Genotype-environment interaction for milk production of Gyr cattle in Brazil and Colombia.

BACKGROUND: Genotype by environment interactions (G × E) can play an important role in cattle populations and should be included in breeding programs in order to select the best animals for different environments. OBJECTIVE: The aim of this study was to investigate the G × E for milk production of Gyr cattle in Brazil and Colombia by applying a reaction norm model used genomics information, and to identify genomic regions associated with milk production in the two countries. METHODS: The Brazilian and Colombian database included 464 animals (273 cows and 33 sires from Brazil and 158 cows from Colombia) and 27,505 SNPs. A two-trait animal model was used for milk yield adjusted to 305 days in Brazil and Colombia as a function of country of origin, which included genomic information obtained with a single-step genomic reaction norm model. The GIBBS3F90 and POSTGSf90 programs were used. RESULTS: The results obtained indicate G × E based on the reranking of bulls between Brazil and Colombia, demonstrating environmental differences between the two countries. The findings highlight the importance of considering the environment when choosing breeding animals in order to ensure the adequate performance of their progeny. Within this context, the reranking of bulls and the different SNPs associated with milk production in the two countries suggest that G × E is an important effect that should be included in the genetic evaluation of Dairy Gyr cattle in Brazil and Colombia. CONCLUSION: The Gyr breeding program can be optimized by choosing a selection environment that will allow maximum genetic progress in milk production in different environments within and between countries.

Analysis of residual feed intake in Nellore bulls of different ages, rib eye area, and backfat thickness.

The aim of the present study was to use different models that include body composition phenotypes for the evaluation of residual feed intake (RFI) in Nellore bulls of different ages. Phenotypic and genotypic data of bulls that had participated in feed efficiency tests of a commercial (COM) and an experimental (EXP) herd between 2007 and 2019 were used. The mean entry age in the two herds was 645 and 279 days, respectively. The phenotypes were evaluated: rib eye area (REA), backfat thickness (BFT), residual feed intake (RFIKOCH), RFI adjusted for REA (RFIREA), RFI adjusted for BFT (RFIBFT), and RFI adjusted for REA and BFT (RFIREA BFT). The (co)variance components and prediction of genomic estimated breeding values (GEBV) were obtained by REML using ssGBLUP in single and two-trait analyses. Spearman's correlations were calculated based on the GEBV for RFIKOCH. The RFI phenotypes exhibited moderate heritability estimates in both herds (0.17 ± 0.03 to 0.27 ± 0.04). The genetic correlation between phenotypes was positive and high (0.99) in the two herds, a fact that permitted the creation of a single database (SDB). The heritability estimates of the SDB were also of moderate magnitude for the different definitions of RFI (0.19 ± 0.04 to 0.21 ± 0.04). The genetic correlations were positive and high between RFI traits 0.97 ± 0.01 to 0.99 ± 0.01), and positive and low/moderate between REA and BFT (0.01 ± 0.10 to 0.31 ± 0.12). The selection of animals based on the GEBV for RFIKOCH did not alter the ranking of individuals selected for RFIREA, RFIBFT, and RFIREA BFT. The results of the present study suggest that records of Nellore bulls of different ages and with different body compositions can be combined in a SDB for RFI calculation. Therefore, young animals can be evaluated in feed efficiency tests in order to reduce costs and the generation interval and possibly to obtain a higher response to selection.

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia).

The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4−8 Mb, 8−16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.

Assessing the accuracy of imputation in the Gyr breed using different SNP panels.

The aim of this study was to evaluate the accuracy of imputation in a Gyr population using two medium-density panels (Bos taurus - Bos indicus) and to test whether the inclusion of the Nellore breed increases the imputation accuracy in the Gyr population. The database consisted of 289 Gyr females from Brazil genotyped with the GGP Bovine LDv4 chip containing 30 000 SNPs and 158 Gyr females from Colombia genotyped with the GGP indicus chip containing 35 000 SNPs. A customized chip was created that contained the information of 9109 SNPs (9K) to test the imputation accuracy in Gyr populations; 604 Nellore animals with information of LD SNPs tested in the scenarios were included in the reference population. Four scenarios were tested: LD9K_30KGIR, LD9K_35INDGIR, LD9K_30KGIR_NEL, and LD9K_35INDGIR_NEL. Principal component analysis (PCA) was computed for the genomic matrix and sample-specific imputation accuracies were calculated using Pearson's correlation (CS) and the concordance rate (CR) for imputed genotypes. The results of PCA of the Colombian and Brazilian Gyr populations demonstrated the genomic relationship between the two populations. The CS and CR ranged from 0.88 to 0.94 and from 0.93 to 0.96, respectively. Among the scenarios tested, the highest CS (0.94) was observed for the LD9K_30KGIR scenario. The present results highlight the importance of the choice of chip for imputation in the Gyr breed. However, the variation in SNPs may reduce the imputation accuracy even when the chip of the Bos indicus subspecies is used.

