Genome-wide association study for stayability at different calvings in Nellore beef cattle.

BACKGROUNDING: Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal's life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female's productive life. RESULTS: The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant. CONCLUSION: Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.

Head of Zebu cattle (Bos Taurus indicus): sectional anatomy and 3D computed tomography.

The research was designed to use computed tomography (CT) with 3D-CT reconstruction imaging techniques and the various anatomical sections-plana transversalia, frontalis, and dorsalia-to describe the anatomical architecture of the Zebu cattle head. Our study used nine mature heads. The CT bone window created detailed images of cranial bones, mandibles, teeth, and hyoid bones. All of the head cavities were evaluated, including the cranial, orbital, oral, auricular, and nasal cavities with their paranasal and conchal sinuses. The septum nasi, attached to the vomer and maxillary bones, did not reach the nasal cavity floor caudally at the level of the second premolar teeth, resulting in a single median channel from the choanae to the nasopharynx. The positions, boundaries, and connections of the paranasal sinuses were clearly identified. There were four nasal conchal sinuses (that were named the dorsal, middle, ethmoidal, and ventral) and five paranasal sinuses that were described as the following: sinus frontalis, maxillaris, palatinorum, and lacrimalis, as defined in the different anatomical sections and computed tomographic images. The complicated sinus frontalis caused the pneumatization of all bones that surrounded the cranial cavity, with the exception of the ethmoidal and body of basisphenoid bones. The sinus maxillaris was connected to the sinus lacrimalis and palatinorum through the maxillolacrimal and palatomaxillary openings, and to the middle nasal meatus through the nasomaxillary opening. Our findings provide a detailed anatomical knowledge for disease diagnosis to internal medicine veterinarians and surgeons by offering a comprehensive atlas of the Zebu cattle anatomy.

Anatomical studies on the PES region of Zebu cattle (Bos Taurus indicus) with special references to 3D computed tomography imaging technique.

The 3D render volume reconstruction CT (3D-RVCT) produced detailed images of the PES region, determining its relationships with the surrounding structures. Despite extensive research in veterinary studies on the PES through gross anatomy and CT, there is a lack of studies on the PES of zebu cattle. The study aimed to analyze the PES of Zebu cattle using gross cross-sectional, radiographic, CT, and morphometric methods, with the use of 3D-RVCT to provide anatomical guidance for surgeons and students. The study was performed on sixteen PES regions to provide hard and soft tissues in CT images. Three are five tarsal bones and two large fused (III and IV) metatarsal bones that were completely fused except for their distal extremities, which were divided distally by the intertrochlear notch. The cortical thickness of the metatarsal bone was equal on both sides. The bony septum divided the medullary cavity between the two fused large metatarsal bones in the proximal distal half only and disappeared in the middle part. The reconstruction showed similar sizes in the right and left limbs, confirming the pes bones. The radiographic and CT images could be used as a normal reference for the interpretation of some clinical diseases in the PES. The 3D CT reconstruction of the pes bones was described by various CT oblique dorsal and plantar views. The study focuses on diagnosing PES disorders using CT imaging, improving medical interventions, improving Zebu cattle health outcomes, and empowering students to contribute to veterinary medicine research and advancements.

Inheritance of genomic regions and genes associated with number of oocytes and embryos in Gir cattle through daughter design.

