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
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
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
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
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
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
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
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
Agriculture, Dairy & Animal Science
A. Nascimento, D. F. Cardoso, D. J. A. Santos, A. R. S. Romero, D. C. B. Scalez, R. R. A. Borquis, F. R. A. Neto, C. Gondro, H. Tonhati
Summary: Characterization of autozygosity is important for monitoring genetic diversity and managing inbreeding levels. In a population of Brazilian Murrah buffalo, inbreeding levels and hotspots were identified, with signatures of selection found in genomic regions related to milk production traits. These findings suggest the need for careful management of inbreeding to avoid negative impacts on important genetic traits.
JOURNAL OF DAIRY SCIENCE
(2021)
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
Biodiversity Conservation
Tatiana Deniskova, Arsen Dotsev, Marina Selionova, Gottfried Brem, Natalia Zinovieva
Summary: This study examines the ROH distribution and genomic inbreeding in 27 Russian local sheep breeds, finding evidence of low to moderate genomic inbreeding in major local sheep populations.
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
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
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
Julie Colpitts, Philip Dunstan McLoughlin, Jocelyn Poissant
Summary: This study reveals that Sable Island horses are more inbred than domestic breeds, and most of this inbreeding is due to historical bottlenecks and founder effects rather than recent mating between close relatives. Unique ROH islands in the Sable Island population suggest adaptation to local selective pressures and/or strong genetic drift, highlighting the value of this population as a reservoir of equine genetic variation.
Article
Biochemistry & Molecular Biology
Hamed Amirpour Najafabadi, Majid Khansefid, Ghassan Ghaith Mahmoud, Ishaku Lemu Haruna, Huitong Zhou, Jon G. H. Hickford
Summary: Advances in the study of reproductive traits suggest that functional variation in fertility genes could enhance sheep fertility. This study investigated variation in the BMP15 gene and its association with litter size in different breeds of sheep in New Zealand. Two variants were identified in exon 1, with one variant (c.31_33del) showing a significant association with litter size in composite sheep. Further research with larger sample sizes is needed to validate these results and determine if c.31_33del could serve as a genetic marker for improving fecundity in some New Zealand sheep.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
S. Shahinfar, M. Khansefid, M. Haile-Mariam, J. E. Pryce
Summary: The study investigated the performance of machine learning algorithms in predicting lameness cases in dairy cows, with Naive Bayes outperforming logistic regression in terms of F1 score. Despite data limitations, the research proved the concept of using predictive models to enhance lameness management in dairy farming.
Article
Agriculture, Dairy & Animal Science
M. Khansefid, M. Haile-Mariam, J. E. Pryce
Summary: Lameness is a significant health and welfare issue affecting cows, particularly on pasture-based dairy farms. This study found that including genetically correlated traits in a multivariate model can improve the accuracy of genetic predictions for lameness. However, to further enhance prediction accuracy, precise identification and recording of hoof or leg disorders, or large-scale recording of locomotion and claw scores by trained personnel should be considered.
JOURNAL OF DAIRY SCIENCE
(2021)
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
Plant Sciences
Huanhuan Zhao, Babu R. Pandey, Majid Khansefid, Hossein V. Khahrood, Shimna Sudheesh, Sameer Joshi, Surya Kant, Sukhjiwan Kaur, Garry M. Rosewarne
Summary: Field pea breeding can benefit from the application of genomic selection, especially when using multivariate models that incorporate normalized difference vegetation index and bacterial blight disease scores. This study found that multivariate models outperformed univariate models in predicting grain yield, leading to a significant improvement in prediction accuracy. The findings highlight the importance of considering multiple traits and using advanced breeding approaches for ongoing improvements in field pea yield and disease resistance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Veterinary Sciences
Sara Abasi-Mousa, Sheida Varkoohi, Sahereh Joezy, Nader Salary, Majid Khansefid
Summary: This study aggregated the results of different studies through meta-analysis to improve the reliability of estimated genetic parameters for growth traits in sheep. The results showed variations in genetic and phenotypic correlations between different growth traits and among different sheep breeds. The small standard errors indicated that the aggregation of results improved the reliability of estimated parameters.
