{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T22:46:46Z","timestamp":1792450006142,"version":"4.5.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T00:00:00Z","timestamp":1790985600000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cientifico e Tecnologico","doi-asserted-by":"publisher","award":["303789\/2022-0"],"award-info":[{"award-number":["303789\/2022-0"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>This organism-independent theoretical study examines genomic evaluation of open-pollinated progeny from partially selfing species when the fitted genetic covariance contains only an additive genomic relationship matrix. Open-pollinated families contain selfed-selfed, selfed-outcrossed, and outcrossed-outcrossed sibling pairs, so their covariance must be averaged using joint pair probabilities rather than probabilities assigned to individual offspring. An offspring-level shortcut overestimates expected additive covariance whenever selfing and outcrossing coexist. Extending the pair calculation to the covariance between additive effects and dominance deviations in homozygotes gives a balanced-reference projection coefficient equal to twice the selfing rate under mating-system equilibrium and random unrelated outcrossing. When the solution is interior, this coefficient represents the exact restricted maximum-likelihood projection for balanced families with exchangeable covariance blocks. An independent Mendelian simulation with biallelic quantitative trait loci recovered the classical pair-specific coefficients without supplying them to the data-generating model and closely reproduced the theoretical coefficient, with a coefficient of determination of 0.9998 and mean absolute error of 0.0073. The additive genomic relationship matrix was constructed in a separate controlled marker simulation by VanRaden scaling, and additive-only restricted maximum-likelihood estimates closely followed the balanced-reference prediction, with a coefficient of determination of 0.9900 and mean absolute departure of 0.0107. The resulting dimensionless index and scale conversion are therefore sensitivity diagnostics rather than universal corrections for genomic evaluation designs.<\/jats:p>","DOI":"10.1093\/genetics\/iyag273","type":"journal-article","created":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T20:24:47Z","timestamp":1791059087000},"source":"Crossref","is-referenced-by-count":2,"title":["Pair-based covariance under mixed mating and its consequences for REML variance estimation"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9478-5379","authenticated-orcid":false,"given":"Evandro Vagner","family":"Tambarussi","sequence":"first","affiliation":[{"name":"Faculdade de Ci\u00eancias Agron\u00f4micas, Departamento de Produ\u00e7\u00e3o Vegetal, Universidade Estadual Paulista (UNESP) , Avenida Universit\u00e1ria, n\u00b0 3780, Botucatu, S\u00e3o Paulo 18610-034 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,3]]},"reference":[{"key":"2026101703010857100_iyag273-B1","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1038\/s41437-025-00792-8","article-title":"Quantifying genetic and genotypic gain gaps in Eucalyptus: the hidden cost of ignoring inbreeding and dominance","volume":"134","author":"Araujo","year":"2025","journal-title":"Heredity (Edinb)"},{"key":"2026101703010857100_iyag273-B2","doi-asserted-by":"publisher","first-page":"1920","DOI":"10.1111\/evo.14304","article-title":"Genetics of quantitative traits with dominance under stabilizing and directional selection in partially selfing species","volume":"75","author":"Clo","year":"2021","journal-title":"Evolution"},{"key":"2026101703010857100_iyag273-B3","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/genetics\/69.2.235","article-title":"Higher order probability functions of identity of alleles by descent","volume":"69","author":"Cockerham","year":"1971","journal-title":"Genetics"},{"key":"2026101703010857100_iyag273-B4","doi-asserted-by":"publisher","first-page":"157","DOI":"10.2307\/2530754","article-title":"Covariances of relatives stemming from a population undergoing mixed self and random mating","volume":"40","author":"Cockerham","year":"1984","journal-title":"Biometrics"},{"key":"2026101703010857100_iyag273-B5","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/s12711-018-0411-0","article-title":"Understanding the potential bias of variance components estimators when using genomic models","volume":"50","author":"Cuyabano","year":"2018","journal-title":"Genet Sel Evol"},{"key":"2026101703010857100_iyag273-B6","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1534\/g3.115.025957","article-title":"Implementation of the realized genomic relationship matrix to open-pollinated white spruce family testing for disentangling additive from nonadditive genetic effects","volume":"6","author":"Gamal El-Dien","year":"2016","journal-title":"G3 (Bethesda)"},{"key":"2026101703010857100_iyag273-B7","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1214\/aos\/1033066209","article-title":"REML estimation: asymptotic behavior and related topics","volume":"24","author":"Jiang","year":"1996","journal-title":"Ann Stat"},{"key":"2026101703010857100_iyag273-B8","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1038\/s41437-021-00450-9","article-title":"Single-step genomic prediction of Eucalyptus dunnii using different identity-by-descent and identity-by-state relationship matrices","volume":"127","author":"Jurcic","year":"2021","journal-title":"Heredity (Edinb)"},{"key":"2026101703010857100_iyag273-B9","doi-asserted-by":"publisher","first-page":"4648","DOI":"10.3168\/jds.2009-2064","article-title":"Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information","volume":"92","author":"Misztal","year":"2009","journal-title":"J Dairy Sci"},{"key":"2026101703010857100_iyag273-B10","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1007\/s11295-021-01534-7","article-title":"Genomic breeding values\u2019 prediction including populational selfing rate in an open-pollinated Eucalyptus globulus breeding population","volume":"18","author":"Quezada","year":"2022","journal-title":"Tree Genet Genomes"},{"key":"2026101703010857100_iyag273-B11","volume-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2026"},{"key":"2026101703010857100_iyag273-B12","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1534\/g3.116.037895","article-title":"Single-step BLUP with varying genotyping effort in open-pollinated Picea glauca","volume":"7","author":"Ratcliffe","year":"2017","journal-title":"G3 (Bethesda)"},{"key":"2026101703010857100_iyag273-B13","doi-asserted-by":"crossref","unstructured":"Tambarussi EV . 2026. 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