Genetic diversity of SNPs associated with candidate genes for heat stress in Coreño Creole cattle in Mexico.

Mexican Coreño Creole cattle are an important genetic resource adapted to local environmental conditions, so the study of their genetic diversity is essential to know their status and implement conservation programs and their use for crossbreeding. This study evaluated the genetic diversity of heat stress tolerance characteristics of Coreño Creole cattle, and a gene ontology enrichment was performed to know the biological processes in which candidate genes are involved. A total of 48 samples from three localities of Nayarit were genotyped using 777 K Illumina BovineHD BeadChip and 34 single nucleotide polymorphisms associated with candidate genes were selected. Genetic diversity was analyzed using allelic frequencies, expected heterozygosity (He), and Wright's fixation index (FST) using PLINK v1.9 software. Candidate genes were uploaded to the open-source GOnet for pathway analysis and linkage to biological processes. Coreño Creole cattle showed low genetic diversity (He = 0.35), the average FST obtained was 0.044, and only eight markers had allele frequencies higher than 0.80 in the three locations. We found that the genes GOT1 and NCAD are related in the biological processes of stress response, cell differentiation, and homeostatic process. The results revealed that Coreño Creole cattle have low genetic diversity; this could be due to the isolation of these populations.

Discovering Genomic Regions Associated with Reproductive Traits and Frame Score in Mexican Simmental and Simbrah Cattle Using Individual SNP and Haplotype Markers.

Reproductive efficiency stands as a critical determinant of profitability within beef production systems. The incorporation of molecular markers can expedite advancements in reproductive performance. While the use of SNPs in association analysis is prevalent, approaches centered on haplotypes can offer a more comprehensive insight. The study used registered Simmental and Simbrah cattle genotyped with the GGP Bovine 150 k panel. Phenotypes included scrotal circumference (SC), heifer fertility (HF), stayability (STAY), and frame score (FS). After quality control, 105,129 autosomal SNPs from 967 animals were used. Haplotype blocks were defined based on linkage disequilibrium. Comparison between haplotypes and SNPs for reproductive traits and FS was conducted using Bayesian and frequentist models. 23, 13, 7, and 2 SNPs exhibited associations with FS, SC, HF, and STAY, respectively. In addition, seven, eight, seven, and one haplotypes displayed associations with FS, SC, HF, and STAY, respectively. Within these delineated genomic segments, potential candidate genes were associated.

Expression of heat shock protein genes in Simmental cattle exposed to heat stress.

OBJECTIVE: In tropical, subtropical and arid zones, heat stress is the main cause of productivity reduction in cattle. When climate stressors occur, animals become thermal adapted through differential expression of some genes, including heat shock proteins (HSP) family. The aim of this study was to determine levels of expression of HSP60, HSP70, and HSP90 genes in Simmental cattle raised in tropical environments of Mexico. METHODS: In this study, expression of HSP60, HSP70, and HSP90 genes was analyzed in 116 Simmental cattle from three farms with tropical climate located in western Mexico. Animals were sampled twice a day, in the morning and noon. Gene expression was evaluated by quantitative polymerase chain reaction using probes marked with fluorescence. The MIXED procedure of SAS with repeated measures was used for all statistical analysis. RESULTS: HSP60 gene expression differences were found for sex (p = 0.0349). HSP70 gene differences were detected for sampling hour (p = 0.0042), farm (p<0.0001), sex (p = 0.0476), and the interaction sampling hour×farm (p = 0.0002). Gene expression differences for HSP90 were observed for farm (p<0.0001) and year (p = 0.0521). HSP70 gene showed to be a better marker of heat stress than HSP60 and HSP90 genes. CONCLUSION: Expression of HSP70 gene in Simmental herds of the tropical region of western México was different during early morning and noon, but the expression of the HSP60 and HSP90 genes was similar. Identification of resilient animals to heat stress will be useful in the genetic improvement of the Simmental breed.

Genome and chromosome wide association studies for growth traits in Simmental and Simbrah cattle.

