Article
Biotechnology & Applied Microbiology
Motohide Nishio, Keiichi Inoue, Shinichiro Ogawa, Kasumi Ichinoseki, Aisaku Arakawa, Yo Fukuzawa, Toshihiro Okamura, Eiji Kobayashi, Masaaki Taniguchi, Mika Oe, Kazuo Ishii
Summary: The use of genomic data allows for more accurate assessment of inbreeding level and depression. Genome-based inbreeding coefficients show stronger correlations with pedigree-based inbreeding coefficients, particularly those based on runs of homozygosity (ROH) segments and heterozygosity by descent segments (HBD). Genome-based inbreeding coefficients have more significant effects on reproductive traits compared to pedigree-based inbreeding coefficients.
Article
Agriculture, Dairy & Animal Science
Matteo Cortellari, Alessio Negro, Arianna Bionda, Silverio Grande, Alberto Cesarani, Antonello Carta, Nicola Macciotta, Stefano Biffani, Paola Crepaldi
Summary: This study investigates the relationship between pedigree-based and genomic inbreeding in Italian sheep and goat populations. The results highlight the importance of accurate pedigree information and calculating genomic-based inbreeding coefficients, especially when pedigree information is not obtainable. This study contributes to improving animal breeding and conservation by providing a better estimation of animals' relatedness.
Article
Agriculture, Dairy & Animal Science
K. Kaseja, S. Mucha, J. Yates, E. Smith, G. Banos, J. Conington
Summary: Genomic variants and animal pedigree are essential in livestock breeding, and the use of genomic information improves prediction accuracy and verifies pedigrees. The inclusion of the genomic relationship matrix (GRM) helps detect and resolve pedigree errors, leading to increased genetic gain.
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
Davinia Isabel Perdomo-Gonzalez, Nora Laseca, Sebastian Demyda-Peyras, Mercedes Valera, Isabel Cervantes, Antonio Molina
Summary: In this study, pedigree and genomic-based inbreeding coefficients were estimated and compared using the entire population of a Spanish horse breed and selected individuals' genotypic data. The results showed a strong correlation between pedigree and genomic inbreeding values, indicating that working with a deep and reliable pedigree is still useful for genetic studies with large population sizes.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
S. Antonios, S. T. Rodriguez-Ramilo, I Aguilar, J. M. Astruc, A. Legarra, Z. G. Vitezica
Summary: Inbreeding depression is associated with decreased performance and fitness of animals. This study evaluated pedigree-based and genomic methods to estimate inbreeding and its effects on sperm traits in Basco-Bearnaise sheep, finding significant impact on sperm motility.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Multidisciplinary Sciences
Lidia Escoda, Oliver Hawlitschek, Jorge Gonzalez-Esteban, Jose Castresana
Summary: Recently, populations with very low genetic diversity have been found, some of which can persist in the long term, while others may face extinction. This study focuses on the Iberian desman population, which exhibits extremely low heterozygosity values and high levels of inbreeding. Some individuals in the population appear to be genetically identical, posing challenges for genetic identification and parentage analysis. However, characterizing these genetically impoverished populations and improving genomic methodologies for their study are crucial for scientific and conservation purposes.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Magnus D. Vigeland
Summary: QuickPed is a user-friendly pedigree tool aimed at researchers, case workers, and teachers. It contains features not found in other similar tools and makes advanced relatedness analyses available for non-bioinformaticians.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Lisa Dickel, Peter Arcese, Pirmin Nietlisbach, Lukas F. Keller, Henrik Jensen, Jane M. Reid
Summary: Immigration into small recipient populations is expected to alleviate inbreeding and increase genetic variation, with immigrants typically being outbred and unrelated to existing natives and each other. This can facilitate population persistence through genetic and/or evolutionary rescue.
Article
Agriculture, Dairy & Animal Science
Shweta Sahoo, Rani Alex, Vikas Vohra, Sabyasachi Mukherjee, G. R. Gowane
Summary: This study investigated the genetic diversity and inbreeding situation of Saanen x Beetal goats. The results showed a high level of inbreeding in the reference population, with only a few ancestors contributing to the genetic diversity. Inbreeding had non-significant effects on reproductive traits, except for age at first service and age at first kidding. To reduce inbreeding and increase genetic diversity, a stratified breeding plan and the introduction of unrelated crosses should be followed.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2023)
Article
Agriculture, Dairy & Animal Science
O. Jarnecka, E. A. Bauer, W. Jagusiak
Summary: This study described the population structure and inbreeding level of Polish Red Cattle (PRC), with an average inbreeding of 4% and 23.8% inbred animals. The results indicate the potential disruption of the balance in small populations like PRC, highlighting the need for continuous monitoring of endangered populations.
Article
Agriculture, Dairy & Animal Science
Jayesh Vyas, Ashish Chopra, Urmila Pannu, H. K. Narula, Ram Kumar Saran
Summary: This study used pedigree data to evaluate the population structure and genetic variability of a closed flock of Marwari sheep in Rajasthan, India. The findings showed evidence of bottlenecks and genetic drift, but also significant genetic diversity in the population, and the continuous flow of genes contributed to maintaining genetic variability.