Over the past decades, daughter designs, including genotyped sires and their genotyped daughters, have been used as an approach to identify QTL related to economic traits. The aim of this study was to identify genomic regions inherited by Gir sire families and genes associated with number of viable oocytes (VO), total number of oocytes (TO), and number of embryos (EMBR) based on a daughter design approach. In total, 15 Gir sire families were selected. The number of daughters per family ranged from 26 to 395, which were genotyped with different SNP panels and imputed to the Illumina BovineHD BeadChip (777K) and had phenotypes for oocyte and embryo production. Daughters had phenotypic data for VO, TO, and EMBR. The search for QTL was performed through GWAS based on GBLUP. The QTL were found for each trait among and within families based on the top 10 genomic windows with the greatest genetic variance. For EMBR, genomic windows identified among families were located on BTA4, BTA5, BTA6, BTA7, BTA8, BTA13, BTA16, and BTA17, and they were most frequent on BTA7 within families. For VO, genomic windows were located on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA23, and BTA27 among families, being most frequent on BTA8 within families. For TO, the top 10 genomic windows were identified on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA26, and BTA27, being most frequent on BTA7 and BTA8 within families. Considering all results, the greatest number of genomic windows was found on BTA7, where the VCAN, XRCC4, TRNAC-ACA, HAPLN1, and EDIL3 genes were identified in the common regions. In conclusion, 15 Gir sire families with 26 to 395 daughters per family with phenotypes for oocyte and embryo production helped to identify the inheritance of several genomic regions, especially on BTA7, where the EDIL3, HAPLN1, and VCAN candidate genes were associated with number of oocytes and embryos in Gir cattle families.

Genetic parameters for oocytes and embryo production and their association with linear type traits in dairy Gyr Cattle.

In vitro embryo production is one of the main reproductive techniques used in dairy Gyr cattle. In addition, linear type measures are well characterized and have been used in dairy Gyr breed selection for the last 4 decades. The estimation of genetic parameters for the number of aspirated oocytes and in vitro-produced embryos associated with the linear type measures would support genetic progress for animal breeding programs toward embryo production. This study aimed to estimate genetic parameters for aspirated oocytes, embryo in vitro production, and linear type traits, exploring the association between them. The repeatability model was applied to 14,251 ovum pick-up events from 1,916 Gyr donors. A subset of 604 donors from the same group had their body measurements taken. Single- and 2-trait analyses were carried out using the BLUPF90 family programs. Heritability estimates of 0.38, 0.34, and 0.20 were obtained for total oocytes, viable oocytes, and embryos, respectively,-and the heritability of the linear type traits ranged from 0.22 to 0.40. High genetic correlations between total oocytes and viable oocytes (0.99), and between oocytes (total and viable) and embryos (0.83) were obtained. Low to high genetic (-0.07 to 0.92) and phenotypic (0.32 to 0.86) correlations were obtained between the linear type traits. Moreover, low phenotypic correlations (0.01 to 0.13) were observed for oocytes (total and viable) and embryos with the linear type traits, whereas low to moderate genetic correlations (0.07 to 0.42) were observed between the same traits, especially for ilium width (0.42), rump area (0.38), and hip height (0.33). Thus, selection for in vitro production is achievable in Gyr dairy cattle, and superior genetic progress is associated with the selection of oocytes (total and viable). Furthermore, the moderate genetic association between oocytes and embryos with linear type traits, especially ilium width suggests that progress on in vitro embryo production may be achieved by accessing these measurements.

The effectiveness of low-dose of eCG in timed AI Nelore (Bos indicus) heifers.

