Seleção e associação genômica para precocidade sexual em bovinos da raça Nelore

The objective of this study was to perform genome-wide association to detect chromosomal regions associated with indicator traits of sexual precocity of Nellore cattle, and evaluating methodologies for prediction of genomic values to use for selection of these traits. Data from Nellore animals belonging to farms integrating animal breeding programs of DeltaGen® and Paint® (CRV Lagoa), were used. Age at first calving (AFC), the occurrence of early pregnancy of heifers (EP) and scrotal circumference (SC) were used as traits associated with sexual precocity. After quality control and consistency of phenotypic data, information of 68,170; 72,675 and 83,911 animals with phenotype, and of 1,738; 1,770 and 1,680 genotypes for AFC, EP and SC, respectively, and 412,993 SNPs, remained for analysis. In chapter 2, the estimates of the SNP effects were obtained using the single-step method (WssGBLUP). All animals were used applying single trait animal model to predict the genetic values and, subsequently, the solutions of the SNP effects were obtained from these genetic values. The 10 windows of 150 SNPs that captured the greatest proportion of variance explained by markers were identified. The 10 windows with greater effect 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 on chromosomes 4, 8, 11, 13, 14, 19, 22 and 23, explaining 6.78% of the total variance. With GWAS analysis it was possible to identify chromosomal regions associated with EP and SC. Identifying these regions enables better understanding and evaluation of these traits, besides indicating candidate genes for future research studies of causal mutations. In Chapter 3, two multi-step methods were used to estimate the marker effects - GBLUP and IBLASSO; besides the single-step method (ssGBLUP). Observed phenotype was used as the dependent variable to estimate the genomic value ...Objetivou-se com este estudo realizar associação genômica ampla, visando detectar regiões cromossômicas associadas a características indicadoras de precocidade sexual de bovinos da raça Nelore, bem como avaliar metodologias para a predição de valores genômicos visando à seleção destas características. Foram utilizados dados de animais da raça Nelore, pertencentes a fazendas que integram os programas de melhoramento genético da DeltaGen® e Paint® (CRV Lagoa). As características associadas à precocidade sexual utilizadas neste estudo foram a idade ao primeiro parto (IPP), a ocorrência de prenhez precoce de novilhas (P16) e o perímetro escrotal (PE). Após o controle de qualidade e consistência dos dados fenotípicos, permaneceram para as análises informações de 68.170, 72.675 e 83.911 animais com fenótipo e de 1.738, 1.770 e 1.680 animais genotipados para IPP, P16 e PE, respectivamente, e 412.993 SNPs. No Capítulo 2, as estimativas dos efeitos dos SNPs foram obtidas utilizando-se a metodologia single-step (WssGBLUP). Todos os animais foram utilizados aplicando-se modelo animal unicaracterística para predizer os valores genéticos e, posteriormente, as soluções dos efeitos dos SNPs foram obtidas a partir destes valores genéticos. Foram identificadas as 10 janelas de 150 SNPs que capturaram a maior proporção da variância explicada pelos marcadores. As 10 janelas de maior efeito obtidas para a P16 estão localizadas nos cromossomos 5, 6, 7, 14, 18, 21 e 27 e somadas explicaram 7,91% da variância genética total. Para o PE, estas janelas estão nos cromossomos 4, 8, 11, 13, 14, 19, 22 e 23, explicando 6,78% da variância total. Com as análises de GWAS foi possível identificar regiões cromossômicas associadas com P16 e PE. A identificação dessas regiões possibilita o melhor entendimento e avaliação destas características, além de indicar genes candidatos para estudos futuros de investigação de..

Genome-wide association study of reproductive traits in Nellore heifers using Bayesian inference

An important goal of Zebu breeding programs is to improve reproductive performance. A major problem faced with the genetic improvement of reproductive traits is that recording the time for an animal to reach sexual maturity is costly. Another issue is that accurate estimates of breeding values are obtained only a long time after the young bulls have gone through selection. An alternative to overcome these problems is to use traits that are indicators of the reproductive efficiency of the herd and are easier to measure, such as age at first calving. Another problem is that heifers that have conceived once may fail to conceive in the next breeding season, which increases production costs. Thus, increasing heifer's rebreeding rates should improve the economic efficiency of the herd. Response to selection for these traits tends to be slow, since they have a low heritability and phenotypic information is provided only later in the life of the animal. Genome-wide association studies (GWAS) are useful to investigate the genetic mechanisms that underlie these traits by identifying the genes and metabolic pathways involved. Data from 1853 females belonging to the Agricultural Jacarezinho LTDA were used. Genotyping was performed using the BovineHD BeadChip (777 962 single nucleotide polymorphisms (SNPs)) according to the protocol of Illumina - Infinium Assay II ® Multi-Sample HiScan with the unit SQ ™ System. After quality control, 305 348 SNPs were used for GWAS. Forty-two and 19 SNPs had a Bayes factor greater than 150 for heifer rebreeding and age at first calving, respectively. All significant SNPs for age at first calving were significant for heifer rebreeding. These 42 SNPs were next or within 35 genes that were distributed over 18 chromosomes and comprised 27 protein-encoding genes, six pseudogenes and two miscellaneous noncoding RNAs. The use of Bayes factor to determine the significance of SNPs allowed us to identify two sets of 42 and 19 significant SNPs for heifer rebreeding and age at first calving, respectively, which explain 11.35 % and 6.42 % of their phenotypic variance, respectively. These SNPs provide relevant information to help elucidate which genes affect these traits

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

<div><p>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.</p></div

Manhattan plot for scrotal circumference (SC) in Nellore cattle.

<p>The y-axis shows the proportion of variance explained by the windows of 150 SNPs and the x-axis indicates the chromosome number.</p

Identification of genes within the 10 windows of 150 SNPs that explained the highest proportion of genetic variance for scrotal circumference in Nellore cattle.

<p>Identification of genes within the 10 windows of 150 SNPs that explained the highest proportion of genetic variance for scrotal circumference in Nellore cattle.</p

Manhattan plot for the occurrence of early pregnancy (EP) in Nellore cattle.

<p>The y-axis shows the proportion of variance explained by the windows of 150 SNPs and the x-axis indicates the chromosome number.</p