Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits.

Although the genetic correlations between complex traits have been estimated for more than a century, only recently we have started to map and understand the precise localization of the genomic region(s) that underpin these correlations. Reproductive traits are often genetically correlated. Yet, we don't fully understand the complexities, synergism, or trade-offs between male and female fertility. In this study, we used reproductive traits in two cattle populations (Brahman; BB, Tropical Composite; TC) to develop a novel framework termed correlation scan (CS). This framework was used to identify local regions associated with the genetic correlations between male and female fertility traits. Animals were genotyped with bovine high-density single nucleotide polymorphisms (SNPs) chip assay. The data used consisted of ~1000 individual records measured through frequent ovarian scanning for age at first corpus luteum (AGECL) and a laboratory assay for serum levels of insulin growth hormone (IGF1 measured in bulls, IGF1b, or cows, IGF1c). The methodology developed herein used correlations of 500-SNP effects in a 100-SNPs sliding window in each chromosome to identify local genomic regions that either drive or antagonize the genetic correlations between traits. We used Fisher's Z-statistics through a permutation method to confirm which regions of the genome harboured significant correlations. About 30% of the total genomic regions were identified as driving and antagonizing genetic correlations between male and female fertility traits in the two populations. These regions confirmed the polygenic nature of the traits being studied and pointed to genes of interest. For BB, the most important chromosome in terms of local regions is often located on bovine chromosome (BTA) 14. However, the important regions are spread across few different BTA's in TC. Quantitative trait loci (QTLs) and functional enrichment analysis revealed many significant windows co-localized with known QTLs related to milk production and fertility traits, especially puberty. In general, the enriched reproductive QTLs driving the genetic correlations between male and female fertility are the same for both cattle populations, while the antagonizing regions were population specific. Moreover, most of the antagonizing regions were mapped to chromosome X. These results suggest regions of chromosome X for further investigation into the trade-offs between male and female fertility. We compared the CS with two other recently proposed methods that map local genomic correlations. Some genomic regions were significant across methods. Yet, many significant regions identified with the CS were overlooked by other methods.

Meta-Analysis of Heifer Traits Identified Reproductive Pathways in Bos indicus Cattle.

Fertility traits measured early in life define the reproductive potential of heifers. Knowledge of genetics and biology can help devise genomic selection methods to improve heifer fertility. In this study, we used ~2400 Brahman cattle to perform GWAS and multi-trait meta-analysis to determine genomic regions associated with heifer fertility. Heifer traits measured were pregnancy at first mating opportunity (PREG1, a binary trait), first conception score (FCS, score 1 to 3) and rebreeding score (REB, score 1 to 3.5). The heritability estimates were 0.17 (0.03) for PREG1, 0.11 (0.05) for FCS and 0.28 (0.05) for REB. The three traits were highly genetically correlated (0.75-0.83) as expected. Meta-analysis was performed using SNP effects estimated for each of the three traits, adjusted for standard error. We identified 1359 significant SNPs (p-value < 9.9 × 10-6 at FDR < 0.0001) in the multi-trait meta-analysis. Genomic regions of 0.5 Mb around each significant SNP from the meta-analysis were annotated to create a list of 2560 positional candidate genes. The most significant SNP was in the vicinity of a genomic region on chromosome 8, encompassing the genes SLC44A1, FSD1L, FKTN, TAL2 and TMEM38B. The genomic region in humans that contains homologs of these genes is associated with age at puberty in girls. Top significant SNPs pointed to additional fertility-related genes, again within a 0.5 Mb region, including ESR2, ITPR1, GNG2, RGS9BP, ANKRD27, TDRD12, GRM1, MTHFD1, PTGDR and NTNG1. Functional pathway enrichment analysis resulted in many positional candidate genes relating to known fertility pathways, including GnRH signaling, estrogen signaling, progesterone mediated oocyte maturation, cAMP signaling, calcium signaling, glutamatergic signaling, focal adhesion, PI3K-AKT signaling and ovarian steroidogenesis pathway. The comparison of results from this study with previous transcriptomics and proteomics studies on puberty of the same cattle breed (Brahman) but in a different population identified 392 genes in common from which some genes-BRAF, GABRA2, GABR1B, GAD1, FSHR, CNGA3, PDE10A, SNAP25, ESR2, GRIA2, ORAI1, EGFR, CHRNA5, VDAC2, ACVR2B, ORAI3, CYP11A1, GRIN2A, ATP2B3, CAMK2A, PLA2G, CAMK2D and MAPK3-are also part of the above-mentioned pathways. The biological functions of the positional candidate genes and their annotation to known pathways allowed integrating the results into a bigger picture of molecular mechanisms related to puberty in the hypothalamus-pituitary-ovarian axis. A reasonable number of genes, common between previous puberty studies and this study on early reproductive traits, corroborates the proposed molecular mechanisms. This study identified the polymorphism associated with early reproductive traits, and candidate genes that provided a visualization of the proposed mechanisms, coordinating the hypothalamic, pituitary, and ovarian functions for reproductive performance in Brahman cattle.

