scholarly journals Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

2020 ◽  
Vol 49 (6) ◽  
pp. 1083-1092
Author(s):  
S Goitom ◽  
M.G. Gicheha ◽  
F.K. Njonge ◽  
N Kiplangat
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Population Differentiation ◽  
Principal Component ◽  
Vital Role ◽  
Group Method ◽  
Indigenous Cattle ◽  
Ecological Zones ◽  
Genome Wide

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

scholarly journals Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10485
Author(s):  
Zhixin Wang ◽  
Yalin Sun ◽  
Xinfang Huang ◽  
Feng Li ◽  
Yuping Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Conservation ◽  
Principal Component ◽  
Snp Markers ◽  
Colocasia Esculenta ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Entire Collection ◽  
Tuber Crop

Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.

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

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.

scholarly journals Climate Change and Fading Genetic Resources of Parkia biglobosa (Jacq.) in Nigeria Based on SSR Markers

2019 ◽  
Author(s):  
Jacob Popoola ◽  
James Agbolade ◽  
Abiodun Ajiboye ◽  
Omotolani Akinola ◽  
Francis Lewu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Principal Component ◽  
Sub Saharan Africa ◽  
Group Method ◽  
Parkia Biglobosa ◽  
Arithmetic Average ◽  
Ecological Zones ◽  
Pair Group

African locust bean (Parkia biglobosa (Jacq.) is a multi-purpose economic tree with genetic potentials in sub-Saharan Africa. Its cultivation and production is declining with increased aging and genetically threatened throughout its natural ranges. Research efforts are needed to change the present scenario to sustainable cultivation and utilization, hence this present study. This study was aimed at evaluating genetic diversity and geographical spread relationships of twenty landraces collected from different ecological zones of Nigeria using simple sequence repeat (SSR) markers. Ten SSR markers were screened and five primers (PbL02, PbL03, PbL04, PbL05 and PbL09) were selected based on clear amplification products and reproducible scorable bands. The SSR primers detected a total of 55 alleles ranged from 10 to 14 alleles with a mean of 11. The percentage polymorphisms were high and ranged from 68.75 % in PbL04 to 84.21 % in PbL05 with a mean of 74.16 %. The polymorphic information content (PIC) was in the range of 0.31 in PbL02 to 0.37 in PbL09. The genetic diversity and heterozygosity values ranged from 0.39 to 0.50 and 0.00 to 0.68 while the average genetic distance for all pair wise comparisons was 0.31.The first five Principal Component (PC) accounted for 70.20 % of the total variation out of which PC1 (31.50%) and PC2 (19.20%) extracted 49.70% molecular similarity. The dendrogram resulted in separation of the 19 landraces into three major clusters based on unweighted pair group method with arithmetic average. Cluster I comprised of five landraces: ABNo130 and BENo023; OYNo11, KANo125 and NiNo262 while cluster II had only one (BANo116). Cluster III was diverse comprising 13 landraces: ZANo188, KNNo162, KENo220, GMNo076 and EbNo260, ADNo64, EdNo164, KANo137, KENo217, KwNo270, NiNo241, OsNo206 and PLNo120. The homogeneity of alleles among the studied landraces suggested suspicion of loss of genetic intra-specific variation among the landraces of P. biglobosa which calls for concerted efforts toward better cultivation, conservation, management, utilization and genetic improvement of the species in Nigeria.

scholarly journals Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography

2020 ◽  
Vol 42 (10) ◽  
pp. 1169-1178
Author(s):  
Agraw Amane ◽  
Gurja Belay ◽  
Yao Nasser ◽  
Martina Kyalo ◽  
Tadelle Dessie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
Genetic Research ◽  
Principal Component ◽  
Conservation Strategies ◽  
Genetic Cluster ◽  
Sheep Population ◽  
Indigenous Sheep ◽  
Genome Wide

Abstract Background Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies. Objective The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations. Methods A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference. Results Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep. Conclusion The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations

scholarly journals Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.)

