Article
Biotechnology & Applied Microbiology
Johannes Geibel, Nora Paulina Praefke, Steffen Weigend, Henner Simianer, Christian Reimer
Summary: This study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate the linkage disequilibrium (LD) patterns between the called SVs and surrounding SNPs. The results indicated that LD between deletions (DELs) and SNPs was similar to LD between SNPs, while LD between other SVs and SNPs was significantly reduced. The main reason for the reduced LD was the presence of local minor allele frequency differences. Genotyping accuracy was lower for duplications (DUP), inversions (INV), and translocation breakpoints (BND) compared to SNPs and deletions (DELs). The presence of tag SNPs was slightly lower for DELs compared to WGS SNPs, but this difference disappeared when considering SNPs located on different chicken genotyping arrays.
Article
Agriculture, Dairy & Animal Science
N. Dementieva, O. Mitrofanova, A. P. Dysin, A. A. Kudinov, O. Stanishevskaya, T. A. Larkina, K. Plemyashov, D. K. Griffin, M. N. Romanov, M. G. Smaragdov
Summary: Phenotypic diversity in poultry is mainly influenced by artificial selection and genetic drift. This study assessed genetic diversity within and between Russian chicken breeds and populations, revealing genetic differences among populations. LD pruning is crucial for studying genetic diversity, with the Russian White RG population showing a significant impact due to its large sample size.
Article
Biotechnology & Applied Microbiology
Jose Marcelo Soriano Viana, Antonio Augusto Franco Garcia
Summary: Additive variance is generally the most important component of genotypic variance. LD and inbreeding have a significant effect on the magnitude of the genetic variances and covariances. In general, the additive x additive variance is the most important component of epistatic variance.
Article
Genetics & Heredity
Shirin Rahimmadar, Mokhtar Ghaffari, Mahdi Mokhber, John L. Williams
Summary: The assessment of LD structure and Ne in different water buffalo breeds revealed potential for the use of Affymetrix Axiom 90 K SNP genomic array in GWAS and GS. Studying the persistency of LD phase and population genetic diversity highlighted the necessity for breeding plans to safeguard these buffalo populations.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Sajal R. Sthapit, Travis M. Ruff, Marcus A. Hooker, Deven R. See
Summary: The population structure and genetic diversity of wheat varieties in the United States were examined using a panel of historical and modern varieties. The results showed that population structure was related to growth habit and kernel characteristics, which also corresponded with geographic distribution. Market class classification accounted for the greatest amount of variation. There was no evidence of decreased genetic diversity after the release of the first semidwarf wheat variety in 1961, and some varieties even showed increases in genetic diversity. The findings suggest that overall genetic diversity in wheat varieties has not declined in the long term, despite occasional fluctuations.
Article
Ecology
Dengcheng Yang, Fan Li, Jing Wang, Ang Dong, Rongling Wu
Summary: LD in tetraploids is studied with a specific model for different loci disequilibrium, using EM algorithm for parameter estimation and experimental verification in populations. Analysis of switchgrass genomic data reveals the importance of LD in inferring evolutionary history.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Suncica Stipoljev, Toni Safner, Pavao Gancevic, Ana Galov, Tina Stuhne, Ida Svetlicic, Stefano Grignolio, Jorge Cassinello, Nikica Sprem
Summary: The genetic diversity of European aoudad populations is relatively low, with individuals likely originating from multiple genetic sources. The Sierra Espuna population in Spain is the only one where multiple haplotypes have been detected.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Dongwon Seo, Sunghyun Cho, Prabuddha Manjula, Nuri Choi, Young-Kuk Kim, Yeong Jun Koh, Seung Hwan Lee, Hyung-Yong Kim, Jun Heon Lee
Summary: Classifying a target population at the genetic level using a minimum number of markers from high-density SNP array data can provide stable results. Utilizing GWAS, PCA, and machine learning algorithms to explore various combinations with the minimum number of markers has proven to be effective in distinguishing target populations.
Article
Biology
George Wanjala, Putri Kusuma Astuti, Zoltan Bagi, Nelly Kichamu, Peter Strausz, Szilvia Kusza
Summary: The Dorper sheep breed was created for harsh environments in South Africa, with two variants developed in the selection process. It has gained popularity worldwide and is reported to do better than locally adapted breeds. Dorper is widely used in crossbreeding to improve other native breeds. However, there has been no research on the genomic status of Dorper in South Africa and other regions. This study compared the genomic architecture of Dorper populations in South Africa and Hungary, finding significant genetic variations potentially influenced by environmental factors and coat color.
