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

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.

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The Genomic Basis of the Genetic Differentiation and Local Adaptive Evolution of Pampus Echinogaster based on SLAF-seq

10.21203/rs.3.rs-640424/v1 ◽

2021 ◽

Author(s):

Yuan Li ◽

Fangrui Lou ◽

Hai Li ◽

Rui Wang ◽

Zizi Cai ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Population Expansion ◽

Nucleotide Polymorphisms ◽

Stress Reactions ◽

Long Distance ◽

Evolutionary Mechanisms ◽

Inflammatory Reactions ◽

Genomic Study

Abstract Background: Factors such as climate change (especially ocean warming) and overfishing have led to a decline in the supply of Pampus echinogaster and a trend of decreasing age. Exploring the genetic structure and local adaptive evolutionary mechanisms is crucial for the management of P. echinogaster. Results: This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the overall genetic diversity among the nine P. echinogaster populations was high. The Shantou population had the lowest genetic diversity, and the Tianjin population had the highest. Meanwhile, the population genetic structure based on all SNPs revealed significant gene exchange and insignificant genetic differentiation between the nine P. echinogaster populations. Based on pairwise genetic differentiation (FST), we further screened 1,852 outlier SNPs that might have been affected by habitat selection and annotated SLAF tags containing these 1,852 outlier SNPs using Blast2GO. The annotation results showed that the genomic sequences at the outlier SNPs were mainly related to material metabolism, ion transport, breeding, stress response, and inflammatory reactions, which may be related to the adaptation of P. echinogaster to different environmental conditions (such as water temperature and salinity) in different sea areas.Conclusions: The high genetic similarity of nine P. echinogaster populations may have been caused by the population expansion after the last glacial period, the lack of balance between migration and genetic drift, and the long-distance diffusion of eggs and larvae. We suspected that variation of these genes associated with material metabolism, ion transfer, breeding, stress reactions, and inflammatory reactions were critical for adaptation to spatially heterogeneous temperatures in natural P. echinogaster populations.

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Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Genes ◽

10.3390/genes11111298 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1298

Author(s):

Caléo Panhoca de Almeida ◽

Jean Fausto de Carvalho Paulino ◽

Sérgio Augusto Morais Carbonell ◽

Alisson Fernando Chiorato ◽

Qijian Song ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Common Bean ◽

Gene Diversity ◽

Association Studies ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Association Mapping Approach

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

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Genome-wide assessment of genetic diversity and population structure in Magnolia odoratissima based on SLAF-Seq

10.21203/rs.3.rs-747821/v1 ◽

2021 ◽

Author(s):

Tao Zhang ◽

Xue Li ◽

Shuilian He

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Natural Populations ◽

Environmental Parameters ◽

Candidate Snps ◽

Small Populations ◽

Nucleotide Polymorphisms ◽

High Genetic Diversity ◽

Genome Wide

Abstract Magnolia odoratissima is a highly threatened species with small populations and scattered distribution due to habitat fragmentation and human activity. The species is recognized as a Plant Species with Extremely Small Populations (PSESP) and is endemic to China. In the current study, the population structure and levels of genetic diversity of M. odoratissima in the five remaining natural populations and three cultivated populations were evaluated using single nucleotide polymorphisms (SNPs) derived from Specific-Locus Amplified Fragment Sequencing (SLAF-seq). A total of 180,650 SNP loci were found in seventy M. odoratissima individuals. The genome-wide Nei’s and Shannon’s nucleotide diversity indexes of the total M. odoratissima population were 0.3035 and 0.4695, respectively. The observed heterozygosity (Ho) and expected heterozygosity (He) were 0.1122 and 0.3011. Our results suggest that M. odoratissima has relatively high genetic diversity at the genomic level. FST and AMOVA indicated that high genetic differentiation existed among populations. A phylogenetic neighbor-joining tree, Bayesian model–based clustering and principal components analysis (PCA) all divided the studied M. odoratissima individuals into three distinct clusters. The Treemix analysis showed that there was low gene flow among the natural populations and a certain gene flow from the wild populations to the cultivated population (LS to KIB, and GN to JD). In addition, a total of 36 unique SNPs were detected as being significantly associated with environmental parameters (altitude, temperature and precipitation). These candidate SNPs were found to be involved in multiple pathways including several molecular functions and biological process, suggesting they may play key roles in environmental adaptation. Our results suggested that three distinct evolutionary significant units (ESUs) should be set up to conserve this critically endangered species.

