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.

Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture-Based Systems.

Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. The measurements based on visual scores were collected in 20,807 animals raised in pasture-based systems in Brazil. In addition, 2775 animals were genotyped using a 35 K SNP chip, which contained 31,737 single nucleotide polymorphisms after quality control. Single-step GWAS was performed using the BLUPF90 software while candidate genes were identified based on the Ensembl Genes 69. PANTHER and REVIGO platforms were used to identify key biological pathways and STRING to create gene networks. Novel candidate genes were revealed associated with CONF, including ALDH9A1, RXRG, RAB2A, and CYP7A1, involved in lipid metabolism. The genes associated with PREC were ELOVL5, PID1, DNER, TRIP12, and PLCB4, which are related to the synthesis of long-chain fatty acids, lipid metabolism, and muscle differentiation. For MUSC, the most important genes associated with muscle development were SEMA6A, TIAM2, UNC5A, and UIMC1. The polymorphisms identified in this study can be incorporated in commercial genotyping panels to improve the accuracy of genomic evaluations for visual scores in beef cattle.

Heat stress response in slick vs normal-haired Criollo Limonero heifers in a tropical environment.

To assess the effect of hair type on the heat stress response, 20 Criollo Limonero heifers with slick (n = 11) or normal hair (n = 9) were studied. Under a high temperature-humidity index (THI) environment, heat stress response was assessed through physiological variables that included respiration rate (RR), heart rate (HR), ruminal frequency (RMF), rectal temperature (RT), saliva pH (SPH), and lymphocyte count (LC) in the morning (5:00 AM, 27.4 °C, 64% relative humidity, THI = 77) and afternoon (1:00 PM, 34.5 °C, 70% relative humidity, THI = 88). A case-control study using a split plot design was used. Data were analyzed using ANOVA (PROC MIXED SAS 2010) and a statistical model comprising the fixed effects of hair length, sampling hour, interaction of hair length by sampling hour, and the random effect of animal nested within hair type on physiological variables associated with heat stress response. Sampling hour influenced (P < 0.0001) RR, RT, and (P < 0.003) SPH. Hair length influenced RR (P < 0.01) and RT (P < 0.04) and tended to influence LC (P < 0.07). The interaction of sampling hour by hair influenced RR (P < 0.04), RT (P < 0.0002), and both SPH and LC (P < 0.05). During afternoon hours, slick-haired heifers had lower values for RR (81 ± 4.2 vs 102 ± 4.7 bpm; P < 0.01), RT (39.5 ± 0.1 vs 40.3 ± 0.1 C°; P < 0.002), and LC (60 ± 3.2 vs 72.3 ± 3.6; P < 0.09) than normal-haired heifers. In normal-haired heifers, SPH increased during afternoon compared to morning-hours (8.66 ± 0.1 vs 9.11 ± 0.1; P < 0.04). It was concluded that slick-coated heifers exhibited an enhanced capability to cope with heat stress compared to normal-haired heifers likely due to an enhanced capacity for heat dissipation.

Genome-wide association study and pathway analysis for fat deposition traits in nellore cattle raised in pasture-based systems.

Genome-wide association study (GWAS) is a powerful tool to identify candidate genes and genomic regions underlying key biological mechanisms associated with economically important traits. In this context, the aim of this study was to identify genomic regions and metabolic pathways associated with backfat thickness (BFT) and rump fat thickness (RFT) in Nellore cattle, raised in pasture-based systems. Ultrasound-based measurements of BFT and RFT (adjusted to 18 months of age) were collected in 11,750 animals, with 39,903 animals in the pedigree file. Additionally, 1,440 animals were genotyped using the GGP-indicus 35K SNP chip, containing 33,623 SNPs after the quality control. The single-step GWAS analyses were performed using the BLUPF90 family programs. Candidate genes were identified through the Ensembl database incorporated in the BioMart tool, while PANTHER and REVIGO were used to identify the key metabolic pathways and gene networks. A total of 18 genomic regions located on 10 different chromosomes and harbouring 23 candidate genes were identified for BFT. For RFT, 22 genomic regions were found on 14 chromosomes, with a total of 29 candidate genes identified. The results of the pathway analyses showed important genes for BFT, including TBL1XR1, AHCYL2, SLC4A7, AADAT, VPS53, IDH2 and ETS1, which are involved in lipid metabolism, synthesis of cellular amino acids, transport of solutes, transport between Golgi Complex membranes, cell differentiation and cellular development. The main genes identified for RFT were GSK3ß, LRP1B, EXT1, GRB2, SORCS1 and SLMAP, which are involved in metabolic pathways such as glycogen synthesis, lipid transport and homeostasis, polysaccharide and carbohydrate metabolism. Polymorphisms located in these candidate genes can be incorporated in commercial genotyping platforms to improve the accuracy of imputation and genomic evaluations for carcass fatness. In addition to uncovering biological mechanisms associated with carcass quality, the key gene pathways identified can also be incorporated in biology-driven genomic prediction methods.

