Estimation of Breeding Values Using Different Densities of Snp to Inform Kinship in Broiler Chickens

Background: Traditionally, breeding values are estimated based on phenotypic and pedigree information using the numerator relationship (A) matrix. With the availability of genomic information, genome-wide markers can be included in the estimation of breeding values through genomic kinship. However, the density of genomic information used can impact the cost of implementation. The aim of this study was to compare the rank, accuracy, and bias of estimated breeding values (EBV) for organs [heart (HRT), liver (LIV), gizzard (GIZ), lungs (LUN)] and carcass [breast (BRST), drumstick (DRM) and thigh (THG)] weight traits in a broiler population using pedigree-based BLUP (PBLUP) and single-step genomic BLUP (ssGBLUP) methods using various densities of SNP and variants imputed from whole-genome sequence (WGS). Results: For both PBLUP and ssGBLUP, heritability estimates varied from low (LUN) to high (fHRT, LIV, GIZ, BRST, DRM and THG.) Regression coefficients values of EBV on genomic estimated breeding values (GEBV) were similar for both the high density (HD) and WGS sets of SNPs ranging from 0.87 to 0.99 across senarios. Conclusion: Results show no benefit of using WGS data compared to HD array data using an unweighted ssGBLUP. Our results suggest that 10% of the content of the HD array can yield unbiased and accurate EBV

Análise fatorial confirmatória e genômica do perfil de ácidos graxos do leite em bovinos leiteiros criados em condições tropicais

The bovine milk fatty acid (FA) profile is one of the most complex and unique among terrestrial mammals. Its composition is extremely variable and depends on factors such as the source of the diet, the physiological state of the animal, and a fraction attributed to the genetic component. FA is mainly synthesized by the new synthesis that occurs in the mammary gland or derived from the ruminal biohydrogenation process. Recently, efforts have been made in an attempt to elucidate the main mechanisms associated with their metabolic pathways. In addition, the FA profile has been investigated as a biomarker for heat stress due to the great influence of diet on its composition. Most of these studies are carried out by analyzing genetic parameter estimation, genome-wide association study (GWAS), and in a complementary tool with enrichment analysis. However, little has been explored on approaches that can assess quantitative characteristics in a multivariate method. In this context, two studies were conducted using different strategies and objectives. The objective of this study was to estimate the genetic parameters for FA under conditions of thermal stress (decline) and without thermal stress (intercept), subsequently to compare genomic values between rankings (intercept and decline). Records of test-day milk of 7 FA (saturated FA - SFA, unsaturated FA - UFA, monounsaturated fatty acid - MUFA, polyunsaturated FA - PUFA, palmitic FA - C16:0, oleic FA - C18:0, and stearic FA - C18:1) were used in genetic analysis. The components of variance were obtained using a repeatability model with random regression of a THI function (temperature and humidity index). Saturated FA (saturated and C16:0) showed lower estimates of heritability under thermal stress conditions. C18:1 showed greater sensitivity to heat under conditions of thermal stress. Correlations between the rankings of genomic genetic values ranged from -0.27 to 0.99. Our results demonstrated an opportunity to investigate new biomarkers and improve selection processes for thermotolerance. In experiment 2, the objective was to adjust latent variables (unobservable variable) and predict factor scores to use them as a phenotype in the estimation of genetic parameters, GWAS, and enrichment analysis. The adjustments were obtained through confirmatory factor analysis (multivariate method) whose main objective is to reduce the size of the data. The set of observable variables that obtained the best fit in the model were SAT, POLI, C18: 0, and C18:1. These variables were combined into a factor that represented 3 stages of lactation (40-60; 160-180; 250-270), based on fixed intervals in days in milk (DIM) and later, were merged to represent lactation order (1 to 3) used in genetic analysis. The heritability estimates for latent variables were low (0.07 to 0.11). From the GWAS results, 11 candidate genes (PLD1, TM6SF2, NUDT7, LIPT1, AKPA1, APOH, RPGRIP1L, FTO, GMDS, ALDH3B1, and PC) were located on 9 chromosomes, mostly including genes that have not yet been discussed in the literature. In the enrichment analysis, functional terms were revealed including fatty acid synthesis, triacylglycerol synthesis, and lipid and lipoprotein metabolism. Overall, our study contributed as a design for further studies and to improve the knowledge base on the genetic mechanisms underlying the composition of FA.O perfil de ácidos graxos do leite (AGL) bovino é um dos mais complexos e únicos entre mamíferos terrestres. A sua composição é extremamente variável e dependente de fatores como fonte da dieta, estado fisiológico do animal e uma fração atribuída ao componente genético. AGL são principalmente sintetizados pela de novo síntese que ocorre na glândula mamária ou derivados do processo de biohidrogrenação ruminal. Recentemente, esforços têm sido realizados na tentativa de elucidar os principais mecanismos associados às suas vias metabólicas. Além disso, o perfil de AGL tem sido investigado como biomarcador para o estresse térmico devido a grande influência da dieta na sua composição. Esses estudos são realizados na sua maioria pela análise de estimação de parâmetros genéticos, associação genômica ampla (GWAS) e de forma complementar com análise de enriquecimento. No entanto, pouco ainda tem sido explorado sobre abordagens que possam avaliar características quantitativas de forma multivariada. Neste contexto, foram conduzidos dois estudos utilizando estratégias e objetivos diferentes. Objetivou-se, no 1 estudo, estimar os parâmetros genéticos para AGL sob condições de estresse térmico (declínio) e sem estresse térmico (intercepto), posteriormente, comparar valores genômicos entre rankings (intercepto e declínio). Dados de produção de 7 AGL (AGL saturado - SAT, ALG insaturado - INSAT, ácido graxo monoinsaturado - MONO, AGL poliinsaturado - POLI, AGL palmítico - C16:0, AGL oleico - C18:0, e AGL esteárico - C18:1) foram utilizados nas análises genéticas. Os componentes de variância foram obtidos por meio de um modelo de repetibilidade com regressão aleatória de uma função de THI (índice de temperatura e umidade). AGL saturados (saturado e C16:0) apresentaram menores estimativas de herdabilidade sobre condições de estresse térmico. C18:1 apresentou maior sensibilidade ao calor em condições de estresse térmico. Correlações entre os rankings de valores genéticos gnômicos variaram entre -0.27 a 0.99. Nossos resultados demonstraram uma oportunidade para investigar novos biomarcadores e melhorar os processos seletivos para termotolerância. No experimento 2, objetivou-se ajustar variáveis latentes (variável não observável) e predizer fator scores para utilizá-las como fenótipo na estimação de parâmetros genéticos, GWAS e análise de enriquecimento. Os ajustes foram obtidos por meio de uma análise fatorial confirmatória (método multivariado) que tem como principal objetivo reduzir a dimensão dos dados. O conjunto de variáveis observáveis que obtiveram melhor ajuste no modelo foram SAT, POLI, C18:0 e C18:1. Essas variáveis foram combinadas em um fator que representou 3 estágios de lactação (início: 40-60; meio: 160-180; final: 250- 270), baseados em intervalos fixos em dias em lactação (DEL) e posteriormente, foram combinadas para representar ordens de parto (1-3) utilizadas nas análises genéticas. As estimativas de herdabilidades para variáveis latentes foram de baixa magnitude (0,07 a 0,11). Dos resultados de GWAS, 11 genes candidatos genes (PLD1, TM6SF2, NUDT7, LIPT1, AKPA1, APOH, RPGRIP1L, FTO, GMDS, ALDH3B1, e PC) foram localizados em 9 cromossomos, incluindo na sua maioria genes que ainda não foram discutidos na literatura. Na análise de enriquecimento, foram revelados termos funcionais incluindo síntese de ácidos graxos, síntese do triglicerol e metabolismo de lipídeos e lipoproteínas. No geral, nosso estudo contribuiu como molde para novos estudos e para melhorar a base de conhecimento sobre os mecanismos genéticos subjacente à composição de AGL

