Multi-Trait GWAS and new candidate genes annotation for growth curve parameters in Brahman cattle

Understanding the genetic architecture of beef cattle growth cannot be limited simply to the genome-wide association study (GWAS) for body weight at any specific ages, but should be extended to a more general purpose by considering the whole growth trajectory over time using a growth curve approach. For such an approach, the parameters that are used to describe growth curves were treated as phenotypes under a GWAS model. Data from 1,255 Brahman cattle that were weighed at birth, 6, 12, 15, 18, and 24 months of age were analyzed. Parameter estimates, such as mature weight (A) and maturity rate (K) from nonlinear models are utilized as substitutes for the original body weights for the GWAS analysis. We chose the best nonlinear model to describe the weight-age data, and the estimated parameters were used as phenotypes in a multi-trait GWAS. Our aims were to identify and characterize associated SNP markers to indicate SNP-derived candidate genes and annotate their function as related to growth processes in beef cattle. The Brody model presented the best goodness of fit, and the heritability values for the parameter estimates for mature weight (A) and maturity rate (K) were 0.23 and 0.32, respectively, proving that these traits can be a feasible alternative when the objective is to change the shape of growth curves within genetic improvement programs. The genetic correlation between A and K was -0.84, indicating that animals with lower mature body weights reached that weight at younger ages. One hundred and sixty seven (167) and two hundred and sixty two (262) significant SNPs were associated with A and K, respectively. The annotated genes closest to the most significant SNPs for A had direct biological functions related to muscle development (RAB28), myogenic induction (BTG1), fetal growth (IL2), and body weights (APEX2); K genes were functionally associated with body weight, body height, average daily gain (TMEM18), and skeletal muscle development (SMN1). Candidate genes emerging from this GWAS may inform the search for causative mutations that could underpin genomic breeding for improved growth rates

Study of inbreeding and population structure of meat quail population under selection

Objetivou-se, com este trabalho, fazer um estudo da estrutura da população, bem como uma análise da tendência genética e avaliação do efeito da endogamia sobre características de crescimento e produção de ovos de duas linhagens de codornas de corte submetidas a seleção por peso. Foi utilizado um banco de dados das linhagens,UFV1 e UFV2, provenientes do programa de melhoramento genético de codornas de corte da Universidade Federal de Viçosa. Para cálculo da endogamia e estrutura de população através do programa Endog, foram utilizadas 11 gerações da UFV1, totalizando 12.965 animais, e 17 gerações da UFV2, totalizando 18.373 animais. Os valores genéticospara as características de crescimento e produção foram preditos através do programa WOMBAT, usando um modelo bicaracterística. As características foram peso ao nascimento (P1), peso aos 28 dias (P28), peso médio do ovo até 112 dias(POM112), número de ovos até 112 dias (NO112) e massa de ovos até 112 dias (MO112).Para estudo de tendência genética foi testada regressão linear e quadrática do valor genético em função das gerações avaliadas. Para estudo do efeito da endogamia sobre as características, foram testadas regressões linear e quadrática do valor genético das características avaliadas em função da taxa de endogamia (F%). A significância das regressões obtidas, utilizando o programa SAS, foi avaliada ao nível de 5% de probabilidade. Para a linhagem UFV1, a taxa de endogamia média foi 0,79% e tamanho efetivo de população 330,18.Para a linhagem UFV2, o coeficiente de endogamia médio foi 1,85% e o tamanho efetivo 194,58. A endogamia média em função das gerações apresentou efeito quadrático para as duas linhagens. O valor genético em função das gerações apresentou efeito quadrático para todas as características e linhagens. O valor genético em função da taxa de endogamia apresentou efeito quadrático para todas as características e linhagens. O ganho genético obtido com a seleção foi superior às perdas por depressão endogâmica. Animais com endogamia superior a 13% sofreram efeitos da depressão endogâmica para P1, P28 e POM112.The objective of this study was to analyse the structure of population, genetic tendency and evaluate the effect of inbreeding ongrowth and production traits of meat type quail selected by weigth. Strains UFV1 and UFV2, from Universidade Federal de Viçosa, was used to calculate inbreeding coefficient (F) and effective population size (Ne), totalizing 12.965 animals and 11generations from UFV1 and 18.273 animals and 17 generations from UFV2. The software Endog was used to calculate the genetic structure of population. The software Wombat was used to predict breeding values for growth and production traits using a bicharacteristicmodel. Traits were birth weight (P1), body weight at 28 days (P28), average egg weight up to 112 days of age (POM112), number of eggs up to 112 days (NO112) and egg mass up to 112 days (MO112).Also, general linear models (GLM) were used to analyze effects of generation on genetic value and the effects of inbreeding on genetic value traits. All regressions was tested for significance (P < 0.05) using the software SAS. The UFV1 strain showed an average F of 0,79% and Ne 330,18. UFV2 strain showed an average F of 1,85% and Ne 194,58. The effect of generations on inbreeding and effect of generations on average of genetic value was quadratic, for both strains. The inbreeding presented a quadratic effect on genetic value, for all traits and strains. The genetic gain with body weight selection was superior to losses by inbreeding depression. Animals with inbreeding over than 13% have suffered the effects of inbreeding depression for P1, P28 and POM112.Conselho Nacional de Desenvolvimento Científico e Tecnológic

