scholarly journals Genomic response to natural selection within alpine cattle breeds

2018 ◽  
Vol 63 (No. 4) ◽  
pp. 136-143
Author(s):  
N. Moravčíková ◽  
M. Simčič ◽  
G. Mészáros ◽  
J. Sölkner ◽  
V. Kukučková ◽  
...  
Keyword(s):  
Natural Selection ◽  
Principal Component ◽  
Selection Response ◽  
Population Based ◽  
Nucleotide Polymorphisms ◽  
Data Quality Control ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Genomic Regions ◽  
Genomic Response

The aim of this study was to analyse the genomic regions that have been target of natural selection with respect to identifying the loci responsible mainly for fitness traits across six alpine cattle breeds. The genome-wide scan for selection signatures was performed using genotyping data from totally 465 animals. After applying data quality control, overall 35 873 single nucleotide polymorphisms were useable for the subsequent analysis. The detection of genomic regions affected by natural selection was carried out using the approach of principal component analysis. The analysis was based on the assumption that markers extremely related to the population structure are also candidates for local adaptation potential of the population. Based on the expected false discovery rate equal to 10% up to 1138 loci were identified as outliers. The strongest signals of selection were found in genomic regions on BTA 1, 2, 3, 6, 9, 11, 13, and 22. Most genes located in the identified regions have been previously associated with immunity system as well as body growth and muscle formation that mainly reflect the pressure of both natural and artificial selection in respect to adaptation of analysed breeds to the local environmental conditions. The results also signalized that those regions represent a correlated selection response in way to maintain the fitness of analysed breeds.

scholarly journals Genome-wide identification of breed-informative single-nucleotide polymorphisms in three South African indigenous cattle breeds

1970 ◽  
Vol 46 (3) ◽  
pp. 302-312
Author(s):  
A.A. Zwane ◽  
A. Maiwashe ◽  
M.L. Makgahlela ◽  
A. Choudhury ◽  
J.F. Taylor ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Single Nucleotide Polymorphisms ◽  
South African ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Indigenous Cattle ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Polymorphic Snps ◽  
Genome Wide

Access to genotyping assays enables the identification of informative markers that discriminate between cattle breeds. Identification of these markers can assist in breed assignment, improvement and conservation. The objective of this study was to identify breed informative markers to discriminate between three South African indigenous cattle breeds. Data from BovineSNP50 and GeneSeek Genomic Profiler (GGP-80K) assays were generated for Afrikaner, Drakensberger and Nguni, and were analysed for their genetic differentiation. Hereford and Angus were included as outgroups. Breeds were differentiated using principal component analysis (PCA). Single-nucleotide polymorphisms (SNPs) within the breeds were determined when minor allele frequency (MAF) was ≥ 0.05. Breed-specific SNPs were identified using Reynolds Fst and extended Lewontin and Krakauer's (FLK) statistics. These SNPs were validated using three African breeds, namely N’Dama, Kuri and Zebu from Madagascar. PCA discriminated among the breeds. A larger number of polymorphic SNPs was detected in Drakensberger (73%) than in Afrikaner (56%) and Nguni (65%). No substantial numbers of informative SNPs (Fst ≥ 0.6) were identified among indigenous breeds. Eleven SNPs were validated as discriminating the indigenous breeds from other African breeds. This is because the SNPs on BovineSNP50 and GGP-80K assays were ascertained as being common in European taurine breeds. Lower MAF and SNP informativeness observed in this study limits the application of these assays in breed assignment, and could have other implications for genome-wide studies in South African indigenous breeds. Sequencing should therefore be considered to discover new SNPs that are common among indigenous South African breeds and also SNPs that discriminate among these indigenous breeds.

scholarly journals Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

2021 ◽  
Vol 7 (11) ◽  
pp. eabd1239
Author(s):  
Mark Simcoe ◽  
Ana Valdes ◽  
Fan Liu ◽  
Nicholas A. Furlotte ◽  
David M. Evans ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Color Variation ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Melanin Pigmentation ◽  
Eye Color ◽  
Human Eye ◽  
Genome Wide ◽  
Genomic Regions

Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.

scholarly journals Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 832
Author(s):  
Nina Moravčíková ◽  
Radovan Kasarda ◽  
Radoslav Židek ◽  
Luboš Vostrý ◽  
Hana Vostrá-Vydrová ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Structure ◽  
Principal Component ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
German Shepherd ◽  
German Shepherd Dog ◽  
Genome Wide ◽  
Scale Population ◽  
History Effect

