Characterization of Runs of Homozygosity, Heterozygosity-Enriched Regions, and Population Structure in Cattle Populations Selected for Different Breeding Goals

Abstract Background: A decline in the level of genetic diversity can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, some metrics have been proposed to assess the levels of populational genetic diversity in selected populations. The main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results: A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3,576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data.Conclusions: The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.

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Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data

Plant Disease ◽

10.1094/pdis-11-16-1586-re ◽

2017 ◽

Vol 101 (5) ◽

pp. 666-673 ◽

Cited By ~ 10

Author(s):

Marie-Claude Gagnon ◽

Nicolas Feau ◽

Angela L. Dale ◽

Braham Dhillon ◽

Richard C. Hamelin ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genome Sequence ◽

Sequence Data ◽

Ornamental Plants ◽

Phytophthora Ramorum ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Data ◽

And Migration

Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.

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Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species

10.7287/peerj.preprints.27690v1 ◽

2019 ◽

Author(s):

Jun Hyoung Bang ◽

Chi Eun Hong ◽

Sebastin Raveendar ◽

Kyong Hwan Bang ◽

Kyung Ho Ma ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Sequence Data ◽

Whole Genome Sequence ◽

Sequence Repeat ◽

Molecular Studies ◽

Simple Sequence ◽

Genomic Simple Sequence Repeat

Background. Licorice (Glycyrrhiza spp. L.) is used as a natural sweetener and medicinal herb. Molecular studies have been conducted to find differences between wild and cultivated species because most wild species are highly resistant to abiotic and biotic stresses compared with their cultivated counterparts. However, few molecular markers have been developed for studying the genetic diversity and population structure of licorice species and to identify differences between cultivars. Thus, the present study aimed to develop a set of genomic simple sequence repeat (SSR) markers for molecular studies of these species. Methods. We designed 100 SSR markers based on the whole-genome sequence data of wild Glycyrrhiza lepidota and selected 62 SSR markers. Results. The genetic diversity analysis using these markers identified 2–23 alleles, and the major allele frequency, observed heterozygosity, genetic diversity, and polymorphism information content were 0.11–0.91, 0–0.90, 0.17–0.94, and 0.15–0.93, respectively. Interspecies transferability values were 93.5%, 91.6%, and 91.1% for G. echinata, G. glabra, and G. uralensis, respectively. Phylogenetic analysis clustered cultivated (group 1) and wild (group 2) species into three and two subgroups, respectively. The SSR markers developed here can be applied to genetic diversity, population structure, and cultivar differentiation studies, as well as to breeding of licorice varieties.

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Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species

10.7287/peerj.preprints.27690 ◽

2019 ◽

Author(s):

Jun Hyoung Bang ◽

Chi Eun Hong ◽

Sebastin Raveendar ◽

Kyong Hwan Bang ◽

Kyung Ho Ma ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Sequence Data ◽

Whole Genome Sequence ◽

Sequence Repeat ◽

Molecular Studies ◽

Simple Sequence ◽

Genomic Simple Sequence Repeat

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Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

Animals ◽

10.3390/ani10081441 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1441

Author(s):

Filippo Cendron ◽

Francesco Perini ◽

Salvatore Mastrangelo ◽

Marco Tolone ◽

Andrea Criscione ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Conservation Status ◽

Geographical Area ◽

Snp Array ◽

Local Economy ◽

Conservation Strategies ◽

Snp Analysis ◽

Runs Of Homozygosity ◽

Chicken Breeds

The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.

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Genetic diversity may help evolutionary rescue in a clonal endemic plant species of Western Himalaya

Scientific Reports ◽

10.1038/s41598-021-98648-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Irshad Ahmad Sofi ◽

Irfan Rashid ◽

Javaid Yousuf Lone ◽

Sandhya Tyagi ◽

Zafar A. Reshi ◽

...

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Population Structure ◽

Plant Species ◽

Ssr Markers ◽

Sequence Data ◽

Endemic Plant ◽

Single Marker Analysis ◽

Endemic Plant Species ◽

Trait Associations

AbstractHabitat loss due to climate change may cause the extinction of the clonal species with a limited distribution range. Thus, determining the genetic diversity required for adaptability by these species in sensitive ecosystems can help infer the chances of their survival and spread in changing climate. We studied the genetic diversity and population structure of Sambucus wightiana—a clonal endemic plant species of the Himalayan region for understanding its possible survival chances in anticipated climate change. Eight polymorphic microsatellite markers were used to study the allelic/genetic diversity and population structure. In addition, ITS1–ITS4 Sanger sequencing was used for phylogeny and SNP detection. A total number of 73 alleles were scored for 37 genotypes at 17 loci for 8 SSRs markers. The population structural analysis using the SSR marker data led to identifying two sub-populations in our collection of 37 S. wightiana genotypes, with 11 genotypes having mixed ancestry. The ITS sequence data show a specific allele in higher frequency in a particular sub-population, indicating variation in different S. wightiana accessions at the sequence level. The genotypic data of SSR markers and trait data of 11 traits of S. wightiana, when analyzed together, revealed five significant Marker-Trait Associations (MTAs) through Single Marker Analysis (SMA) or regression analysis. Most of the SSR markers were found to be associated with more than one trait, indicating the usefulness of these markers for working out marker-trait associations. Moderate to high genetic diversity observed in the present study may provide insurance against climate change to S. wightiana and help its further spread.

