Heritability estimates and genome-wide association study of methane emission traits in Nellore cattle.

The objectives of the present study were to estimate the heritability for daily methane emission (CH4) and residual daily methane emission (CH4res) in Nellore cattle, as well as to perform genome-wide association studies (GWAS) to identify genomic regions and candidate genes influencing the genetic variation of CH4 and CH4res. Methane emission phenotypes of 743 Nellore animals belonging to 3 breeding programs were evaluated. CH4 was measured using the sulfur hexafluoride (SF6) tracer technique (which involves an SF6 permeation tube introduced into the rumen, and an appropriate apparatus on each animal), and CH4res was obtained as the difference between observed CH4 and CH4 adjusted for dry matter intake. A total of 6,252 genotyped individuals were used for genomic analyses. Data were analyzed with a univariate animal model by the single-step GBLUP method using the average information restricted maximum likelihood (AIREML) algorithm. The effects of single nucleotide polymorphisms (SNPs) were obtained using a single-step GWAS approach. Candidate genes were identified based on genomic windows associated with quantitative trait loci (QTLs) related to the 2 traits. Annotation of QTLs and identification of candidate genes were based on the initial and final coordinates of each genomic window considering the bovine genome ARS-UCD1.2 assembly. Heritability estimates were of moderate to high magnitude, being 0.42 ±â€…0.09 for CH4 and 0.21 ±â€…0.09 for CH4res, indicating that these traits will respond rapidly to genetic selection. GWAS revealed 11 and 15 SNPs that were significantly associated (P < 10-6) with genetic variation of CH4 and CH4res, respectively. QTLs associated with feed efficiency, residual feed intake, body weight, and height overlapped with significant markers for the traits evaluated. Ten candidate genes were present in the regions of significant SNPs; 3 were associated with CH4 and 7 with CH4res. The identified genes are related to different functions such as modulation of the rumen microbiota, fatty acid production, and lipid metabolism. CH4 and CH4res presented sufficient genetic variation and may respond rapidly to selection. Therefore, these traits can be included in animal breeding programs aimed at reducing enteric methane emissions across generations.

Genetic selection designed to reduce the amount of enteric methane emission from livestock is a mitigation strategy to ensure more sustainable production over generations since genetic gains are cumulative. Brazil is a large producer of beef, and the Nellore breed (Bos taurus indicus) plays a very important role in this production. There are a few studies evaluating genetic and genomic aspects of enteric methane emission in Nellore cattle. The objectives of the present study were to estimate the heritability of daily methane emission (CH4) and residual daily methane emission (CH4res) in Nellore cattle, as well as to identify genomic regions and candidate genes associated with genetic variation of these traits. The heritability estimates for CH4 and CH4res were of moderate to high magnitude (0.42 ±â€…0.09 and 0.21 ±â€…0.09, respectively). Genome-wide association analyses revealed new loci associated with methane emission in Nellore cattle on chromosomes 5, 11, 17, and 20, where 10 candidate genes were identified, 3 for CH4 and 7 for CH4res. The 2 traits possess sufficient genetic variability to be included as selection criteria in breeding programs.

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.

Genetic parameters and genome-wide association studies for mozzarella and milk production traits, lactation length, and lactation persistency in Murrah buffaloes.