Canonical correlation analysis applied to production and reproduction traits of meat type quails

ABSTRACT: Data from 629 meat type quails were used to study association between two different sets of traits: egg production and reproduction. Traits related to reproduction were: body weight at 42 days (W42), average egg weight (AEW), age at sexual maturity (ASM); and production traits: number of eggs produced from 42 until 182th day considering intervals of 35 days each period (P1, P2, P3 and P4). Canonical correlations were used to describe the association between these two sets of traits. The canonical coefficients indicated that egg production and reproductive traits were moderately related (0.3475). The first partial period of production (P1) and age at sexual maturity were the most relevant traits among the analyzed variables. Results show that selecting animals with lower age at sexual maturity might lead to an increase on number of eggs produced until 77 days, although it might also lead to a decrease on egg weight. Breeding programs aiming to improve quails production should consider selection strategies to decrease age at sexual maturity and then, as correlated response, increased egg production might be observed

Genetic evaluation for egg mass in partial periods and complete period in meat quails

The objective of this study was to obtain estimates of genetic and phenotypic parameters for egg mass of meat quails and also to propose an optimal age for selection of birds through the egg mass. The data used in this study came from 3,503 female meat quails (UFV1: 1.811 quails; UFV2: 1.692 quails) of the Poultry Breeding Program from Universidade Federal de Viçosa. The traits examined were egg mass in partial periods until 77, 112, 147 and 182 days, and egg mass in the total period of 407 days by the use of single and bi-trait animal models. For the genetic group UFV1, the heritability values for the periods were high: 0.58, 0.59, 0.57, 0.59 and 0.24 (until 77, 112, 147,182 and 407 days, respectively). The values of genetic correlations were medium, ranging from 0.51 (77 and 407 days) to 0.61 (112 and 407, 147 and 407 days). For the genetic group UFV2, the estimates of heritability were of low magnitude: 0.05, 0.03, 0.04, 0.05, and 0.11 (until 77, 112, 147, 182, and 407 days, respectively). The values for genetic correlation ranged from 0.61 (112 and 407 days) to 0.93 (77 and 407 days). For the genetic group UFV1, the second partial period (112 days) for selection of meat quails using the egg mass trait is recommended, due to a higher value of heritability and a higher value of genetic correlation with the total and relative efficiency close to the unity in this period. In the genetic group UFV2, the first partial period (77 days) is indicated, since it had a higher estimation of genetic correlation and a higher relative efficiency. The choice of these partial periods reduces the generation interval, increasing the intensity of selection and an increase in genetic gain per unit of time

Genetic parameters for egg production in meat quails through partial periods

ABSTRACT: We estimated genetic and phenotypic parameters for egg production in meat-type quails aiming to propose an optimal age for selection through partial record egg production. Data of 3,503 female quails from two strains (namely, UFV1, with 1,811 and UFV2 with 1,692 females) were used. Egg production was assessed by the number of eggs recorded after 42 days of age and each partial period consisted on 35 days of egg production forward. Covariance components were estimated by using single and bivariate animal model, comprising each partial period of egg production and full egg production period (one year of egg laying). Regarding strain UFV1, heritability estimates ranges from 0.03 to 0.16, and for strain UFV2 0.20 to 0.25. The highest genetic correlation with full egg production was with second period (0.64) for strain UFV1 and with third period (0.47) for UFV2. Therefore, animal selection based on egg production until 112 days for the strain UFV1 and 147 days for the strain UFV2 provided increased genetic gain by reducing generation interval

Estimated growth curves based on the Brody nonlinear model for genotypes of the most significant SNPs for maturity rate (BovineHD2000000873).

<p>Estimated growth curves based on the Brody nonlinear model for genotypes of the most significant SNPs for maturity rate (BovineHD2000000873).</p

Means and standard deviations for the parameter estimates, and goodness of fit(GOF) results based on convergence rate (C%), adjusted coefficient of determination (R²); mean square error (MSE); mean-absolute deviation for periods 1 (until 12 months–MAD₁) and 2 (older than 12 months–MAD₂), and Akaike's information criterion (AIC).

<p>Means and standard deviations for the parameter estimates, and goodness of fit(GOF) results based on convergence rate (C%), adjusted coefficient of determination (R²); mean square error (MSE); mean-absolute deviation for periods 1 (until 12 months–MAD₁) and 2 (older than 12 months–MAD₂), and Akaike's information criterion (AIC).</p

Manhattan plots for the growth curve parameter maturity rate (K) in Brahman cattle.

<p>Chromosomes 1 to 29 and X are shown, separated by alternating colors. The corresponding horizontal lines indicate the genome-wide significance levels for both traits.</p