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Genome-Wide Association Study of Body Weight Traits in Chinese Fine-Wool Sheep

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 170 ◽  
Author(s):  
Zengkui Lu ◽  
Yaojing Yue ◽  
Chao Yuan ◽  
Jianbin Liu ◽  
Zhiqiang Chen ◽  
...  
Keyword(s):  
Body Weight ◽  
Muscle Development ◽  
Genome Wide Association Study ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Economic Trait ◽  
Significance Levels ◽  
Genomic Regions ◽  
Selection Of

Body weight is an important economic trait for sheep and it is vital for their successful production and breeding. Therefore, identifying the genomic regions and biological pathways that contribute to understanding variability in body weight traits is significant for selection purposes. In this study, the genome-wide associations of birth, weaning, yearling, and adult weights of 460 fine-wool sheep were determined using resequencing technology. The results showed that 113 single nucleotide polymorphisms (SNPs) reached the genome-wide significance levels for the four body weight traits and 30 genes were annotated effectively, including AADACL3, VGF, NPC1, and SERPINA12. The genes annotated by these SNPs significantly enriched 78 gene ontology terms and 25 signaling pathways, and were found to mainly participate in skeletal muscle development and lipid metabolism. These genes can be used as candidate genes for body weight in sheep, and provide useful information for the production and genomic selection of Chinese fine-wool sheep.

scholarly journals Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora

2017 ◽  
Vol 284 (1846) ◽  
pp. 20162182 ◽  
Author(s):  
Natalie L. Rosser ◽  
Luke Thomas ◽  
Sean Stankowski ◽  
Zoe T. Richards ◽  
W. Jason Kennington ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Future Research ◽  
Nucleotide Polymorphisms ◽  
Coral Genus ◽  
Genome Wide ◽  
A Genome ◽  
Different Seasons ◽  
Genetic Clusters ◽  
Genome Level ◽  
Genomic Regions

Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC . Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora , including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species; however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC , provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.

scholarly journals Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

2021 ◽  
Vol 12 ◽  
Author(s):  
Kelechi Uchendu ◽  
Damian Ndubuisi Njoku ◽  
Agre Paterne ◽  
Ismail Yusuf Rabbi ◽  
Daniel Dzidzienyo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome ◽  
Breeding Programmes ◽  
Vegetables And Fruits ◽  
Genomic Regions

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

scholarly journals Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish

2018 ◽  
Author(s):  
Reid S. Brennan ◽  
Timothy M. Healy ◽  
Heather J. Bryant ◽  
Man Van La ◽  
Patricia M. Schulte ◽  
...  
Keyword(s):  
Natural Selection ◽  
Salinity Tolerance ◽  
Hypoxia Tolerance ◽  
Physiological Traits ◽  
Adaptive Divergence ◽  
Genome Wide ◽  
Native Populations ◽  
Genomic Regions ◽  
Insight Into ◽  
Freshwater Environments

AbstractAdaptive divergence between marine and freshwater environments is important in generating phyletic diversity within fishes, but the genetic basis of adaptation to freshwater habitats remains poorly understood. Available approaches to detect adaptive loci include genome scans for selection, but these can be difficult to interpret because of incomplete knowledge of the connection between genotype and phenotype. In contrast, genome wide association studies (GWAS) are powerful tools for linking genotype to phenotype, but offer limited insight into the evolutionary forces shaping variation. Here, we combine GWAS and selection scans to identify loci important in the adaptation of complex physiological traits to freshwater environments. We focused on freshwater (FW)-native and brackish water (BW)-native populations of the Atlantic killifish (Fundulus heteroclitus) as well as a population that is a natural admixture of these two populations. We measured phenotypes for multiple physiological traits that differ between populations and that may contribute to adaptation across osmotic niches (salinity tolerance, hypoxia tolerance, metabolic rate, and body shape) and used a reduced representation approach for genome-wide genotyping. Our results show patterns of population divergence in physiological capabilities that are consistent with local adaptation. Selection scans between BW-native and FW-native populations identified genomic regions that presumably aect fitness between BW and FW environments, while GWAS revealed loci that contribute to variation for each physiological trait. There was substantial overlap in the genomic regions putatively under selection and loci associated with the measured physiological traits, suggesting that these phenotypes are important for adaptive divergence between BW and FW environments. Our analysis also implicates candidate genes likely involved in physiological capabilities, some of which validate a priori hypotheses. Together, these data provide insight into the mechanisms that enable diversification of fishes across osmotic boundaries.Author SummaryIdentifying the genes that underlie adaptation is important for understanding the evolutionary process, but this is technically challenging. We bring multiple lines of evidence to bear for identifying genes that underlie adaptive divergence. Specifically, we integrate genotype-phenotype association mapping with genome-wide scans for signatures of natural selection to reveal genes that underlie phenotypic variation and that are adaptive in populations of killifish that are diverging between marine and freshwater environments. Because adaptation is likely manifest in multiple physiological traits, we focus on hypoxia tolerance, salinity tolerance, and metabolic rate; traits that are divergent between marine and freshwater populations. We show that each of these phenotypes is evolving by natural selection between environments; genetic variants that contribute to variation in these physiological traits tend to be evolving by natural selection between marine and freshwater populations. Furthermore, one of our top candidate genes provides a mechanistic explanation for previous hypotheses that suggest the adaptive importance of cellular tight junctions. Together, these data demonstrate a powerful approach to identify genes involved in adaptation and help to reveal the mechanisms enabling transitions of fishes across osmotic boundaries.