Genetic and genomic analyses of longitudinal traits related to milk production efficiency are paramount for optimizing water buffaloes breeding schemes. Therefore, this study aimed to (1) compare single-trait random regression models under a single-step genomic BLUP setting based on alternative covariance functions (i.e., Wood, Wilmink, and Ali and Schaeffer) to describe milk (MY), fat (FY), protein (PY), and mozzarella (MZY) yields, fat-to-protein ratio (FPR), somatic cell score (SCS), lactation length (LL), and lactation persistency (LP) in Murrah dairy buffaloes (Bubalus bubalis); (2) combine the best functions for each trait under a multiple-trait framework; (3) estimate time-dependent SNP effects for all the studied longitudinal traits; and (4) identify the most likely candidate genes associated with the traits. A total of 323,140 test-day records from the first lactation of 4,588 Murrah buffaloes were made available for the study. The model included the average curve of the population nested within herd-year-season of calving, systematic effects of number of milkings per day, and age at first calving as linear and quadratic covariates, and additive genetic, permanent environment, and residual as random effects. The Wood model had the best goodness of fit based on the deviance information criterion and posterior model probabilities for all traits. Moderate heritabilities were estimated over time for most traits (0.30 ± 0.02 for MY; 0.26 ± 0.03 for FY; 0.45 ± 0.04 for PY; 0.28 ± 0.05 for MZY; 0.13 ± 0.02 for FPR; and 0.15 ± 0.03 for SCS). The heritability estimates for LP ranged from 0.38 ± 0.02 to 0.65 ± 0.03 depending on the trait definition used. Similarly, heritabilities estimated for LL ranged from 0.10 ± 0.01 to 0.14 ± 0.03. The genetic correlation estimates across days in milk (DIM) for all traits ranged from -0.06 (186-215 DIM for MY-SCS) to 0.78 (66-95 DIM for PY-MZY). The SNP effects calculated for the random regression model coefficients were used to estimate the SNP effects throughout the lactation curve (from 5 to 305 d). Numerous relevant genomic regions and candidate genes were identified for all traits, confirming their polygenic nature. The candidate genes identified contribute to a better understanding of the genetic background of milk-related traits in Murrah buffaloes and reinforce the value of incorporating genomic information in their breeding programs.

Candidate genes for longitudinal traits under sequential sampling in beef cattle.

Both the measurement age of a longitudinal trait and the common pre-sampling procedures used in beef cattle herds may affect the identification of a functional candidate gene (FCG) that is potentially associated with a trait. To identify the FCG that takes part in the genetic control of body weight at five different ages in a beef cattle population with and without sequential sampling, the animals were weighed at different measurement events, around 330, 385, 440, 495 and 550 days old. Genetic parameters were estimated for body weight at each age using a single trait (STM) and a random regression model (RRM). In addition, two different databases were used to estimate the genetic parameters: the first (DB100) was formed by all animals that were weighed in the five measurement events, and the second (DB70) has records of the same population, considering that 70% of the heaviest animals were selected after each measurement event. For DB100, genome-wide association studies (GWAS) were performed with 21,667 SNP markers to identify genomic windows that explained at least 1% of the genetic variance. Additionally, prioritization analyses were performed and FCGs were selected. We associated seven different FCGs with body weight at different ages. Among them, the gene DUSP10 was suggested as FCG in all five ages evaluated. Genetic parameters estimated for body weight using DB100 were similar when STM and RRM were applied. However, when DB70 was used as phenotypic data, there were differences between the two models. When the STM was applied, there were differences between the genetic parameters estimated for body weight when DB100 or DB70 were used as sources of phenotypes, but not for the estimates obtained with RRM. The importance of each gene for animal growth can change at different ages, and different genes may be more relevant to body weight at each different growth stage for beef cattle. Besides, sequential sampling can affect the GWAS results of a longitudinal trait. The age of the animal when a longitudinal trait is measured and pre-sampling can also contribute to inconsistencies in GWAS results for body weight in beef cattle, depending on the time when that data were collected, and consequently on the identification of FCG between studies, even when models that consider a covariance structure are used.

Genome-wide association and functional genomic analyses for various hoof health traits in North American Holstein cattle.

Hoof diseases are a major welfare and economic issue in the global dairy cattle production industry, which can be minimized through improved management and breeding practices. Optimal genetic improvement of hoof health could benefit from a deep understanding of the genetic background and biological underpinning of indicators of hoof health. Therefore, the primary objectives of this study were to perform genome-wide association studies, using imputed high-density genetic markers data from North American Holstein cattle, for 8 hoof-related traits: digital dermatitis, sole ulcer, sole hemorrhage, white line lesion, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, and toe ulcer, and a hoof health index. De-regressed estimated breeding values from 25,580 Holstein animals were used as pseudo-phenotypes for the association analyses. The genomic quality control, genotype phasing, and genotype imputation were performed using the PLINK (version 1.9), Eagle (version 2.4.1), and Minimac4 software, respectively. The functional genomic analyses were performed using the GALLO R package and the DAVID platform. We identified 22, 34, 14, 22, 28, 33, 24, 43, and 15 significant markers for digital dermatitis, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, sole hemorrhage, sole ulcer, toe ulcer, white line lesion disease, and the hoof health index, respectively. The significant markers were located across all autosomes, except BTA10, BTA12, BTA20, BTA26, BTA27, and BTA28. Moreover, the genomic regions identified overlap with various previously reported quantitative trait loci for exterior, health, meat and carcass, milk, production, and reproduction traits. The enrichment analyses identified 44 significant gene ontology terms. These enriched genomic regions harbor various candidate genes previously associated with bone development, metabolism, and infectious and immunological diseases. These findings indicate that hoof health traits are highly polygenic and influenced by a wide range of biological processes.

