Genomic Uniqueness of Local Sheep Breeds From Morocco

Sheep farming is a major source of meat in Morocco and plays a key role in the country’s agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

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Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Genes ◽

10.3390/genes10110938 ◽

2019 ◽

Vol 10 (11) ◽

pp. 938 ◽

Cited By ~ 4

Author(s):

Islam ◽

Li ◽

Liu ◽

Berihulay ◽

Abied ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Positive Selection ◽

Candidate Genes ◽

Runs Of Homozygosity ◽

Selection Signatures ◽

Effective Population ◽

Signature Of Selection ◽

Genomic Regions ◽

Insight Into

: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

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Evaluating the use of ABBA-BABA statistics to locate introgressed loci

10.1101/001347 ◽

2013 ◽

Cited By ~ 17

Author(s):

Simon H. Martin ◽

John W. Davey ◽

Chris D. Jiggins

Keyword(s):

Population Structure ◽

Population Size ◽

Effective Population Size ◽

Ancestral Population ◽

Whole Genome ◽

Effective Population ◽

Genome Data ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson?s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f̂d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f̂d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f̂d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

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Changes in Genetic Diversity and Demographic History of Jankowski’s Bunting (Emberiza Jankowskii), as Revealed by Mitochondrial DNA and Microsatellite Markers

10.21203/rs.3.rs-265651/v1 ◽

2021 ◽

Author(s):

Long Huang ◽

Guochen Feng ◽

Dan Li ◽

Weiping Shang ◽

Lishi Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Genetic Variation ◽

Microsatellite Markers ◽

Population Size ◽

Demographic History ◽

Effective Population ◽

High Genetic Diversity ◽

History Of ◽

Eastern Inner Mongolia

Abstract The genetic variation and distribution of a population depend largely on the demographic history. For instance, populations that have recently experienced shrinkage usually have a lower genetic diversity. However, some endangered species with a narrow distribution have a high genetic diversity resulting from large historical population sizes and long generation times. In addition, very recent population bottlenecks may not be reflected in the population’s genetic information. In this study, we used a mitochondrial DNA marker and 15 microsatellite markers to reveal the genetic diversity, recent changes, inbreeding, and demographic history of a Jankowski’s bunting (Emberiza jankowskii) population in eastern Inner Mongolia. The results show that the genetic diversity of the population remained at a relatively stable and high level until recently. Severe population shrinkage did not result in a considerable lack of genetic variation because of the large historical population size and relatively short periods of human disturbance. In addition, introgression and gene flow among populations compensate for the loss of genetic variation to some extent. Considering the current small effective population size and the existence of inbreeding, we recommend that habitat protection be continued to maximize the genetic diversity of the Jankowski’s bunting population.

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An examination of genetic diversity and effective population size in Atlantic salmon populations

Genetics Research ◽

10.1017/s0016672309990346 ◽

2009 ◽

Vol 91 (6) ◽

pp. 395-412 ◽

Cited By ~ 14

Author(s):

NATACHA NIKOLIC ◽

JAMES R. A. BUTLER ◽

JEAN-LUC BAGLINIÈRE ◽

ROBERT LAUGHTON ◽

IAIN A. G. McMYN ◽

...

Keyword(s):

Genetic Diversity ◽

Atlantic Salmon ◽

Population Size ◽

Effective Population Size ◽

Demographic History ◽

Effective Population ◽

High Genetic Diversity ◽

Historical Processes ◽

Wide Range ◽

Microsatellite Dna Markers

SummaryEffective population size (Ne) is an important parameter in the conservation of genetic diversity. Comparative studies of empirical data that gauge the relative accuracy of Ne methods are limited, and a better understanding of the limitations and potential of Ne estimators is needed. This paper investigates genetic diversity and Ne in four populations of wild anadromous Atlantic salmon (Salmo salar L.) in Europe, from the Rivers Oir and Scorff (France) and Spey and Shin (Scotland). We aimed to understand present diversity and historical processes influencing current population structure. Our results showed high genetic diversity for all populations studied, despite their wide range of current effective sizes. To improve understanding of high genetic diversity observed in the populations with low effective size, we developed a model predicting present diversity as a function of past demographic history. This suggested that high genetic diversity could be explained by a bottleneck occurring within recent centuries rather than by gene flow. Previous studies have demonstrated the efficiency of coalescence models to estimate Ne. Using nine subsets from 37 microsatellite DNA markers from the four salmon populations, we compared three coalescence estimators based on single and dual samples. Comparing Ne estimates confirmed the efficiency of increasing the number and variability of microsatellite markers. This efficiency was more accentuated for the smaller populations. Analysis with low numbers of neutral markers revealed uneven distributions of allelic frequencies and overestimated short-term Ne. In addition, we found evidence of artificial stock enhancement using native and non-native origin. We propose estimates of Ne for the four populations, and their applications for salmon conservation and management are discussed.

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Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing

Tropical Animal Health and Production ◽

10.1007/s11250-021-02605-6 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Lei-Lei Li ◽

Shi-Ke Ma ◽

Wei Peng ◽

You-Gui Fang ◽

Hai-Rui Duo ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Whole Genome ◽

Genome Resequencing ◽

Sheep Breeds ◽

Tibetan Sheep ◽

Whole Genome Resequencing

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Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

10.1101/732750 ◽

2019 ◽

Author(s):

Quentin Rougemont ◽

Jean-Sébastien Moore ◽

Thibault Leroy ◽

Eric Normandeau ◽

Eric B. Rondeau ◽

...

Keyword(s):

Genetic Diversity ◽

Coho Salmon ◽

Pacific Salmon ◽

Demographic History ◽

Glacial Refugium ◽

Human Populations ◽

Deleterious Mutations ◽

Effective Population ◽

Geographical Patterns ◽

Genome Wide Data

AbstractA thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

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Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.2613 ◽

2020 ◽

Vol 287 (1922) ◽

pp. 20192613 ◽

Cited By ~ 2

Author(s):

Elisa G. Dierickx ◽

Simon Yung Wa Sin ◽

H. Pieter J. van Veelen ◽

M. de L. Brooke ◽

Yang Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Sex Chromosomes ◽

Demographic History ◽

Large Population ◽

Effective Population ◽

Island Species ◽

Population Sizes ◽

Approaches To Study ◽

Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

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Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽

10.3390/ani9060361 ◽

2019 ◽

Vol 9 (6) ◽

pp. 361 ◽

Cited By ~ 3

Author(s):

Shuqi Diao ◽

Shuwen Huang ◽

Zhiting Xu ◽

Shaopan Ye ◽

Xiaolong Yuan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Conservation Status ◽

Snp Array ◽

Size Analysis ◽

Selection Signatures ◽

Effective Population ◽

Low Genetic Diversity ◽

Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

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