Article
Multidisciplinary Sciences
Jose G. Cortes-Hernandez, Felipe J. Ruiz-Lopez, Carlos G. Vasquez-Pelaez, Adriana Garcia-Ruiz
Summary: This study aimed to investigate the runs of homozygosity (ROH) in the Mexican Holstein population and their associations with milk, fat and protein yields, and conformation final score. The results showed evidence of genomic regions preserved by genetic selection, which were associated with improved productivity and functionality of dairy cattle.
Article
Agriculture, Dairy & Animal Science
Sindy Caivio-Nasner, Albeiro Lopez-Herrera, Luis G. Gonzalez-Herrera, Juan C. Rincon
Summary: In this study, genetic characteristics of Blanco Orejinegro (BON) cattle with 500 years of adaptation to the Colombian tropic were investigated, revealing recent inbreeding and identifying single nucleotide polymorphisms associated with milk yield, external appearance, production, reproduction, health, and meat carcass.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Ahmed M. Sallam, Henry Reyer, Klaus Wimmers, Francesca Bertolini, Adel Aboul-Naga, Camila U. Braz, Alaa Emara Rabee
Summary: Understanding the genomic features of local goat breeds in Egypt is crucial for successful breeding programs and conservation. This study identified genomic regions with selection signatures and detected runs of homozygosity, genomic inbreeding coefficients, and fixation index in different goat breeds. The results revealed differences in genomic structure and adaptation among breeds, providing valuable information for preservation and breeding programs.
Article
Agriculture, Dairy & Animal Science
Laura Falchi, Alberto Cesarani, Salvatore Mastrangelo, Gabriele Senczuk, Baldassare Portolano, Fabio Pilla, Nicolo P. P. Macciotta
Summary: The distribution and characteristics of runs of homozygosity in different breeds and their crosses of Bos taurus taurus and Bos taurus indicus cattle farmed globally were analyzed using SNP genotypes. The analysis included 3,263 cattle from 204 different breeds, with 23,311 SNPs retained. The results showed that runs of homozygosity can be used to identify genomic signatures related to environmental adaptation, disease resistance, coat color determinism, and production traits.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Shuaishuai Tian, Wendan Tang, Ziqi Zhong, Ziyi Wang, Xinfeng Xie, Hong Liu, Fuwen Chen, Jiaxin Liu, Yuxin Han, Yao Qin, Zhen Tan, Qian Xiao
Summary: In this study, the genetic variations and runs of homozygosity (ROH) of 235 Wenchang chickens were systematically investigated. The ROH of Wenchang chicken consists mainly of short segments, and the chickens exhibit relatively high genetic diversity. Additionally, several genes related to growth performance, stress resistance, meat traits, and fat deposition were identified. These findings are valuable for future breeding, conservation, and utilization of Wenchang and other chicken breeds.
Article
Genetics & Heredity
Hendyel A. Pacheco, Attilio Rossoni, Alessio Cecchinato, Francisco Penagaricano
Summary: Intensive selection for improved productivity has led to increased inbreeding rates and decreased genetic diversity. Inbreeding negatively impacts male fertility. This study examined the presence of runs of homozygosity (ROH) in Italian Brown Swiss cattle and their association with bull fertility.
FRONTIERS IN GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Muhammad Saif-Ur-Rehman, Faiz-Ul Hassan, James Reecy, Tingxian Deng
Summary: Runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds using genotyping technology. The dairy group showed the highest level of inbreeding, while the dual group showed the lowest level. ROH islands were found to be associated with economically important traits in dairy cattle.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Yuqiang Liu, Guoyao Zhao, Xiaojue Lin, Jiahao Zhang, Guanyu Hou, Luepei Zhang, Dewu Liu, Yaokun Li, Junya Li, Lingyang Xu
Summary: This study assessed the runs of homozygosity (ROH) pattern in three representative cattle populations in China and identified candidate genes related to important traits. The findings provide valuable insights into the genetic basis of adaptive traits and promote the conservation of Chinese indigenous cattle genetic resources.