Genome-wide association study for reproduction traits in Colombian Creole Blanco Orejinegro cattle.

The profitability of the beef cattle production system relies heavily on reproductive traits. Unfortunately, certain traits, such as age at first calving (AFC), calving interval (CI), and gestation length (GL), can pose challenges in traditional breeding programs because of their low heritability (0.01-0.12) and sex-limited characteristics. Another important aspect is the conservation of the genetic resources of animals adapted to the Colombian regions, which implies the preservation and rational use of the creole breeds in the country market. Therefore, this study aimed to identify genomic regions in the creole cattle breed Blanco Orejinegro (BON) that influence the reproductive traits in females. The dataset comprised 439 animals and 118,116 single-nucleotide polymorphisms' (SNPs) markers. The GS3 program was used to identify the SNP effects employing the BAYES Cπ methodology. The number of SNPs with effect for AFC was 25, 1527 for CI, and 23 for GL. Some of the genes found associated with reproductive and growth traits as well as immune response and environmental adaptation ECE1, EPH, EPHB2, SMARCAL1, IGFBP5, IGFBP2, FCGRT, EGFR, MUL1, PINK1, STPG1, CNGB1, TGFB1, OXTR, IL22RA1, MYOM3, OXTR, CNR2, HIVEP3, CTPS1, CXCL8, FCGRT, MREG, TMEM169, PECR, and MC1R. Our results evidenced a high contribution of the genetic architecture of the Colombian creole cattle breed Blanco Orejinegro that may impact should be included in implementing genetic improvement and conservation programs.

Unravelling the genetic variability of host resilience to endo- and ectoparasites in Nellore commercial herds.

BACKGROUND: Host resilience (HR) to parasites can affect the performance of animals. Therefore, the aim of this study was to present a detailed investigation of the genetic mechanisms of HR to ticks (TICK), gastrointestinal nematodes (GIN), and Eimeria spp. (EIM) in Nellore cattle that were raised under natural infestation and a prophylactic parasite control strategy. In our study, HR was defined as the slope coefficient of body weight (BW) when TICK, GIN, and EIM burdens were used as environmental gradients in random regression models. In total, 1712 animals were evaluated at five measurement events (ME) at an average age of 331, 385, 443, 498, and 555 days, which generated 7307 body weight (BW) records. Of the 1712 animals, 1075 genotyped animals were used in genome-wide association studies to identify genomic regions associated with HR. RESULTS: Posterior means of the heritability estimates for BW ranged from 0.09 to 0.54 across parasites and ME. The single nucleotide polymorphism (SNP)-derived heritability for BW at each ME ranged from a low (0.09 at ME.331) to a moderate value (0.23 at ME.555). Those estimates show that genetic progress can be achieved for BW through selection. Both genetic and genomic associations between BW and HR to TICK, GIN, and EIM confirmed that parasite infestation impacted the performance of animals. Selection for BW under an environment with a controlled parasite burden is an alternative to improve both, BW and HR. There was no impact of age of measurement on the estimates of genetic variance for HR. Five quantitative trait loci (QTL) were associated with HR to EIM but none with HR to TICK and to GIN. These QTL contain genes that were previously shown to be associated with the production of antibody modulators and chemokines that are released in the intestinal epithelium. CONCLUSIONS: Selection for BW under natural infestation and controlled parasite burden, via prophylactic parasite control, contributes to the identification of animals that are resilient to nematodes and Eimeria ssp. Although we verified that sufficient genetic variation existed for HR, we did not find any genes associated with mechanisms that could justify the expression of HR to TICK and GIN.

