Article
Biotechnology & Applied Microbiology
Jisung Jang, Kwondo Kim, Young Ho Lee, Heebal Kim
Summary: This study called and compared autosome-wide CNVs in Eurasian taurine, Asian indicine, African taurine, and African humped cattle using NGS data, revealing significant population differentiated CNVRs and genes that may be under selection, including those related to various traits. Additionally, breed- and individual-level comparisons of CNVR presence or copy number showed important CNVs potentially influencing cattle adaptation to different environments, based on the largest dataset of 336 individuals and 39 breeds analyzed with short Illumina reads.
Article
Agriculture, Dairy & Animal Science
Y. T. Utsunomiya, A. A. A. D. Fortunato, M. Milanesi, B. B. Trigo, N. F. Alves, T. S. Sonstegard, J. F. Garcia
Summary: Brazil is the largest exporter of beef in the world, with most of its beef derived from Nellore cattle. The history of Nellore cattle in Brazil involves importation of bulls from India, leading to genetic influences from both zebu and taurine breeds. Despite the small average taurine ancestry of approximately 1%, some taurine variants significantly impact traits such as body size and horn characteristics in Nellore cattle.
Article
Agriculture, Dairy & Animal Science
Gerardo Alves Fernandes Junior, Elisa Peripolli, Patricia Iana Schmidt, Gabriel Soares Campos, Lucio Flavio Macedo Mota, Maria Eugenia Zerlotti Mercadante, Fernando Baldi, Roberto Carvalheiro, Lucia Galvao de Alnuquerque
Summary: In this review, the current status of genomic selection (GS) in Bos indicus cattle and its influence on beef breeds raised in pasture-based tropical conditions is discussed. Traditional breeding programs have achieved significant genetic gains for growth-related traits, but GS has shown even higher gains compared to pedigree-based evaluations. Genomics has allowed for intensified use of young bulls and increased genetic progress for traits that are difficult to measure and record. Other important applications include screening non-proven sires for commercial herds and selecting genetically superior young females using a combination of genomic selection and embryo transfer.
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Multidisciplinary Sciences
Jessica Moraes Malheiros, Banny Silva Barbosa Correia, Caroline Ceribeli, Daniel Rodrigues Cardoso, Luiz Alberto Colnago, Stanislau Bogusz Junior, James Mark Reecy, Gerson Barreto Mourao, Luiz Lehmann Coutinho, Julio Cesar Pascale Palhares, Alexandre Berndt, Luciana Correia de Almeida Regitano
Summary: The study found a close relationship between fecal metabolite profile and ruminal metabolism in Nelore steers, with many common polar metabolites identified in both samples. The rumen had higher concentrations of polar compounds compared to feces, but fecal metabolites still represented ruminal fluid metabolites.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Heming Wu, Qingyan Huang, Xia Zhang, Zhikang Yu, Zhixiong Zhong
Summary: This study identified a high rate of chromosomal abnormalities in fetuses with miscarriage during early and middle pregnancy, with a significantly higher numerical chromosomal abnormality rate in pregnant women aged >=35 compared to <35. The early fetal chromosomal abnormality rate was higher than the middle fetal rate, and there were 168 genes enriched in the VOUS + pCNV regions, associated with 41 functions and 12 pathways.
FRONTIERS IN GENETICS
(2021)
Article
Reproductive Biology
Rafael Herrera Alvarez, Bernardo Marcozzi Bayeux, Daniel A. Joaquim, Yeda Fumie Watanabe, Patrice Humblot
Summary: The research compared antral follicle count, oocyte production, and embryonic development competence of young, long-lived, and senescent Bos indicus cows. The study found that long-lived and senescent cows had lower AFC compared to young cows, but young cows had higher oocyte production. In terms of embryonic development, young and long-lived cows had higher blastocyst formation rates.
Review
Biochemistry & Molecular Biology
Brett Trost, Livia O. Loureiro, Stephen W. Scherer
Summary: Over the past 30 years, advances in genomics technologies have revealed significant variation in the human genome, providing a foundation for the study of human genetic diseases. Each human genome contains millions of single nucleotide variants, with approximately 1% difference compared to the reference genome, and fewer than 100 new genetic variants are typically detected in the euchromatic portion of a child's genome across a generation.