This study evaluated the efficacy of the administration of different doses of equine chorionic gonadotropin (eCG; 0 IU, 200 IU, or 300 IU) at the time of the progesterone device removal in 2-year-old Nelore (Bos indicus) heifers synchronized for fixed-timed artificial insemination (FTAI). On day 0 (D0), a total of 398 heifers received 2 mg of oestradiol benzoate i.m., 0.53 mg of cloprostenol i.m., and an eight-day previously used (second use) intravaginal device containing 1 g of progesterone (P4). Eight days later (D8), simultaneous with the P4 device removal, 0.5 mg of oestradiol cypionate i.m. and 0.53 mg of cloprostenol i.m. were administered. At the same time, heifers were randomly assigned to receive one of the following treatments: G-0 IU (n = 141; no eCG treatment), G-200 IU (n = 132; treated with 200 IU of eCG), and G-300 IU (n = 125; treated with 300 IU of eCG). FTAI was performed 48 h after the P4 device removal (D10). Ultrasonographic evaluations were performed at D0, D10, and D17. Heifers were scanned to measure the size of the largest follicle (LF), the presence, number, and size of the corpus luteum (CL), and the ovulation rate. Subsequently, at D40, the heifers underwent scanning to determine the pregnancy rate and identify any twin pregnancies. Additionally, at D70, scans were performed to assess pregnancy loss (PG). Data were analysed by orthogonal contrasts [C1 (eCG effect): control x (200 IU + 300 IU) and C2 (eCG dose effect): 200 IU × 300 IU]. On D0, CL presence was similar between the groups [G-0 IU = 65.2% (92/141), G-200 IU = 55.3% (73/132), and G-300 IU = 63.2% (79/125); p = .16]. No interactions between the presence of CL on D0 and eCG treatment were found for any of the variables (p > .05). The diameter of the LF at FTAI (D10) was not influenced by eCG treatment (p = .22) or eCG dose (p = .18). However, treatment with eCG increased the diameter of the CL at D17 (G-0 IU = 15.7 ± 0.3 mmb , G-200 IU = 16.6 ± 0.2 mma , and G-300 IU = 16.6 ± 0.3 mma ; p = .001), regardless of the dose used (p = .94). The ovulation rate was higher in heifers treated with eCG [G-0 IU = 79.4%b (112/141), G-200 IU = 90.2%a (119/132), and G-300 IU = 93.6%a (117/125); p = .002], but there was no effect of eCG dose (p = .36). Pregnancy per AI (P/AI) on D40 [G-0 IU = 32.6%b (46/141), G-200 IU = 42.4%a (56/132), and G-300 IU = 42.4%a (53/125); P = 0.05] and D70 [G-0 IU = 29.1%b (41/141), G-200 IU = 40.9%a (54/132), and G-300 IU = 40.8%a (51/125); p = .02] were higher on heifers that received eCG; however, no dose effect was observed for P/AI on D40 (p = .89) nor D70 (p = .98). Pregnancy loss between D40 and D70 tended to reduce (p = .07) in eCG-treated heifers without dose effect (p = .91). Heifers with CL at D0 presented a greater follicle diameter (LF) on D10 (With CL = 11.2 ± 0.2 mm and Without CL = 10.2 ± 0.2 mm; p = .05), CL diameter on D17 (With CL = 15.8 ± 0.03 mm and Without CL = 11.8 ± 0.6 mm; p = .01), and ovulation rate [With CL = 95.5% (233/244) and Without CL = 74.7% (115/154); p = .01]. However, no difference in pregnancy rate at D40 (p = .52) and D70 (p = .84) was found. In conclusion, eCG treatment increases ovulation and pregnancy rates of heifers submitted to a FTAI protocol. Furthermore, eCG treatment increases the diameter of the CL after FTAI and reduces pregnancy losses. No dose effect was observed, suggesting Nelore (Bos indicus) heifers respond to 200 IU of eCG treatment for FTAI.

Relationship among thermal environment, stage of lactation, body characteristics, yield and milk constituents of dairy Gyr cows managed on pasture.

Our aims were to evaluate changes in body characteristics, milk yield and milk constituents as well as to determine the relationship between the thermal environment and production characteristics during the first lactation of dairy Gyr cows managed on pasture. Between 2013 and 2015, forty-five primiparous dairy Gyr cows were evaluated from prepartum to 10 months of lactation in Southeast of Brazil. Body weight, body condition score (BCS), subcutaneous fat thickness (SFT), milk yield (305 d), and milk constituents were collected monthly and progesterone was collected weekly. Additionally, we determined the temperature humidity index (THI) based on microclimate data. Overall, the cows lost body weight until six months of lactation and there was a progressive decrease in BCS, SFT, milk yield and milk lactose as the months in lactation progressed. In contrast, there was an increase in milk fat, milk protein and milk solids. The thermal environment did not pose a consistent heat challenge, nevertheless, we found a positive correlation between the average THI two days before milk collection with milk yield, fat and lactose contents, but in contrast a negative correlation was found with total solids and protein. In conclusion, the THI and months of lactation affected the yield and constituents of milk. However, more studies are necessary to understand the impacts of body characteristics and thermal environment on yield and milk constituents throughout the productive life of Gyr dairy cows.

