Article
Agriculture, Dairy & Animal Science
Rebeka Sinha, Beena Sinha, Ragini Kumari, M. R. Vineeth, Nisha Sharma, Archana Verma, Ishwar Dayal Gupta
Summary: This study measured udder traits in different breeds of cows and investigated the association between these traits and genetic polymorphisms. The results showed that specific genotypes were associated with udder characteristics in different breeds of cows.
ANIMAL BIOTECHNOLOGY
(2022)
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
Manish Kumar Sinha, Arumugam Kumaresan, Thirumala Rao Talluri, John Peter Ebenezer Samuel King, Mani Arul Prakash, Pradeep Nag, Nilendu Paul, Kathan Raval, Elango Kamaraj, V Aranganathan
Summary: In this study, high-throughput next-generation sequencing was used to identify important SNPs and novel variants associated with fertility in high-fertile (HF) and low-fertile (LF) breeding bulls. The results showed a higher number of SNPs in HF bulls compared to LF bulls. GO analysis revealed the involvement of genes with significant variations in oxidative phosphorylation and metabolic pathways in HF bulls, while genes related to Ca2++ ion binding, ribosomal structure, translation, and ribosomal small subunit assembly were found to have significant variations in LF bulls. Several candidate genes including TPT1, BOLA-DRA, CD74, RPS17, RPS28, RPS29, RPL14, RPL13, and RPS27A were identified, which are associated with sperm functionality, survival, oxidative stress, and bull fertility.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Xiaona Chen, Xinyu Duan, Qingqing Chong, Chunqing Li, Heng Xiao, Shanyuan Chen
Summary: This study analyzed the differences in DNA methylation between zebu and taurine cattle and identified pathways and candidate genes associated with disease, disease resistance, and economic traits. These findings provide a foundation for further screening of characteristic epigenetic molecular markers in zebu and support genetic improvement of domestic cattle.
Article
Agriculture, Dairy & Animal Science
Maulana M. Naji, Yuri T. Utsunomiya, Johann Solkner, Benjamin D. Rosen, Gabor Meszaros
Summary: This study compared the alignment of sequence data from different breeds of cattle to two different reference genomes, revealing that aligning to UOA_Brahman_1 detected more SNVs, especially in cross-subspecies alignments. Unexpectedly low SNV counts in certain regions suggest the presence of taurine DNA in the UOA_Brahman_1 reference genome. Analysis of taurine-introgressed loci using principal component and admixture analyses confirmed the presence of these loci.
GENETICS SELECTION EVOLUTION
(2021)
Article
Genetics & Heredity
Babette Abanda, Markus Schmid, Archile Paguem, Hanna Iffland, Siegfried Preuss, Alfons Renz, Albert Eisenbarth
Summary: Autochthonous taurine and zebu cattle from Cameroon show significant differences in resistance to endemic pathogens, potentially influenced by genetic background and breed history. Genomic analysis identified trait-associated genomic regions for different pathogens, suggesting potential for breeding resistant cattle in Northern Cameroon. Further research using larger datasets is necessary to improve resistance to pathogen infections and understand genetic structures of African multi-breed cattle populations.
Article
Genetics & Heredity
Robert N. Vaughn, Kelli J. Kochan, Aline K. Torres, Min Du, David G. Riley, Clare A. Gill, Andy D. Herring, James O. Sanders, Penny K. Riggs
Summary: The study revealed a relationship between the expression of the ACTN3 gene in skeletal muscle and feed efficiency in crossbred steers. The inefficient group showed higher expression of ACTN3 and a maternal effect was observed in ACTN3 inheritance. Additionally, a significant breed effect was found in other genes related to feed efficiency, suggesting a possible link between muscle fiber type ratio and feed efficiency.
FRONTIERS IN GENETICS
(2022)
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
Rakesh Kumar, Ishwar Dayal Gupta, Archana Verma, Sohanvir Singh, Ragini Kumari, Nishant Verma
Summary: This study identified genetic variations of the HSPB6 gene in Karan Fries cattle and found associations between certain SNPs and heat tolerance traits, suggesting potential use of these SNPs as markers for genetic selection in breeding programs.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Biology
Bosco Jose, Hari Abdul Samad, Jaya Bharati, V. Tejaswi, Pranay Konda, Khan Sharun, Manoj K. Tripathi, Sai Kumar, Meeti Punetha, Divya Mohan, V. Verma, Vikrant Singh Chouhan, V. P. Maurya, G. Taru Sharma, Puneet Kumar, Mihir Sarkar, Gyanendra Singh
Summary: Global warming has made livestock more susceptible to heat stress, threatening the sustainability of marginal farmers. This study compared the thermo-adaptability of Tharparkar calves, an indigenous breed, and crossbred calves during heat stress. The results showed that Tharparkar calves exhibited better thermo-adaptability than crossbred calves in different heat stress conditions.
