A comprehensive characterization of longevity and culling reasons in Canadian Holstein cattle based on various systematic factors.

The decision of premature culling cows directly impacts the profitability of dairy farms. A comprehensive characterization of the primary causes of culling reasons would greatly improve both management and selection objectives in dairy cattle breeding programs. Therefore, this study aimed to analyze the temporal frequencies of 34 culling reasons in Canadian Holstein cows. After data editing and quality control, records from 3,096,872 cows culled from 9,683 herds spread across Canada were used for the analyses covering the periods from 1996 to 2020. Reproductive issues were the main culling reason accounting for 23.02%, followed by milk production (20.82%), health (20.39%), conformation problems (13.69%), economic factors (13.10%), accidents (5.67%), age-related causes (1.67%), and workability (1.63%). Nearly fifty-eight percent of cows were culled after 47 months of age. The observed frequencies of culling due to economic factors were lower than expected from 1996 to 2014 and higher than expected between 2015 and 2020. Reproduction issues had the highest culling frequencies during fall (24.54%), winter (24.02%), and spring (22.51%), while health issues were the most frequent (22.51%) culling reason in the summer season. Health issues (25.50%) and milk production (27.71%) were the most frequent culling reasons in the provinces of Quebec and Ontario, respectively. Reproductive issues showed the highest frequency across climates based on the Köppen climate classification, except for Csb (Dry-summer subtropical or Mediterranean climate) and Bsk (Middle latitude steppe climate), which correspond to small regions in Canada, where production was the most frequent culling reason (29.42% and 21.56%, respectively). Reproductive and milk performance issues were the two main culling reasons in most ecozones, except in Boreal Shield and Atlantic Marine, where health issues had the highest frequencies (25.12 and 23.75%, respectively). These results will contribute to improving management practices and selective decisions to reduce involuntary culling of Holstein cows.

Genetic origin of donkeys in Brazil.

INTRODUCTION: The genetic groups of native donkeys in Brazil are characterized by adaptation to the local environment. However, the donkey population in the country is declining, mainly because of agricultural mechanization and transportation that has led to the abandonment and the consequent indiscriminate slaughter of these animals. There are three local genetic groups of distinct geographic and temporal formation. However, analyses of their origin, phylogenetic relationship, and population structure are scarce. Within this context, molecular markers such as the mitochondrial control region (D-loop) are useful for these analyses. MATERIAL AND METHODS: This study aimed to evaluate the variation and origin of maternal lineages of groups of naturalized donkeys in Brazil (Brazilian, Nordestino, and Pêga). RESULTS AND DISCUSSION: We detected five mitochondrial haplotypes with 19 polymorphic sites, two of them exclusively found in the Nordestino donkey; this group is in fact more distant from the others. Phylogenetic analysis indicates maternal contributions of two clades (Nubian and Somali) to the formation of the genetic groups of donkeys, a fact that explains the high diversity, structure, and distances of the groups, reported here for the first time. CONCLUSION : This analysis contributes production and conservation of native donkey breeds. It also gives clues about the formation of the Iberian breeds from which Brazilian donkeys originated.

Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals.

BACKGROUND: A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. RESULTS: A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data. CONCLUSIONS: The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.

Flaxseed added to the diet of Alpine goats affects the nutrients intake and blood parameters.

The flaxseed is a nutraceutical food used as a source of α-linolenic acid, which can bring benefits to the health of mammals. This study was carried out to examine the effect of flaxseed inclusion in the diets on the intake of nutrients, body weight, and blood parameters of Alpine goats. Twenty-one adult females with an initial average weight of 41.06 ± 1.84 kg were used in a completely randomized design, with four experimental treatments (0, 5, 10, and 15% of flaxseed in the total diet) and five replications per treatment. The intake of the dry matter presented a decreasing linear effect (P < 0.001), with a reduction of 53.5% between the control diet (0% of flaxseed) and 15% of flaxseed, but no effect was observed on weight gain (P > 0.05). Inclusion of flaxseed from 0 to 15% linearly decreased the intakes of organic matter, crude protein, non-fibrous carbohydrates, and neutral detergent fiber, but increased the ether extract intake (P < 0.001). Regarding plasma concentration traits, increasing the flaxseed levels from 0 to 15% had linear positive effect on LDL, VLDL, and triglycerides (P < 0.05), but no effect on cholesterol, HDL, glucose, creatinine, and urea (P > 0.05). The inclusion of flaxseed in the diet for 80 days changes the nutrients intake and blood parameters but shows no impact on body weight. However, further studies are required to determine the impact of flaxseed on the goat's health in the long term since there has been an increase in the concentration of triglycerides, LDL, and VLDL.