Identification of genomic regions and pathways associated with traits related to rumen acidosis in feedlot Nellore cattle.

There may be an increased risk of metabolic disorders, such as rumen acidosis, in cattle fed high-concentrate diets, particularly those from Bos taurus indicus genotypes, which have shown to be more sensitive to ruminal acidification. Therefore, this study aimed to estimate (co)variance components and identify genomic regions and pathways associated with ruminal acidosis in feedlot Nellore cattle fed high-concentrate diets. It was utilized a dataset containing a total of 642 Nellore bulls that were genotyped from seven feedlot nutrition studies. The GGP Indicus 35k panel was used with the single step genome-wide association study methodology in which the effects of the markers were obtained from the genomic values estimated by the GBLUP model. A bivariate model to estimate genetic correlations between the economically important traits and indicator traits for acidosis was used. The traits evaluated in this study that were nutritionally related to rumen acidosis included average daily gain (ADG), final body weight, time spent eating (TSE), time spent ruminating, rumenitis score (RUM), rumen absorptive surface area (ASA), rumen keratinized layer thickness (KER) and hot carcass weight (HCW). The identified candidate genes were mainly involved in the negative or non-regulation of the apoptotic process, salivary secretion, and transmembrane transport. The genetic correlation between HCW and ASA was low positive (0.27 ± 0.23), and between ADG and ASA was high moderate (0.58 ± 0.59). A positive genetic correlation between RUM and all performance traits was observed, and TSE correlated negatively with HCW (-0.33 ± 0.21), ASA (-0.75 ± 0.48), and KER (-0.40 ± 0.27). The genetic association between economically important traits and indicator traits for acidosis suggested that Nellore cattle may be more sensitive to acidosis in feedlot systems.

Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle.

For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (FROH ), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (FGRM ), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (FGRM_0.5 ), and by the proportion of homozygous loci (FHOM ) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. FROH was equal to 0.095 ± 0.084, and its Spearman correlation with FGRM was low (0.44) and moderate-high with FHOM (0.79) and with FGRM_0.5 (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree-based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied.

Effects of inbreeding on production traits and genetic evaluations in Guzerá beef cattle raised under tropical conditions.

The objectives of this study were to evaluate the influence of inbreeding on growth traits and body measurements, as well as on the estimation of genetic parameters and genetic trends in Guzerá cattle. Phenotypic records of 4,212 animals selected for postweaning weight from Guzerá Breeding Program of Advanced Beef Cattle Research Center were utilized. The pedigree file contained records from 7,213 animals born from 1928 to 2019. The traits analyzed were: birth weight (BW), weights adjusted to 210, 378 and 550 days of age (W210, W378 and W550, respectively), chest girth at 378 and 550 days of age (CG378 and CG550), scrotal circumference (SC), and hip height at 378 and 550 days of age (HH378 and H550). Linear regression was used to evaluate the effects of inbreeding on traits. Genetic parameters were obtained using models including or not the effect of inbreeding as a covariate. Inbreeding had negative effects (P ≤ 0.01) on BW (-0.09 kg), W378 (-2.86 kg), W550 (-2.95 kg), HH378 (-0.10 cm), and H550 (-0.29 cm). The lowest and highest heritability estimates were obtained for W210 (0.21 ± 0.07) and HH550 (0.57 ± 0.06), respectively. The genetic correlations were strong and positive between all traits, ranging from 0.44 ± 0.08 (SC x HH) to 0.99 ± 0.01 (W378 x W550). Spearman correlations between EBVs obtained with or without inbreeding effect ranged from 0.968 to 0.995 (P < 0.01). The results indicate loss of productive performance in inbred animals. However, the inclusion of inbreeding coefficient in genetic evaluation models did not alter the magnitude of genetic parameters or genetic trends for the traits studied.