OBJECTIVE: The objective of this study was to perform genome (genome wide association studies [GWAS]) and chromosome (CWAS) wide association analyses to identify single nucleotide polymorphisms (SNPs) associated with growth traits in registered Simmental and Simbrah cattle. METHODS: The phenotypes were deregressed BLUP EBVs for birth weight, weaning weight direct, weaning weight maternal, and yearling weight. The genotyping was performed with the GGP Bovine 150k chip. After the quality control analysis, 105,129 autosomal SNP from 967 animals (473 Simmental and 494 Simbrah) were used to carry out genotype association tests. The two association analyses were performed per breed and using combined information of the two breeds. The SNP associated with growth traits were mapped to their corresponding genes at 100 kb on either side. RESULTS: A difference in magnitude of posterior probabilities was found across breeds between genome and chromosome wide association analyses. A total of 110, 143, and 302 SNP were associated with GWAS and CWAS for growth traits in the Simmental-, Simbrah-and joint -data analyses, respectively. It stands out from the enrichment analysis of the pathways for RNA polymerase (POLR2G, POLR3E) and GABAergic synapse (GABRR1, GABRR3) for Simmental cattle and p53 signaling pathway (BID, SERPINB5) for Simbrah cattle. CONCLUSION: Only 6,265% of the markers associated with growth traits were found using CWAS and GWAS. The associated markers using the CWAS analysis, which were not associated using the GWAS, represents information that due to the model and priors was not associated with the traits.

Genetic diversity evolution in the Mexican Charolais cattle population.

OBJECTIVE: The aim was to characterize the genetic diversity evolution of the registered Mexican Charolais cattle population by pedigree analysis. METHODS: Data consisted of 331,390 pedigree records of animals born from 1934 to 2018. Average complete generation equivalent, generation interval, effective population size (Ne), and effective numbers of founders (fe), ancestors (fa), and founder genomes (Ng) were calculated for seven five-year periods. The inbreeding coefficient was calculated per year of birth, from 1984 to 2018, whereas the gene contribution of the most influential ancestors was calculated for the latter period. RESULTS: Average complete generation equivalent consistently increased across periods, from 4.76, for the first period (1984 through 1988), to 7.86, for the last period (2014 through 2018). The inbreeding coefficient showed a relative steadiness across the last seventeen years, oscillating from 0.0110 to 0.0145. During the last period, the average generation interval for the father-offspring pathways was nearly 1 yr. longer than that of the mother-offspring pathways. The effective population size increased steadily since 1984 (105.0) and until 2013 (237.1), but showed a minor decline from 2013 to 2018 (233.2). The population displayed an increase in the fa since 1984 and until 2008; however, showed a small decrease during the last decade. The effective number of founder genomes increased from 1984 to 2003, but revealed loss of genetic variability during the last fifteen years (from 136.4 to 127.7). The fa:fe ratio suggests that the genetic diversity loss was partially caused by formation of genetic bottlenecks in the pedigree; in addition, the Ng:fa ratio indicates loss of founder alleles due to genetic drift. The most influential ancestor explained 1.8% of the total genetic variability in the progeny born from 2014 to 2018. CONCLUSION: Inbreeding, Ne, fa, and Ng are rather beyond critical levels; therefore, the current genetic status of the population is not at risk.

Hybrid Versus Autochthonous Turkey Populations: Homozygous Genomic Regions Occurrences Due to Artificial and Natural Selection.