Can Bos indicus cattle breeds be discriminated by differences in the changes of their sweat gland traits across summer and winter seasons?

This study addresses the hypothesis that Bos indicus cattle breeds can be discriminated by the changes that occur in their sweat gland traits between summer and winter seasons in tropical conditions. Samples of the skin were taken from six Bos indicus cattle breeds (eight subjects per breed), including Nellore, Cangaian, Gyr, Guzerat, Punganur, and Sindhi in winter and summer. The sweat gland epithelium (µm), glandular portion length (µm), sweat gland duct length (µm), gland depth (µm), and sweat gland density (cm2) were determined. Principal component analyses were performed to address the overall structure of breed's group, together with confirmatory analyses by the least squares procedures. Exploratory analysis showed that cattle breeds presented patterns of dissimilarity in the changes in their skin and sweat glands traits between winter and summer seasons. Breeds were separated into three groups under the two principal components, which represented 77.26% of the total variance. The first group was composed of Sindh and Guzerat cattle, which did not present modifications in the parameters assessed between seasons. The most visible alterations were observed in Gyr cattle (third group). In fact, confirmatory analyses showed that glandular portion length, sweat gland duct length, gland depth, and sweat gland density of the Gyr cattle increased (P < 0.05) during the summer season. In conclusion, the results of this investigation demonstrated that morphological traits of the skin and sweat glands associated with seasonal changes in tropical conditions were able to discriminate among Bos indicus cattle breeds.

Genomic clues of the evolutionary history of Bos indicus cattle.

Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.

RAPID COMMUNICATION: Multi-breed validation study unraveled genomic regions associated with puberty traits segregating across tropically adapted breeds1.

An efficient strategy to improve QTL detection power is performing across-breed validation studies. Variants segregating across breeds are expected to be in high linkage disequilibrium (LD) with causal mutations affecting economically important traits. The aim of this study was to validate, in a Tropical Composite cattle (TC) population, QTL associations identified for sexual precocity traits in a Nellore and Brahman meta-analysis genome-wide association study. In total, 2,816 TC, 8,001 Nellore, and 2,210 Brahman animals were available for the analysis. For that, genomic regions significantly associated with puberty traits in the meta-analysis study were validated for the following sexual precocity traits in TC: age at first corpus luteum (AGECL), first postpartum anestrus interval (PPAI), and scrotal circumference at 18 months of age (SC). We considered validated QTL those underpinned by significant markers from the Nellore and Brahman meta-analysis (P ≤ 10-4) that were also significant for a TC trait, i.e., presenting a P-value of ≤10-3 for AGECL, PPAI, or SC. We also considered as validated QTL those regions where significant markers in the reference population were at ±250 kb from significant markers in the validation population. Using this criteria, 49 SNP were validated for AGECL, 4 for PPAI, and 14 for SC, from which 5 were in common with AGECL, totaling 62 validated SNP for these traits and 30 candidate genes surrounding them. Considering just candidate genes closest to the top SNP of each chromosome, for AGECL 8 candidate genes were identified: COL8A1, PENK, ENSBTAG00000047425, BPNT1, ADAMTS17, CCHCR1, SUFU, and ENSBTAG00000046374. For PPAI, 3 genes emerged as candidates (PCBP3, KCNK10, and MRPS5), and for SC 8 candidate genes were identified (SNORA70, TRAC, ASS1, BPNT1, LRRK1, PKHD1, PTPRM, and ENSBTAG00000045690). Several candidate regions presented here were previously associated with puberty traits in cattle. The majority of emerging candidate genes are related to biological processes involved in reproductive events, such as maintenance of gestation, and some are known to be expressed in reproductive tissues. Our results suggested that some QTL controlling early puberty seem to be segregating across cattle breeds adapted to tropical conditions.

Sustainable Cattle Ranching in Practice: Moving from Theory to Planning in Colombia's Livestock Sector.

A growing population with increasing consumption of milk and dairy require more agricultural output in the coming years, which potentially competes with forests and other natural habitats. This issue is particularly salient in the tropics, where deforestation has traditionally generated cattle pastures and other commodity crops such as corn and soy. The purpose of this article is to review the concepts and discussion associated with reconciling food production and conservation, and in particular with regards to cattle production, including the concepts of land-sparing and land-sharing. We then present these concepts in the specific context of Colombia, where there are efforts to increase both cattle production and protect tropical forests, in order to discuss the potential for landscape planning for sustainable cattle production. We outline a national planning approach, which includes disaggregating the diverse cattle sector and production types, identifying biophysical, and economic opportunities and barriers for sustainable intensification in cattle ranching, and analyzing areas suitable for habitat restoration and conservation, in order to plan for both land-sparing and land-sharing strategies. This approach can be used in other contexts across the world where there is a need to incorporate cattle production into national goals for carbon sequestration and habitat restoration and conservation.