Genome-Wide Association Study of Meat Quality Traits in Nellore Cattle

<div><p>The objective of this study was to identify genomic regions that are associated with meat quality traits in the Nellore breed. Nellore steers were finished in feedlots and slaughtered at a commercial slaughterhouse. This analysis included 1,822 phenotypic records of tenderness and 1,873 marbling records. After quality control, 1,630 animals genotyped for tenderness, 1,633 animals genotyped for marbling, and 369,722 SNPs remained. The results are reported as the proportion of variance explained by windows of 150 adjacent SNPs. Only windows with largest effects were considered. The genomic regions were located on chromosomes 5, 15, 16 and 25 for marbling and on chromosomes 5, 7, 10, 14 and 21 for tenderness. These windows explained 3,89% and 3,80% of the additive genetic variance for marbling and tenderness, respectively. The genes associated with the traits are related to growth, muscle development and lipid metabolism. The study of these genes in Nellore cattle is the first step in the identification of causal mutations that will contribute to the genetic evaluation of the breed.</p></div

Genomic association for sexual precocity in beef heifers using pre-selection of genes and haplotype reconstruction

<div><p>Reproductive traits are of the utmost importance for any livestock farming, but are difficult to measure and to interpret since they are influenced by various factors. The objective of this study was to detect associations between known polymorphisms in candidate genes related to sexual precocity in Nellore heifers, which could be used in breeding programs. Records of 1,689 precocious and non-precocious heifers from farms participating in the Conexão Delta G breeding program were analyzed. A subset of single nucleotide polymorphisms (SNP) located in the region of the candidate genes at a distance of up to 5 kb from the boundaries of each gene, were selected from the panel of 777,000 SNPs of the High-Density Bovine SNP BeadChip. Linear mixed models were used for statistical analysis of early heifer pregnancy, relating the trait with isolated SNPs or with haplotype groups. The model included the contemporary group (year and month of birth) as fixed effect and parent of the animal (sire effect) as random effect. The fastPHASE® and GenomeStudio® were used for reconstruction of the haplotypes and for analysis of linkage disequilibrium based on r² statistics. A total of 125 candidate genes and 2,024 SNPs forming haplotypes were analyzed. Statistical analysis after Bonferroni correction showed that nine haplotypes exerted a significant effect (p<0.05) on sexual precocity. Four of these haplotypes were located in the Pregnancy-associated plasma protein-A2 gene (<i>PAPP-A2)</i>, two in the Estrogen-related receptor gamma gene <i>(ESRRG)</i>, and one each in the Pregnancy-associated plasma protein-A gene <i>(PAPP-A)</i>, Kell blood group complex subunit-related family <i>(XKR4)</i> and <i>mannose-binding lectin genes (MBL-1)</i> genes. Although the present results indicate that the <i>PAPP-A2</i>, <i>PAPP-A</i>, <i>XKR4</i>, <i>MBL-1</i> and <i>ESRRG</i> genes influence sexual precocity in Nellore heifers, further studies are needed to evaluate their possible use in breeding programs.</p></div

Manhattan plot of additive genetic variance explained by windows of 150 adjacent SNPs for Marbling.

<p>Manhattan plot of additive genetic variance explained by windows of 150 adjacent SNPs for Marbling.</p

Descriptive statistics and heritability (h²) estimates of meat quality traits in Nellore cattle.

<p>Descriptive statistics and heritability (h²) estimates of meat quality traits in Nellore cattle.</p

Chromosome (Chr), location, identification of genes and proportion of variance (VAR) explained by windows with largest effects on tenderness^a.

<p>Chromosome (Chr), location, identification of genes and proportion of variance (VAR) explained by windows with largest effects on tenderness<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157845#t003fn001" target="_blank">^a</a>.</p

Chromosome (Chr), location, identification of genes and proportion of variance (VAR) explained by windows with largest effects on marbling^a.

<p>Chromosome (Chr), location, identification of genes and proportion of variance (VAR) explained by windows with largest effects on marbling<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157845#t002fn001" target="_blank">^a</a>.</p

Frequency, average effect, and respective standard error of the haplotype alleles located in the <i>MBL-1</i> gene.

<p>Frequency, average effect, and respective standard error of the haplotype alleles located in the <i>MBL-1</i> gene.</p

Frequency, average effect, and respective standard error of haplotype alleles located in the <i>PAPP-A</i> gene.

<p>Frequency, average effect, and respective standard error of haplotype alleles located in the <i>PAPP-A</i> gene.</p

Frequency, average effect, and respective standard error of haplotype alleles located in the <i>XKR4</i> gene.

<p>Frequency, average effect, and respective standard error of haplotype alleles located in the <i>XKR4</i> gene.</p