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
Biodiversity Conservation
Wilber Hernandez-Montiel, Nubia Noemi Cob-Calan, Lilia E. Cahuich-Tzuc, Jose A. Rueda, Jorge Quiroz-Valiente, Victor Meza-Villalvazo, Roberto Zamora-Bustillos
Summary: This study analyzed the runs of homozygosity, inbreeding coefficient, and effective population size in Pelibuey sheep, and compared them between two groups of ewes. The results revealed that the length distribution of runs of homozygosity and the genes associated with prolificacy were located near LINGO2, FLRT2, ADGRB3, DGKG, DGKE, DGKB, and DGKI. These findings are important for understanding the economic activity of this species.
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
Genetics & Heredity
Anna Letko, Benoit Hedan, Anna Snell, Alexander C. Harris, Vidhya Jagannathan, Goran Andersson, Bodil S. Holst, Elaine A. Ostrander, Pascale Quignon, Catherine Andre, Tosso Leeb
Summary: Bernese mountain dogs are a large dog breed with a complex genomic architecture due to high levels of inbreeding and relatedness. They are multi-purpose companion and family dogs, but are predisposed to several genetic disorders. The analysis of whole-genome sequencing data revealed limited clustering between European and USA dogs and identified several fixed regions harboring genetic variants associated with morphological traits and diseases. The breed's strong predisposition to hematopoietic cancers may be attributed to the presence of immune cell-regulating genes in shared runs of homozygosity.
Article
Biotechnology & Applied Microbiology
Maryam Nosrati, Hojjat Asadollahpour Nanaei, Arash Javanmard, Ali Esmailizadeh
Summary: The study revealed patterns, distributions, and levels of ROHs in the sheep genome, with most ROHs being small and the level of genomic inbreeding relatively low. The inbreeding coefficients based on ROH increased with distance from Southwest Asia, with maximum values detected in North European breeds. Multiple ROH hotspots were identified across 25 different autosomes, with most detected genes related to growth, body weight, meat production, wool production, and pigmentation.
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
Biochemistry & Molecular Biology
Eleonore Lavanchy, Jerome Goudet
Summary: Genomic measures of inbreeding based on IBD segments are widely used but often rely on assumptions that can affect the accuracy of estimation. In this study, we simulated data from different genomic representations and compared the performance of two software programs for estimating IBD segments. We found that the density of SNPs required for accurate estimation varied between the two programs and was influenced by the demographic history of the population. We recommend researchers consider the specific characteristics of their data and choose the appropriate method for inbreeding estimation.
MOLECULAR ECOLOGY RESOURCES
(2023)
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
Zhong Xu, Shuqi Mei, Jiawei Zhou, Yu Zhang, Mu Qiao, Hua Sun, Zipeng Li, Lianghua Li, Binke Dong, Favour Oluwapelumi Oyelami, Junjing Wu, Xianwen Peng
Summary: The study assessed genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig, identifying genes associated with fat deposition and muscular development in ROH islands. The findings shed light on the effects of environmental and artificial selection on genome structure of composite pigs, providing a basis for genomic selection (GS) and hybrid utilization of other pig breeds.
FRONTIERS IN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Shen-He Liu, Xiao-Ya Ma, Faiz-Ul Hassan, Teng-Yun Gao, Ting-Xian Deng
Summary: The study used ROH analysis to evaluate genomic inbreeding patterns and levels in Mediterranean buffaloes, identifying ROH hotspots, candidate genes related to production traits, and genetic improvement potential through selective breeding.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Tomasz Szmatola, Artur Gurgul, Igor Jasielczuk, Ewa Oclon, Katarzyna Ropka-Molik, Monika Stefaniuk-Szmukier, Grazyna Polak, Iwona Tomczyk-Wrona, Monika Bugno-Poniewierska
Summary: This study examined the distribution of runs of homozygosity (ROH) in six different horse breeds, and found differences in the length, quantity, and frequency of ROH between breeds. The study also identified ROH islands, which may represent signals of recent selection events, and found several genes involved in important horse breed characteristics. The results can be used for further research in identifying markers unique to specific horse breed characteristics.
