformatics"},{"issue":"11","key":"pone.0357452.ref032","doi-asserted-by":"crossref","first-page":"2383","DOI":"10.1534\/g3.115.021667","article-title":"LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms","volume":"5","author":"D Money","year":"2015","journal-title":"G3 (Bethesda)"},{"key":"pone.0357452.ref033","unstructured":"USDA Natural Resources Conservation Service. Field Office Technical Guide Useful Conversions. https:\/\/efotg.sc.egov.usda.gov\/references\/public\/NH\/Useful_Conversions.pdf. 2026."},{"key":"pone.0357452.ref034","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v067.i01","article-title":"Fitting linear mixed-effects models using lme4","volume":"67","author":"D Bates","year":"2015","journal-title":"Journal of Statistical Software"},{"key":"pone.0357452.ref035","unstructured":"Venables WN, Ripley BD. Modern Applied Statistics with S. Fourth ed. New York, NY, USA: Springer."},{"issue":"4","key":"pone.0357452.ref036","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1016\/j.cj.2018.03.001","article-title":"Genomic selection methods for crop improvement: Current status and prospects","volume":"6","author":"X Wang","year":"2018","journal-title":"The Crop Journal"},{"issue":"6","key":"pone.0357452.ref037","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s41437-022-00539-9","article-title":"Performance of Bayesian and BLUP alphabets for genomic prediction: analysis, comparison and results","volume":"128","author":"PK Meher","year":"2022","journal-title":"Heredity (Edinb)"},{"key":"pone.0357452.ref038","volume-title":"R: A language and environment for statistical computing","author":"R Core Team","year":"2023"},{"issue":"3","key":"pone.0357452.ref039","doi-asserted-by":"crossref","first-page":"250","DOI":"10.3835\/plantgenome2011.08.0024","article-title":"Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP","volume":"4","author":"JB Endelman","year":"2011","journal-title":"The Plant Genome"},{"issue":"2","key":"pone.0357452.ref040","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1534\/genetics.114.164442","article-title":"Genome-wide regression and prediction with the BGLR statistical package","volume":"198","author":"P P\u00e9rez","year":"2014","journal-title":"Genetics"},{"issue":"6","key":"pone.0357452.ref041","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0156744","article-title":"Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer","volume":"11","author":"G Covarrubias-Pazaran","year":"2016","journal-title":"PLoS One"},{"issue":"9","key":"pone.0357452.ref042","doi-asserted-by":"crossref","first-page":"3039","DOI":"10.1534\/g3.118.200435","article-title":"BGGE: A New Package for Genomic-Enabled Prediction Incorporating Genotype \u00d7 Environment Interaction Models","volume":"8","author":"I Granato","year":"2018","journal-title":"G3 (Bethesda)"},{"issue":"12","key":"pone.0357452.ref043","doi-asserted-by":"crossref","first-page":"3813","DOI":"10.1534\/g3.118.200740","article-title":"Multi-environment Genomic Prediction of Plant Traits Using Deep Learners With Dense Architecture","volume":"8","author":"A Montesinos-L\u00f3pez","year":"2018","journal-title":"G3 (Bethesda)"},{"key":"pone.0357452.ref044","unstructured":"de los Campos G, Gr\u00fcneberg A. MTM Package. http:\/\/quantgen.github.io\/MTM\/vignette.html"},{"issue":"10","key":"pone.0357452.ref045","doi-asserted-by":"crossref","first-page":"932","DOI":"10.3390\/agriculture11100932","article-title":"Development of a Genomic Prediction Pipeline for Maintaining Comparable Sample Sizes in Training and Testing Sets across Prediction Schemes Accounting for the Genotype-by-Environment Interaction","volume":"11","author":"R Persa","year":"2021","journal-title":"Agriculture"},{"issue":"12","key":"pone.0357452.ref046","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btu279","article-title":"Cross-study validation for the assessment of prediction algorithms","volume":"30","author":"C Bernau","year":"2014","journal-title":"Bioinformatics"},{"issue":"5","key":"pone.0357452.ref047","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.2135\/cropsci2009.11.0662","article-title":"Plant Breeding with Genomic Selection: Gain per Unit Time and Cost","volume":"50","author":"EL Heffner","year":"2010","journal-title":"Crop Science"},{"key":"pone.0357452.ref048","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/bs.agron.2019.05.001","article-title":"Chapter Four - A practical guide to genetic gain.","author":"JE. 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