The RNA structurome in the asexual blood stages of malaria pathogen plasmodium falciparum.

Plasmodium falciparum is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and non-coding transcripts from the asexual developmental cycle in P. falciparum in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite's asexual RBC cycle. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, approximately 71% of the genes with secondary structures are found to be protein coding mRNAs. The mapping pattern of these base-paired RNAs corresponded to all regions of mRNAs, including the 5' UTR, CDS and 3' UTR as well as the start and stop codons. Histone family genes which are known to form secondary structures in their mRNAs and transcripts from genes which are important for transcriptional and post-transcriptional control, such as the unique plant-like transcription factor family, ApiAP2, DNA-/RNA-binding protein, Alba3 and proteins important for RBC invasion and malaria cytoadherence also showed strong accumulation of duplex RNA reads in various asexual stages in P. falciparum. Intriguingly, our study determined stage-specific, dynamic relationships between mRNA structural contents and translation efficiency in P. falciparum asexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs. Abbreviations: CDS: Coding Sequence; DNA: Deoxyribonucleic Acid; dsRNA: double-stranded RNA; IDC: Intra-erythrocytic Developmental Cycle (IDC); m6A: N6-methyladenosine; mRNA: Messenger RNA; ncRNA: Non-coding RNA; RBC: Red Blood cells; RBP: RNA-Binding Protein; REC: Relative Expression Counts; RNA-seq: RNA-sequencing; RNA: Ribonucleic Acid; RNP: Ribonucleoprotein; RPKM: Reads Per Kilobase of transcript Per Million; rRNA: Ribosomal RNA 16. RUFs: RNAs of Unknown Function; SHAPE: Selective 2'-hydroxyl acylation analysed by primer extension; snoRNA: Small Nucleolar RNA; snRNA: Small Nuclear RNA; SRP-RNA: Signal Recognition Particle RNA; ssRNA: (Single-stranded RNA); TE: Translation Efficiency; tRNA: transfer RNA; UTR: Untranslated Region.

Genetic principal components for reproductive and productive traits in Holstein cows reared under tropical conditions.

The objective of this study was to compare the standard multi-trait model and five reduced-rank models fitted to the first principal components and genetic parameter estimates in order to determine the most appropriate method to model the covariance structure of reproductive and productive traits in Brazilian Holstein cows. Individual records of the following traits from 5217 cows were analyzed: 305-day milk yield (MY305), peak yield, milk yield per day of calving interval, days from calving to first estrus, days from calving to last service (CLS), calving interval (CI), and gestation length. Schwarz's Bayesian information criterion was used to compare the different models. The results indicated that four principal components were necessary to model the genetic (co)variance structure, reducing the number of parameters to be estimated. Analysis of genetic and phenotypic correlations showed that milk production-related traits were strongly correlated with each other (ranging from 0.74 to 0.99), while the correlation of these traits with the reproductive traits was weak (ranging from - 0.14 to 0.27). Heritability estimates for the traits ranged from 0.03 to 0.18. The reproductive traits CLS and CI and the production trait MY305 should be included as selection criteria in dairy cattle breeding programs because they are correlated with the first two principal components, retaining 91% of the genetic variability of the data.