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Genetic Diversity and Population Differentiation of Pinus koraiensis in China

Horticulturae ◽

10.3390/horticulturae7050104 ◽

2021 ◽

Vol 7 (5) ◽

pp. 104

Author(s):

Xiang Li ◽

Minghui Zhao ◽

Yujin Xu ◽

Yan Li ◽

Mulualem Tigabu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Genetic Information ◽

Expressed Sequence Tag ◽

Association Studies ◽

Genetic Erosion ◽

Principal Component ◽

Pinus Koraiensis ◽

Genome Wide Association Studies ◽

Ecological Value

Pinus koraiensis is a well-known precious tree species in East Asia with high economic, ornamental and ecological value. More than fifty percent of the P. koraiensis forests in the world are distributed in northeast China, a region with abundant germplasm resources. However, these natural P. koraiensis sources are in danger of genetic erosion caused by continuous climate changes, natural disturbances such as wildfire and frequent human activity. Little work has been conducted on the population genetic structure and genetic differentiation of P. koraiensis in China because of the lack of genetic information. In this study, 480 P. koraiensis individuals from 16 natural populations were sampled and genotyped. Fifteen polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers were used to evaluate genetic diversity, population structure and differentiation in P. koraiensis. Analysis of molecular variance (AMOVA) of the EST-SSR marker data showed that 33% of the total genetic variation was among populations and 67% was within populations. A high level of genetic diversity was found across the P. koraiensis populations, and the highest levels of genetic diversity were found in HH, ZH, LS and TL populations. Moreover, pairwise Fst values revealed significant genetic differentiation among populations (mean Fst = 0.177). According to the results of the STRUCTURE and Neighbor-joining (NJ) tree analyses and principal component analysis (PCA), the studied geographical populations cluster into two genetic clusters: cluster 1 from Xiaoxinganling Mountains and cluster 2 from Changbaishan Mountains. These results are consistent with the geographical distributions of the populations. The results provide new genetic information for future genome-wide association studies (GWAS), marker-assisted selection (MAS) and genomic selection (GS) in natural P. koraiensis breeding programs and can aid the development of conservation and management strategies for this valuable conifer species.

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Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks

10.1101/238840 ◽

2017 ◽

Cited By ~ 1

Author(s):

Eltohamy A. A. Yousef ◽

Thomas Müller ◽

Andreas Börner ◽

Karl J. Schmid

Keyword(s):

Genetic Diversity ◽

Missing Data ◽

Genetic Differentiation ◽

Brassica Oleracea ◽

Principal Component ◽

Genotyping By Sequencing ◽

Ex Situ ◽

Nucleotide Polymorphisms ◽

Phenotypic Differences ◽

Seed Regeneration

AbstractCauliflower (Brassica oleracea var. botrytis) is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS). They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs) with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (<1%) of SNPs that are highly differentiated between the two genebanks, which indicates that selection during seed regeneration is not a major cause of differentiation between genebanks. Seed regeneration procedures of both genebanks do not result in different levels of genetic drift and loss of genetic variation. We therefore conclude that the composition and type of accessions mainly influence the level of genetic diversity and explain the strong genetic differentiation between the two ex situ collections. In summary, GBS is a useful method for characterizing genetic diversity in cauliflower genebank material and our results suggest that it may be useful to incorporate routine genotyping into accession management and seed regeneration to monitor the diversity present in ex situ collections and to reduce the loss of genetic diversity during seed regeneration.

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Variation in breeding practices and geographic isolation drive subpopulation differentiation, contributing to the loss of genetic diversity within dog breed lineages

10.21203/rs.3.rs-15717/v2 ◽

2020 ◽

Author(s):

Sara Lampi ◽

Jonas Donner ◽

Heidi Anderson ◽

Jaakko L. O. Pohjoismäki

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Association Studies ◽

Genome Wide Association Studies ◽

Population Fragmentation ◽

Genome Wide ◽

A Genome ◽

Loss Of Genetic Diversity ◽

Subpopulation Differentiation

Abstract Background: Discrete breed ideals are not restricted to delimiting dog breeds from another, but also are key drivers of subpopulation differentiation. As genetic differentiation due to population fragmentation results in increased rates of inbreeding and loss of genetic diversity, detecting and alleviating the reasons of population fragmentation can provide effective tools for the maintenance of healthy dog breeds. Results: Using a genome wide SNP array, we detected genetic differentiation to subpopulations in six breeds, Belgian Shepherd, English Greyhound, Finnish Lapphund, Italian Greyhound, Labrador Retriever and Shetland Sheepdog, either due to geographical isolation or as a result of differential breeding strategies. The subpopulation differentiation was strongest in show dog lineages.Conclusions: Besides geographical differentiation caused by founder effect and lack of gene flow, selection on champion looks or restricted pedigrees is a strong driver of population fragmentation. Artificial barriers for gene flow between the different subpopulations should be recognized, their necessity evaluated critically and perhaps abolished in order to maintain genetic diversity within a breed. Subpopulation differentiation might also result in false positive signals in genome-wide association studies of different traits.Lay summary: Purebred dogs are, by definition, reproductively isolated from other breeds. However, similar isolation can also occur within a breed due to conflicting breeder ideals and geographic distances between the dog populations. We show here that both of these examples can contribute to breed division, with subsequent loss of genetic variation in the resulting breed lineages. Breeders should avoid creating unnecessary boundaries between breed lineages and facilitate the exchange of dogs between countries.