Genome-wide association study for growth traits in Blanco Orejinegro and Romosinuano cattle.

Growth traits are economically important characteristics for the genetic improvement of local cattle breeds. Genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to perform a GWAS to identify genomic regions and genes associated to birth weight, weaning weight adjusted for 240 days, 16 months, and 24 months weight in Romosinuano (ROMO) and Blanco Orejinegro (BON) cattle. A single-step genomic-BLUP was implemented using 596 BON and 569 ROMO individuals that were genotyped with an Illumina BovineSNP50 BeadChip. There were 25 regions of interest identified on different chromosomes, with few of them simultaneously associated with two or more growth traits and some were common to both breeds. The gene mapping allowed to find 173 annotations on these regions, from which 49 represent potential candidate genes with known growth-related functions in cattle and other species. Among the regions that were associated with several growth traits, that at 24 - 27 MB of BTA14, has important candidate genes such as LYPLA1, XKR4, TMEM68 and PLAG1. Another region of interest at 0.40-0.77 Mb of BTA23 was identified in both breeds, containing KHDRBS2 as a potential candidate gene influencing body weight. Future studies targeting these regions could provide more knowledge to uncover the genetic architecture underlying growth traits in BON and ROMO cattle. The genomic regions and genes identified in this study could be used to improve the prediction of genetic merit for growth traits in these creole cattle breeds.

Genome-wide association study reveals candidate genes for traits related to meat quality in Colombian Creole hair sheep.

Genome-wide association studies (GWAS) allow identifying genomic regions related to traits of economic importance in animals of zootechnical interest. The objective of this research was to conduct a genome-wide association study on meat quality traits using the Illumina OvineSNPs50 BeadChip array. The animals were sampled in the departments of Córdoba, Cesar, and Valle del Cauca. The genotypes obtained with the Illumina OvineSNP50 BeadChip microarray were analyzed SNP (single-nucleotide polymorphism) data to conduct a GWAS for pH and water-holding capacity (WHC) traits measured after 7 days of maturation, in the Longissimus dorsi (LD) muscle, in 167 Creole hair sheep of 12 months old belonging to Pelibuey (CHSP, n = 60), Ethiopian (CHSE, n = 44), and Sudan (CHSS, n = 63) breeds. The GWAS was done using a mixed linear model (MLMA) and based on the Ovis aries v3.1 genome. The CHSE showed the lowest meat juice release and, consequently, the highest water-holding capacity (WHC = 30.6 ± 0.1), suggesting that this breed has better performance in the meat industry compared with CHSS (WHC = 41.7 ± 0.1) and CHSP (WHC = 36.8 ± 0.1), since there is a relationship between WHC and juiciness. For the character pH, it was not possible to annotate genes related to meat quality, while, for the WHC, they have obtained 11 candidate genes associated (ELOVL2, ARAP2, LOC101102527, SHOC2, AIPL1, CSRNP3, IFRD, KDM8, NANS, DAPK1, IBN2, TPM2). Particularly, ELOVL2, ARAP2, IBN2, and TPM2 genes are involved in muscle contraction and fatty acid composition in sheep. In this study, we generated a baseline for GWAS related to meat quality traits in Colombian Creole hair sheep that can be used for future genomic selection plans.

Genomic association using principal components of morphometric traits in horses: identification of genes related to bone growth.

The measurement of morphometric traits in horses is important for determining breed qualification and is one of the main selection criteria for the species. The development of an index (HPC) that consists of principal components weighted by additive genetic values allows to explore the most relevant relationships using a reduced number of variables that explain the greatest amount of variation in the data. Genome-wide association studies (GWAS) using HPC are a relatively new approach that permits to identify regions related to a set of traits. The aim of this study was to perform GWAS using HPC for 15 linear measurements as the explanatory variable in order to identify associated genomic regions and to elucidate the biological mechanisms linked to this index in Campolina horses. For GWAS, weighted single-step GBLUP was applied to HPC. The eight genomic windows that explained the highest proportion of additive genetic variance were identified. The sum of the additive variance explained by the eight windows was 95.89%. Genes involved in bone and cartilage development were identified (SPRY2, COL9A2, MIR30C, HEYL, BMP8B, LTBP1, FAM98A, and CRIM1). They represent potential positional candidates for the HPC of the linear measurements evaluated. The HPC is an efficient alternative to reduce the 15 usually measured traits in Campolina horses. Moreover, candidate genes inserted in region that explained high additive variance of the HPC were identified and might be fine-mapped for searching putative mutation/markers.