The Mexican turkey population is considered to be the descendant of the original domesticated wild turkey and it is distinct from hybrid strains obtained by the intense artificial selection activity that has occurred during the last 40 years. In this study 30 Mexican turkeys were genomically compared to 38 commercial hybrids using 327,342 SNP markers in order to elucidate the differences in genome variability resulting from different types of selection, i.e., only adaptive for Mexican turkey, and strongly directional for hybrids. Runs of homozygosity (ROH) were detected and the two inbreeding coefficients (F and FROH) based on genomic information were calculated. Principal component and admixture analyses revealed two different clusters for Mexican turkeys (MEX_cl_1 and MEX_cl_2) showing genetic differentiation from hybrids (HYB) (FST equal 0.168 and 0.167, respectively). A total of 3602 ROH were found in the genome of the all turkeys populations. ROH resulted mainly short in length and the ROH_island identified in HYB (n = 9), MEX_cl_1 (n = 1), and MEX_cl_2 (n = 2) include annotated genes related to production traits: abdominal fat (percentage and weight) and egg characteristics (egg shell color and yolk weight). F and FROH resulted correlated to each other only for Mexican populations. Mexican turkey genomic variability allows us to separate the birds into two subgroups according to the geographical origin of samples, while the genomic homogeneity of hybrid birds reflected the strong directional selection occurring in this population.

Genetic parameters for scrotal circumference, frame score and yearling weight of Mexican Charolais and Charbray young bulls / Parámetros genéticos de circunferencia escrotal, talla corporal y peso al año de toros jóvenes mexicanos Charolais y Charbray / Parâmetros genéticos de perímetro escrotal, escore de frame e peso ao ano de idade de touros jovens mexicanos Charolês e Charbray

Abstract Background: Knowledge of genetic correlations and the economics of traits are essential to decide which traits should be used as selection criteria. Objective: To estimate heritabilities and genetic, environmental, and phenotypic correlations, and direct (DRS) and correlated (CRS) responses to selection by scrotal circumference (SC), frame score (FS), and yearling weight (YW) of Mexican Charolais (CH), and Charbray (CB) young bulls. Methods: Actual SC, height and YW records (10,078 for CH, and 500 for CB) were adjusted to 365 d. The 0.0505 adjustment factor recommended by the Beef Improvement Federation was used to obtain the 365-d adjusted SC for both breeds. Height and age records were used to obtain FS. Data were analyzed using a three-trait animal model. The animal model for each trait included bull breed, contemporary group (groups of young bulls born in the same herd, year, and season of the year), and age of dam as a linear covariate as fixed effects, and direct additive genetic and residual as random effects. Results: Heritability estimates for SC, FS and YW were 0.21 ± 0.04, 0.25 ± 0.04, and 0.29 ± 0.04, respectively. The genetic correlation between YW with SC was 0.37 ± 0.16, and between YW with FS was 0.42 ± 0.16. The estimate of genetic correlation between SC and FS was low and positive (0.15 ± 0.14). The DRS was 0.38 cm, 0.18 units, and 8.30 kg for SC, FS and YW. The CRS was 0.16 cm, and 0.08 units for SC and FS from indirect selection on YW. Conclusions: Direct selection for YW is expected to be effective. Indirect selection for SC and FS based on YW would not be expected to be as effective as direct selection for improving SC and FS.

Resumen Antecedentes: el conocimiento de las correlaciones genéticas y el aspecto económico de las características son necesarios para decidir qué características usar como criterios de selección. Objetivo: estimar las heredabilidades y correlaciones genéticas, ambientales y fenotípicas, y respuesta directa (DRS) y correlacionada (CRS) a la selección por circunferencia escrotal (SC), talla corporal (FS), y peso al año (YW) de toros jóvenes mexicanos Charolais (CH), y Charbray (CB). Métodos: registros (10.078 para CH y 500 para CB) de SC, altura y YW se ajustaron a 365 d. El factor de ajuste de 0,0505 recomendado por la Beef Improvement Federation se usó para obtener la SC ajustada a 365 d para ambas razas. Registros de altura y edad del animal se usaron para calcular FS. Los datos se analizaron usando un modelo animal para tres características. El modelo animal para cada característica incluyó raza del toro, grupo contemporáneo (grupos de toros jóvenes nacidos en el mismo hato, año y época del año) y edad de la madre como covariable lineal como efectos fijos, y el genético aditivo directo y el error como efectos aleatorios. Resultados: los estimadores de heredabilidad de SC, FS y YW fueron 0,21 ± 0,04, 0,25 ± 0,04 y 0,29 ± 0,04, respectivamente. La correlación genética de YW con SC fue 0,37 ± 0,16, y de YW con FS fue 0,42 ± 0,16. El estimador de la correlación genética entre SC y FS fue bajo y positivo (0,15 ± 0,14). La DRS fue 0,38 cm, 0,18 unidades, y 8,30 kg para SC, FS y YW. La CRS fue 0,16 cm y 0,08 unidades para SC y FS al seleccionar YW. Conclusiones: se espera que la selección directa de YW sea efectiva. La selección indirecta de SC y FS basada en YW no se espera que sea tan efectiva como la selección directa para mejorar SC y FS.