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Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing

Frontiers in Zoology ◽

10.1186/s12983-021-00432-x ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Buweihailiqiemu Ababaikeri ◽

Yucong Zhang ◽

Huiying Dai ◽

Wenjuan Shan

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Differentiation ◽

Tarim Basin ◽

Principal Component ◽

Northwest China ◽

The North ◽

Genome Wide ◽

Specific Length

Abstract Background The Yarkand hare (Lepus yarkandensis Günther, 1875) is endemic to oasis and desert areas around the Tarim Basin in the Xinjiang Uyghur Autonomous Region of northwest China; however, genome-wide information for this species remains limited. Moreover, the genetic variation, genetic structure, and phylogenetic relationships of Yarkand hare from the plateau mountain regions have not been reported. Thus, we used specific-length amplified fragment sequencing (SLAF-seq) technology to evaluate the genetic diversity of 76 Yarkand hares from seven geographic populations in the northern and southwestern parts of the Tarim Basin to investigate single-nucleotide polymorphism (SNP) marker-based population differentiation and evolutionary processes. Selective sweep analysis was conducted to identify genetic differences between populations. Results Using SLAF-seq, a total of 1,835,504 SNPs were initially obtained, of which 308,942 high-confidence SNPs were selected for further analysis. Yarkand hares exhibited a relatively high degree of genetic diversity at the SNP level. Based on pairwise FST estimates, the north and southwest groups showed a moderate level of genetic differentiation. Phylogenetic tree and population structure analyses demonstrated evident systematic phylogeographical structure patterns consistent with the geographical distribution of the hares. Hierarchical analysis of molecular variation further indicated that genetic variation was mainly observed within populations. Low to moderate genetic differentiation also occurred among populations despite a common genomic background, likely due to geographical barriers, genetic drift, and differential selection pressure of distinct environments. Nevertheless, the observed lineage-mixing pattern, as indicated by the evolutionary tree, principal component analysis, population structure, and TreeMix analyses, suggests a certain degree of gene flow between the north and southwest groups. This may be related to the migration of hares to high-altitude water sources southwest of the basin during glacial climatic oscillations, as well as river re-diffusion and oasis restoration in the basin following the glacial period. We also identified candidate genes, and their associated gene ontology terms and pathways, related to the adaptation of Yarkand hares to different environmental habitats. Conclusions The identified genome-wide SNPs, genetic diversity, and population structure of Yarkand hares expand our understanding of the genetic background of this endemic species and provide valuable insights into its environmental adaptation, allowing for further exploration of the underlying mechanisms.

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Genetic Diversity of South African Indigenous Goat Population from Four Provinces Using Genome-Wide SNP Data

Sustainability ◽

10.3390/su122410361 ◽

2020 ◽

Vol 12 (24) ◽

pp. 10361

Author(s):