SMALL RUMINANT RESEARCH
(2022)
Article
Genetics & Heredity
Grazyna Polak, Artur Gurgul, Igor Jasielczuk, Tomasz Szmatola, Jedrzej Krupinski, Monika Bugno-Poniewierska
Summary: Traditionally, pedigree-based methods were used to manage inbreeding in populations, but the use of genomic data provides a more accurate estimation of shared genetic material. This study found that genomic inbreeding measures are effective in controlling inbreeding in rare horse populations, suggesting that genomics should be considered as an alternative in population structure analysis.
Article
Agriculture, Dairy & Animal Science
Jiaxin Liu, Liangyu Shi, Yang Li, Liang Chen, Dorian Garrick, Lixian Wang, Fuping Zhao
Summary: By analyzing ROH in five Chinese indigenous sheep breeds, we observed different ROH patterns and genetic characteristics among the breeds. Large-tailed Han sheep exhibited the highest level of genomic inbreeding, while candidate genes within ROH islands could be used to illustrate the genetic characteristics of these sheep breeds.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Shweta Sahoo, Rani Alex, Vikas Vohra, Sabyasachi Mukherjee, G. R. Gowane
Summary: The aim of this study was to investigate the genetic diversity and population structure in the Alpine x Beetal goat population. The results showed that the average inbreeding coefficient and average relatedness were 4.77% and 7.84% for the whole population, and 9.65% and 11.98% for the reference population, respectively. The high inbreeding coefficient and average relatedness in the reference population indicated the impact of a closed gene pool, emphasizing the need for immediate intervention to manage genetic diversity.
SMALL RUMINANT RESEARCH
(2023)
Article
Agronomy
Hanna Haikka, Timo Knurr, Outi Manninen, Leena Pietila, Mika Isolahti, Esa Teperi, Esa A. Mantysaari, Ismo Stranden
Article
Agriculture, Dairy & Animal Science
M. Koivula, I Stranden, G. P. Aamand, E. A. Mantysaari
Summary: The study focuses on the computational and predictive performance of ssGTBLUP with residual polygenic effect and unknown parent groups (UPG) in the context of increasing genomic information in dairy cattle. Proper consideration of UPG effects and the use of complete QP transformation are key factors for successful implementation of the model.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Environmental Sciences
Javier Sanchez Romano, Anna Omazic, Mikael Leijon, Asa Hagstrom, Morten Tryland, Juha Kantanen, Tiina Reilas, Ulrika Rockstrom, Valery Fedorov, Ann Albihn
Summary: Reindeer husbandry is crucial for indigenous peoples in the Arctic, but it may also contribute to the transmission of viruses between species. This study revealed a variety of viruses in reindeer, including some previously unknown species, which could potentially pose a threat to both human and animal health in the future.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2021)
Article
Agriculture, Dairy & Animal Science
Ulla Ovaska, Auli Blauer, Charlotte Krolokke, Maria Kjetsa, Juha Kantanen, Mervi Honkatukia
Summary: Native breeds are domestic animals that have adapted to their habitats, with high genetic and cultural values. Conservation efforts are maintained by national programmes and agricultural support schemes in Nordic countries. It is crucial to widely understand and recognize the importance of native breeds in society, especially in local communities. Farmers should be motivated to utilize these breeds and engage more in the design of conservation practices and support schemes.
Article
Agriculture, Dairy & Animal Science
Andrei A. Kudinov, Esa A. Mantysaari, Timo J. Pitkanen, Ekaterina Saksa, Gert P. Aamand, Pekka Uimari, Ismo Stranden
Summary: Genomic data are crucial in dairy cattle breeding value prediction, with accuracy depending on reference population size and relatedness of candidate animals. In populations with limited data, incorporating external information is necessary for improved reliability.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2022)
Article
Biology
Ze-Hui Chen, Ya-Xi Xu, Xing-Long Xie, Dong-Feng Wang, Diana Aguilar-Gomez, Guang-Jian Liu, Xin Li, Ali Esmailizadeh, Vahideh Rezaei, Juha Kantanen, Innokentyi Ammosov, Maryam Nosrati, Kathiravan Periasamy, David W. Coltman, Johannes A. Lenstra, Rasmus Nielsen, Meng-Hua Li
Summary: The study revealed multiple introgression events from wild sheep to domestic sheep, involving adaptive and gene-related aspects post-domestication. Introgression events from different wild sheep species to Asiatic and European mouflons during domestication process provided more insights into the diversity of genomic regions.