The structure of associations: Method insights from analyzing 28 clinical isolates of Cryptococcus neoformans.

Clinical isolates of a fungal pathogen from a single region or country often exhibit structural clonality or phylogenetic clustering at the sequence or MLST level; such population structure can persist also in larger samples. In efforts to improve causal understanding of pathogenesis at the molecular level, genome-wide association screening methods initially designed for other kingdoms have been applied to fungi. The example of a Colombian dataset of 28 clinical Cryptococcus neoformans VNI isolates indicates where the output from standard pipelines may need to be analyzed in new ways in order to efficiently extract hypotheses for experiments from fungal genotype-phenotype data.

Collections of clinical isolates of a human fungal pathogen can consist of clusters of genetically similar isolates. Such clustering complicates the screening for genetic associations with clinically relevant traits. We propose new methods, illustrating them for the fungus causing cryptococcosis.

Bivariate GWAS reveals pleiotropic regions among feed efficiency and beef quality-related traits in Nelore cattle.

Feed-efficient cattle selection is among the most leading solutions to reduce cost for beef cattle production. However, technical difficulties in measuring feed efficiency traits had limited the application in livestock. Here, we performed a Bivariate Genome-Wide Association Study (Bi-GWAS) and presented candidate biological mechanisms underlying the association between feed efficiency and meat quality traits in a half-sibling design with 353 Nelore steers derived from 34 unrelated sires. A total of 13 Quantitative Trait Loci (QTL) were found explaining part of the phenotypic variations. An important transcription factor of adipogenesis in cattle, the TAL1 (rs133408775) gene located on BTA3 was associated with intramuscular fat and average daily gain (IMF-ADG), and a region located on BTA20, close to CD180 and MAST4 genes, both related to fat accumulation. We observed a low positive genetic correlation between IMF-ADG (r = 0.30 ± 0.0686), indicating that it may respond to selection in the same direction. Our findings contributed to clarifying the pleiotropic modulation of the complex traits, indicating new QTLs for bovine genetic improvement.

Genome-wide association study in thoroughbred horses naturally infected with cyathostomins.

Cyathostomins are considered one of the most important parasites of horses. A group of horses within a herd can be responsible for eliminating the majority of parasite eggs. This phenotype might be explained by genetic factors. This study aimed to identify genomic regions associated with fecal egg count (FEC) and hematological parameters by performing a genomic-wide association study (GWAS) in Thoroughbred horses naturally infected with cyathostomins. Packed cell volume (PCV), differential leukocyte, and FEC were determined from 90 horses. All animals were genotyped using the Illumina Equine 70 K BeadChip panel containing 65,157 SNP markers. The five genomic windows that have explained the highest percentage of the additive genetic variance of a specific trait (top 5) were further explored to identify candidate genes. A total of 33, 21, 30, 21, and 19 genes were identified for FEC, PCV, eosinophils, neutrophils, and lymphocyte count, respectively. The top 5 marker regions explained 2.86, 2.56, 2.73, 2.33, and 2.37% of the additive genetic variation of FEC, PCV, eosinophils, neutrophils, and lymphocytes count, respectively. This is the first study correlating phenotypic horse health traits to GWAS analysis, which may be used for animal breeding activities, reducing losses due to parasite infections.

Testicular hypoplasia in Nellore Cattle: Genetic analysis and functional analysis of genome-wide association study results.