CNV detection and their association with growth, efficiency and carcass traits in Santa Inês sheep.

Copy number variations (CNV) are an important source of genetic variation. CNV has been increasingly studied and frequently associated with diseases and productive traits in livestock animals. However, CNV-based genome-wide association studies (GWAS) in Santa Inês sheep, one of the principal sheep breeds in Brazil, have not yet been reported. Thus, the aim of this study was to investigate the association between CNV and growth, efficiency and carcass traits in sheep. The Illumina OvineSNP50 BeadChip array was used to detect CNV in 491 Santa Inês individuals. Then, CNV-based GWAS was performed with a linear mixed model approach considering a genomic relationship matrix, for ten traits: (1) growth: body weight at three (W3) and six (W6) months of age; (2) efficiency: residual feed intake (RFI) and feed efficiency (FE) and (3) carcass: external carcass length (ECL), leg length (LL), carcass yield (CY), commercial cuts weight (CCW), loin eye area (LEA) and subcutaneous fat thickness (SFT). We identified 1,167 autosomal CNV in 438 sheep, with 294 non-redundant CNV, ranging from 21.8 to 861.9 kb, merged into 216 distinct copy number variation regions (CNVRs). One significant CNV segment (pFDR -value<0.05) in OAR3 was associated with CY, while another significant CNV in OAR6 was associated with RFI. Additionally, another 5 CNV segments were considered relevant for investigation in the future studies. The significant segments overlapped 4 QTLs and spanned 8 genes, including the SPAST,TGFA and ADGRL3 genes, involved in cell differentiation and energy metabolism. Therefore, the results of the present study increase knowledge about CNV in sheep, their possible impacts on productive traits, and provide information for future investigations, being especially useful for those interested in structural variations in the sheep genome.

Variants in myostatin and MyoD family genes are associated with meat quality traits in Santa Inês sheep.

Myostatin and MyoD family genes play vital roles in myogenesis and this study aimed to identify association of variants in MyoD1, MyoG, MyF5, MyF6, and MSTN genes with meat traits in Santa Inês sheep. A dataset with 44 variants and records of seven meat traits in 192 lambs (pH0, pH24, a*, b*, L*, tenderness assessed by shear force, and water-holding capacity) was used. Single-locus and haplotype association analyses were performed, and the significance threshold was established according to Bonferroni's method. Single-locus analysis revealed two associations at a Bonferroni level, where the variant c.935-185C > G in MyoD1 had an additive effect (-4.31 ± 1.08 N) on tenderness, while the variant c.464 + 185G > A in MyoG had an additive effect (-2.86 ± 0.64) on a*. Additionally, the haplotype replacement GT>AC in MSTN was associated with pH0 (1.26 ± 0.31), pH24 (1.07 ± 0.27), a* (-1.40 ± 0.51), and tenderness (3.83 ± 1.22 N), while the replacement GT > AG in MyoD1 was associated with pH0 (1.43 ± 0.26), pH24 (1.25 ± 0.22), b* (-1.06 ± 0.39), and tenderness (-4.13 ± 1.16 N). Our results have demonstrated that some variants in MyoG, MyF6, MyoD1, and MSTN can be associated with physicochemical meat traits in Santa Inês sheep.

Identification of novel candidate genes for age at first calving in Nellore cows using a SNP chip specifically developed for Bos taurus indicus cattle.