HUMAN MOLECULAR GENETICS
(2021)
Article
Agronomy
Qianqian Zhang, Anna Amanda Schonherz, Mogens Sando Lund, Bernt Guldbrandtsen
Summary: This study demonstrates the combined effects of positive selection and adaptive introgression on the modern bovine genome through in-depth assessment of sequence variation on a whole-genome scale. The observed hotspots of runs of homozygosity (ROH) haplotypes were confirmed to be results of positive selection and were associated with productive traits in modern Bos taurus cattle breeds. The study also identifies the introgression events of haplotypes from Bos indicus to Bos taurus, contributing to the formation of the current bovine genome.
Article
Agriculture, Dairy & Animal Science
Nora Laseca, Antonio Molina, Mercedes Valera, Alicia Antonini, Sebastian Demyda-Peyras
Summary: This study provides a detailed characterization of CNV regions in the Pura Raza Espanola horse breed, revealing a unique pattern of genomic regions enriched in CNVs and the incidence of CNVs across the entire genome. The study also identifies genes related to olfactory pathways and immune response. The findings contribute to our understanding of CNVs in equines and their impact on genetic and phenotypic variations.
Article
Agriculture, Dairy & Animal Science
J. R. Bevilaqua, N. N. Rodrigues, G. F. Rossi, M. A. F. Pupin, M. O. Silva, M. S. Borges, L. G. Fernandes, M. E. Z. Mercadante, F. M. Monteiro, M. E. F. Oliveira
Summary: This study evaluated the potential fertility predictors in prepubertal heifers of different breeds during different follicular wave stages. The results showed that both breed and follicular wave stage had an impact on the predictors, and most of the phenotypic reproductive parameters could be characterized using a single measure.
Article
Multidisciplinary Sciences
Thaina Cortez, Horacio Montenegro, Luiz L. Coutinho, Luciana C. A. Regitano, Sonia C. S. Andrade
Summary: Evolutionary history and intense selective pressures can lead to changes in the genome of species. The genomic evolution of Bos species, particularly the economically important Nelore cattle breed in Brazil, was investigated in this study. Positive selection was observed in genes related to transport protein cobalamin, glycolipid metabolism, and hormone signaling in Nelore and B. indicus. The high gene contraction rate and the association of rapidly evolving gene families with amino acid biosynthesis, reproductive, and immune system-related pathways demonstrate the relevance of these traits from a domestication perspective. This research provides insights into how the genome responds to artificial selection and highlights the importance of selective pressures on traits relevant for animal breeding.
Article
Psychiatry
Camillo Thomas Gualtieri
Summary: The genetic origins of neuropsychiatric disorders such as autism and schizophrenia are complex and characterized by irregular behavior and variable expression. High-resolution genomewide analysis techniques have begun to illuminate the unpredictable behavior of the human genome, revealing a high degree of structural and behavioral variability that is especially relevant to brain development and function. Genomic variability is a key window into the origins of complex diseases, particularly neuropsychiatric disorders and neurodevelopmental disorders. Evolutionary genomic events are over-represented in patients with autism and schizophrenia, suggesting that the special qualities of the human genome that drove evolution might play a role in the development of these disorders.
FRONTIERS IN PSYCHIATRY
(2021)
Article
Genetics & Heredity
Foad J. Rouhani, Xueqing Zou, Petr Danecek, Tauanne Dias Amarante, Gene Koh, Qianxin Wu, Yasin Memari, Richard Durbin, Inigo Martincorena, Andrew R. Bassett, Daniel Gaffney, Serena Nik-Zainal
Summary: The study explores human induced pluripotent stem cells derived from different tissues, finding UV-related damage and mutations in skin fibroblast-derived cells, while blood-derived cells show a high prevalence of acquired mutations.
Article
Agriculture, Dairy & Animal Science
Maria Gabriela C. D. Peixoto, Maria Raquel S. Carvalho, Andrea A. Egito, Raphael S. Steinberg, Frank Angelo T. Bruneli, Marco Antonio Machado, Fernanda C. Santos, Izinara C. Rosse, Pablo Augusto S. Fonseca
Summary: The Guzera breed in Brazil has experienced genetic bottlenecks, but efforts by the scientific community and breeders have maintained high genetic diversity. The dual-purpose herds are more uniform, with beef herds preserving greater amounts of genetic diversity among groups, while the dairy herd is genetically distant from others.