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
Agriculture, Dairy & Animal Science
Bethany Pilon, Kelly Hinterneder, El Hamidi A. Hay, Breno Fragomeni
Summary: Inbreeding depression refers to the decreased fitness of offspring of closely related individuals, which is a common issue in the livestock industry. The relationship between homozygosity and decreased performance is complex and varies by chromosome. Evaluating inbreeding per individual regions of the genome and focusing on specific ROH with negative effects may help to avoid inbreeding depression and increase prediction accuracy in genomic selection programs.
Article
Agriculture, Dairy & Animal Science
Xudong Wu, Ren Zhou, Yuanlang Wang, Wei Zhang, Xianrui Zheng, Guiying Zhao, Xiaodong Zhang, Zongjun Yin, Yueyun Ding
Summary: This study analyzed the genome of the local Chinese pig breed AQ pigs using resequencing technology and found that inbreeding levels were a concern and influenced by artificial selection. The study also identified genes related to immune biological processes in the ROH islands of AQ pigs.
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
Ryley J. Vanderhout, Emily M. Leishman, Heather Hiscock, Emhimad A. Abdalla, Bayode O. Makanjuola, Jeff Mohr, Alexandra Harlander-Matauschek, Shai Barbut, Benjamin J. Wood, Christine F. Baes, Nienke van Staaveren
Summary: White striping, a recent issue in the turkey industry, affects meat quality and economic value. A study found 88% of turkeys have white striping, with severity related to weight and meat yield. Evaluation of white striping in turkey genetic selection programs is needed for future research.
Article
Veterinary Sciences
Emily M. Leishman, Ryley J. Vanderhout, Nienke van Staaveren, Shai Barbut, Jeff Mohr, Benjamin J. Wood, Christine F. Baes
Summary: This study evaluated post mortem activity in turkeys during slaughter and analyzed the effects of activity, genetic line, and season on meat quality traits. The results showed that post mortem activity influenced color, drip loss, and shear force, while genetic line and season had significant effects on various meat quality traits.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Veterinary Sciences
Emily M. Leishman, Nienke van Staaveren, Vern R. Osborne, Benjamin J. Wood, Christine F. Baes, Alexandra Harlander-Matauschek
Summary: Injurious pecking is a significant welfare and economic issue in turkey production. This study investigated the risk factors for integument injuries in Canadian turkey flocks through a survey and analysis. The results showed that flock age and sex were associated with different types of pecking injuries. Aggressive pecking injuries appeared to be influenced by human interaction, while feather pecking injuries were related to litter condition and the management of sick birds. Future research should focus on these factors to better understand their relationship with the prevalence and severity of these conditions.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Editorial Material
Agriculture, Dairy & Animal Science
Joana G. P. Jacinto, Irene M. Hafliger, Christine F. Baes, Hinayah R. de Oliveira, Cord Drogemuller
Review
Agriculture, Dairy & Animal Science
Saranya G. Narayana, Ellen de Jong, Flavio S. Schenkel, Pablo A. S. Fonseca, Tatiane C. S. Chud, Diana Powell, Garrett Wachoski-Dark, Paul E. Ronksley, Filippo Miglior, Karin Orsel, Herman W. Barkema
Summary: This study conducted a systematic review and gene prioritization analysis of genome-wide association studies on resistance to mastitis in dairy cattle, and identified potential functional candidate genes associated with mastitis resistance. The findings are important for developing enhanced genomic strategies to combat mastitis by increasing mastitis resistance through genetic selection.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
L. M. Alcantara, F. S. Schenkel, C. Lynch, G. A. Oliveira, C. F. Baes, D. Tulpan