The age at first calving has a great economic impact on the beef cattle system and calving at 24 months is an objective of selection for a more efficient herd. However, an age at first calving around 36 months has been observed for Nellore cattle in Brazil. Thus, a genome-wide association study (GWAS) was carried out with 8376 records of age at first calving and 3239 animals genotyped with the GGP-Indicus 35K, which has been developed specifically for Bos taurus indicus. The weighted single-step genomic best linear unbiased prediction method was used, with adjacent SNPs (single nucleotide polymorphisms) in genomic windows of 1.0 Mb. After quality control, 3239 (2161 males and 1078 females) animals genotyped for 30,519 SNPs were used in GWAS analysis. The average and standard deviation of age at first calving were 1041.7 and 140.6 days, respectively. The heritability estimate was 0.10 ± 0.02. The GWAS analysis found seven genomic regions in BTA1, 2, 5, 12, 18, 21, and 24, which explained a total of 11.24% of the additive genetic variance of age at first calving. In these regions were found 62 protein coding genes, and the genes HSD17B2, SERPINA14, SERPINA1, SERPINA5, STAT1, NFATC1, ATP9B, CTDP1, THPO, ECE2, PSMD2, EIF4G1, EIF2B2, DVL3, POLR2H, TMTC2, and GPC6 are possible candidates for age at first birth due their function. Moreover, two molecular functions ("serine-type endopeptidase inhibitor activity" and "negative regulation of endopeptidase activity") were significant, which depend on several serpin genes. The use of a SNP chip developed especially for Bos taurus indicus allowed to find genomic regions for age at first calving, which are close to QTLs previously reported for other reproduction-related traits. Future studies can reveal the causal variants and their effects on reproductive precocity of Nellore cows.

Genotype by environment interaction for fat and protein yields via reaction norms in Holstein cattle of southern Brazil.

Our objective was to evaluate the genetic merit of Holstein cattle population in southern Brazil in response to variations in the regional temperature by analyzing the genotype by environment interaction using reaction norms. Fat yield (FY) and protein yield (PY) data of 67 360 primiparous cows were obtained from the database of the Paraná Holstein Breeders Association, Brazil (APCBRH). The regional average annual temperature was used as the environmental variable. A random regression model was adopted applying mixed models with Restricted Maximum Likelihood (REML) algorithm using WOMBAT software. The genetic merit of the 15 most representative bulls, depending on the temperature gradient, was evaluated. Heritability ranged from 0.21 to 0.27 for FY and from 0.14 to 0.20 for PY. The genetic correlation observed among the environmental gradients proved to be higher than 0.80 for both traits. Slight reranking of bulls for both traits was detected, demonstrating that non-relevant genotype by environment interaction for FY and PY were observed. Consequently, no inclusion of the temperature effect in the model of genetic evaluation in southern Brazilian Holstein breed is required.

Water buffaloes (Bubalus bubalis) only have A2A2 genotype for beta-casein.

Beta-casein is a milk protein that has two variants: A1 and A2. Some individuals have difficulties digesting beta-casein A1, which can cause gastrointestinal disorders. A2 milk has emerged as an alternative. This milk only contains beta-casein A2 and is obtained from females carrying the A2A2 genotype of the gene. In cattle, allele and genotype frequencies vary according to breed and marker-assisted selection is performed to obtain A2A2 animals and the consequent production of A2 milk that is easier to digest. This study aimed to evaluate the alleles of beta-casein in buffaloes. A total of 657 buffaloes of four different breeds were genotyped and all animals carried the A2A2 genotype, i.e., allele A1 does not exist in the buffalo species. Thus, all milk products of buffaloes are naturally A2. This result adds value to products derived from buffalo milk.

Genotype by environment interaction for somatic cell score in Holstein cattle of southern Brazil via reaction norms.

OBJECTIVE: The objective of this study was to evaluate the genetic behavior of a population of Holstein cattle in response to the variation of environmental temperature by analyzing the effects of genotype by environment interaction (GEI) through reaction norms for the somatic cell score (SCS). METHODS: Data was collected for 67,206 primiparous cows from the database of the Paraná Holstein Breeders Association in Brazil, with the aim of evaluating the temperature effect, considered as an environmental variable, distinguished under six gradients, with the variation range found being 17°C to 19.5°C, over the region. A reaction norm model was adopted utilizing the fourth order under the Legendre polynomials, using the mixed models of analysis by the restricted maximum likelihood method by the WOMBAT software. Additionally, the genetic behavior of the 15 most representative bulls was assessed, in response to the changes in the temperature gradient. RESULTS: A mean score of 2.66 and a heritability variation from 0.17 to 0.23 was found in the regional temperature increase. The correlation between the environmental gradients proved to be higher than 0.80. Distinctive genetic behaviors were observed according to the increase in regional temperature, with an observed increase of up to 0.258 in the breeding values of some animals, as well as a reduction in the breeding of up to 0.793, with occasional reclassifications being observed as the temperature increased. CONCLUSION: Non-relevant GEI for SCS were observed in Holstein cattle herds of southern Brazil. Thus, the inclusion of the temperature effect in the model of genetic evaluation of SCS for the southern Brazilian Holstein breed is not required.