Article
Biochemistry & Molecular Biology
Lydia K. Wooldridge, Beth L. Dumont
Summary: This study constructed broad- and fine-scale sex-averaged recombination maps in nine geographically isolated wild house mouse populations using a coalescent-based approach. The results showed low conservation of recombination maps across subspecies and populations, with most hotspots being unique to one population due to minimal sharing of Prdm9 alleles. Additionally, population-specific differences in the degree and direction of sex dimorphism for recombination were observed. Overall, this study highlights the variability of recombination landscape in M. musculus and emphasizes the functional impact of Prdm9 allelic variation in wild populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Ecology
Lisa Mazumder, Rick Kesseli
Summary: Dandelions have a worldwide distribution in urban environments despite the lack of sexual reproduction in most areas. The impact of this unusual natural history on population structure and diversity is investigated using genetic markers, showing high levels of genetic diversity within populations and seasonal genotypic differentiation.
ECOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Santiago G. Medina-Munoz, Diego Ortega-Del Vecchyo, Luis Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Lourdes Garcia-Garcia, Andres Moreno-Estrada, Aaron P. Ragsdale
Summary: This study used high-coverage whole-genome data and existing genomes from Latin America to infer the complex evolutionary history of Latin American populations. The models developed in this study provide a more accurate prediction of genetic variation in admixed populations and can be a valuable resource for future studies.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Veterinary Sciences
Hehe Tang, Yanchao Ma, Jianzeng Li, Zhenzhen Zhang, Wenting Li, Chunxia Cai, Lujie Zhang, Zhuanjian Li, Yadong Tian, Yanhua Zhang, Jinqing Ji, Lu Han, Xiangtao Kang, Ruirui Jiang, Ruili Han
Summary: In this study, we identified 8 SNPs and found that 4 of them were completely linked to each other, and these SNPs were highly correlated with the level of alkaline phosphatase (ALP). Furthermore, individuals with the AA genotype showed the highest ALP level and better growth performance, indicating that these SNPs could serve as potential molecular breeding markers for predicting early ALP level and improving growth performance in chickens.
RESEARCH IN VETERINARY SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Krystyna Nadachowska-Brzyska, Ludovic Dutoit, Linnea Smeds, Martin Kardos, Lars Gustafsson, Hans Ellegren
Summary: Long-term effective population size (N-e) is crucial in evolutionary biology and population genetics, with numerous estimates available for various species and populations. However, estimating contemporary N-e remains challenging, especially with LD-based methods. Whole-genome sequencing data offers new possibilities in estimating high contemporary N-e.
Article
Multidisciplinary Sciences
Dat Thanh Nguyen, Trang T. H. Tran, Mai Hoang Tran, Khai Tran, Duy Pham, Nguyen Thuy Duong, Quan Nguyen, Nam S. Vo
Summary: Regardless of the overwhelming use of next-generation sequencing technologies, microarray-based genotyping combined with the imputation of untyped variants remains a cost-effective means to interrogate genetic variations across the human genome. This study comprehensively evaluates the performance of 23 available human genotyping arrays in different ancestry groups, and finds that higher density arrays do not necessarily have better imputation performance. Additionally, PGS estimated from imputed SNP arrays correlates highly with PGS estimated from whole-genome sequencing data. The study highlights the importance of selecting a suitable genotyping array for PGS applications.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
E. F. Dzomba, M. Chimonyo, R. Pierneef, F. C. Muchadeyi
Summary: This study examined the frequency and distribution patterns of runs of homozygosity (ROH) in South African sheep breeds, finding that it corresponded to the breed history and selection pressures. Different breeds exhibited varying levels of autozygosity, with genes within ROH islands associated with important traits and predomestic selection factors.
Article
Genetics & Heredity
Magriet A. van der Nest, Nompilo Hlongwane, Khanyisile Hadebe, Wai-Yin Chan, Nicolaas A. van der Merwe, Lieschen De Vos, Ben Greyling, Bhaveni B. Kooverjee, Pranisha Soma, Edgar F. Dzomba, Michael Bradfield, Farai C. Muchadeyi
Summary: The study evaluated the genetic architecture of an admixed South African Simbra crossbred population and identified genomic regions showing signatures of selection. These regions contain genes affecting cattle health and production, potentially contributing to the phenotype of the Simbra hybrid cattle breed.