Resumo Antecedentes: o conhecimento das correlações genéticas, e aspecto econômico de as características são necessário para decidir que características usar como critérios de seleção. Objetivo: estimar herdabilidades e correlações genéticas, ambientais e fenotípicas, e resposta direta (DRS), e correlacionada (CRS) à seleção do perímetro escrotal (SC), escore de frame (FS), e peso ao ano de idade (YW) de touros jovens mexicanos Charolês (CH), e Charbray (CB). Métodos: registros (10.078 para CH e 500 para CB) de SC, altura e YW foram ajustados a 365 d. O fator de ajuste 0,0505 recomendado por a Beef Improvement Federation foi usado para obter o SC ajustado aos 365 d para ambas raças. Registros de altura na garupa e idade do animal foram usados para obter o FS. Os dados foram analisados usando um modelo animal para três características. O modelo animal para cada característica incluiu raça do touro, grupo contemporâneo (grupos de touros jovens nascidos no mesmo fazenda, ano e época do ano) e idade materna como covariável linear como efeitos fixos, e genético aditivo direto e o erro como efeitos aleatórios. Resultados: as estimativas de herdabilidade para SC, FS e YW foram 0,21 ± 0,04, 0,25 ± 0,04 e 0,29 ± 0,04, respetivamente. A correlação genética do YW com SC foi 0,37 ± 0,16, e de YW com FS foi 0,42 ± 0,16. A estimativa da correlação genética entre SC e FS foi baixa e positiva (0,15 ± 0,14). A DRS foi 0,38 cm, 0,18 unidades, e 8,30 kg para SC, FS e YW. A CRS foi 0,16 cm e 0,08 unidades para SC e FS al selecionar YW. Conclusões: espera-se que a seleção direta do YW seja eficaz. A seleção indireta de SC e FS com base no YW não se espera que seja tão efetiva como a seleção direta para melhorar SC e FS.

Genetic footprints of Iberian cattle in America 500 years after the arrival of Columbus.

BACKGROUND: American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of the genetic status of Creole cattle is essential for the establishment of conservation programs of these historical resources. METHODOLOGY/PRINCIPAL FINDINGS: We sampled 27 Creole populations, 39 Iberian, 9 European and 6 Zebu breeds. We used microsatellite markers to assess the origins of Creole cattle, and to investigate the influence of different breeds on their genetic make-up. The major ancestral contributions are from breeds of southern Spain and Portugal, in agreement with the historical ports of departure of ships sailing towards the Western Hemisphere. This Iberian contribution to Creoles may also include some African influence, given the influential role that African cattle have had in the development of Iberian breeds, but the possibility of a direct influence on Creoles of African cattle imported to America can not be discarded. In addition to the Iberian influence, the admixture with other European breeds was minor. The Creoles from tropical areas, especially those from the Caribbean, show clear signs of admixture with Zebu. CONCLUSIONS/SIGNIFICANCE: Nearly five centuries since cattle were first brought to the Americas, Creoles still show a strong and predominant signature of their Iberian ancestors. Creole breeds differ widely from each other, both in genetic structure and influences from other breeds. Efforts are needed to avoid their extinction or further genetic erosion, which would compromise centuries of selective adaptation to a wide range of environmental conditions.