COMMUNICATIONS BIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Hafedh Ben Zaabza, Matti Taskinen, Esa A. Mantysaari, Timo Pitkanen, Gert Pedersen Aamand, Ismo Stranden
Summary: Approximate multistep methods were developed to calculate reliabilities for estimated breeding values in large genetic evaluations. This study utilized a traditional animal model and genomic data to approximate the reliabilities for genotyped animals in a single-step genomic BLUP model. Reliabilities for nongenotyped animals were also calculated using a traditional animal model with pseudo-record counts. The developed approach was found to be efficient and suitable for large datasets.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Biology
Li Ang, Gabriel Vinderola, Akihito Endo, Juha Kantanen, Chen Jingfeng, Ana Binetti, Patricia Burns, Shi Qingmiao, Ding Suying, Yu Zujiang, David Rios-Covian, Anastasia Mantziari, Shea Beasley, Carlos Gomez-Gallego, Gueimonde . Miguel, Seppo Salminen
Summary: Compared with their wild ancestors, domesticated horses have a different fecal microbiome composition and abundance, potentially influenced by diet and antibiotic use.
COMMUNICATIONS BIOLOGY
(2022)
Article
Agronomy
Minna Koivula, Ismo Stranden, Gert P. Aamand, Esa A. Mantysaari
Summary: Genomic selection is widely used in dairy cattle breeding, but the use of single-step models in national dairy cattle evaluations is rare. This study compared three approaches for accounting for missing pedigree information and tested different models using Nordic Holstein test-day production data. The results showed that the MF approach had the lowest bias.
Article
Agriculture, Dairy & Animal Science
Jon H. Eiriksson, Ismo Stranden, Guosheng Su, Esa A. Mantysaari, Ole F. Christensen
Summary: In genomic prediction of crossbred animals, accounting for the breed origin of alleles (BOA) can improve the accuracy of genomic breeding value prediction. This study investigated different measures of breed proportions and heterozygosity derived from BOA, and validated their effectiveness for predicting production traits in crossbred dairy cows. The results showed that models incorporating BOA had higher predictive ability compared to models using only global breed proportions.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Multidisciplinary Sciences
Rayner Gonzalez-Prendes, Catarina Ginja, Juha Kantanen, Nasser Ghanem, Donald R. Kugonza, Mahlako L. Makgahlela, Martien A. M. Groenen, Richard P. M. A. Crooijmans
Summary: This study aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle breeds, with a focus on candidate genes associated with coat color and/or eye-protective phenotypes. By analyzing whole genome sequences of 170 animals from eight breeds, the researchers identified five genomic regions under selection that contain candidate genes associated with retinal degeneration, ultraviolet protection, and pigmentation. These findings provide insights into the molecular basis of GWH phenotypes and its adaptation.
Article
Genetics & Heredity
Melak Weldenegodguad, Juha Kantanen, Jaana Peippo, Kisun Pokharel
Summary: This study investigated the transcriptome profiles of different adipose tissues in reindeer and found distinct patterns in the metacarpal adipose tissue compared to perirenal and prescapular adipose tissues. Furthermore, 10 genes, including the important PRDM9 gene involved in reindeer adaptation and speciation, were consistently upregulated in all three tissues of male reindeer.
Article
Agriculture, Dairy & Animal Science
Eve Rannamae, Urmas Saarma, Juha Kantanen, Auli Blauer
Summary: Countries in the northern Baltic Sea region have a long history of connection, and animal husbandry provides valuable information about these historical connections. Despite limited archaeological evidence, zooarchaeological and historical research has shown that goat husbandry has continued in this part of Europe since the Late Iron Age. A study analyzing mitochondrial DNA from ancient and present-day goats in Finland and Estonia revealed a high level of diversity among the ancient goats, as well as shared maternal lineages between ancient and medieval individuals. The analysis also demonstrated a maternal affinity between ancient Finnish and Estonian goats and present-day Finngoat and Swedish Landrace breeds, confirming the historical connections in the region.
Article
Agriculture, Dairy & Animal Science
Nurbiy S. Marzanov, Davud A. Devrishov, Mikhail Y. Ozerov, Oleg P. Maluchenko, Saida N. Marzanova, Elena B. Shukurova, Elena A. Koreckaya, Juha Kantanen, Daniel Petit
Summary: The history of the Romanov breed can be traced back to 1802. This breed has unique qualities such as resistance to harsh environments, high ovulation rates, early maturation, and excellent fur coat qualities. Genetic markers have been identified that are associated with these characteristics, such as polymorphism in two genes linked to ovulation rate and heterozygosity linked to adaptation to harsh environments. Blood group and genetic marker analysis showed that Romanov sheep have distinct characteristics compared to other breeds, with a higher frequency of certain alleles and fewer genotypes at specific loci. The proximity of 12 Romanov breed populations was confirmed through cluster analysis, indicating a common origin in the Yaroslavl region.
Article
Agriculture, Dairy & Animal Science
Ismo Stranden, Gert P. Aamand, Esa A. Mantysaari
Summary: The use of J factors in genomic estimated breeding values can improve computation efficiency and eliminate the influence of marker information centering.
GENETICS SELECTION EVOLUTION
(2022)