Genome-Wide Association Study for Indicator Traits of Sexual Precocity in Nellore Cattle

Abstract

The objective of this study was to perform a genome-wide association study (GWAS) to detect chromosome regions associated with indicator traits of sexual precocity in Nellore cattle. Data from Nellore animals belonging to farms which participate in the DeltaGen® and Paint® animal breeding programs, were used. The traits used in this study were the occurrence of early pregnancy (EP) and scrotal circumference (SC). Data from 72,675 females and 83,911 males with phenotypes were used; of these, 1,770 females and 1,680 males were genotyped. The SNP effects were estimated with a single-step procedure (WssGBLUP) and the observed phenotypes were used as dependent variables. All animals with available genotypes and phenotypes, in addition to those with only phenotypic information, were used. A single-trait animal model was applied to predict breeding values and the solutions of SNP effects were obtained from these breeding values. The results of GWAS are reported as the proportion of variance explained by windows with 150 adjacent SNPs. The 10 windows that explained the highest proportion of variance were identified. The results of this study indicate the polygenic nature of EP and SC, demonstrating that the indicator traits of sexual precocity studied here are probably controlled by many genes, including some of moderate effect. The 10 windows with large effects obtained for EP are located on chromosomes 5, 6, 7, 14, 18, 21 and 27, and together explained 7.91% of the total genetic variance. For SC, these windows are located on chromosomes 4, 8, 11, 13, 14, 19, 22 and 23, explaining 6.78% of total variance. GWAS permitted to identify chromosome regions associated with EP and SC. The identification of these regions contributes to a better understanding and evaluation of these traits, and permits to indicate candidate genes for future investigation of causal mutations.

Rewiring of gene expression in circulating white blood cells is associated with pregnancy outcome in heifers (Bos taurus)

“…For instance, prevalence of infertility may reach 16% 2 and 15% 3 in humans and beef female calves, respectively. Similar to what has been observed in humans 4 , the genetic architecture of fertility in beef heifers is very complex 5,6,7,8,9,10,11,12 . In line with this complexity, female reproductive traits have low heritability.…”

“…The examination of the genetic components of fertility in beef heifers have yielded several genes potentially associated with fertility traits 5,6,7,8,9,10,11,12 , but the effect of these markers are minimal, and there is no clear redundancy in genetic markers identified across breeds. Beyond the genomic profiling, the analysis of multiple layers of an individual’s molecular blueprint is likely key for understanding the underlying biology of complex traits 29 .…”

Genome-wide association study provides strong evidence of genes affecting the reproductive performance of Nellore beef cows

“…Failure in this stage can result in a non-viable pregnancy, a fact that would explain this association. Genes associated with male fertility [32, 36, 37, 56] were also found within the top 20 windows ( CIB4 , UCN , and PGAM1 ), a finding that would explain the genetic correlation between male and female reproductive traits as reported by Irano et al [11]. Another possible explanation is that sperm quality influences pregnancy success.…”

A combination of nutrition and genetics is able to reduce age at puberty in Nelore heifers to below 18 months

“…Our second hypothesis was not accepted because 100% of the heifers from sires with low EPD for age at first calving reached puberty before 36 months of age, whereas only 38% of heifers from sires with high EPD for age at first calving reached puberty at the same age. Irano et al (2016) suggested that the genetic control of puberty is susceptible to a pattern of complex polygenic inheritance. Several researchers attempted to identify the physiological processes that lead to this difference, and it seems that puberty onset is controlled by the hypothalamus.…”