scholarly journals Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis

2022 ◽  
Vol 12 ◽  
Author(s):  
Hanli Dang ◽  
Tao Zhang ◽  
Yuanyuan Li ◽  
Guifang Li ◽  
Li Zhuang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Unsaturated Fatty Acids ◽  
Principal Component ◽  
Glycyrrhiza Uralensis ◽  
Alpha Linolenic Acid ◽  
High Quality ◽  
Illumina Hiseq ◽  
Sequencing Platform ◽  
Population Evolution ◽  
Genetic Diversity And Structure

Glycyrrhiza uralensis is a valuable medicinal legume, which occurs widely in arid and semi-arid regions. G. uralensis demand has risen steeply due to its high medical and commercial value. Interpret genome-wide information can stimulate the G. uralensis development as far as its increased bioactive compound levels, and plant yield are concerned. In this study, leaf nutrient concentration and photosynthetic chlorophyll index of G. uralensis were evaluated to determine the G. uralensis growth physiology in three habitats. We observed that G. uralensis nutrient levels and photosynthesis differed significantly in three regions (p < 0.05). Whole-genome re-sequencing of the sixty G. uralensis populations samples from different habitats was performed using an Illumina HiSeq sequencing platform to elucidate the distribution patterns, population evolution, and genetic diversity of G. uralensis. 150.06 Gb high-quality clean data was obtained after strict filtering. The 895237686 reads were mapped against the reference genome, with an average 89.7% mapping rate and 87.02% average sample coverage rate. A total of 6985987 SNPs were identified, and 117970 high-quality SNPs were obtained after filtering, which were subjected to subsequent analysis. Principal component analysis (PCA) based on interindividual SNPs and phylogenetic analysis based on interindividual SNPs showed that the G. uralensis samples could be categorized into central, southern, and eastern populations, which reflected strong genetic differentiation due to long periods of geographic isolation. In this study, a total of 131 candidate regions were screened, and 145 candidate genes (such as Glyur001802s00036258, Glyur003702s00044485, Glyur001802s00036257, Glyur007364s00047495, Glyur000028s00003476, and Glyur000398s00034457) were identified by selective clearance analysis based on Fst and θπ values. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed significant enrichment of 110 GO terms including carbohydrate metabolic process, carbohydrate biosynthetic process, carbohydrate derivative biosynthetic process, and glucose catabolic process (p < 0.05). Alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, and fatty acid degradation pathways were significantly enriched (p < 0.05). This study provides information on the genetic diversity, genetic structure, and population adaptability of the medicinal legumes, G. uralensis. The data obtained in this study provide valuable information for plant development and future optimization of breeding programs for functional genes.

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2020 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
De Novo ◽  
Average Length ◽  
Species Conservation ◽  
Illumina Hiseq ◽  
Bottleneck Analysis ◽  
Genetic Diversity And Structure ◽  
Geographical Distances ◽  
High Level

Abstract Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeqTM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2020 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Species Conservation ◽  
Group Method ◽  
Arithmetic Means ◽  
Illumina Hiseq ◽  
Genetic Diversity And Structure

Abstract Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population is unknown due to lack of efficient molecular markers.Results: In this study, we employed Illumina HiSeq TM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). A total of 23,741,783 raw reads were obtained and assembled, from which, 89,271 unigenes with an average length of 598.3191 nt were generated. During functional annotation, 31,686 unigenes were annotated in Gene Ontology categories, Kyoto Encyclopedia of Genes and Genomes pathways, Swiss-Prot database, and Nucleotide Collection (NR/NT) database. In addition, 11,343 expressed sequence tag-simple sequence repeat (EST-SSRs) were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which, 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used to analyze genetic diversity and structure of the natural populations. The obtained results revealed that the shows high levels of genetic diversity in populations, the average observed and expected heterozygosity were H O = 0.422 and H E = 0.479. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of bottleneck in all populations. Genetic differentiation among populations was moderate (F ST = 0.133) and indicating limited gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. These results showed a moderate genetic structure of P. vietnamensis. STRUCTURE analysis and the unweighted pair-group method with arithmetic means (UPGMA) tree revealed strong genetic structure and two genetic clusters related to geographical distances, as well. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2020 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Species Conservation ◽  
Group Method ◽  
Arithmetic Means ◽  
Illumina Hiseq ◽  
Genetic Diversity And Structure