FRONTIERS IN GENETICS
(2021)
Article
Microbiology
Evelyn Madoroba, Kudakwashe Magwedere, Nyaradzo Stella Chaora, Itumeleng Matle, Farai Muchadeyi, Masenyabu Aletta Mathole, Rian Pierneef
Summary: The study aimed to determine microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Results revealed diverse and highly variable microbial communities in animal products, which is crucial for food safety.
Article
Agriculture, Dairy & Animal Science
Simon F. Lashmar, Donagh P. Berry, Rian Pierneef, Farai C. Muchadeyi, Carina Visser
Summary: Genomic selection in less-developed countries can be hindered by high genotyping costs, but imputation from lower to higher densities can reduce these costs. This study found that SNP selection strategies and density can significantly impact imputation accuracy in locally adapted cattle breeds. Ultimately, a genotyping panel of around 10,000 SNP chosen based on a combination of MAF and LD criteria can achieve a low error rate in genomic imputation for admixed breeds like the SA Drakensberger.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Multidisciplinary Sciences
T. Mafuna, P. Soma, A. M. Tsotetsi-Khambule, C. A. Hefer, F. C. Muchadeyi, O. M. M. Thekisoe, R. E. Pierneef
Summary: This study used metagenomic approach to investigate the gut microbiome of Haemonchus contortus field strains and its predilection site in Dohne Merino sheep. The research identified differences and similarities in bacterial composition between male and female H. contortus gut microbiomes, as well as the predominant genera in the abomasum of Dohne Merino sheep. The study provides insight into the complex interactions of different gastrointestinal nematode microbiomes with the host.
SCIENTIFIC REPORTS
(2021)
Review
Agriculture, Dairy & Animal Science
Vivien J. Chebii, Emmanuel A. Mpolya, Farai C. Muchadeyi, Jean-Baka Domelevo Entfellner
Summary: Ungulates are essential sources of food, labor, clothing, and transportation for humans, and they possess unique adaptive traits in various habitats. Genomics resources have helped identify genes associated with the adaptability of ungulates to their environments.
Article
Agriculture, Dairy & Animal Science
Keabetswe Tebogo Ncube, Edgar Farai Dzomba, Khanyisile Hadebe, Pranisha Soma, Lorinda Frylinck, Farai Catherine Muchadeyi
Summary: South Africa is a major goat producing country in Africa, but there is still a growing demand for chevon. Despite being easily accessible and having health benefits, chevon is less preferred due to perceived low meat quality. This study investigates the carcass quality and associated genomic regions of different goat breeds in South Africa, providing insights for future breed improvement programs.
Article
Agriculture, Dairy & Animal Science
Nyaradzo Stella Chaora, Khulekani Sedwell Khanyile, Kudakwashe Magwedere, Rian Pierneef, Frederick Tawi Tabit, Farai Catherine Muchadeyi
Summary: This study utilized gene sequencing and bioinformatics analysis to determine mislabeling of processed meat products using the mitochondrial 16S ribosomal RNA gene. The results showed that pork was the major contaminant in most meat samples. This method can be used to authenticate meat products and manage mislabeling.
Article
Genetics & Heredity
Langelihle Mbali Kunene, Farai Catherine Muchadeyi, Khanyisile Hadebe, Gabor Meszaros, Johann Soelkner, Trevor Dugmore, Edgar Farai Dzomba
Summary: Nguni cattle are a breed with mixed ancestry that show resistance to African conditions. This study investigated the genetics of coat colour and patterns in Nguni cattle, finding associations with specific genes and signalling pathways. The results provide insights for breeding and improvement, and suggest different genetic mechanisms for coat colour and forehead stripe phenotypes.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Njabulo M. Dlamini, Edgar F. Dzomba, Mpumelelo Magawana, Sphamandla Ngcamu, Farai C. Muchadeyi
Summary: This study investigated the genetic diversity and similarities and differences within and between two conservation herds of the South African Nguni Cattle. The results showed reduced genetic diversity in the two herds, calling for measures to protect the diversity of the South African Nguni cattle.
Article
Ecology
Stephane Blondeau Da Silva, Joram M. Mwacharo, Menghua Li, Abulgasim Ahbara, Farai Catherine Muchadeyi, Edgar Farai Dzomba, Johannes A. Lenstra, Anne Da Silva
Summary: This study investigated how shared IBD patterns between individuals of the same breed can indicate the level of admixture. The findings showed that breeds with higher genetic isolation had more shared and longer IBD segments. This study paves the way for further research on the development of admixture indicators based on intra-breed shared IBD segments.