scholarly journals Inference of Population Genetic Structure and High Linkage Disequilibrium Among Alternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing

2019 ◽  
Author(s):  
Tika B. Adhikari ◽  
Brian J. Knaus ◽  
Niklaus J. Grünwald ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Plant Pathogens ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Allelic Association ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Genome Wide ◽  
A Genome

ABSTRACTGenotyping by sequencing (GBS) is considered a powerful tool to discover single nucleotide polymorphisms (SNPs), which are useful to characterize closely related genomes of plant species and plant pathogens. We applied GBS to determine genome-wide variations in a panel of 187 isolates of three closely related Alternaria spp. that cause diseases on tomato and potato in North Carolina (NC) and Wisconsin (WI). To compare genetic variations, reads were mapped to both A. alternata and A. solani draft reference genomes and detected dramatic differences in SNPs among them. Comparison of A. linariae and A. solani populations by principal component analysis revealed the first (83.8% of variation) and second (8.0% of variation) components contained A. linariae from tomato in NC and A. solani from potato in WI, respectively, providing evidence of population structure. Genetic differentiation (Hedrick’s G’ST) in A. linariae populations from Haywood, Macon, and Madison counties in NC were little or no differentiated (G’ST 0.0 - 0.2). However, A. linariae population from Swain county appeared to be highly differentiated (G’ST > 0.8). To measure the strength of the linkage disequilibrium (LD), we also calculated the allelic association between pairs of loci. Lewontin’s D (measures the fraction of allelic variations) and physical distances provided evidence of linkage throughout the entire genome, consistent with the hypothesis of non-random association of alleles among loci. Our findings provide new insights into the understanding of clonal populations on a genome-wide scale and microevolutionary factors that might play an important role in population structure. Although we found limited genetic diversity, the three Alternaria spp. studied here are genetically distinct and each species is preferentially associated with one host.

scholarly journals Population Differentiation at the HLA Genes

2017 ◽  
Author(s):  
Débora Y. C. Brandt ◽  
Jônatas César ◽  
Jérôme Goudet ◽  
Diogo Meyer
Keyword(s):  
Population Differentiation ◽  
Balancing Selection ◽  
Global Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Hla Genes ◽  
Genome Wide ◽  
Different Populations ◽  
Genomic Regions

ABSTRACTBalancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To tackle this issue, we investigated population differentiation at the HLA genes, which constitute the most striking example of balancing selection in humans. We found that population differentiation of single nucleotide polymorphisms (SNPs) at the HLA genes is on average lower than that of SNPs in other genomic regions. However, this result depends on accounting for the differences in allele frequency between selected and putatively neutral sites. Our finding of reduced differentiation at SNPs within HLA genes suggests a predominant role of shared selective pressures among populations at a global scale. However, in pairs of closely related populations, where genome-wide differentiation is low, differentiation at HLA is higher than in other genomic regions. This pattern was reproduced in simulations of overdominant selection. We conclude that population differentiation at the HLA genes is generally lower than genome-wide, but it may be higher for recently diverged population pairs, and that this pattern can be explained by a simple overdominance regime.

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