Characterized by the incomplete development of the germinal epithelium of the seminiferous tubules, Testicular hypoplasia (TH) leads to decreased sperm concentration, increased morphological changes in sperm and azoospermia. Economic losses resulting from the disposal of affected bulls reduce the efficiency of meat production systems. A genome-wide association study and functional analysis were performed to identify genomic windows and the underlying positional candidate genes associated with TH in Nellore cattle. Phenotypic and pedigree data from 207,195 animals and genotypes (461,057 single nucleotide polymorphism, SNP) from 17,326 sires were used in this study. TH was evaluated as a binary trait measured at 18 months of age. A possible correlated response on TH resulting from the selection for scrotal circumference was evaluated by using a two-trait analysis. Thus, estimated breeding values were calculated by fitting a linear-threshold animal model in a Bayesian approach. The SNP effects were estimated using the weighted single-step genomic BLUP method. Twelve non-overlapping windows of 20 adjacent SNP that explained more than 1% of the additive genetic variance were selected for candidate gene annotation. Functional and gene prioritization analysis of the candidate genes identified genes (KHDRBS3, GPX5, STAR, ERLIN2), which might play an important role in the expression of TH due to their known roles in the spermatogenesis process, synthesis of steroids and lipid metabolism.

Revealing the genetic basis of eyelid pigmentation in Hereford cattle.

Ocular squamous cell carcinoma and infectious keratoconjunctivitis are common ocular pathologies in Hereford cattle with considerable economic impact. Both pathologies have been associated with low eyelid pigmentation, and thus, genetic selection for higher eyelid pigmentation could reduce their incidence. The objective of the present study was to reveal the genetic basis of eyelid pigmentation in Hereford cattle. The analysis included a single-step genome-wide association study (ssGWAS) and a subsequent gene-set analysis in order to identify individual genes, genetic mechanisms, and biological pathways implicated in this trait. Data consisted of eyelid pigmentation records in 1,165 Hereford bulls and steers, visually assessed in five categories between 0% and 100%. Genotypic data for 774,660 single-nucleotide polymorphism markers were available for 886 animals with pigmentation records. Pedigree information of three generations of ancestors of animals with phenotype was considered in this study, with a total of 4,929 animals. Our analyses revealed that eyelid pigmentation is a moderately heritable trait, with heritability estimates around 0.41. The ssGWAS identified at least eight regions, located on BTA1, BTA3, BTA5, BTA14, BTA16, BTA18, BTA19, and BTA24, associated with eyelid pigmentation. These regions harbor genes that are directly implicated in melanocyte biology and skin pigmentation, such as ADCY8, PLD1, KITLG, and PRKCA. The gene-set analysis revealed several functional terms closely related to melanogenesis, such as positive regulation of melanocyte differentiation and regulation of ERK1 and ERK2 cascade. Overall, our findings provide evidence that eyelid pigmentation is a heritable trait influenced by many loci. Indeed, the ssGWAS detected several candidate genes that are directly implicated in melanocyte biology, including melanogenesis. This study contributes to a better understanding of the genetic and biological basis of eyelid pigmentation and presents novel information that could aid to design breeding strategies for reducing the incidence of ocular pathologies in cattle. Additional research on the genetic link between eyelid pigmentation and ocular pathologies is needed.

Low eyelid pigmentation is considered as a predisposing factor associated with common ocular pathologies in cattle, such as ocular squamous cell carcinoma and infectious keratoconjunctivitis, with considerable economic impact. The aim of our study was to investigate the genetic basis of eyelid pigmentation in Hereford cattle. The analysis included estimation of genetic parameters, a genome-wide association study, and a subsequent gene-set analysis to identify individual genes, genetic mechanisms, and biological pathways implicated in eyelid pigmentation. Our results indicate that eyelid pigmentation is a complex trait, with a moderate heritability around 0.41, and affected by multiple loci, including genes related to melanocyte biology, melanogenesis, skin pigmentation, and development of melanoma. Evidence that biological processes such as melanocyte development and melanocyte differentiation explain part of the observed variation in eyelid pigmentation were also found. Overall, this study provides a better understanding of the genetics underlying eyelid pigmentation in Hereford. Our findings could contribute to point out breeding strategies for reducing the incidence of ocular pathologies in cattle.

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.

Genomic study of the resilience of buffalo cows to a negative energy balance.