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Short Communication: A Within- and Across-country Assessment of the Genomic Diversity and Autozygosity of South African and Eswatini Nguni Cattle

10.21203/rs.3.rs-1060515/v1 ◽

2021 ◽

Author(s):

Simon Frederick Lashmar ◽

Carina Visser ◽

Moses Okpeku ◽

Farai Catherine Muchadeyi ◽

Ntanganedzeni Olivia Mapholi ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Standard Deviation ◽

Cattle Breed ◽

Principal Component ◽

Genomic Diversity ◽

Potential Threat ◽

Inbreeding Coefficients ◽

Agroecological Zones ◽

Nguni Cattle

Abstract In southern Africa, the Nguni cattle breed is classified as an indigenous and transboundary animal genetic resource that manifests unique adaptation abilities across distinct agroecological zones. The genetic integrity of various ecotypes is under potential threat due to both indiscriminate crossbreeding and uncontrolled inbreeding. The aim of this study was to assess the genetic diversity and autozygosity that exists both across countries (ES: eSwatini; SA: South Africa) and within-country (SA), between purebred stud animals (SA-S) and research herds (SA-R). Subsets of 96 ES, 96 SA-S and 96 SA-R genotyped for 40 930 common SNPs were used to study inbreeding, runs of homozygosity (ROH) and heterozygosity (ROHet) profiles as well as population structure. The highest proportion (0.513) of the 3 595 ROH was <4Mb in length, while the majority (0.560) of the 4 409 ROHet segments fell within the 0.5-1Mb length category. Inbreeding coefficients indicated low inbreeding (FROH range: 0.025 for SA-S to 0.029 for SA-R). Principal component (PCA) and population structure (K=5) analyses illustrated genomic distinctiveness between SA and ES populations, greater admixture for SA-R (mean±standard deviation proportion shared=0.631±0.353) compared to SA-S (mean±standard deviation proportion shared=0.741±0.123), and three subpopulations for ES. Overall, results illustrated that genetic distinctiveness in the Nguni resulted from both geographic isolation and exposure to different production strategies. Although no impending threat to genetic diversity was observed, further loss should be monitored to prevent endangerment of unique and beneficial indigenous resources.

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Population genomics of East Asian ethnic groups

Hereditas ◽

10.1186/s41065-020-00162-w ◽

2020 ◽

Vol 157 (1) ◽

Author(s):

Ziqing Pan ◽

Shuhua Xu

Keyword(s):

Genetic Diversity ◽

East Asia ◽

Ethnic Groups ◽

Population Genomics ◽

Sequence Data ◽

East Asian ◽

Whole Genome Sequence ◽

Whole Genome ◽

Evolutionary Forces ◽

Asian Populations

AbstractEast Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.

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Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.665872 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhiying Wang ◽

Bohan Zhou ◽

Tao Zhang ◽

Xiaochun Yan ◽

Yongsheng Yu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Inbreeding Depression ◽

Inner Mongolia ◽

Inbreeding Coefficient ◽

Production Performance ◽

Pedigree Information ◽

Economic Traits ◽

Inbreeding Coefficients ◽

Cashmere Goats

Objective: The purpose of this study was to discover the population structure and genetic diversity of Inner Mongolia White Cashmere goats (IMCGs) and demonstrate the effect of inbreeding on the live body weight (LBW), cashmere yield (CY), fiber length (FL), and fiber diameter (FD) of IMCGs.Materials and Methods: All data were collected from pedigree information and production performance records of IMCGs from 1983 to 2019. The population structure and genetic diversity were analyzed by Endog 4.8 software. Inbreeding coefficients were obtained by the pedigree package in R. Then, a linear regression model was used to analyze how inbreeding influences economic traits in IMCGs. Four levels of inbreeding coefficients (Fi) were classified in this study, including Fi = 0, 0< Fi ≤ 6.25, 6.25< Fi ≤ 12.5 and Fi≥12.5. Variance analysis was performed to determine whether inbreeding levels had a significant effect on economic traits in IMCGs.Results: The proportions of rams and dams in IMCGs for breeding were relatively small, with values of 0.8 and 20.5%, respectively. The proportion of inbred animals in the entire population was high, with values up to 68.6%; however, the average inbreeding coefficient and relatedness coefficient were 4.50 and 8.48%, respectively. To date, the population has experienced 12 generations. The average generation interval obtained in the present study was 4.11 ± 0.01 years. The ram-to-son pathway was lowest (3.97 years), and the ewe-to-daughter pathway was highest (4.24 years). It was discovered that the LBW, CY, and FL increased by 3.88 kg, 208.7 g, and 1.151 cm, respectively, with every 1% increase in the inbreeding coefficient, and the FD decreased by 0.819 μm with every 1% increase in the inbreeding coefficient. Additionally, multiple comparison analysis indicated that when the inbreeding coefficient was higher than 6.25%, the LBW showed an obvious decreasing trend. The threshold value of inbreeding depression in the CY is 12.5%. However, inbreeding depression has not been observed in the FL and FD.Conclusion: Pedigree completeness needs to be further strengthened. The degree of inbreeding in this flock should be properly controlled when designing breeding programs.

