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This study aimed to estimate heritability (<jats:italic>h<\/jats:italic>\n<jats:sup>2<\/jats:sup>) and test the applicability of GS and GWAS for milk production, body conformation and novel heat tolerance traits using single test day phenotypic data. Thirty\u2010two SDFs located in either the north (a lowland vs. a highland) or the south (a lowland vs. a highland) of Vietnam were each visited for an afternoon and the next morning to collect phenotype data of all lactating cows (<jats:italic>n<\/jats:italic>\u2009=\u2009345). Tail hair from each cow was sampled for subsequent genotyping with a 50K SNP chip at that same visit. Milk production traits (single\u2010test day) were milk yield (MILK, kg\/cow\/day), energy corrected milk yield adjusted for body weight (ECMbw, kg\/100 kg BW\/day), fat (mFA, %), protein (mPR, %) and dry matter (mDM, %). Conformation traits were body weight (BW, kg) and body condition score (BCS, 1\u2009=\u2009thin to 5\u2009=\u2009obese). Heat tolerance traits were panting score (PS, 0\u2009=\u2009normal to 4.5\u2009=\u2009extremely heat\u2010stressed) and infrared temperatures (IRTs, \u00b0C) at 11 areas on the external body surface of the cow (inner vulval lip, outer vulval surface, inner tail base surface, ocular area, muzzle, armpit area, paralumbar fossa area, fore udder, rear udder, forehoof and hind hoof), assessed by an Infrared Camera. Univariate linear mixed models and a 10\u2010fold cross\u2010validation approach were applied for GS. Univariate single SNP mixed linear models were applied for the GWAS. Estimated <jats:italic>h<\/jats:italic>\n<jats:sup>2<\/jats:sup> (using the genotype information to build relationships among animals) were moderate (0.20\u20130.37) for ECMbw, mFA, mPR, mRE, BW, BCS and IRT at rear udder; low (0.08\u20130.19) for PS and other IRTs; and very low (\u2264\u20090.07) for MILK, ECM and mDM. Accuracy of genomic estimated breeding values (GEBVs) was low (\u2264\u20090.12) for MILK, ECM, mDM and IRT at hind hoof; and moderate to high (0.32\u20130.46) for all other traits. The most significant regions on chromosomes (BTA) associated with milk production traits were 0.47\u20131.18\u2009Mb on BTA14. Moderate to high <jats:italic>h<\/jats:italic>\n<jats:sup>2<\/jats:sup> and moderate accuracies of GEBVs for mFA, mPR, ECMbw, BCS, BW, PS and IRTs at rear udder and outer vulval surface suggested that GS using single test day phenotypic data could be applied for these traits. However, a greater sample size is required to decrease the bias of GEBVs by GS and increase the power of detecting significant quantitative trait loci (QTLs) by GWAS.<\/jats:p>","DOI":"10.1111\/jbg.12907","type":"journal-article","created":{"date-parts":[[2024,10,27]],"date-time":"2024-10-27T11:15:36Z","timestamp":1730027736000},"page":"322-341","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Genomic Prediction and Genome\u2010Wide Association Studies for Productivity, Conformation and Heat Tolerance Traits in Tropical Smallholder Dairy Cows"],"prefix":"10.1111","volume":"142","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4083-0872","authenticated-orcid":false,"given":"Nguyen N.","family":"Bang","sequence":"first","affiliation":[{"name":"School of Veterinary Science The University of Queensland  Gatton Queensland Australia"},{"name":"Faculty of Animal Science Vietnam National University of Agriculture  Hanoi Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5606-3970","authenticated-orcid":false,"given":"Ben J.","family":"Hayes","sequence":"additional","affiliation":[{"name":"Queensland Alliance for Agriculture and Food Innovation The University of Queensland  St Lucia Queensland Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Russell E.","family":"Lyons","sequence":"additional","affiliation":[{"name":"School of Veterinary Science The University of Queensland  Gatton Queensland Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7224-191X","authenticated-orcid":false,"given":"Imtiaz A. 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