Comparison of Marker Effects and Breeding Values at Two Levels at THI for Milk Yield and Quality Traits in Brazilian Holstein Cows

Genomic tools can help in the selection of animals genetically resistant to heat stress, especially the genome-wide association studies (GWAS). The objective of this study was to compare the variance explained by SNPs and direct genomic breeding values (DGVs) at two levels of a temperature and humidity index (THI). Records of milk yield (MY), somatic cell score (SCS), and percentages of casein (CAS), saturated fatty acids (SFA), and unsaturated fatty acids (UFA) in milk from 1157 Holstein cows were used. Traditional breeding values (EBV) were determined in a previous study and used as pseudo-phenotypes. Two levels of THI (heat comfort zone and heat stress zone) were used as environments and were treated as “traits” in a bi-trait model. The GWAS was performed using the genomic best linear unbiased prediction (GBLUP) method. Considering the top 50 SNPs, a total of 36 SNPs were not common between environments, eight of which were located in gene regions related to the evaluated traits. Even for those SNPs that had differences in their explained variances between the two environments, the differences were very small. The animals showed virtually no rank order, with rank correlation values of 0.90, 0.88, 1.00, 0.88, and 0.97 for MY, CAS, SCS, SFA, and UFA, respectively. The small difference between the environments studied can be attributed to the small difference in the pseudo-phenotypes used between the environments, on-farm acclimation, the polygenic nature of the traits, and the THI values studied near the threshold between comfort and heat stress. It is recommended that future studies be conducted with a larger number of animals and at more extreme THI levels