Single-step genome-wide association studies (GWAS) and post-GWAS analyses to identify genomic regions and candidate genes for milk yield in Brazilian Girolando cattle

Pamela I. Otto, Simone E.F. Guimarães, Mario P.L. Calus, Jeremie Vandenplas, Marco A. Machado, João Cláudio C. Panetto, Marcos Vinícius G.B. da Silva*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Milk production is economically important to the Brazilian agribusiness, and the majority of the country's milk production derives from Girolando (Gir × Holstein) cows. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with 305-d milk yield (305MY) in Girolando cattle. In addition, we investigated the SNP-specific variances for Holstein and Gir breeds of origin within the sequence of candidate genes. A single-step genomic BLUP procedure was used to identify QTL associated with 305MY, and the most likely candidate genes were identified through follow-up analyses. Genomic breeding values specific for Holstein and Gir were estimated in the Girolando animals using a model that uses breed-specific partial relationship matrices, which were converted to breed of origin SNP effects. Differences between breed of origin were evaluated by comparing estimated SNP variances between breeds. From 10 genome regions explaining most additive genetic variance for 305MY in Girolando cattle, 7 candidate genes were identified on chromosomes 1, 4, 6, and 26. Within the sequence of these 7 candidate genes, Gir breed of origin SNP alleles showed the highest genetic variance. These results indicated QTL regions that could be further explored in genomic selection panels and which may also help in understanding the gene mechanisms involved in milk production in the Girolando breed.

Original languageEnglish
Pages (from-to)10347-10360
Number of pages14
JournalJournal of Dairy Science
Volume103
Issue number11
DOIs
Publication statusPublished - Nov 2020

Keywords

  • breed of origin of alleles model
  • breed origin effect
  • gene network
  • tropical dairy cattle

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