JOURNAL OF THERMAL BIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Juliana Ranches, Rhaiza Alves, Marcelo Vedovatto, Elizabeth A. Palmer, Philipe Moriel, John D. Arthington
Summary: This study observed significant differences in the metabolism of copper and selenium between Angus and Brahman cattle, including concentration in the liver and variations at different stages.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Ankit Magotra, Y. C. Bangar, C. S. Patil, Pradeep Kamaldeep, Vikas Sindhu, Deepak Malik, Pradeep Chaudhary, Asha Rani Garg, Sandeep Kumar
Summary: The present study investigated the association between CXCR1 gene polymorphisms and clinical mastitis, reproductive disorders, and performance traits in Hardhenu cattle. A targeted SNP rs211042414 (C>T) in the CXCR1 gene was genotyped using PCR amplification and Bsa1 restriction enzyme digestion. Significant associations were found between the SNP and clinical mastitis occurrence. The CC genotype showed higher susceptibility to clinical mastitis and higher milk yields compared to CT and TT genotypes.
REPRODUCTION IN DOMESTIC ANIMALS
(2023)
Article
Genetics & Heredity
Seyed Milad Vahedi, Siavash Salek Ardestani, Kian Pahlevan Afshari, Seyed Mohammad Ghoreishifar, Sima Moghaddaszadeh-Ahrabi, Mohammad Hossein Banabazi, Luiz Fernando Brito
Summary: Genetic introgression from interbreeding hybridization of European and Indian cattle breeds has led to changes in the genomic composition of composite beef cattle populations. Population genetics analyses revealed historical introgression events in CB populations, and selection signal analyses identified different patterns of selection in different CB breeds.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Multidisciplinary
Narian Romanello, Andrea do Nascimento Barreto, Marco Antonio Paula de Sousa, Julio Cesar de Carvalho Balieiro, Felipe Zandonadi Brandao, Felipe Tonato, Alberto Carlos de Campos Bernardi, Jose Ricardo Macedo Pezzopane, Jose Alberto Bastos Portugal, Alexandre Rossetto Garcia
Summary: This study evaluated the microclimate and thermoregulatory and endocrine responses of zebu and composite bulls in a non-shaded pasture system (NS) and an integrated crop-livestock-forestry system (ICLF). The results showed that the ICLF system can reduce air temperature, Black Globe Temperature and Humidity Index (BGHI), and Radiant Thermal Load, providing better thermal comfort and homeothermy for the cattle.
AGRICULTURAL SYSTEMS
(2023)
Article
Biotechnology & Applied Microbiology
Xiuge Wang, Zhihua Ju, Qiang Jiang, Jifeng Zhong, Chengkun Liu, Jinpeng Wang, Jesse L. Hoff, Robert D. Schnabel, Han Zhao, Yaping Gao, Wenhao Liu, Lingling Wang, Yundong Gao, Chunhong Yang, Minghai Hou, Ning Huang, Luciana C. A. Regitano, Laercio R. Porto-Neto, Jared E. Decker, Jeremy F. Taylor, Jinming Huang
Summary: The domestication and subsequent selection of cattle led to the partitioning of ancestral genetic diversity into distinct modern lineages, with detectable genome-wide signatures of adaptation to extreme environments. The study identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds and revealed introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses highlighted candidate genes and pathways involved in hypoxia adaptation, and suggested that high altitude adaptation involved introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus.
Article
Genetics & Heredity
Muhammad S. Tahir, Laercio R. Porto-Neto, Cedric Gondro, Olasege B. Shittu, Kimberley Wockner, Tan W. L. Andre, Hugo R. Smith, Gabriela C. Gouveia, Jagish Kour, Marina R. S. Fortes
Summary: Genomic regions associated with heifer fertility were identified through GWAS and multi-trait meta-analysis, leading to the discovery of numerous candidate genes related to known fertility pathways. Functional enrichment analysis highlighted the importance of various signaling pathways in reproductive performance of Brahman cattle.
