Review
Biochemistry & Molecular Biology
Robin S. Waples
Summary: This article reviews and summarizes performance evaluations of the method to estimate contemporary effective population size (Ne) based on patterns of linkage disequilibrium (LD), with a focus on practical application to real populations in nature.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Enrique Santiago, Armando Caballero, Carlos Kopke, Irene Novo
Summary: A new method is developed to estimate the contemporary effective population size (Ne) based on linkage disequilibrium (LD) in non-model species. It can be applied to different mating systems and variations in family size distribution. The method uses an artificial neural network to predict confidence intervals, providing more consistent estimates.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Genetics & Heredity
Hai Jin, Shuanping Zhao, Yutang Jia, Lei Xu
Summary: Dabieshan cattle (DBSC) are a valuable genetic resource for indigenous cattle breeds in China, with good meat quality and fat deposition. Genetic markers were used to estimate the genetic structure and parameters of the DBSC breeding population. Genotype data of 222 individuals and 81,579 SNPs were retained after quality control. The results showed the extent of inbreeding and history of the current cattle population, and highlighted the potential of genomic breeding for genetic progress.
Article
Agriculture, Dairy & Animal Science
Marykutty Thomas, Radhika Gopalakrishnan, Thirupathy Venkattachalapathy, Aravindakshan Thazhathuveetil
Summary: A population genomic study was conducted to investigate the genomic linkage disequilibrium (LD) in two Indian goat breeds. The results showed that the LD in these breeds was low, indicating high genetic diversity. Significant differences in LD were found among chromosomes, breeds, and marker intervals. The study suggests that a denser SNP panel would be more beneficial for genomic applications.
SMALL RUMINANT RESEARCH
(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
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
Biodiversity Conservation
Luis Santos-del-Blanco, Sanna Olsson, Katharina B. Budde, Delphine Grivet, Santiago C. Gonzalez-Martinez, Ricardo Alia, Juan J. Robledo-Arnuncio
Summary: Estimating contemporary effective population size (N-e) is crucial for genetic conservation and monitoring. However, commonly used genetic estimators may have limitations when applied to widespread forest tree populations. Factors such as genetic isolation, small and restricted samples, gene flow between populations, and overlapping generations can affect the accuracy of these estimators.
BIOLOGICAL CONSERVATION
(2022)
Article
Ecology
Ivan Galvan-Femenia, Carles Barcelo-Vidal, Lauro Sumoy, Victor Moreno, Rafael de Cid, Jan Graffelman
Summary: The study focuses on detecting family relationships in genetic databases, particularly first and second-degree relatives. The paper extends existing LR methods to accurately infer the existence of three-quarter siblings in between first and second-degree relationships, considering linkage disequilibrium through marker pruning.
Article
Fisheries
Baltasar F. Garcia, Alvaro Bonaguro, Carolina Araya, Roberto Carvalheiro, Jose M. Yanez
Summary: The inclusion of genomic information has accelerated genetic gain in shrimp breeding. Evaluating LD decay is crucial for assessing the feasibility of genomic selection. A study using a 50K SNP array tool characterized genomic diversity and LD in a farmed shrimp population.
AQUACULTURE REPORTS
(2021)
Article
Genetics & Heredity
Erik F. Bergseth, Andreas Tillmar, Jorgen T. Haddeland, Daniel Kling
Summary: The use of X-chromosomal markers in forensic genetics has increased, benefiting from commercial kits and increased awareness. This study analyzes a sample of 631 unrelated males from a Norwegian population, comparing the resulting haplotypes and conducting a deeper analysis of the linkage disequilibrium structure. The study demonstrates the importance of population frequency databases and proposes the use of simulations to assess the utility of STR markers.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
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
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
Agronomy
Linfeng Chen, Shouping Yang, Susan Araya, Charles Quigley, Earl Taliercio, Rouf Mian, James E. Specht, Brian W. Diers, Qijian Song
Summary: Genotype imputation is a strategy to increase marker density of existing datasets without additional genotyping. This study compared the performance of different imputation software in soybean populations and found that AlphaPlantImpute had higher imputation accuracy. Factors such as linkage disequilibrium extent, minor allele frequency, and reference panel size were found to positively influence imputation accuracy.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Genetics & Heredity
Cheng-long Zhang, Jihu Zhang, Mirenisa Tuersuntuoheti, Qianqian Chang, Shudong Liu
Summary: Extreme environmental conditions pose a major challenge to livestock production and can lead to reduced productivity. The screening of genes and molecular markers is crucial for understanding the genetic mechanism of prolific traits in sheep living in the Taklimakan Desert environment.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Gordon Luikart, Tiago Antao, Brian K. Hand, Clint C. Muhlfeld, Matthew C. Boyer, Ted Cosart, Brian Trethewey, Robert Al-Chockhachy, Robin S. Waples
Summary: Estimating the effective population size and effective number of breeders per year using computer simulations showed a bias of 5%-10% when using SNPs or microsatellites across different species. However, precision was higher for SNPs than for microsatellites, and confidence intervals were narrow enough to achieve high statistical power in rejecting null hypotheses for different true values of N-b and sample sizes.
MOLECULAR ECOLOGY RESOURCES
(2021)