Article
Agriculture, Dairy & Animal Science
S. T. Amorim, N. B. Stafuzza, S. Kluska, E. Peripolli, A. S. C. Pereira, L. F. Muller da Silveira, L. G. de Albuquerque, F. Baldi
Summary: This study identified potential candidate genes associated with lipid profile, meat quality, carcass, and feed efficiency traits in Nellore cattle through analyzing gene-gene interactions in fatty acid profile traits. These genetic interactions provide new insights into the genetic and physiological mechanisms involved in lipid-related traits and could contribute to improving human health by selecting healthier meat products. The study highlights the importance of understanding the complex genetic interactions in natural populations for better breeding and selection strategies.
Article
Multidisciplinary Sciences
Ludmilla C. Brunes, Fernando S. Baldi, Marcos F. Oliveira E. Costa, Graciela Quintans, Georgett Banchero, Raysildo B. Lobo, Claudio U. Magnabosco
Summary: This study evaluated the association between growth, carcass, and visual scores traits with precocious calving in Nellore cattle. The results showed that birth weight and backfat thickness had the highest discrimination value for early heifer pregnancy. Additionally, bone structure, musculature, depth, tail insertion, and rump scores also had high discrimination value for precocious calving.
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS
(2022)
Article
Agriculture, Dairy & Animal Science
Gustavo Pimenta Schettini, Elisa Peripolli, Pamela Almeida Alexandre, Wellington Bizarria Santos, Joao Barbosa Silva Neto, Angelica Simone Cravo Pereira, Lucia Galvao Albuquerque, Rogerio Abdallah Curi, Fernando Baldi
Summary: This study identified the transcriptomic FA profile in Nellore beef cattle and discovered genes associated with FA phenotypes. The study also conducted enrichment analysis on gene ontology and pathways.
Article
Biochemistry & Molecular Biology
Gustavo Pimenta Schettini, Elisa Peripolli, Pamela Almeida Alexandre, Wellington Bizarria dos Santos, Angelica Simone Cravo Pereira, Lucia Galvao de Albuquerque, Fernando Baldi, Rogerio Abdallah Curi
Summary: This study identified potential regulatory genes of the essential fatty acid profile in Nellore cattle finished in feedlot through differentially expressed genes analysis and two co-expression methodologies. Functional enrichment analysis was also conducted to provide insights into the genetic mechanisms underlying the beef EFA profile.
Article
Agriculture, Dairy & Animal Science
Fernando Brito Lopes, Fernando Baldi, Ludmilla Costa Brunes, Marcos Fernando Oliveira e Costa, Eduardo da Costa Eifert, Guilherme Jordao Magalhaes Rosa, Raysildo Barbosa Lobo, Claudio Ulhoa Magnabosco
Summary: This study evaluates the advantage of preselecting SNP markers using the Markov blanket algorithm in genomic prediction for carcass and meat quality traits in Nellore cattle. The results show that using the Markov blanket SNP markers can result in lower prediction accuracy compared to using all SNPs, but in certain cases, still achieve high prediction accuracy. The use of Markov blanket-identified SNP markers can improve genomic selection efficiency and management decisions.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Bianca Vilela Pires, Ana Claudia Freitas, John Lenon Klein, Thaise Pinto de Melo, Nedenia Bonvino Stafuzza, Claudia Cristina Paro de Paz
Summary: Heat stress affects the vaginal and rectal temperatures of cattle, with Bos taurus and Bos taurus indicus responding differently in terms of core body temperature. Climate zone and temperature-humidity index also impact the temperature changes in cattle.
Article
Biotechnology & Applied Microbiology
Ludmilla Costa Brunes, Carina Ubirajara de Faria, Claudio Ulhoa Magnabosco, Raysildo Barbosa Lobo, Elisa Peripolli, Ignacio Aguilar, Fernando Baldi
Summary: This study aimed to estimate the prediction ability and genetic parameters of RFI in Nellore beef cattle using regression equations for each test and the entire population. The study also evaluated the correlations between RFI and various traits. The results showed that the RFI population had higher additive genetic variance and genetic correlations with growth, reproductive, and carcass traits compared to the RFI from individual tests.
JOURNAL OF APPLIED GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Bianca Pires, Henrique G. Reolon, Natalya G. Abduch, Luana L. Souza, Leandro S. Sakamoto, Maria Eugenia Z. Mercadante, Rafael M. O. Silva, Breno O. Fragomeni, Fernando Baldi, Claudia C. P. Paz, Nedenia B. Stafuzza
Summary: This study examined the relationship between feed efficiency, water efficiency, ingestive behavior, performance, and carcass traits in beef cattle. Findings showed that utilizing residual water intake and residual feed intake can enhance environmental sustainability in beef cattle production. Furthermore, improving factors such as water and feed efficiency can contribute to economic and environmental sustainability in beef cattle production.