Article
Biotechnology & Applied Microbiology
Liu Yang, Yahui Gao, Mingxun Li, Ki-Eun Park, Shuli Liu, Xiaolong Kang, Mei Liu, Adam Oswalt, Lingzhao Fang, Bhanu P. Telugu, Charles G. Sattler, Cong-Jun Li, John B. Cole, Eyal Seroussi, Lingyang Xu, Lv Yang, Yang Zhou, Li Li, Hongping Zhang, Benjamin D. Rosen, Curtis P. Van Tassell, Li Ma, George E. Liu
Summary: This study conducted the first large-scale whole-genome sequencing of single sperm in livestock, revealing the distribution patterns of meiotic recombination in cattle sperm genomes. The findings provide valuable information for future studies on meiotic recombination, genome instability, and male infertility.
Article
Biotechnology & Applied Microbiology
Liu Yang, Yahui Gao, Adam Oswalt, Lingzhao Fang, Clarissa Boschiero, Mahesh Neupane, Charles G. Sattler, Cong-Jun Li, Eyal Seroussi, Lingyang Xu, Lv Yang, Li Li, Hongping Zhang, Benjamin D. Rosen, Curtis P. Van Tassell, Yang Zhou, Li Ma, George E. Liu
Summary: This study used single-cell sequencing to predict CNV events in individual sperms of two Holstein bulls and compared the results with bulk-cell sequencing. The results showed that although only some of the single sperm CNVs were validated by trio CNVs, they still had significant associations with chromosomal distribution patterns and segmental duplications.
Article
Genetics & Heredity
Gabrielle M. Becker, Joan M. Burke, Ronald M. Lewis, James E. Miller, James L. M. Morgan, Benjamin D. Rosen, Curtis P. Van Tassell, David R. Notter, Brenda M. Murdoch
Summary: Gastrointestinal nematodes pose a severe threat to sheep production. Drug resistance and environmental concerns have led to the exploration of alternative control methods. This study identified genetic variants associated with resistance to nematode infection in Katahdin sheep, providing insights into the genetic mechanisms of host response to nematodes.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Shuli Liu, Yahui Gao, Oriol Canela-Xandri, Sheng Wang, Ying Yu, Wentao Cai, Bingjie Li, Ruidong Xiang, Amanda J. Chamberlain, Erola Pairo-Castineira, Kenton D'Mellow, Konrad Rawlik, Charley Xia, Yuelin Yao, Pau Navarro, Dominique Rocha, Xiujin Li, Ze Yan, Congjun Li, Benjamin D. Rosen, Curtis P. Van Tassell, Paul M. Vanraden, Shengli Zhang, Li Ma, John B. Cole, George E. Liu, Albert Tenesa, Lingzhao Fang
Summary: Characterizing genetic regulatory variants that affect livestock gene expression is crucial for understanding the molecular mechanisms underlying economically important traits and improving genetic gain through artificial selection. In this study, we construct a Cattle Genotype-Tissue Expression atlas based on publicly available RNA-sequencing samples to provide valuable resources for the research community. We analyze the transcriptomic landscape of over 100 tissues/cell types, identify genetic associations with gene expression and alternative splicing in 23 distinct tissues, and investigate the functional implications of these regulatory effects using multiomics data. Additionally, we link gene expression in different tissues to 43 economically important traits in cattle, decoding the molecular regulatory mechanisms underlying these agronomic traits. The integration with genome-wide association studies also allows us to identify candidate genes and variants associated with these economically important traits.
Article
Genetics & Heredity
Xiao-Lin Wu, George R. Wiggans, H. Duane Norman, Asha M. Miles, Curtis P. Van Tassell, Ransom L. Baldwin, Javier Burchard, Joao Durr
Summary: This study evaluated the performance of various statistical methods for estimating daily milk yields (DMY) in Holstein and Jersey cows and found that the MCF and linear regression models had smaller biases and higher accuracies for estimating DMY.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Babatunde S. Olasege, Laercio R. Porto-Neto, Muhammad S. Tahir, Gabriela C. Gouveia, Angela Canovas, Ben J. Hayes, Marina R. S. Fortes
Summary: This study identified local genomic regions associated with the genetic correlations between male and female fertility traits using a novel framework called correlation scan (CS). The results highlighted the polygenic nature of these traits and pointed to genes of interest, providing insights into the trade-offs between male and female fertility for further investigation.