Article
Biotechnology & Applied Microbiology
Guoyao Zhao, Yuqiang Liu, Qunhao Niu, Xu Zheng, Tianliu Zhang, Zezhao Wang, Lei Xu, Bo Zhu, Xue Gao, Lupei Zhang, Huijiang Gao, Junya Li, Lingyang Xu
Summary: This study analyzed ROH in Chinese Simmental beef cattle and identified several candidate genes associated with production traits, as well as significant regions related to production traits through association analysis. The results provide valuable insights for better understanding the association between production traits and genome homozygosity in farm animals.
Article
Agriculture, Dairy & Animal Science
Soumya Dash, Avtar Singh, S. P. Dixit, Avnish Kumar, Rajalaxmi Behera
Summary: This study investigated the haplotype structure, runs of homozygosity (ROH), effective population size, and gametic phase persistence of three indigenous dairy cattle breeds using the BovineHD SNP genotyping assay. The results showed variations in SNP quality control and haplotype block numbers among the different breeds. Gir cattle displayed the highest number of ROH regions, indicating a higher inbreeding rate. The effective population size decreased gradually over generations. The high gametic phase correlation between Sahiwal and Tharparkar suggests the potential for genomic selection among dairy breeds. The decline in effective population size emphasizes the need for conservation and genetic improvement of native germplasm.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2023)
Article
Biotechnology & Applied Microbiology
Stefano Pallotti, Matteo Picciolini, Marco Antonini, Carlo Renieri, Valerio Napolioni
Summary: This study investigated the occurrence and distribution of Runs Of Homozygosity (ROHs) across the genome of four South American Camelid species. The results showed signatures of selection in genomic regions related to production traits and adaptation to harsh environments. This information is important for further ecological and animal production studies.
Article
Genetics & Heredity
Yifei Fang, Xinyu Hao, Zhong Xu, Hao Sun, Qingbo Zhao, Rui Cao, Zhe Zhang, Peipei Ma, Yanxiao Sun, Zengmin Qi, Qingkui Wei, Qishan Wang, Yuchun Pan
Summary: Through analyzing data from Genotyping by Genome Reducing and Sequencing, the study found a high level of inbreeding in Laiwu pigs and identified genes associated with economically important traits.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Sowah Addo, Lisa Jung
Summary: This study investigated the genetic diversity and selection signatures in Blond, Swallow-bellied, and Red Mangalitsa pigs. The results showed differences between the breeds, with the closest relatedness found between Red and Blond Mangalitsa pigs. Some runs of homozygosity islands were associated with genes related to synaptic signaling and meat quality traits in Swallow-bellied and Red Mangalitsa pigs respectively.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Jan Berghoefer, Nadia Khaveh, Stefan Mundlos, Julia Metzger
Summary: This study utilizes rule-based and model-based approaches to perform ROH analysis in different pig populations, finding that both methods are highly efficient. The results demonstrate the potential of ROH analysis in detecting potential footprints of selection in pigs and identifying regions related to genetic characteristics and adaptability.
Article
Agriculture, Dairy & Animal Science
Alana Selli, Ricardo V. Ventura, Pablo A. S. Fonseca, Marcos E. Buzanskas, Lucas T. Andrietta, Julio C. C. Balieiro, Luiz F. Brito
Summary: This study focused on identifying and characterizing factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep populations worldwide, with a special emphasis on different breeding purposes and local adaptations. The use of a business intelligence tool allowed for integrated visualization of results, with findings suggesting small and frequent HRRs in the sheep genome. Further studies are recommended with higher density SNP chips for more comprehensive research. Common regions with candidate genes related to various traits, such as body size and brain functions, were also identified, indicating selective pressure in sheep breeds for different purposes.
Article
Agronomy
Seema Yadav, Xianming Wei, Priya Joyce, Felicity Atkin, Emily Deomano, Yue Sun, Loan T. Nguyen, Elizabeth M. Ross, Tony Cavallaro, Karen S. Aitken, Ben J. Hayes, Kai P. Voss-Fels
Summary: Non-additive genetic effects are important in the expression of complex traits in sugarcane, and including non-additive effects in genomic prediction models significantly improves the prediction accuracy of clonal performance. The study showed that prediction accuracies for TCH were improved using extended-GBLUP model, but no improvement was observed for CCS and Fibre.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Imtiaz A. S. Randhawa, Michael R. McGowan, Laercio R. Porto-Neto, Ben J. Hayes, Russell E. Lyons
Summary: The beef industry has seen a recent rise in the trend of polled cattle in certain breeds in Australia. While there was historical reluctance towards poll breeding due to perceived negative correlations with production, recent studies show that polledness does not have consistently negative impacts on production traits. Further research is needed to support the continued breeding of polled animals to eradicate horns naturally and reduce management costs and health risks.