The research article was carried out with the objective of studying the genetic variation on the resilience of buffaloes to negative energy balance-NEB (measured by changes in body weight in early lactation)-as well as investigating genomic regions of interest for this trait. A model of reaction norms was used, considering milk production as the trait to be analyzed and solutions of the contemporary groups to weight changes as environmental gradient. In this methodology, the genetic value of the slope represents the measure of resilience of the animals. After the estimation step, a genome-wide association analysis was performed for the slope of the reaction norms model, to obtain a list of windows and associated genes. The heritability estimates for milk production over the resilience gradient ranged from 0.13 to 0.28, with lower values in the intermediate environmental groups. Regarding the productive resilience of dairy buffalo cows to NEB, the genomic windows with the highest contribution to the genetic variance were detected on chromosomes BBU 1, 2, 3, 4, 9, 12, 19, and 21. A functional analysis of the genes described in the selected windows indicated association with metabolic routes related to growth and immunity of the animals, with an emphasis on the STAT6 gene. The results presented indicate that there is for this trait genetic variation to be used as selection criteria, in addition to genomic regions that can increase the precision of the selection.

Genome-wide interaction study reveals epistatic interactions for beef lipid-related traits in Nellore cattle.

Gene-gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene-gene interactions using the empirical Hilbert-Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where P < 10 - 8 were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms ( P < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP-SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products.

Discovering of Genomic Variations Associated to Growth Traits by GWAS in Braunvieh Cattle.

A genome-wide association study (GWAS) was performed to elucidate genetic architecture of growth traits in Braunvieh cattle. Methods: The study included 300 genotyped animals by the GeneSeek® Genomic Profiler Bovine LDv.4 panel; after quality control, 22,734 SNP and 276 animals were maintained in the analysis. The examined phenotypic data considered birth (BW), weaning (WW), and yearling weights. The association analysis was performed using the principal components method via the egscore function of the GenABEL version 1.8-0 package in the R environment. The marker rs133262280 located in BTA 22 was associated with BW, and two SNPs were associated with WW, rs43668789 (BTA 11) and rs136155567 (BTA 27). New QTL associated with these liveweight traits and four positional and functional candidate genes potentially involved in variations of the analyzed traits were identified. The most important genes in these genomic regions were MCM2 (minichromosome maintenance complex component 2), TPRA1 (transmembrane protein adipocyte associated 1), GALM (galactose mutarotase), and NRG1 (neuregulin 1), related to embryonic cleavage, bone and tissue growth, cell adhesion, and organic development. This study is the first to present a GWAS conducted in Braunvieh cattle in Mexico providing evidence for genetic architecture of assessed growth traits. Further specific analysis of found associated genes and regions will clarify its contribution to the genetic basis of growth-related traits.

Susceptibility of Field-Collected Nyssorhynchus darlingi to Plasmodium spp. in Western Amazonian Brazil.

Mosquito susceptibility to Plasmodium spp. infection is of paramount importance for malaria occurrence and sustainable transmission. Therefore, understanding the genetic features underlying the mechanisms of susceptibility traits is pivotal to assessing malaria transmission dynamics in endemic areas. The aim of this study was to investigate the susceptibility of Nyssorhynchus darlingi-the dominant malaria vector in Brazil-to Plasmodium spp. using a reduced representation genome-sequencing protocol. The investigation was performed using a genome-wide association study (GWAS) to identify mosquito genes that are predicted to modulate the susceptibility of natural populations of the mosquito to Plasmodium infection. After applying the sequence alignment protocol, we generated the variant panel and filtered variants; leading to the detection of 202,837 SNPs in all specimens analyzed. The resulting panel was used to perform GWAS by comparing the pool of SNP variants present in Ny. darlingi infected with Plasmodium spp. with the pool obtained in field-collected mosquitoes with no evidence of infection by the parasite (all mosquitoes were tested separately using RT-PCR). The GWAS results for infection status showed two statistically significant variants adjacent to important genes that can be associated with susceptibility to Plasmodium infection: Cytochrome P450 (cyp450) and chitinase. This study provides relevant knowledge on malaria transmission dynamics by using a genomic approach to identify mosquito genes associated with susceptibility to Plasmodium infection in Ny. darlingi in western Amazonian Brazil.