2021 ◽  
Author(s):  
Amber Bassett ◽  
Kelvin Kamfwa ◽  
Daniel Ambachew ◽  
Karen Cichy
Keyword(s):  
Genetic Variability ◽  
Seed Coat ◽  
Principal Component ◽  
Breeding Programs ◽  
Flavor Intensity ◽  
Genome Wide ◽  
White Bean ◽  
The Usa ◽  
New Varieties ◽  
End Use

Abstract Key message Cooked bean flavor and texture vary within and across 20 Andean seed types; SNPs are significantly associated with total flavor, beany, earthy, starchy, bitter, seed-coat perception, and cotyledon texture. Abstract Common dry beans are a nutritious food recognized as a staple globally, but their consumption is low in the USA. Improving bean flavor and texture through breeding has the potential to improve consumer acceptance and suitability for new end-use products. Little is known about genetic variability and inheritance of bean sensory characteristics. A total of 430 genotypes of the Andean Diversity Panel representing twenty seed types were grown in three locations, and cooked seeds were evaluated by a trained sensory panel for flavor and texture attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Extensive variation in sensory attributes was found across and within seed types. A set of genotypes was identified that exhibit extreme attribute intensities generally stable across all three environments. seed-coat perception and total flavor intensity had the highest broad-sense heritability (0.39 and 0.38, respectively), while earthy and vegetative intensities exhibited the lowest (0.14 and 0.15, respectively). Starchy and sweet flavors were positively correlated and highest in white bean genotypes according to principal component analysis. SNPs associated with total flavor intensity (six SNPs across three chromosomes), beany (five SNPs across four chromosomes), earthy (three SNPs across two chromosomes), starchy (one SNP), bitter (one SNP), seed-coat perception (three SNPs across two chromosomes), and cotyledon texture (two SNPs across two chromosomes) were detected. These findings lay a foundation for incorporating flavor and texture in breeding programs for the development of new varieties that entice growers, consumers, and product developers alike.

scholarly journals Genetic diversity and population structure analysis of Lateolabrax maculatus from Chinese coastal waters using polymorphic microsatellite markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wei Wang ◽  
Chunyan Ma ◽  
Longling Ouyang ◽  
Wei Chen ◽  
Ming Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Analysis ◽  
Principal Component ◽  
Genetic Constitution ◽  
Southern Group ◽  
Population Structure Analysis ◽  
Lateolabrax Maculatus ◽  
Geographic Populations ◽  
Geographic Separation

AbstractIn order to provide valuable guidelines for the conservation of germplasm of Lateolabrax maculatus, the genetic diversity and population structure analysis were evaluated for eight geographic populations along coastal regions of China, using 11 microsatellite DNA markers. The genetic parameters obtained showed that, eight populations can be clustered into two groups, the Northern group and the Southern group, concordant with their geographical positions. The UPGMA tree constructed according to the Nei’s genetic distance along with the structure analysis and discriminant analysis of principal component also supported this result. This might be explained by the geographic separation and the divergent environmental conditions among the populations. It's worth noting that, QD (Qingdao) population from northern area was assigned to the Southern group and showed a close genetic relationship and similar genetic constitution with the southern populations. We speculated that large scales of anthropogenic transportation of wild fries from QD populations to the southern aquaculture areas in history should be the primary cause. The populations from GY (Ganyu), RD (Rudong) and BH (Binhai) had higher genetic diversity and showed limited genetic exchange with other populations, indicating better conservation of the natural resources in these regions. All populations were indicated to have experienced bottleneck events in history.

scholarly journals Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0154353 ◽  
Author(s):  
Carina Visser ◽  
Simon F. Lashmar ◽  
Este Van Marle-Köster ◽  
Mario A. Poli ◽  
Daniel Allain
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
South African ◽  
Snp Data ◽  
Genome Wide ◽  
Angora Goats

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.

Sign in / Sign up

Export Citation Format

Share Document