Article
Biotechnology & Applied Microbiology
Katie M. O'Connor, Ben J. Hayes, Craig M. Hardner, Mobashwer Alam, Robert J. Henry, Bruce L. Topp
Summary: The study suggests that incorporating genomic selection for yield in the Australian macadamia breeding program may accelerate genetic gain due to reduction in generation length, though the cost of genotyping appears to be a constraint at present.
Article
Agriculture, Dairy & Animal Science
Nguyen N Bang, Ben J. Hayes, Russell E. Lyons, Imtiaz A. S. Randhawa, John B. Gaughan, David M. McNeill
Summary: The study found that Vietnamese smallholder dairy cows (VDC) are primarily composed of Holstein genetics, but also contain small percentages of Jersey, Brown Swiss, and zebu genes. The genetic makeup of VDC consists of various dairy breeds, making them a good genetic base for selecting high milk-producing cows with some degree of adaptation to tropical conditions.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Chian Teng Ong, Elizabeth M. Ross, Gry B. Boe-Hansen, Conny Turni, Ben J. Hayes, Ala E. Tabor
Summary: This study compares the effectiveness of different sequencing methods for profiling bovine vaginal metagenomic samples. It finds that ONT adaptive sequencing yields a higher amount of metagenomic data per 1 Gb of sequence data and has increased sequencing efficiency and long read continuity. This method improves the amount and accuracy of metagenomic data for samples with high host-to-microbe DNA ratio.
JOURNAL OF ANIMAL SCIENCE
(2022)
Review
Evolutionary Biology
Jose M. Yanez, Peng Xu, Roberto Carvalheiro, Ben Hayes
Summary: The increasing global demand for food and the challenges facing animal farming require improvements in efficiency and sustainable practices. Genomic technologies can accelerate genetic progress in animal breeding and help meet the protein needs of future human consumption.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Agriculture, Dairy & Animal Science
Bailey N. Engle, Ben J. Hayes
Summary: The allele of PLAG1 genotype is significantly and positively related to Brahman heifer fertility, but the effect diminishes with age and does not affect mature cow weight.
JOURNAL OF ANIMAL SCIENCE
(2022)
Correction
Multidisciplinary Sciences
Rajeev K. Varshney, Manish Roorkiwal, Shuai Sun, Prasad Bajaj, Annapurna Chitikineni, Mahendar Thudi, Narendra P. Singh, Xiao Du, Hari D. Upadhyaya, Aamir W. Khan, Yue Wang, Vanika Garg, Guangyi Fan, Wallace A. Cowling, Jose Crossa, Laurent Gentzbittel, Kai Peter Voss-Fels, Vinod Kumar Valluri, Pallavi Sinha, Vikas K. Singh, Cecile Ben, Abhishek Rathore, Ramu Punna, Muneendra K. Singh, Bunyamin Tar'an, Chellapilla Bharadwaj, Mohammad Yasin, Motisagar S. Pithia, Servejeet Singh, Khela Ram Soren, Himabindu Kudapa, Diego Jarquin, Philippe Cubry, Lee T. Hickey, Girish Prasad Dixit, Anne-Celine Thuillet, Aladdin Hamwieh, Shiv Kumar, Amit A. Deokar, Sushil K. Chaturvedi, Aleena Francis, Reka Howard, Debasis Chattopadhyay, David Edwards, Eric Lyons, Yves Vigouroux, Ben J. Hayes, Eric von Wettberg, Swapan K. Datta, Huanming Yang, Henry T. Nguyen, Jian Wang, Kadambot H. M. Siddique, Trilochan Mohapatra, Jeffrey L. Bennetzen, Xun Xu, Xin Liu
Article
Genetics & Heredity
Elizabeth M. Ross, Hari Sanjana, Loan T. Nguyen, YuanYuan Cheng, Stephen S. Moore, Ben J. Hayes
Summary: This study investigates the expression variation of fertility-related genes in cattle using different sequencing technologies. The findings reveal a large amount of transcriptional variation within fertility genes and highlight the limitations of using a single technology to fully characterize the transcriptional landscape.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Emily F. Mantilla Valdivieso, Elizabeth M. Ross, Ali Raza, Muhammad Noman Naseem, Muhammad Kamran, Ben J. Hayes, Nicholas N. Jonsson, Peter James, Ala E. Tabor
Summary: This study investigated the gene expression profiles of leukocytes in Brangus cattle with different resistance phenotypes to tick infestation. The findings revealed that tick infestation leads to changes in leukocyte gene expression related to chemotaxis, cytokine secretion, and inflammatory response. The altered expression of genes from the bovine MHC complex in highly resistant animals also supports the relevance of this genomic region for disease resilience.
