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
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
Biochemical Research Methods
Dat Thanh Nguyen, Quan Hoang Nguyen, Nguyen Thuy Duong, Nam S. Vo
Summary: Despite the advancement of sequencing technology, SNP arrays remain the most cost-effective genotyping solution for large-scale genomic research. This study introduces a novel method called LmTag for tag SNP selection, which improves imputation performance and prioritizes highly functional SNP markers. It is particularly suitable for under-represented populations and non-model species in developing countries.
BRIEFINGS IN BIOINFORMATICS
(2022)
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
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
Biotechnology & Applied Microbiology
Pablo Federico Roncallo, Adelina Olga Larsen, Ana Laura Achilli, Carolina Saint Pierre, Cristian Andres Gallo, Susanne Dreisigacker, Viviana Echenique
Summary: This study evaluated the genetic diversity, population structure and linkage disequilibrium patterns in a durum wheat collection consisting of 197 genotypes using a 35K SNP array. The results showed a slight increase in genetic diversity over time, with a reduction in rare allelic variants after 1979. The level of pairwise loci in LD was low, and LD patterns varied across different breeding periods.
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)
Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
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
Agriculture, Dairy & Animal Science
Katri Sarviaho, Pekka Uimari, Katja Martikainen
Summary: Genomic selection has been utilized in dairy cattle breeding to predict breeding values accurately and increase genetic gain. However, there is a concern that genetic diversity may decrease due to increased inbreeding rate and decreased effective population size. This research aimed to estimate the impact of genomic selection on inbreeding rate and effective population size using both pedigree and genomic data.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(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
Biochemistry & Molecular Biology
Irene Novo, Noelia Perez-Pereira, Enrique Santiago, Humberto Quesada, Armando Caballero
Summary: The availability of high-density markers allows the estimation of historical effective population size. Recent refinement methods have been shown to be accurate with simulation data and have been applied to real data of various species. An experimental design with Drosophila melanogaster was carried out to test the method, which showed generally good performance. The limitations of the method and its application were discussed.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Kate D. Lee, Craig D. Millar, Patricia Brekke, Annabel Whibley, John G. Ewen, Melanie Hingston, Amy Zhu, Anna W. Santure
Summary: Next-generation sequencing technology has revolutionized ecological and evolutionary genetics, enabling cost-effective identification of genome-wide variation. In this study, researchers developed a 50K SNP chip for the threatened species hihi by combining RAD-seq and WGS data, demonstrating its utility in identifying SNPs for genotyping and revealing high rates of linkage disequilibrium in the hihi genome, indicative of population bottleneck events.
MOLECULAR ECOLOGY RESOURCES
(2022)