Abstract Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population is unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeq TM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). A total of 23,741,783 raw reads were obtained and assembled, from which, 89,271 unigenes with an average length of 598.3191 nt were generated. During functional annotation, 31,686 unigenes were annotated in Gene Ontology categories, Kyoto Encyclopedia of Genes and Genomes pathways, Swiss-Prot database, and Nucleotide Collection (NR/NT) database. In addition, 11,343 expressed sequence tag-simple sequence repeat (EST-SSRs) were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which, 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used to analyze genetic diversity and structure of the natural populations. The obtained results revealed that the shows high levels of genetic diversity in populations, the average observed and expected heterozygosity were H O = 0.422 and H E = 0.479. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of bottleneck in all populations. Genetic differentiation among populations was moderate (F ST = 0.133) and indicating limited gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. These results showed a moderate genetic structure of P. vietnamensis. STRUCTURE analysis and the unweighted pair-group method with arithmetic means (UPGMA) tree revealed strong genetic structure and two genetic clusters related to geographical distances, as well. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

scholarly journals The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Yongtan Li ◽  
Jun Zhang ◽  
Shijie Wang ◽  
Yiwen Zhang ◽  
Minsheng Yang
Keyword(s):  
Morphological Characteristics ◽  
Principal Component ◽  
Sequencing Depth ◽  
Natural Hybridization ◽  
Wild Plant ◽  
Sphingolipid Metabolism ◽  
Whole Genome ◽  
Depth Range ◽  
Illumina Hiseq ◽  
Sequencing Platform

Pyrus hopeiensis is a valuable but endangered wild resource in the genus Pyrus. It has been listed as one of the 120 wild species with tiny population in China. The specie has been little studied. A preliminary study of propagation modes in P. hopeiensis was performed through seed propagation, hybridization, self-crossing trials, bud grafting, branch grafting, and investigations of natural growth. The results showed that the population size of P. hopeiensis was very small, the distribution range was limited, and the habitat was extremely degraded. In the wild population, natural hybridization and root tiller production were the major modes of propagation. Whole genome re-sequencing of the 23 wild and cultivated accessions from Pyrus species collected was performed using an Illumina HiSeq sequencing platform. The sequencing depth range was 26.56x−44.85x and the average sequencing depth was 32x. Phylogenetic tree and principal component analyses (PCA) based on SNPs showed that the wild Pyrus species, such as PWH06, PWH07, PWH09, PWH10, PWH13, and PWH17, were closely related to both P. hopeiensis HB-1 and P. hopeiensis HB-2. Using these results in combination with morphological characteristics, it speculated that P. hopeiensis populations may form a natural hybrid group with frequent gene exchanges between and within groups. A selective elimination analysis on the P. hopeiensis population were performed using Fst and π radio and a total of 381 overlapping genes including SAUR72, IAA20, HSFA2, and RKP genes were obtained. These genes were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) function enrichment. And four KEGG pathways, including lysine degradation, sphingolipid metabolism, other glycan degradation, and betaine biosynthesis were significantly enriched in the P. hopeiensis population. Our study provided information on genetic variation, evolutionary relationships, and gene enrichment in P. hopeiensis population. These data will help reveal the evolutionary history and origin of P. hopeiensis and provide guidelines for subsequent research on the locations of functional genes.