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Homogeneity of Arabian Peninsula dromedary camel populations with signals of geographic distinction based on whole genome sequence data

Scientific Reports ◽

10.1038/s41598-021-04087-w ◽

2022 ◽

Vol 12 (1) ◽

Author(s):

Hussain Bahbahani ◽

Faisal Almathen

Keyword(s):

Genetic Diversity ◽

Genome Sequence ◽

Arabian Peninsula ◽

Sequence Data ◽

Whole Genome Sequence ◽

Whole Genome ◽

Dromedary Camels ◽

Genome Sequence Data ◽

Similarity Indices ◽

Bactrian Camels

AbstractDromedary camels in the Arabian Peninsula distribute along different geographical and ecological locations, e.g. desert, mountains and coasts. Here, we are aiming to explore the whole genome sequence data of ten dromedary populations from the Arabian Peninsula to assess their genetic structure, admixture levels, diversity and similarity indices. Upon including reference dromedary and Bactrian camel populations from Iran and Kazakhstan, we characterise inter-species and geographic genetic distinction between the dromedary and the Bactrian camels. Individual-based alpha genetic diversity profiles are found to be generally higher in Bactrian camels than dromedary populations, with the exception of five autosomes (NC_044525.1, NC_044534.1, NC_044540.1, NC_044542.1, NC_044544.1) at diversity orders (q ≥ 2). The Arabian Peninsula camels are generally homogenous, with a small degree of genetic distinction correlating with three geographic groups: North, Central and West; Southwest; and Southeast of the Arabian Peninsula. No significant variation in diversity or similarity indices are observed among the different Arabian Peninsula dromedary populations. This study contributes to our understanding of the genetic diversity of Arabian Peninsula dromedary camels. It will help conserve the genetic stock of this species and support the design of breeding programmes for genetic improvement of favorable traits.

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Simulation of African and non-African low and high coverage whole genome sequence data to assess variant calling approaches

Briefings in Bioinformatics ◽

10.1093/bib/bbaa366 ◽

2020 ◽

Author(s):

Shatha Alosaimi ◽

Noëlle van Biljon ◽

Denis Awany ◽

Prisca K Thami ◽

Joel Defo ◽

...

Keyword(s):

Genetic Diversity ◽

False Positive ◽

Sequence Data ◽

False Negative ◽

Variant Calling ◽

High Rate ◽

Whole Genome Sequence ◽

Whole Genome ◽

Sequence Coverage ◽

High Coverage

Abstract Current variant calling (VC) approaches have been designed to leverage populations of long-range haplotypes and were benchmarked using populations of European descent, whereas most genetic diversity is found in non-European such as Africa populations. Working with these genetically diverse populations, VC tools may produce false positive and false negative results, which may produce misleading conclusions in prioritization of mutations, clinical relevancy and actionability of genes. The most prominent question is which tool or pipeline has a high rate of sensitivity and precision when analysing African data with either low or high sequence coverage, given the high genetic diversity and heterogeneity of this data. Here, a total of 100 synthetic Whole Genome Sequencing (WGS) samples, mimicking the genetics profile of African and European subjects for different specific coverage levels (high/low), have been generated to assess the performance of nine different VC tools on these contrasting datasets. The performances of these tools were assessed in false positive and false negative call rates by comparing the simulated golden variants to the variants identified by each VC tool. Combining our results on sensitivity and positive predictive value (PPV), VarDict [PPV = 0.999 and Matthews correlation coefficient (MCC) = 0.832] and BCFtools (PPV = 0.999 and MCC = 0.813) perform best when using African population data on high and low coverage data. Overall, current VC tools produce high false positive and false negative rates when analysing African compared with European data. This highlights the need for development of VC approaches with high sensitivity and precision tailored for populations characterized by high genetic variations and low linkage disequilibrium.

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