Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil

Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (N_e), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, N_e, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low N_e values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.

Genomic evaluation for novel stayability traits in Nellore cattle

Cow stayability plays a major role on the overall profitability of the beef cattle industry, as it is directly related to reproductive efficiency and cow's longevity. Stayability (STAY63) is usually defined as the ability of the cow to calve at least three times until 76 months of age. This is a late-measured and lowly heritable trait, which consequently constrains genetic progress per time unit. Thus, the use of genomic information associated with novel stayability traits measured earlier in life will likely result in higher prediction accuracy and faster genetic progress for cow longevity. In this study, we aimed to compare pedigree-based and single-step GBLUP (ssGBLUP) methods as well as to estimate genetic correlations between the proposed stayability traits: STAY42, STAY53 and STAY64, which are measured at 52, 64 and 76 months of cow's age, considering at least 2, 3 and 4 calving, respectively. ssGBLUP yielded the highest prediction accuracy for all traits. The heritability estimates for STAY42, STAY53, STAY63 and STAY64 were 0.090, 0.151, 0.152 and 0.143, respectively. The genetic correlations between traits ranged from 0.899 (STAY42 and STAY53) to 0.985 (STAY53 and STAY63). The high genetic correlation between STAY42 and STAY53 suggests that besides being related to cow longevity, STAY53 is also associated with the early-stage reproductive efficiency. Thus, STAY53 is recommended as a suitable selection criterion for reproductive efficiency due to its higher heritability, favourable genetic correlation with other traits, and measured earlier in life, compared with the conventional stayability trait, that is STAY63.

PARÂMETROS E TENDÊNCIAS GENÉTICAS PARA CARACTERÍSTICAS PRODUTIVAS DE BOVINOS DA RAÇA NELORE

Resumo A região Centro-Oeste tem se destacado como produtora de carne bovina e, para tanto, produzir com eficiência tem sido a meta dos produtores. Nesse sentido, objetivou-se estimar parâmetros e tendências genéticas para pesos aos 240 (P240) e 420 (P420) dias de idade em bovinos da raça Nelore, criados na região de Goiás, Brasil. Utilizaram-se 48.580 dados para P240 e 28.685 para P420. Os parâmetros genéticos foram obtidos por análises univariadas em que o modelo continha os efeitos fixos de grupo de contemporâneos (estação de nascimento - águas e seca -, ano de nascimento, sexo e fazenda) e a covariável idade da vaca. Como efeito aleatório, utilizou-se o efeito aditivo direto e materno para P240 e apenas direto para P420. As tendências genéticas foram obtidas por meio da análise de regressão do valor genético do animal sobre ano de nascimento. Os resultados obtidos de herdabilidade direta foram 0,15 ± 0,02 para P240 e 0,24 ± 0,00 para P420. O ganho genético anual foi de 0,274 kg para P240 e de 0,506 kg P420. Os resultados indicam a possibilidade de se obterem maiores ganhos genéticos por meio da seleção, que está sendo mais eficiente sobre o P420.

Genetic analyses on bodyweight, reproductive, and carcass traits in composite beef cattle

In beef cattle, growth, reproductive, and carcass traits have been studied for improving productivity and quality of meat products. The aim of this study was to estimate genetic parameters for birth (BW), weaning (WW) and yearling (YW) weights, scrotal circumferences at weaning (SCW) and yearling (SCY), age at first calving (AFC), ribeye area (REA) and back fat thickness (BFT) in order to provide support for the evaluation program of the composite Canchim breed. Data on 12 967 (BW), 7481 (WW), 5131 (YW), 1447 (SCW), 1224 (SCY), 1400 (AFC), and 2082 (REA and BFT) animals were analysed using the Average Information Restricted Maximum Likelihood method under an animal model (single and multi-trait analyses). A substantial proportion of the variation in the bodyweights, scrotal circumferences and carcass traits was associated with the additive genetic term indicating that these traits may respond to the selection process. For AFC, a low heritability estimate was observed. Genetic correlations among bodyweights varied from 0.41 to 0.93. The genetic correlation among scrotal circumferences was 0.91. Important genetic correlations among YW, SCW, and SCY with AFC were observed (–0.48, –0.61, and –0.71, respectively), indicating that indirect responses to selection for these traits would be expected in the age of which the heifers calve. Furthermore, BFT presented an interesting result with calving performance due to the genetic correlation (–0.69) with AFC. Post-weaning weights showed moderate genetic correlations with REA. Many of the traits considered in the genetic evaluation of this breed are genetically correlated in a favourable manner. Genetic improvement through selection is expected for production, reproduction, and carcass traits in Canchim beef cattle.

Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle

High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

Divergência genética entre touros da raça Gir

Estudou-se a divergência genética entre 73 reprodutores da raça Gir, por meio de medidas de dissimilaridade, métodos de agrupamento e análises gráficas por componentes principais, com base nas diferenças esperadas em suas progênies relativas a caracteres ponderais e reprodutivos. As distâncias Euclidianas médias padronizadas obtidas foram 4,3743 entre os mais dissimilares e 0,1135 para os mais similares. Quatro grupos de reprodutores com a mesma similaridade foram obtidos por métodos de agrupamento por otimização. Os três primeiros componentes principais explicaram 82,01% da variância total, o primeiro explicou 37,09%, o segundo respondeu por 26,58% e o terceiro por 18,34% da variância. Os escores dos componentes principais possibilitaram a avaliação visual da divergência genética, por meio de gráficos de dispersão. Os resultados encontrados permitiram identificar entre os animais avaliados, os mais divergentes, recomendando que suas progênies possam ser utilizadas como genitores de acasalamentos em programas de melhoramento que visem obter bezerros com melhor desempenho que os pais.

Parâmetros e tendências genéticas para pesos de várias idades em bovinos Nelore

Objetivou-se estimar parâmetros, correlações e tendências genéticas para os pesos de animais da raça Nelore criados na região da Mata e no Agreste Nordestino aos 205 (P205), 365 (P365) e 550 (P550) dias de idade. Para realização das análises genéticas, utilizou-se da metodologia de modelos mistos. O modelo estatístico continha os efeitos aleatórios aditivos diretos, aditivos maternos, ambiente permanente e o erro; efeitos fixos de grupo contemporâneo - fazenda, sexo, estação (água e seca), mês e ano de nascimento do bezerro e a covariável idade da vaca ao parto. As tendências genéticas foram estimadas pela regressão dos valores genéticos sobre o ano de nascimento dos animais. As estimativas da herdabilidade direta foram 0,13 ± 0,03 para P205; 0,03 ± 0,02 para P365 e 0,12 ± 0,04 para P550. As correlações variaram de 0,55 a 0,85. Os parâmetros genéticos permitem ganhos por meio da seleção e, de acordo com as correlações, a seleção para peso a determinada idade possibilitará ganhos as idades posteriores, podendo assim realizar-se seleções em idades mais jovens, apesar dos ganhos serem lentos devido aos baixos coeficientes de herdabilidade.