Article
Agriculture, Dairy & Animal Science
Luara A. Freitas, Rodrigo P. P. Savegnago, Anderson A. C. Alves, Ricardo L. D. Costa, Danisio P. P. Munari, Nedenia B. B. Stafuzza, Guilherme J. M. Rosa, Claudia C. P. Paz
Summary: This study investigated the feasibility of using easy-to-measure phenotypic traits to predict sheep resistant, resilient, and susceptible to gastrointestinal nematodes and compared the classification performances of different methods. The results showed that multinomial logistic regression and linear discriminant analysis models had the best classification performances. The use of readily available records and easily measurable traits may contribute to the identification of susceptible animals, supporting management decisions at the farm level and potentially reducing economic losses.
Article
Agriculture, Dairy & Animal Science
Joao Barbosa da Silva Neto, Elisa Peripoli, Angelica S. C. Pereira, Nedenia Bonvino Stafuzza, Raysildo B. Lobo, Heigde Fukumasu, Jose Bento Sterman Ferraz, Fernando Baldi
Summary: This study aimed to assess the impact of weighting candidate causal loci on the prediction accuracy and dispersion for growth and carcass-related traits in Nelore cattle. The heritability estimates for the traits ranged from moderate to low. The use of weighted single-step genome-wide association study improved the prediction accuracy for some traits, but not for others.
Article
Agriculture, Dairy & Animal Science
Elisa Peripolli, Nedenia Bonvino Stafuzza, Marco Antonio Machado, Joao Claudio do Carmo Panetto, Andrea Alves do Egito, Fernando Baldi, Marcos Vinicius Gualberto Barbosa da Silva
Summary: Further characterization of genetic structural variations should focus on small and endangered local breeds. A comprehensive genome-wide assessment of copy number variations (CNVs) in Brazilian cattle breeds revealed important genes and variants. The CNVR distribution is non-uniform and strongly associated with immunity and cattle resilience to harsh environments. QTLs associated with body conformation and dairy-related traits were also identified.
Article
Agriculture, Dairy & Animal Science
Juan Diego Rodriguez, Elisa Peripolli, Marisol Londono-Gil, Rafael Espigolan, Raysildo Barbosa Lobo, Rodrigo Lopez-Correa, Ignacio Aguilar, Fernando Baldi
Summary: This study evaluated the impact of SNP marker density and MAF on genomic predictions and imputation performance for beef cattle using ssGBLUP methodology. The results showed that at least 5% of SNP markers from a high-density array are necessary to obtain reliable genomic predictions and imputed genotypes. The findings suggest that developing low-density customised arrays based on MAF and even distribution of SNPs could be a cost-effective approach for implementing genomic selection in beef cattle.
ANIMAL PRODUCTION SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Leticia Silva Pereira, Ludmilla Costa Brunes, Fernando Baldi, Adriana Santana do Carmo, Byanka Bueno Soares, Valentina Magnabosco, Eduardo da Costa Eifert, Claudio Ulhoa Magnabosco
Summary: The objective of this study was to estimate genetic parameters and correlations for feed efficiency traits in Guzerat cattle using multi-trait analysis. The heritability estimates of the evaluated traits ranged from low to moderate. Residual feed intake (RFI) and dry matter intake (DMI) showed enough genetic variability to be used as selection criteria. Selection for RFI would not compromise productive, reproductive, and carcass performance, contributing to reduce production costs and increase profitability and sustainability in tropical beef cattle production.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2023)
Article
Agriculture, Dairy & Animal Science
Marisol Londono-Gil, Daniel Cardona-Cifuentes, Rafael Espigolan, Elisa Peripolli, Raysildo B. Lobo, Angelica S. C. Pereira, Ignacio Aguilar, Fernando Baldi
Summary: The aim of this study was to assess the impact of using genomic information in situations of pedigree uncertainty on genetic evaluations for growth and cow productivity traits in Nelore commercial herds. Different approaches were used to estimate genetic values, including with or without genomic information and varying pedigree structures. The results showed that the accuracy of genetic value estimation decreased as the proportion of unknown sires and maternal grandsires increased. The use of genomic information improved the accuracy of prediction for young animals without known pedigrees.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2023)