Genetic parameters for various semen production and quality traits and indicators of male and female reproductive performance in Nellore cattle.

BACKGROUND: Given the economic relevance of fertility and reproductive traits for the beef cattle industry, investigating their genetic background and developing effective breeding strategies are paramount. Considering their late and sex-dependent phenotypic expression, genomic information can contribute to speed up the rates of genetic progress per year. In this context, the main objectives of this study were to estimate variance components and genetic parameters, including heritability and genetic correlations, for fertility, female precocity, and semen production and quality (andrological attributes) traits in Nellore cattle incorporating genomic information. RESULTS: The heritability estimates of semen quality traits were low-to-moderate, while moderate-to-high estimates were observed for semen morphological traits. The heritability of semen defects ranged from low (0.04 for minor semen defects) to moderate (0.30 for total semen defects). For seminal aspect (SMN_ASPC) and bull reproductive fitness (BULL_FIT), low (0.19) and high (0.69) heritabilities were observed, respectively. The heritability estimates for female reproductive traits ranged from 0.16 to 0.39 for rebreeding of precocious females (REBA) and probability of pregnancy at 14 months (PP14), respectively. Semen quality traits were highly genetically correlated among themselves. Moderate-to-high genetic correlations were observed between the ability to remain productive in the herd until four years of age (stayability; STAY) and the other reproductive traits, indicating that selection for female reproductive performance will indirectly contribute to increasing fertility rates. High genetic correlations between BULL_FIT and female reproductive traits related to precocity (REBA and PP14) and STAY were observed. The genetic correlations between semen quality and spermatic morphology with female reproductive traits ranged from -0.22 (REBA and scrotal circumference) to 0.48 (REBA and sperm vigor). In addition, the genetic correlations between REBA with semen quality traits ranged from -0.23 to 0.48, and with the spermatic morphology traits it ranged from -0.22 to 0.19. CONCLUSIONS: All male and female fertility and reproduction traits evaluated are heritable and can be improved through direct genetic or genomic selection. Selection for better sperm quality will positively influence the fertility and precocity of Nellore females. The findings of this study will serve as background information for designing breeding programs for genetically improving semen production and quality and reproductive performance in Nellore cattle.

A structural variant at ASIP associated with the darkness of hair coat is found in multiple zebu cattle populations.

A structural variant (SV) in the agouti signaling protein gene (ASIP), namely ASIP-SV1, has been found to strongly correlate with the darkness of hair coat in specific regions of the body of bulls from the zebu (Bos indicus) Nellore breed. Here we visually analyzed the whole-genome sequence of zebu and taurine (Bos taurus) cattle to elucidate the extent of spread of ASIP-SV1 in different cattle populations. Of 216 sequences analyzed, 63 zebu (45.9%) and five taurine (6.3%) animals had at least one copy of ASIP-SV1. Four of the taurine animals presenting the SV were Romagnola cattle, a breed with history of zebu introgression. The remaining taurine animal was a Simmental, a breed frequently used in crossbreeding. These data provide evidence that ASIP-SV1 is commonly found in zebu populations, in addition to taurine animals with zebu admixture.

Effect of food supplementation on in vitro embryo production and growth performance in prepubertal Nelore heifers.

In vitro embryos production from prepubertal heifers can help contribute to breeding programs; however, strategies are necessary to increase their embryo production. The aim of this study was to investigate the effects of two nutritional plans on oocyte recovery, embryo production and growth performance of prepubertal Nelore heifers. Thirty-four Nelore heifers with age of 6.5 months were divided into two feeding treatments (NP1 and NP2). The NP1 diets served as the control and NP2 diets were formulated to contain an average of 1.22-fold more energy than NP1. After 3 months of supplementation, the animals underwent follicular aspiration (ovum pick-up, OPU) every 21 d for 3 months and embryos were produced in vitro. Wither height, chest depth, body weight and subcutaneous fat of animals were measured. The number of retrieved and viable oocytes per OPU were 1.49-fold and 1.42-fold greater in NP2 heifers (p = 0.018 and p = 0.049, respectively) than those in NP1 heifers. Heifers administered NP2 produced 29.7% blastocysts, a percentage higher than NP1 animals that produced 24.40% embryos (p < 0.05). Consequently, females in the NP2 treatment showed improved body development. These results indicate a positive effect of a higher energy diet on assisted reproduction and body development in prepubertal heifers.