Article
Agriculture, Dairy & Animal Science
James P. Copley, Bailey N. Engle, Elizabeth M. Ross, Shannon Speight, Geoffry Fordyce, Benjamin J. Wood, Kai P. Voss-Fels, Benjamin J. Hayes
Summary: This study aimed to understand the impact of environmental conditions on the reproductive performance of beef cattle in Northern Australia. The results showed that early puberty is important for reproductive success. The temperature humidity index had a negative effect on first lactation pregnancy and puberty, while deviation from long-term average rainfall did not significantly affect reproductive traits. Average daily weight gain was positively correlated with first lactation pregnancy and heifer pregnancy.
TRANSLATIONAL ANIMAL SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Babatunde S. Olasege, Muhammad S. Tahir, Gabriela C. Gouveia, Jagish Kour, Laercio R. Porto-Neto, Ben J. Hayes, Marina R. S. Fortes
Summary: The study used genomic information to estimate genetic parameters of female and male fertility traits in Australian tropical cattle, finding that selection for female fertility traits can benefit male fertility and vice versa. The results suggest that early-life fertility traits can be selected for within and across sexes, with potential benefits for breeding rates in tropical herds.
ANIMAL PRODUCTION SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Christie L. Warburton, Roy Costilla, Bailey N. Engle, Nicholas J. Corbet, Jack M. Allen, Geoffry Fordyce, Michael R. McGowan, Brian M. Burns, Ben J. Hayes
Summary: This study investigated quantifying population stratification in a multibreed population of cattle, finding that using breed-adjusted genomic relationship matrices did not improve prediction accuracy for lowly heritable traits, but allowed for capturing a higher proportion of additive genetic effects when estimating variance components.
ANIMAL PRODUCTION SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Beatriz B. Trigo, Adam T. H. Utsunomiya, Alvaro A. A. D. Fortunato, Marco Milanesi, Rafaela B. P. Torrecilha, Harrison Lamb, Loan Nguyen, Elizabeth M. Ross, Ben Hayes, Romulo C. M. Padula, Thayla S. Sussai, Ludmilla B. Zavarez, Rafael S. Cipriano, Maria M. T. Caminhas, Flavia L. Lopes, Cassiano Pelle, Tosso Leeb, Danika Bannasch, Derek Bickhart, Timothy P. L. Smith, Tad S. Sonstegard, Jose F. Garcia, Yuri T. Utsunomiya
Summary: The study identified a major association signal near the agouti signaling protein gene (ASIP) for darkness of hair coat (DHC) in Nellore bulls. Functional variants associated with DHC, including a structural rearrangement involving ASIP, were found through analysis of whole-genome sequence data.
GENETICS SELECTION EVOLUTION
(2021)
Article
Agriculture, Dairy & Animal Science
Gerardo A. Fernandes Junior, Roberto Carvalheiro, Henrique N. de Oliveira, Mehdi Sargolzaei, Roy Costilla, Ricardo V. Ventura, Larissa F. S. Fonseca, Haroldo H. R. Neves, Ben J. Hayes, Lucia G. de Albuquerque
Summary: The study investigated the feasibility of imputing whole-genome sequence in Nellore beef cattle, achieving high imputation accuracies per individual. The software-dependent SNP-wise imputation accuracy is particularly important for rare variants. The accuracy of imputation appears to be relatively independent of annotation classification.
GENETICS SELECTION EVOLUTION
(2021)