Resumo
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In beef cattle breeding programs, the study of reproductive traits in females is of great importance to meet the growing demand for meat in the world. Currently, strategies are being created that contribute to increasing the genetic gain of productive and reproductive traits, which may lead to the use of a small group of reproducers, which may increase inbreeding levels in populations. The aim of this study was (i) to identify genomic regions and biological factors that affect the heifer early calving (HC) at 24 (HC24), 26 (HC26), 28 (HC28), and 30 (HC30) months of age in Nelore cattle and (ii) to estimate inbreeding coefficients based on pedigree and genomic data on traits of economic interest. A total of 66,496 phenotypic records and 8,652 heifer genotypes for the HC24 - HC30 study were used. For the inbreeding study, 22,680 genotypes were used, the traits studied were adjusted scrotal circumference at 365 days (SC365), HC30; adjusted body weight at 210 (BW210) and 450 (BW450) days of age, ribeye area (REA); backfat thickness (BFT) and rump fat thickness (RFT). The w-ssGWAS results pointedout shared and specific window regions for HC at different ages, which varied according to their genetic correlation. These regions house key genes in the biological process of hormonal, lipid, and metabolic regulation, essential for developing bones, muscles, and reproductive organs. A total of four regions of shared windows between HC24, HC26, HC28, and HC30 were identified in BTA 5, 6, 14, and 16 harboring candidate genes with a direct effect on processes related to the control of functions associated with metabolism, endocrinology, reproduction, and aspects of growth (IGF1, UBA6, GNRHR, LYN, MOS, PLAG1, ETNK2, KISS1, and REN). The average inbreeding depression was -0.241% and -1.102% per 1% of inbreeding for linear regression coefficients scaled on the percentage of mean (m) and standard deviation (sd), respectively. The means for m (and sd) were -0.18% (-1.271%) for sexual precocity traits(SC365 and HC30); -0.37% (-0.985%) for carcass traits (REA; BFT and RFT) and -0.17% (-1.051%) for weight traits (BW120 maternal and animal and BW455). Findings showed differences in physiological processes linked to HC at different ages and metabolic processes that help the genetic control of sexually precocious Nelore heifers. Hence, inbreeding depression is more pronounced in carcass traits than in sexual precocity and weight traits. These findings highlight the need for the management of inbreeding in the breeding programmes. For all traits, long and short ROH contributed to inbreeding depression. The results obtained from inbreeding depression will allow establishing that they allow monitoring and maintaining genetic diversity, which will improve the traits that are part of the genetic improvement program of the Nelore breed.
Resumo
O conhecimento da estrutura de uma população é importante quando se deseja manter a variabilidade genética em programas de melhoramento genético. As estimativas dos parâmetros genéticos permitem identificar as características de interesse econômico que podem responder a seleção direta ou indireta. Neste trabalho, objetivou-se avaliar a estrutura genética populacional e estimar os parâmetros genéticos para as características peso corporal da fêmea na entrada (PEP) e na saída (PSP) da primeira estação de monta, idade ao primeiro parto (IPP), peso corporal da vaca ao primeiro parto (PPP), peso corporal da vaca ao primeiro desmame (PPD) e perímetro escrotal aos 378 dias (PE378) em bovinos da raça Caracu, para avaliar critérios de seleção e os procedimentos de acasalamento para manter a variabilidade genética da população. A estrutura genética da população foi avaliada pelo tamanho efetivo (Ne), número efetivo de fundadores (fe), número efetivo de ancestrais (fa), intervalos de geração, coeficiente de endogamia (F), coeficiente de parentesco médio (AR) e integridade do pedigree. Os parâmetros genéticos foram estimados pelo método de máxima verossimilhança restrita (REML) por meio de modelo animal multi-característica. Os resultados obtidos para Ne na geração máxima, completa e equivalente, foram 180,90; 57,39; e 92,38, respectivamente. O valor para fe foi de 199 e para fa de 27. O coeficiente de endogamia médio e o parentesco médio foram 2,14% e 5,72%, respectivamente. Na avaliação da integridade do pedigree foram identificados 94,83% das mães e 93,82% dos pais com registros de origem. As estimativas de herdabilidade para as características de peso corporal variaram de 0,37 ± 0,09 (PPP) a 0,46 ± 0,08 (PPD). Para as características reprodutivas, as estimativas de herdabilidade foram 0,31 ± 0,10 para PE378 e 0,10 ± 0,06 para IPP. As correlações genéticas variaram de -0,37 ± 0,30 (PE378 e IPP) a 0,94 ± 0,06 (PSP e PPP). As correlações genéticas entre os pesos corporais medidos durante o primeiro ciclo reprodutivo e IPP indicaram que a seleção visando controlar o peso corporal nesse período não irá afetar a idade ao primeiro parto. A correlação genética favorável obtida entre PE378 e IPP (-0,37±0,30) indicou que a seleção para PE378 nos machos poderá favorecer a redução de idade ao primeiro parto das fêmeas. A partir dos parâmetros populacionais, concluiu-se que a variabilidade genética da população tem sido mantida, assim como os níveis de endogâmia, em decorrência do controle dos acasalamentos no decorrer das gerações.
The knowledge of the structure of the population is important to desired to maintain genetic variability in breeding programs. The genetic parameters estimates allow identifying economic interest traits that can respond to direct or indirect selection. The goal of this study was to evaluate the population genetic structure and to estimate the genetic parameters for the body weight of the cow at the beginning (WBF) and at the end (WEF) of the first breeding season, age at first calving (AFC), body weight of cow at first calving (WFC), body weight of cow at first weaning (WFW) and scrotal circumference measured at 378 days (SC378) in Caracu beef cattle, to assess the selection criteria and to indicate mating procedures to maintain the genetic diversity of the population. The genetic structure of the population was verified of the effective population size (Ne), the effective number of the founders (fe), the effective number of the ancestors (fa), the generational intervals, the inbreeding coefficient (F), the average relatedness (AR) and of the pedigree integrity. The restricted maximum likelihood method (REML) was used to estimate the genetic parameters under multitrait animal model. The maximum, complete and equivalent generation for Ne was 180.90; 57.39 and 92.38, respectively. For the fe were 199 and for fa 27. The average of the inbreeding coefficient and the AR were 2.14% and 5.72%, respectively. The integrity of the pedigree identified was 94.83% of the dam and 93.82% of the sire with known initial records Estimates of heritability for body weight traits ranged from 0.37 ± 0.09 (WFC) to 0.46 ± 0.08 (WFW). For the reproductive traits, the heritability estimates were 0.31 ± 0.10 for SC378 and 0.10 ± 0.06 for AFC. Genetic correlations ranged from -0.37 ± 0.30 (SC378 and AFC) to 0.94 ± 0.06 (WEF and WFC). Genetic correlations between body weights measured during the first reproductive cycle and the AFC indicated that selection to control body weight in this period will not affect age at first calving. The favorable genetic correlation obtained between SC378 and AFC (-0.37 ± 0.30) indicated that selection for SC378 of males may reduce the age at first calving of females. The population parameters showed that the genetic variability of the population has been maintained, as well as the levels of the inbreeding due to the control of mating during the generations.