Kappa and beta-casein alleles in dairy zebu cattle.

The kappa (CSN3) and beta-casein (CSN2) genes are intensively genotyped in dairy cattle for selection purposes. This information is also generated and disseminated for Zebu breeds adapted to tropical climates. The objective of this work was to gather information on the genotypes for the CSN3 and CSN2 genes in three breeds (Gyr, Guzerat and Sindhi), and to verify the genotypic frequencies in the populations. The genotype AA and allele A frequencies are high for the CSN3 gene, without changes in values over the years, possibly indicating a small gene participation in traits under selection. In addition, the A2A2 frequencies are high for the CSN2 gene (<∼0.80). It is recommended to verify the association and contribution of CSN3 genotypes in productive traits for these breeds. The potential of A2 milk production by these genetic groups is also confirmed.

Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle.

BACKGROUND: Indigenous Sudanese cattle are mainly indicine/zebu (humped) type. They thrive in the harshest dryland environments characterised by high temperatures, long seasonal dry periods, nutritional shortages, and vector disease challenges. Here, we sequenced 60 indigenous Sudanese cattle from six indigenous breeds and analysed the data using three genomic scan approaches to unravel cattle adaptation to the African dryland region. RESULTS: We identified a set of gene-rich selective sweep regions, detected mostly on chromosomes 5, 7 and 19, shared across African and Gir zebu. These include genes involved in immune response, body size and conformation, and heat stress response. We also identified selective sweep regions unique to Sudanese zebu. Of these, a 250 kb selective sweep on chromosome 16 spans seven genes, including PLCH2, PEX10, PRKCZ, and SKI, which are involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. CONCLUSIONS: Our results suggest that environmental adaptation may involve recent and ancient selection at gene-rich regions, which might be under a common regulatory genetic control, in zebu cattle.

Estimates of genetic and phenotypic parameters for feeding behaviour and feed efficiency-related traits in Nelore cattle.

The objective of this study was to obtain (co)variance components, heritability, and genetic and phenotypic correlation estimates for feed efficiency and feed behaviour-related indicator traits. Further, it aimed to predict the direct and correlated responses for feed efficiency traits when selection was applied for feeding behaviour-related traits in Nelore cattle. Phenotypic records (n = 4840) from 125 feed efficiency tests (RFI: Residual feed intake and DMI: Dry matter intake) carried out between 2011 and 2018 were considered in this study. Animals belonged to five farms located in two Brazilian geographical regions (Midwest and Southeast). Animals under similar management and environmental conditions in the feedlot were evaluated when they attained an average of 13.5 ± 4.15 months of age. Feed behaviour-related traits were also obtained, including meal criteria (MC), meal frequency (MF), average meal duration (AMD), meal duration (MD), average consumption per meal (ACM), and consumption rate (CR) through the GrowSafe System® electronic bunk system. The contemporary groups for all traits were composed of farm, management group, feed efficiency test, sex, and birth year. The (co)variance components were estimated using the restricted maximum likelihood method considering a multi-trait (n = 8) animal model. The heritability estimates for RFI (0.23 ± 0.02), DMI (0.31 ± 0.02), MF (0.65 ± 0.02), AMD (0.29 ± 0.02), ACM (0.24 ± 0.02), MD (0.41 ± 0.02), MC (0.48 ± 0.02), and CR (0.42 ± 0.02) were moderate to high. The highest genetic correlation was obtained between CR and MD (-0.91 ± 0.04), MD and AMD (0.73 ± 0.03), CR and AMD (-0.68 ± 0.04), and RFI and DMI (0.81 ± 0.02). The highest phenotypic correlation was between ACM and AMD (0.76 ± 0.02), DMI and MD (0.77 ± 0.02), and DMI and RFI (0.77 ± 0.02). Genetic improvement for feed efficiency and feeding behaviour-related traits is feasible and the results obtained herein provided valuable information regarding the genetic background of Nelore feeding behaviour-related traits. The genetic association between feeding behaviour and feed efficiency-related traits suggested that animals spending less time feeding at a low feeding rate also had lower DMI and higher feed efficiency (RFI), and likely had lower energy maintenance requirements. The relative efficiency of selection showed that feeding behaviour-related traits were not adequate indicator traits to improve RFI and DMI. The DMI might be an effective selection criterion to improve RFI and reduce the herd's maintenance requirements.