Proceso de alimentación en indígenas Curripaco: experiencias y significados "Ji Pai Inacu Petcha Fáa" / Feeding process in Curripaco indigenous: experiences and meanings "Ji Pai Inacu Petcha Fáa" / Processo de alimentação em indígenas Curripaco: experiências e significados "Ji Pai Inacu Petcha Fáa"

Resumen El conocimiento del proceso de la alimentación permite diseñar programas específicos en materia de seguridad alimentaria y nutricional para los diferentes grupos sociales, como es el caso de las comunidades indígenas que ameritan un enfoque diferencial. Objetivo: comprender las experiencias de los indígenas Curripaco asentados en el resguardo de Tierra Alta con relación al proceso de alimentación y el significado que le dan a este. Metodología: estudio de tipo cualitativo, con enfoque etnográfico y con técnicas para la recolección de información como la observación participante y la entrevista semiestructurada. Resultados: se obtuvieron las siguientes categorías emergentes: obtención de alimentos, con las subcategorías: el conuco, el rio o caño y la selva; preparación de los alimentos, que incluye el proceso desde que se obtienen los alimentos hasta el plato final; alimentos especiales, con dos subcategorías: los alimentos sagrados y los alimentos prohibidos; y servir el alimento, que comprende entre otras cosas la temperatura de los alimentos y el orden jerárquico dentro del grupo familiar, para servirlo. Conclusión: la preservación de las prácticas ancestrales relacionadas con el proceso de alimentación, es un elemento importante que han contribuido a la conservación de la salud de sus integrantes en el tiempo, de modo que se debe propender por proteger dichas prácticas e incluirlas como componente esencial de la promoción de la salud en los planes de seguridad alimentaria y nutricional que se gesten en el territorio.

Abstract Knowledge of the feeding process allows the design of specific programs on food and nutritional security for different social groups, as is the case of indigenous communities that deserve a differential approach. Objective: to understand the experiences of the Curripaco indigenous people settled in the Tierra Alta reservation in relation to the feeding process and the meaning they give to it. Methodology: qualitative study with an ethnographic approach and techniques such as participant observation and semi-structured interviews for collecting information. Results: the following emerging categories were obtained: obtaining food, with the subcategories the conuco, the river or pipe and the jungle; food preparation, which includes the process from the time when the food is obtained to the final dish; special foods, with two subcategories, sacred foods and forbidden foods; and serving the food which includes, among other things, the temperature of the food and the hierarchical order within the family group to serve it. Conclusion: the preservation of ancestral practices related to the feeding process is an important element that has contributed to the conservation of the health of its members over time, so that it is necessary to tend to protect these practices and include them as an essential component of health promotion in the food and nutritional security plans that are developed in the territory.

Resumo O conhecimento do processo da alimentação permite desenhar programas específicos em matéria de segurança alimentaria e nutricional para os diferentes grupos sócias, como é o caso das comunidades indígenas que merece um enfoque diferencial. Objetivo: compreender as experiências dos indígenas Curripaco assentados no resguardo de Terra Alta com relação ao processo de alimentação e o significado que lhe dão a este. Metodologia: estudo de tipo qualitativo, com enfoque etnográfico e com técnicas para a recopilação de informação como a observação participante e a entrevista semiestruturada. Resultados: obvieram-se as seguintes categorias emergentes: obtenção de alimentos, com as subcategorias: o sitio, o rio o cano e a floresta; preparação dos alimentos, que inclui o processo desde que se obtém os alimentos até o prato final; alimentos especiais, com dois subcategorias: os alimentos sagrados e os alimentos proibidos; e servir o alimento, que compreende entre outras coisas a temperatura dos alimentos e a ordem hierárquico dentro do grupo familiar, para servi-lo. Conclusão: a preservação das práticas ancestrais relacionadas com o processo de alimentação, é um elemento importante que tem contribuído à conservação da saúde de seus integrantes no tempo, de modo que se deve propender por proteger ditas práticas e inclui-las como componente essencial da promoção da saúde nos planos de segurança alimentaria e nutricional que se gestem no território.

Genome-wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus).

Runs of homozygosity (ROH) are contiguous homozygous regions of the genome. These regions can be used to identify genes associated with traits of economic interest, as well as inbreeding levels. The aim of the present study was to analyse the length and distribution of ROH islands in Gyr cattle and to identify genes within these regions. A population of 173 animals selected for beef production and a population of 291 animals selected for dairy production were used. Differences in the number of short ROH (ROH1-2 Mb ) were observed between the two populations, while the number of long ROH (ROH>16 Mb ) was similar. ROH islands with the highest incidences (>0.50) overlapped in several segments of the genome in the two populations. The genes identified were associated with milk production, growth, reproduction, immune response and resistance traits. Our results contribute to the understanding of how selection can shape the distribution of ROH and ROH islands within the same breed when animals are selected for different purposes such as dairy or beef production.

Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight.

Linkage disequilibrium (LD) plays an important role in genomic selection and mapping of quantitative trait loci (QTL). This study investigated the pattern of LD and effective population size (Ne ) in Gir cattle selected for yearling weight. For this purpose, 173 animals with imputed genotypes (from 18 animals genotyped with the Illumina BovineHD BeadChip and 155 animals genotyped with the Bovine LDv4 panel) were analysed. The LD was evaluated at distances of 25-50 kb, 50-100 kb, 100-500 kb and 0.5-1 Mb. The Ne was estimated based on 5 past generations. The r2 values (a measure of LD) were, respectively, .35, .29, .18 and .032 for the distances evaluated. The LD estimates decreased with increasing distance of SNP pairs and LD persisted up to a distance of 100 kb (r2  = .29). The Ne was greater in generations 4 and 5 (24 and 30 animals, respectively) and declined drastically after the last generation (12 animals). The results showed high levels of LD and low Ne , which were probably due to the loss of genetic variability as a consequence of the structure of the Gir population studied.

Exome sequencing in genomic regions related to racing performance of Quarter Horses.

Among horses selected for speed, the racing line of Quarter Horses is characterized by high performance in sprint races, with these animals being considered the fastest horses in the world. However, few studies have investigated in more detail the polymorphisms and genes that act on this trait. The objective of this study was to analyze exomes and UTRs in regions previously associated with this trait by GWAS in Quarter Horse racehorses with contrasting maximum speed index (SImax), prospecting causal gene polymorphisms that are related to or are in strong linkage disequilibrium with racing performance. Genotypic and phenotypic records from 360 animals of the racing line of Quarter Horses, previously genotyped with an SNP chip to obtain individual genomic estimated breeding values for performance, were used for the formation and sequencing of two groups of animals with contrasting racing performance (20 animals with superior SImax and 20 with inferior SImax). Two rapid runs were performed using two pools of libraries containing 20 and 19 samples randomly chosen among the 40 samples with contrasting SIs. A total of 1203 variants (1105 SNPs and 93 InDels) were identified in 33 regions of interest obtained previously by GWAS. Twenty-nine of the polymorphisms (24 SNPs and 5 InDels) were considered to be important based on three different and independent approaches: SIFT scores classified as deleterious (< 0.05), degree of impact on the consensus region of each polymorphism, and different allele frequencies identified by Fisher's exact test (p < 0.01) between the groups of horses with contrasting SImax. Thus, eight genes described as functional and positional candidates in previous studies (ABCG5, COL11A1, GEN1, SOCS3, MICAL1, SPTBN1, EPB41L3, and SHQ1) and nine new candidate genes (AKNA, ARMC2, FKBP15, LHX1, NOL10, TMEM192, ZFP37, FIG4, and HNRNPU), some of them with known function, were related to racing performance in Quarter Horses.

Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information.

Gir is one of the main cattle breeds raised in tropical South American countries. Strong artificial selection through its domestication resulted in increased genetic differentiation among the countries in recent years. Over the years, genomic studies in Gir have become more common. However, studies of population structure and signatures of selection in divergent Gir populations are scarce and need more attention to better understand genetic differentiation, gene flow, and genetic distance. Genotypes of 173 animals selected for growth traits and 273 animals selected for milk production were used in this study. Clear genetic differentiation between beef and dairy populations was observed. Different criteria led to genetic divergence and genetic differences in allele frequencies between the two populations. Gene segregation in each population was forced by artificial selection, promoting isolation, and increasing genetic variation between them. Results showed evidence of selective forces in different regions of the genome. A total of 282 genes were detected under selection in the test population based on the fixation index (Fst), integrated haplotype score (iHS), and cross-population extend haplotype homozygosity (XP-EHH) approaches. The QTL mapping identified 35 genes associated with reproduction, milk composition, growth, meat and carcass, health, or body conformation traits. The investigation of genes and pathways showed that quantitative traits associated to fertility, milk production, beef quality, and growth were involved in the process of differentiation of these populations. These results would support further investigations of population structure and differentiation in the Gir breed.