Chitosan and cottonseed processing method association on carcass traits and meat quality of feedlot lambs.

The objective of this study was to evaluate the effects of the association of cottonseed processing method with chitosan on carcass traits and meat quality of lambs finished in feedlot. Eighty lambs with an average body weight of 20.6 kg, with 04 months of age, were distributed in a completely randomized design, in a 2 x 2 factorial arrangement. The factors were represented by two cottonseed processing method (whole or ground) and two levels of chitosan (0 and 136 mg/kg BW). The association of cottonseed processing method with chitosan in the lamb diet did not affect (P>0.05) carcasses traits. The pH, color, cooking losses, shear force, and proximate composition of meat were also not affected (P>0.05) by the processing method of cottonseed or its association with chitosan in the lamb diets. There was an increase in palmitoleic (c9-C16:1; P = 0.01) and conjugated linoleic (P = 0.02) fatty acids when ground cottonseed was associated with chitosan. Ground cottonseed associated with chitosan increases the concentration of unsaturated fatty acids in the meat of feedlot lambs.

Evaluation of genotype by environment interactions on milk production traits of Holstein cows in southern Brazil.

OBJECTIVE: This study assessed the possible existence of genotype by environment interactions for milk, fat and protein yields in Holstein cattle raised in one of the most important milk production basins in Brazil. METHODS: Changes in the genetic parameters and breeding values were evaluated for 57,967 animals from three distinct regions of southern Brazil, divided according to differences in climate. The genotype by environment interaction was determined by genetic correlations between regions, estimated by the restricted maximum likelihood, considering the animal model. Bull rankings were investigated to verify the ratio of coincident selected animals between regions for each trait. RESULTS: The estimates of heritability coefficients were similar between two regions, but were lower in the third evaluated area, for all traits. Genetic correlations between regions were high, ranging from 0.91 to 0.99 for milk, fat and protein yields, representing the absence of a genotype by environment interaction for productive traits. The percentage of selection error between regions for the top 10% of animals ranged from 0.88% to 2.07% for milk yield, 0.99% to 2.46% for fat yield and 0.59% to 3.15% for protein yield. CONCLUSION: A slight change in genotype between areas was expected since no significant genotype by environment interactions were identified, facilitating the process of selecting Holstein cattle in southern Brazil.

Linkage disequilibrium in Brazilian Santa Inês breed, Ovis aries.

For genomic selection to be successful, there must be sufficient linkage disequilibrium between the markers and the causal mutations. The objectives of this study were to evaluate the extent of LD in ovine using the Santa Inês breed and to infer the minimum number of markers required to reach reasonable prediction accuracy. In total, 38,168 SNPs and 395 samples were used. The mean LD between adjacent marker pairs measured by r2 and |D'| were 0.166 and 0.617, respectively. LD values between adjacent marker pairs ranged from 0.135 to 0.194 and from 0.568 to 0.650 for r2 for |D'| across all chromosomes. The average r2 between all pairwise SNPs on each chromosome was 0.018. SNPs separated by between 0.10 to 0.20 Mb had an estimated average r2 equal to 0.1033. The identified haplotype blocks consisted of 2 to 21 markers. Moreover, estimates of average coefficients of inbreeding and effective population size were 0.04 and 96, respectively. LD estimated in this study was lower than that reported in other species and was characterized by short haplotype blocks. Our results suggest that the use of a higher density SNP panel is recommended for the implementation of genomic selection in the Santa Inês breed.

Principal components for the in vivo and carcass conformations of Anglo-Nubian crossbred goats / Componentes principais para conformações in vivo e das carcaças em caprinos mestiços da raça Anglo-Nubiana

ABSTRACT: This study aimed to identify the principal components (PC) that explain the highest percentages of total variance and best characterize the in vivo and carcass morphologies of Anglo-Nubian crossbred goats. Nineteen carcass morphometric traits and six in vivo morphometric traits were measured in 28 kids at eight months of age. Principal component analysis indicated that five PC were able to explain 83.57% of the total variance in the 19 original carcass traits. Those components were termed PC1-Carcass Size, PC2 - Body Condition, PC3-Carcass Width, PC4-Chest Depth, and PC5 - Hindquarter. For in vivo morphometric traits, the first two principal components explained 78.86% of the total variance. These components were called PC1-In vivo Size and PC2-In vivo Conformation.