Phenotypic variation in milk fatty acid composition and its association with stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in Gir cows.

Individual variation in milk fatty acid (FA) composition has been partially attributed to stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in taurine breeds, but much less is known for Zebu breeds. This study investigated the phenotypic variation in milk FA composition, and the influence of SCD1 variants on this trait and on milk fat desaturase indices (DI) in Gir cows. The functional impact of SCD1 variants was predicted using bioinformatics tools. Milk and blood samples were collected from 312 cows distributed in 10 herds from five states of Brazil. SCD1 variants were identified through target sequencing, and milk FA composition was determined by gas chromatography. Phenotypic variation in milk FA composition fell within the range reported for taurine breeds, with SCD18 index showing the lowest variation among the DI. Fourteen SCD1 variants were identified, six of which not previously described. Regarding the A293V polymorphism, all cows were homozygous for the C allele (coding for alanine), whereas all genotypes were detected for the second SNP affecting the 293 codon (G > A), with compelling evidence for functional effects. Significant associations (based on raw p-values) were found between this SNP and C12:0, cis-9, trans-11 CLA and short-chain FA, and between another SNP (rs523411937) and C15:0 and odd-chain linear FA. A new SNP on Chr26:21277069 was associated with trans-11 C18:1, cis-9, trans-11 CLA, C18:3 n-3 and n-3 FA. These findings indicate that SCD1 polymorphisms also contributes to the phenotypic variation in milk FA composition of Gir cows, with potential use in their breeding programmes.

Sensor validation to record rumination and analysis of behavioral parameters of dairy Gyr heifers in feedlot systems.

The use of sensors for livestock monitoring has grown in the last decade, motivated not only by the search for improvements in animal production and health, but also by the better use of physical, financial, and human resources in the management of livestock. Since precision livestock farming depends on technological innovation, including the use of sensors, it is essential to validate their applicability in confined animals. Therefore, the objective was to evaluate the functioning of the SCR Heatime® HR System sensor in heifers and analyze the behavioral differences of these animals in two feedlot systems (tie-stall and loose-housing). Eleven Gyr heifers of 10 months of age and an average body weight of 179 ± 26 kg were used. Animals were equipped with the SCR Heatime® HR System 7 days before the evaluations for adaptation, with the behavioral and system studies carried out during two periods each of 5 days, for 8 h a day. Five heifers were housed in tie-stall bedding and six were housed in loose-housing. After the evaluations for a period, animals have been switched systems in the following period. While the animals had the sensors attached to their bodies, behavioral evaluations were also performed visually, every 3 min by two evaluators per system. Behavior activities were characterized as standing, lying, idle standing, idle lying, ruminating standing, ruminating lying, feed, and water intake. The regression for the rumination activity recorded between the sensor and the visual assessment was significant only for loose-housing (P = 0.0002), but the Pearson correlation between both was negative and low (r = - 0.25; P = 0.0002). The sensor overestimated rumination by 27.3% in loose-housing (28 vs. 22 min/2 h) and 38.5% in tie-stall (36 vs. 26 min/2 h). Thus, when considering the different feedlot systems, validation was not possible due to the overestimation of time spent on rumination activity determined by the sensor. In the behavioral comparison between the systems by visual assessment, there was a significant difference (P < 0.05) for the behaviors of motor activity, idle lying, total idle time, and feed intake between the animals in the two housing systems. As for idle standing, ruminating standing, total rumination time, and water intake, there was no difference (P > 0.05). However, the time spent ruminating lying was greater from 10:00 to 12:00 h (43 ± 3 min/2 h) in the tie-stall, whereas in the loose-housing the animals distribute more uniformly their rumination from 08:00 to 16:00 h (26 min/2 h on average). Therefore, the use of the SCR Heatime® HR System sensor is not recommended for Gyr heifers housed in tie-stall and loose-housing systems. Regarding the daytime range of rumination and the accuracy improvements of similar sensors, it is recommended to develop them in both feedlot systems using the periods of less rumination in early morning in tie-stall and late afternoon in loose-housing.