Summary: This study investigated the use of machine learning algorithms to classify different breeding protocols in dairy cattle. The results showed that a stacking classifier algorithm had the highest accuracy and recall in identifying TAI protocols, opening the opportunity for unbiased genetic evaluation based on natural fertility.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Saeed Shadpour, Tatiane C. S. Chud, Dagnachew Hailemariam, Hinayah R. Oliveira, Graham Plastow, Paul Stothard, Jan Lassen, Ransom Baldwin, Filippo Miglior, Christine F. Baes, Dan Tulpan, Flavio S. Schenkel
Summary: This study aimed to improve DMI predictions of Canadian Holstein cows using milk MIRS data with the help of artificial neural networks (ANN). Different ANN architectures were explored to predict unobserved DMI, and the robustness of developed prediction models was validated by analyzing data from dairy cows in Canada, Denmark, and the United States.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Multidisciplinary Sciences
Audrey A. A. Martin, Samir Id-Lahoucine, Pablo A. S. Fonseca, Christina M. Rochus, Lucas M. Alcantara, Dan Tulpan, Stephen J. LeBlanc, Filippo Miglior, Joaquim Casellas, Angela Canovas, Christine F. Baes, Flavio S. Schenkel
Summary: This study aimed to determine the genetic background of gametic incompatibility in Holstein cattle. By conducting a transmission ratio distortion analysis on a large number of genotyped Holstein cattle, genomic regions and functional candidate genes associated with gametic incompatibility were identified. The findings suggest that further investigation of gametic incompatibility will provide opportunities to improve mate allocation for the dairy cattle industry.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Samir Id-Lahoucine, Joaquim Casellas, Pablo A. S. Fonseca, Aroa Suarez-Vega, Flavio S. Schenkel, Angela Canovas
Summary: This study discovered the phenomenon of transmission ratio distortion (TRD) on the X-chromosome and revealed different TRD patterns and functional candidate genes.
Article
Agriculture, Dairy & Animal Science
Nienke van Staaveren, Emma Hyland, Kerry Houlahan, Colin Lynch, Filippo Miglior, David F. Kelton, Flavio S. Schenkel, Christine F. Baes
Summary: Calf diseases pose challenges for dairy producers in terms of economics and animal welfare. Genetic selection for disease resistance in calves is a promising approach for sustainable dairy farming. However, clear definitions, standardized recording practices, and data transfer procedures are needed to successfully include calf health traits in genetic evaluations.
CANADIAN JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Genetics & Heredity
Samir Id-Lahoucine, Joaquim Casellas, Filippo Miglior, Flavio S. Schenkel, Angela Canovas
Summary: This study identified biological mechanisms affecting fertility and viability of sperm and ova, leading to observable transmission ratio distortion. Gene-by-gene interactions were found to cause specific transmission distortion patterns. Using genotypic and allelic parameterization, several pairs of loci with epistatic transmission ratio distortion were identified, providing insights into economically important traits such as reproduction.
FRONTIERS IN GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Stephanie Kamalanathan, Kerry Houlahan, Filippo Miglior, Tatiane C. S. Chud, Dave J. Seymour, Dagnachew Hailemariam, Graham Plastow, Hinayah R. de Oliveira, Christine F. Baes, Flavio S. Schenkel
Summary: Dairy cows contribute to greenhouse gas emissions from livestock, and strategies involving genetics and breeding can be used to reduce methane emissions. This study assessed three definitions for methane emission traits and their genetic parameters in Holstein cattle. The heritability of daily methane production, methane yield, and methane intensity was estimated, and a high genetic correlation was found between daily methane production and methane intensity. This study suggests that genetic selection can potentially mitigate methane emissions in Holstein cattle.
Meeting Abstract
Agriculture, Dairy & Animal Science
K. Hoeksema, K. Houlahan, H. R. Oliveira, F. Miglior, F. S. Schenkel, C. F. Baes
JOURNAL OF DAIRY SCIENCE
(2022)
Meeting Abstract
Agriculture, Dairy & Animal Science
R. Bongers, K. Houlahan, F. Miglior, H. Oliveira, F. S. Schenkel, C. F. Baes
JOURNAL OF DAIRY SCIENCE
(2022)