RESUMO: Este estudo buscou identificar componentes principais (CP) que explicam os maiores percentuais de variância total e que melhor caracterizam cabritos mestiços da raça Anglo Nubiana, quanto à medidas morfológicas obtidas in vivo, e na carcaça de 28 animais com 8 meses de idade. Foram conduzidas duas análises de componentes principais, sendo uma para 19 características de carcaça e outra para seis características morfométricas in vivo. Os cinco primeiros CP explicaram 82,54% da variância total das 19 características incluídas nessa análise. Estes componentes foram chamados de: CP1 - Tamanho da Carcaça, CP2 - Condição Corporal, CP3 - Largura da Carcaça, CP4 - Profundidade do Tórax e, CP5 - Comprimento do Pernil. Os dois primeiros componentes principais das morfometrias obtidas in vivo explicaram 78,86% da variância total e foram chamados de CP1 - Tamanho in vivo e CP2 - Conformação in vivo.

Effects of birth type and family on the variation of carcass and meat traits in Santa Ines sheep.

This study aimed to evaluate the effects of birth type and family on quantitative and qualitative meat traits in Santa Ines lambs and to do a descriptive study of variation inside of breed. A total of 50 carcass and meat traits were evaluated in up to 101 lambs slaughtered at 424 days of age. Random effect of family, the fixed effect of birth type (single or double) and year, and the covariates of dam's weight at weaning and age (in days) at slaughter were inserted in the model. This study shows that some carcass and meat traits in Santa Ines raised on pasture has large variability, specially for meat cut yields, several carcass non-components yields, and rib eye area, subcutaneous fat thickness, shear force, cooking losses, and b* color parameter. The birth type effect influenced (P < 0.05) rump width; reticulum, leg, heart and kidney yields; and the carcass pH at 24 h after slaughter. The family effect was significant (P < 0.05) for cold carcass weight; hot, cold and true carcass yields; external carcass and leg lengths; perimeter and width of the rump; kidney, liver and tail yields; and carcass pH at slaughter.

Performance of the Santa Ines breed raised on pasture in semiarid tropical regions and factors that explain trait variation.

This study aimed to evaluate sex, the number of lambs per birth, and the family effects on production traits in the Santa Ines breed of sheep by estimating the least square means and coefficient of variance for those traits. A total of 484 lambs were evaluated for the following traits: weight at birth, at weaning, and at 240 days of age; weight gain during the pre-weaning and post-weaning periods; height, width, and length of different body regions; and rib eye area and fat thickness between the 12th and 13th ribs. We observed coefficients of variation higher than 10 % for several traits. Generally, males were larger than females (P < 0.05), while lambs from single and double births were larger than lambs from triple births (P < 0.05). Family effect was significant (P < 0.05) for most traits and explained the highest percentage of residual variance. The results showed good development of Santa Ines sheep, especially during the pre-weaning period but no in post-weaning. Our study also showed that there is an effect of sex, birth type, and family, which must be included in any statistical model for the estimation of least square means and residual variance in ANOVA.

Live weight, carcass ultrasound images, and visual scores in Angus cattle under feeding regimes in Brazil.

This study aimed to evaluate visual precocity, muscling, conformation, skeletal, and breed scores; live weights at birth, at 205, and at 550 days of age; and, besides, rib eye area and fat thickness between the 12th and 13th ribs obtained by ultrasound. Those traits were evaluated in 1,645 Angus cattle kept in five feeding conditions as follows: supplemented or non-supplemented, grazing native pasture or grazing cultivated pasture, and feedlot. Descriptive statistics, Pearson's correlations, and principal component analysis were carried out. Gender and feeding conditions were fixed effects, while animal's age and mother's weight at weaning were the covariates analyzed. Gender and feeding conditions were very significant for the studied traits, but visual scores were not influenced by gender. Animal's age and mother's weight at weaning influenced many traits and must be appropriately adjusted in the statistical models. An important correlation between visual scores, live weights, and carcass traits obtained by ultrasound was found, which can be analyzed by univariate procedure. However, the multivariate approach revealed some information that cannot be neglected in order to ensure a more detailed assessment.