Genetic association between feed efficiency, growth, scrotal circumference, and carcass traits in Guzerat cattle.

The objective of this study was to estimate the genetic parameters for feed efficiency-related traits and their genetic correlations with growth, male fertility, and carcass traits using multi-trait analysis in Guzerat cattle. Further, it aimed to predict the direct and correlated responses for feed efficiency traits when selection was applied for growth, male fertility, and carcass traits. The evaluated traits were adjusted weight at 120 (W120), 210 (W210), 365 (W365), and 450 days of age (W450), adjusted scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), scrotal circumference, ribeye area (REA), backfat thickness (BFT), rump fat thickness (RFT), residual feed intake (RFI), and dry matter intake (DMI). The genetic parameters were obtained by the restricted maximum likelihood method (REML), using an animal model in multi-trait analyses. The heritability estimates for W120, W210, W365, W450, SC365, and SC450 varied from low to high (0.17 to 0.39). The carcass traits, REA, BFT, and RFT, displayed low to moderate heritability estimates, 0.27, 0.10, and 0.31, respectively. The heritability estimates for RFI (0.15) and DMI (0.23) were low and moderate, respectively. The RFI showed low genetic correlations with growth traits, ranging from - 0.07 to 0.22, from 0.03 to 0.05 for scrotal circumference, and from - 0.35 to 0.16 for carcass, except for DMI, which ranged from 0.42 to 0.46. The RFI and DMI presented enough additive genetic variability to be used as selection criteria in Guzerat breed genetic improvement program. Additionally, the response to selection for RFI would be higher when selection is performed directly for this trait. The selection for residual feed intake would not promote unfavorable correlated responses for scrotal circumference, carcass (yield and finish), and growth traits. Therefore, the selection for more efficient animals would not compromise the productive, reproductive, and carcass performance, contributing to reduce the production costs, increasing the profitability and sustainability of beef cattle production in tropical areas.

Genetic differentiation and structuration of the Gobra zebu cattle breeds reared in Senegal.

The Gobra zebu genetic breeding program has resulted in the genetic improvement of a new population. This population gained genetic characteristics that set them apart from the other cattle populations reared in Senegal. The cause of these differences might be the reproductive isolation and selection to which this population of the "Centre de Recherches Zootechniques" of Dahra has been subjected since the 1950s. This study aimed to assess the genetic differentiation and structuration of this population compared to the main cattle breeds used in Senegal. A total of 180 individuals, selected from the Gobra selection nucleus and bovine populations from four main breeds in Senegal, were included in this study. We used a panel of 21 microsatellite markers among those recommended by the Food Agriculture Organization, to conduct the molecular genotyping of our sampled populations. The basic genetic parameters of differentiation and structuration were calculated using various bioinformatics software. The results of this study, particularly the degrees of genetic differentiation (Fst), the coefficient of genetic homogeneity (Gst), and the gene flow (Nm), show a significant genetic differentiation of the Gobra from the station compared to the other populations studied. Structuring and phylogeny analyses reveal a micro-structuring within the Gobra population as a novelty. This micro-structuring clearly identifies the Gobra individuals from Dahra's station among the other Gobra populations studied. The main causes of these observations would be reproductive isolation and the selection pressure exerted on this population for several decades.