Tlou Caswell Chokoe ◽

Khanyisile Mdladla-Hadebe ◽

Farai Muchadeyi ◽

Edgar Dzomba ◽

Tlou Matelele ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

South African ◽

Principal Component ◽

Chromosome 8 ◽

Nucleotide Polymorphisms ◽

North West ◽

Genome Wide ◽

Goat Population ◽

Indigenous Goat

Genome-wide assessments of the genetic landscape of Farm Animal Genetic Resources (FAnGR) are key to developing sustainable breed improvements. Understanding the FAnGR adaptation to different environments and supporting their conservation programs from community initiative to national policymakers is very important. The objective of the study was to investigate the genetic diversity and population structure of communal indigenous goat populations from four provinces of South Africa. Communal indigenous goat populations from the Free State (FS) (n = 24), Gauteng (GP) (n = 28), Limpopo (LP) (n = 30), and North West (NW) (n = 35) provinces were genotyped using the Illumina Goats SNP50 BeadChip. An Illumina Goats SNP50 BeadChip data from commercial meat-type breeds: Boer (n = 33), Kalahari Red (n = 40), and Savanna (n = 31) was used in this study as reference populations. The Ho revealed that the genetic diversity of a population ranged between 0.39 ± 0.11 Ho in LP to 0.42 ± 0.09 Ho in NW. Analysis of molecular variance revealed variations of 3.39% (p < 0.0001) and 90.64% among and within populations, respectively. The first two Principal Component Analyses (PCAs) revealed a unique Limpopo population separated from GP, FS, and NW communal indigenous goat populations with high levels of admixture with commercial goat populations. There were unique populations of Kalahari and Savanna that were observed and admixed individuals. Marker FST (Limpopo versus commercial goat populations) revealed 442 outlier single nucleotide polymorphisms (SNPs) across all chromosomes, and the SNP with the highest FST value (FST = 0.72; chromosome 8) was located on the UHRF2 gene. Population differentiation tests (PCAdapt) revealed PC2 as optimal and five outlier SNPs were detected on chromosomes 10, 15, 20, and 21. The study revealed that the SNPs identified by the first two principal components show high FST values in LP communal goat populations and allowed us to identify candidate genes which can be used in the development of breed selection programs to improve this unique LP population and other communal goat population of FS, GP, and NW, and find genetic factors contributing to the adaptation to harsh environments. Effective management and utilization of South African communal indigenous goat populations is important, and effort should be made to maintain unique genetic resources for conservation.

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DNA polymorphism, genetic originality and identification of sterlet populations and replacement broodstock (Acipenser ruthenus)

Вестник Пермского университета. Серия «Биология»=Bulletin of Perm University. Biology ◽

10.17072/1994-9952-2021-1-53-60 ◽

2021 ◽

pp. 53-60

Author(s):

L. V. Komarova ◽

◽

A. R. Peleeva ◽

N. V. Kostitsyna ◽

A. G. Melnikova ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Gene Pool ◽

Dna Polymorphism ◽

Molecular Genetic ◽

Natural Populations ◽

Federal District ◽

Acipenser Ruthenus ◽

Sterlet Acipenser Ruthenus

DNA polymorphism has been studied, indicators of genetic diversity and genetic originality have been de-termined for three natural populations and three replacement broodstocks of sterlet (Acipenser ruthenus Linnaeus, Acipenseridae) from the Volga Federal District. In the group of A. ruthenus replacement broodstock, 106 ISSR-PСR markers were identified, and in the group of natural populations, 103 ISSR-PСR markers. The indicators of genetic diversity and the coefficient of genetic originality (CGO) were slightly higher in the group of natural populations. Analysis of genetic structure of natural populations and groups of broodstock herds A. ruthenus showed that the coefficient of genetic differentiation are also slightly higher in the group of natural populations and equal 0,377. As a result of molecular genetic iden-tification, generic and species identification fragments of sterlet DNA were revealed, as well as combina-tions of polymorphic fragments for identification of the studied natural populations and stocks. The data obtained can be used to preserve the gene pool of populations, which is characteristic for a particular re-gion.

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Pharmacogenomics of Lithium Response in Bipolar Disorder

Pharmaceuticals ◽

10.3390/ph14040287 ◽

2021 ◽

Vol 14 (4) ◽

pp. 287

Author(s):

Courtney M. Vecera ◽

Gabriel R. Fries ◽

Lokesh R. Shahani ◽

Jair C. Soares ◽

Rodrigo Machado-Vieira

Keyword(s):

Bipolar Disorder ◽

Association Studies ◽

Mood Stabilizer ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Non Coding Rna ◽

Genome Wide ◽

Lithium Response ◽

Genetic Loading ◽

Long Non Coding Rna

Despite being the most widely studied mood stabilizer, researchers have not confirmed a mechanism for lithium’s therapeutic efficacy in Bipolar Disorder (BD). Pharmacogenomic applications may be clinically useful in the future for identifying lithium-responsive patients and facilitating personalized treatment. Six genome-wide association studies (GWAS) reviewed here present evidence of genetic variations related to lithium responsivity and side effect expression. Variants were found on genes regulating the glutamate system, including GAD-like gene 1 (GADL1) and GRIA2 gene, a mutually-regulated target of lithium. In addition, single nucleotide polymorphisms (SNPs) discovered on SESTD1 may account for lithium’s exceptional ability to permeate cell membranes and mediate autoimmune and renal effects. Studies also corroborated the importance of epigenetics and stress regulation on lithium response, finding variants on long, non-coding RNA genes and associations between response and genetic loading for psychiatric comorbidities. Overall, the precision medicine model of stratifying patients based on phenotype seems to derive genotypic support of a separate clinical subtype of lithium-responsive BD. Results have yet to be expounded upon and should therefore be interpreted with caution.

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