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

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.

scholarly journals Genetic diversity of Indigofera kirilowii Maxim. ex Palibin using AFLP makers

2019 ◽  
Vol 48 (4) ◽  
pp. 1237-1241
Author(s):  
Qikui Wu ◽  
Limin Sun ◽  
Xiaojing Liu ◽  
Xuan Wang ◽  
Xia Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Length Polymorphism ◽  
North China ◽  
Fragment Length Polymorphism ◽  
Natural Populations ◽  
Geographic Location ◽  
High Genetic Diversity

The present studies were conducted to assess the genetic diversity and to infer population structure of 220 individuals of Indigofera kirilowii from 8 natural populations of Shandong province, north China, using amplified fragment length polymorphism (AFLP) markers. A total of 1589 AFLP bands were produced, of which 99.87% were polymorphic. High genetic diversity was considered (H = 0.1401; I = 0.2346), with high genetic differentiation (GST = 0.1058), while estimates of gene flow (Nm) were high in all analysis. No correlations were observed between geographic location and genetic diversity (r = –0.0901; p = 0.3293). Based on the results, here a strategy for the conservation of I. kirilowii germplasm was proposed.

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

Genes ◽  
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.

scholarly journals Genetic diversity and population structure of sheep (Ovis aries) in Sichuan, China

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257974
Author(s):  
Mingliang Zhou ◽  
Gaofu Wang ◽  
Minghua Chen ◽  
Qian Pang ◽  
Shihai Jiang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ovis Aries ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genome Wide ◽  
High Quality Snps ◽  
Exotic Breed ◽  
Population Structures

Sichuan, China, has abundant genetic resources of sheep (Ovis aries). However, their genetic diversity and population structure have been less studied, especially at the genome-wide level. In the present study, we employed the specific-locus amplified fragment sequencing for identifying genome-wide single nucleotide polymorphisms (SNPs) among five breeds of sheep distributed in Sichuan, including three local pure breeds, one composite breed, and one exotic breed of White Suffolk. From 494 million clean paired-end reads, we obtained a total of 327,845 high-quality SNPs that were evenly distributed among all 27 chromosomes, with a transition/transversion ratio of 2.56. Based on this SNP panel, we found that the overall nucleotide diversity was 0.2284 for all five breeds, with the highest and lowest diversity observed in Mage sheep (0.2125) and Butuo Black (0.1963) sheep, respectively. Both Wright’s fixation index and Identity-by-State distance revealed that all individuals of Liangshan Semifine-wool, White Suffolk, and Butuo Black sheep were respectively clustered together, and the breeds could be separated from each other, whereas Jialuo and Mage sheep had the closest genetic relationship and could not be distinguished from each other. In conclusion, we provide a reference panel of genome-wide and high-quality SNPs in five sheep breeds in Sichuan, by which their genetic diversity and population structures were investigated.

scholarly journals Putative Variants, Genetic Diversity and Population Structure among Soybean Cultivars Bred at Different Ages in Huang-Huai-Hai Region

2021 ◽  
Author(s):  
Jialin Liu ◽  
Huimin Xie ◽  
Ting Lin ◽  
Congxiao Tie ◽  
Huolin Luo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variants ◽  
Pedigree Information ◽  
Biological Processes ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Soybean Cultivars ◽  
Genome Wide

Abstract Soybean cultivars bred in the Huang-Huai-Hai region (HR) are rich in pedigree information. To data, few reports have exposed the genetic variants, population structure and genetic diversity of cultivars in this region by making use of genome-wide resequencing data. To depict genetic variation, population structure and composition characteristics of genetic diversity, a sample of soybean population that composed all by cultivars was constructed. We re-sequenced 181 soybean cultivar genomes with an average depth of 10.38x. In total, 11185589 single nucleotide polymorphisms (SNPs) and 2520208 insertion-deletions (InDels) were identified on all 20 chromosomes. A considerable number of putative variants existed in important genome regions that may have an incalculable influence on genes, which participated in momentous biological processes. PCA and population structure figured out that there was no obvious grouping trend. The LD semi-decay distances of the five sub-populations were 290kb, 380kb, 753kb, 182kb, and 227kb, respectively. Sub-population A (SA) had the highest value of nucleotide polymorphism (π). With the passage of time, the nucleotide polymorphism of SB and SC decreased gradually, however that of SD and SE, opposite to SB and SC, gave a rapid up-climbing trend, which meant a sharp increasing in genetic diversity during the latest 20 years, hinting that breeders may have different breeding goals in different breeding periods in HR. Analysis of the PIC statistics exhibited very similar results with π. The current study was to analyze the genetic variants and characterize the structure and genetic diversity of soybean cultivars bred in different decades in HR, and in the hope of providing a theoretical reference for other identical studies.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

2020 ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background: Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and an important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus, we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analysed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei. Results: The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci (PPL) from 69.23% to 100%, an expected heterozygosity (He) of 0.504 and an average Shannon's Information Index (I) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow (Nm) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R2 = 0.352, P < 0.01) indicated that geographically closely located populations are clustered together with some exceptions. Conclusions: Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

2019 ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus , we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analyzed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei.Results The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci ( PPL ) from 69.23% to 100%, an expected heterozygosity ( He ) of 0.504 and an average Shannon's Information Index ( I ) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow ( Nm ) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R 2 = 0.352, P < 0.01) indicated that geographically closely located populations are cluster together with some exceptions.Conclusions Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and an important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus, we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analysed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei. Results The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci (PPL) from 69.23 to 100%, an expected heterozygosity (He) of 0.504 and an average Shannon’s Information Index (I) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow (Nm) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R2 = 0.352, P < 0.01) indicated that geographically closely located populations are clustered together with some exceptions. Conclusions Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

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