Management practices to control gastrointestinal parasites in sheep farms in Minas Gerais, southeastern Brazil / Práticas de manejo para controle de parasitas gastrointestinais em fazendas com ovinos em Minas Gerais, Sudeste do Brasil

Parasite related problems are considered one of the major health problems for sheep breeding, causing considerable economic losses to commercial husbandry. The aim of this study was to determine the technological level and the level of knowledge of farmers regarding management practices to control gastrointestinal parasites in sheep in Minas Gerais state, southeastern Brazil. The analysis was based on 213 questionnaires applied by official veterinarians of the State Government Agency for Animal Health (Instituto Mineiro de Agropecuária, IMA), covering 16.6% of all counties. From two hundred and thirteen sheep farms sampled, 117 farms had their technological level determined. From the samples, 0.9% were characterized as high level, 45.3% as medium, and 53.0% as low technological level. The flock size ranged from 2 to 1843 with an average of 80.5 sheep per farm. The majority of the sheep production systems was extensive/semi-extensive (74.5%). The management practices adopted by the farmers to reduce parasitism were: split young and adult animals (5.6%), change pasture after deworm the animals (5.2%), use quarantine for incoming animals (2.3%), deworm newly arrived sheep (1.5%), and have regular technical assistance (31.9%). Although 76.5% of the farmers medicate the animals, treatments were performed without any major technical criteria, with an average interval of 4.6 months. The most commonly used drug families were macrocyclic lactones (38.5%) and benzimidazoles (24.9%). The management practices adopted in Minas Gerais are based on old recommendations and may not return in a good set of strategies to prevent parasite infections. Field observations reinforce the finding where farmers have obtained unsatisfactory results in maintaining the health and productivity level of their enterprises.

Problemas relacionados com parasitas são considerados um dos principais problemas sanitários na criação de ovinos, causando consideráveis perdas econômicas para criação comercial. O objetivo deste estudo foi determinar o nível tecnológico e o nível de conhecimento dos criadores sobre práticas de manejo para o controle de parasitas gastrintestinais em ovinos no estado de Minas Gerais, sudeste do Brasil. A análise foi baseada em 213 questionários aplicados pelos veterinários oficiais da Agência de Governo Estudal de Saúde Animal (Instituto Mineiro de Agropecuária, IMA), cobrindo 16,6% de todos os municípios. Duzentos e treze propriedades com ovinos foram amostradas e 117 tiveram o seu nível tecnológico determinado. A partir da amostra, 0,9% foi caracterizado como nível elevado, de 45,3%, como de médio e 53,0% como baixo nível tecnológico. O tamanho do rebanho variou de 2 a 1843 com uma média de 80,5 ovinos por propriedade. A maioria dos sistemas de produção de ovinos eram extensivos/semi-extensivos (74,5%). As práticas de manejo adotadas pelos criadores para reduzir o parasitismo foram: separar animais jovens e adultos (5,6%), mudança de pastagem após vermifugar os animais (5,2%), uso de quarentena para animais recem adiquiridos (2,3%), vermifugação de ovelhas recém-chegadas (1,5%) e assistência técnica regular (31,9%). Apesar de 76,5% dos criadores vermifugarem os animais, os tratamentos foram realizados sem qualquer critério técnico importante, com um intervalo médio de 4,6 meses. As famílias de drogas mais comumente usadas foram lactonas macrocíclicas (38,5%) e benzimidazóis (24,9%). As práticas de manejo adotadas em Minas Gerais são baseadas em recomendações antigas e não em estratégias para prevenir infecções parasitárias. As observações de campo reforçam os achados em que os proprietários obtiveram resultados insatisfatórios na manutenção dos níveis de saúde e produtividade de seus empreendimentos.