Article
Biochemistry & Molecular Biology
Yang Zhou, Lv Yang, Xiaotao Han, Jiazheng Han, Yan Hu, Fan Li, Han Xia, Lingwei Peng, Clarissa Boschiero, Benjamin D. Rosen, Derek M. Bickhart, Shujun Zhang, Aizhen Guo, Curtis P. Van Tassell, Timothy P. L. Smith, Liguo Yang, George E. Liu
Summary: A cattle pangenome representation was created based on the genome sequences of 898 cattle representing 57 breeds. The pangenome identified novel sequence and structural variants, providing valuable insights into the diversity and evolutionary history of cattle.
Article
Agriculture, Dairy & Animal Science
Muhammad S. Tahir, Laercio R. Porto-Neto, Toni Reverter-Gomez, Babatunde S. Olasege, Mirza R. Sajid, Kimberley B. Wockner, Andre W. L. Tan, Marina R. S. Fortes
Summary: Biologically informed SNP set did not show significantly better performance in predicting fertility traits in Tropical Composites compared to other SNP sets, but it captured all observed genetic variance when modeled together with biologically uninformed SNP set.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Multidisciplinary Sciences
M. Jennifer Woodward-Greene, Jason M. Kinser, Tad S. Sonstegard, Johann Soelkner, Iosif I. Vaisman, Curtis P. Van Tassell
Summary: Computer vision is a tool that can provide livestock producers with digital body measurements important for animal health and production. The scarcity of labeled training data sets poses a challenge in building these tools. To address this, the PreciseEdge image segmentation algorithm is introduced, which employs a standard image collection protocol and a semi-automated image labeling method for efficient and accurate body measurement extraction.
Article
Agriculture, Dairy & Animal Science
F. L. Guinan, G. R. Wiggans, H. D. Norman, J. W. Durr, J. B. Cole, C. P. Van Tassell, I. Misztal, D. Lourenco
Summary: Genomic selection accelerates genetic changes in populations by increasing accuracy and decreasing generation interval. The genetic gain and inbreeding levels of US dairy cattle breeds since the implementation of genomic evaluations in 2009 were examined. The Holstein and Jersey breeds have seen the most significant increase in genetic gain since then.
JOURNAL OF DAIRY SCIENCE
(2023)
Review
Agriculture, Dairy & Animal Science
Hafedh Ben Zaabza, Curtis P. Van Tassell, Jeremie Vandenplas, Paul VanRaden, Zengting Liu, Herwin Eding, Stephanie McKay, Katrine Haugaard, Martin H. Lidauer, Esa A. Mantysaari, Ismo Stranden
Summary: This paper provides an overview of different methods and computational approaches for calculating reliability, from the animal model era to the single-step genomic model era. It also discusses the challenges faced in reliability computation and presents efficient and accurate algorithms developed recently for large-scale genomic evaluations.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Multidisciplinary Sciences
Laercio R. Porto-Neto, Pamela A. Alexandre, Nicholas J. Hudson, John Bertram, Sean M. McWilliam, Andre W. L. Tan, Marina R. S. Fortes, Michael R. McGowan, Ben J. Hayes, Antonio Reverter
Summary: Worldwide, the identification and selection of fertile bulls plays a crucial role in beef production. In this study, fertility-related phenotypes and high-density DNA genotypes were collected for thousands of bulls from six tropical breeds, revealing both genetic correlations and the importance of breed representation for accurate genomic estimated breeding values. Several candidate genes associated with bull fertility traits were identified, contributing to early-life selection and genetic improvement strategies. This study also enhances our knowledge of the molecular basis of male fertility in mammals.
Article
Agriculture, Dairy & Animal Science
Badjibassa Akounda, Dominique Ouedraogo, Albert Soudre, Pamela A. Burger, Benjamin D. Rosen, Curtis P. Van Tassell, Johann Soelkner
Summary: This study explores the morphological differences between different goat populations in Burkina Faso using morphometric traits. The results show that there is no strict distinction between the two populations, indicating a close genetic relationship. Four groups were identified based on body size, representing the main breeds and their crosses. These different goat morphotypes are the result of farmers breeding practices. The study highlights the need for sustainable genetic improvement approaches for the use of these adapted local goat genetic resources.