VETERINARY MEDICINE AND SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Mohammad Ghoreishifar, Seyed Milad Vahedi, Siavash Salek Ardestani, Majid Khansefid, Jennie E. Pryce
Summary: Inbreeding depression adversely affects semen traits, with longer runs of homozygosity being especially detrimental. Genomic regions associated with semen traits and fertility were identified, suggesting the potential need to avoid homozygosity in these regions for artificial insemination sires.
Article
Genetics & Heredity
Huanhuan Zhao, Zibei Lin, Majid Khansefid, Josquin F. Tibbits, Matthew J. Hayden
Summary: In plant breeding programs, incorporating correlated traits into genomic selection models can improve prediction accuracy. This study explored the genetic correlation between important agronomic traits in safflower and found moderate correlations between grain yield and plant height, as well as low correlations between grain yield and days to flowering. Including plant height in the models led to a 4%-20% improvement in prediction accuracy for grain yield. Selection responses for grain yield varied across sites, but simultaneous selection for grain yield and seed oil content showed positive gains across all sites. Incorporating gxE interaction into genomic selection resulted in more balanced selection responses across sites. Genomic selection is a valuable tool for breeding high grain yield, oil content, and adaptable safflower varieties.
FRONTIERS IN GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Craig Mckimmie, Majid Khansefid, Hamed Amirpour-Najafabadi
Summary: This study compares breeding indexes between Australia and New Zealand and explores the use of Australian genomics to predict the productivity of New Zealand sires. A new genomic index for selecting New Zealand bulls was developed and found to have high correlations with traditional indexes through regression analysis.
ANIMAL PRODUCTION SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
M. Haile-Mariam, M. Khansefid, M. Axford, M. E. Goddard, Jennie E. Pryce
Summary: The longevity of dairy cattle is influenced by mortality and slaughter rates on the farm. This study examined the genetic parameters and trends of mortality rates and slaughter rates in Holstein and Jersey breeds. It found that the mortality rate of cows has increased in recent years, and most dead cows leave the herd before 120 days of lactation. The study also identified genetic correlations between traits such as milk yield, calving interval, somatic cell count, and protein yield with mortality rates and slaughter rates.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Fazel Almasi, Michael J. Stear, Majid Khansefid, Hien Nguyen, Aniruddha Desai, Jennie E. Pryce
Summary: This study aimed to estimate the repeatability and heritability of traits related to grazing and rumination activities and their correlations with other traits. The results showed that the repeatability of grazing traits was high, indicating that wearable sensors and SVM methods are reliable for recording sheep activities on pasture and have potential applications in selective breeding.
FRONTIERS IN ANIMAL SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
M. Khansefid, J. E. Pryce, S. Shahinfar, M. Axford, M. E. Goddard, M. Haile-Mariam
Summary: Partitioning cow survival into early and late survival and analyzing them as two correlated traits can improve the accuracy and stability of genetic predictions compared with analyzing overall survival as a single trait.
ANIMAL PRODUCTION SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Sunduimijid Bolormaa, Iona M. MacLeod, Majid Khansefid, Leah C. Marett, William J. Wales, Filippo Miglior, Christine F. Baes, Flavio S. Schenkel, Erin E. Connor, Coralia I. Manzanilla-Pech, Paul Stothard, Emily Herman, Gert J. Nieuwhof, Michael E. Goddard, Jennie E. Pryce
Summary: Sharing individual cow data between international partners and using sequence variants from international cow data's GWAS to evaluate the accuracy of genomic estimated breeding values (GEBV) for residual feed intake (RFI) in Australian cows can improve the accuracy of GEBV. The study suggests that a meta-analysis of summary GWAS statistics could provide selected SNPs for custom panels to use in genomic selection programs. Further confirmation through larger studies is recommended.
GENETICS SELECTION EVOLUTION
(2022)
Article
Agriculture, Dairy & Animal Science
Rostam Abdollahi-Arpanahi, Daniela Lourenco, Ignacy Misztal
Summary: Different core definitions were investigated for genomic prediction accuracy, revealing that the core definition becomes arbitrary when the core size reaches an optimal value equivalent to the number of largest eigenvalues explaining 99% of the variation of G.
GENETICS SELECTION EVOLUTION
(2022)