Analysis of genetic diversity and structure in a genebank collection of red clover (Trifolium pratense L.) using SSR markers

2016 ◽  
Vol 15 (4) ◽  
pp. 376-379 ◽  
Author(s):  
Mamta Gupta ◽  
Vikas Sharma ◽  
Sunil K. Singh ◽  
Rakesh K. Chahota ◽  
Tilak R. Sharma
Keyword(s):  
Genetic Diversity ◽  
Trifolium Pratense ◽  
Fragment Size ◽  
Red Clover ◽  
Principal Component ◽  
Model Based Clustering ◽  
Average Value ◽  
Genetic Diversity And Structure ◽  
Trifolium Pratense L ◽  
High Level

AbstractGenetic diversity of a red clover global collection was assessed using 36 simple sequence repeat (SSR) primers representing all seven linkage groups (LGs). The number of fragments amplified ranged from 1 to 6 for all the primers. Primer RCS0060 detected highest number of fragments, whereas four SSRs viz., RCS0899, RCS1594, TPSSR40 and RCS6927 amplified single fragment. Size range of amplicons generated by all the primers varied from 100 to 400 bp. Polymorphism information content values ranged from 0.301 to 0.719 with an average value of 0.605. LG wise diversity analysis showed that LG 3 was most diverse (I = 0.65, Ht = 0.44), whereas LG-1 showed minimum diversity (I = 0.48, Ht = 0.26) for the microsatellites used. Bayesian model-based clustering inferred three genetically distinct populations in the red clover germplasm holding and showed considerable admixture in individuals within clusters. Neighbour-joining analysis showed intermixing of accessions within groups. Principal component analysis plot complemented the clustering shown by Structure and distinguished three populations to greater extent. Analysis of molecular variance showed that 91% of the genetic variation was residing within populations, while 9% variation was among populations. Overall, the results showed that a high level of genetic diversity is prevailing in this worldwide collection of red clover, which can be exploited for its genetic improvement through breeding approaches.

scholarly journals Genetic Diversity and Structure Analysis of a Worldwide Collection of Faba bean (Vicia faba) Genotypes using ISSR Markers

2021 ◽  
Vol 25 (03) ◽  
pp. 683-691
Author(s):  
Ahmed A. Qahtan
Keyword(s):  
Genetic Diversity ◽  
Vicia Faba ◽  
Faba Bean ◽  
Gene Diversity ◽  
Principal Component ◽  
Issr Markers ◽  
Discrimination Power ◽  
Software Analysis ◽  
Inter Simple Sequence Repeats ◽  
Genetic Diversity And Structure

The success of breeding programs depends on the extent of genetic variability. Inter-simple sequence repeats (ISSR) have been widely utilized in investigations, including the characterization of many plant species genetically. This research aimed to examine both the genetic diversity and relationships of 92 faba bean (Vicia faba L.) genotypes from different geographical areas using ISSR markers. Eleven ISSR primers generated a total of 189 repeatable amplified bands, of which 109 were polymorphic. Values of polymorphism information content (PIC) and gene diversity averaged 0.3484 and 0.1438 and ranged 0.089–0.715 and 0.0742–0.2065, respectively. The studied accessions of faba bean plant differentiated into four main clusters, prevalently based on geographical origin through UPGMA clustering analysis and principal component analysis (PCA), deriving four major groupings based on pedigree and origin relationships. The STRUCTURE software analysis results were significantly aligned with the PCA and showed five main clusters; each one represents one continent. AMOVA showed high variation and differentiation among nations from different continents. The discrimination power of ISSR markers obtained in this study suggests that they could be used to examine the diversity of faba bean genotypes efficiently and precisely and encourage targeted crossing strategies. © 2021 Friends Science Publishers

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2019 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Genetic Structure ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Group Method ◽  
Arithmetic Means ◽  
Illumina Hiseq ◽  
Genetic Diversity And Structure

Abstract Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population is unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeq TM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). A total of 23,741,783 raw reads were obtained and assembled, from which, 89,271 unigenes with an average length of 598.3191 nt were generated. During functional annotation, 31,686 unigenes were annotated in Gene Ontology categories, Kyoto Encyclopedia of Genes and Genomes pathways, Swiss-Prot database, and Nucleotide Collection (NR/NT) database. In addition, 11,343 expressed sequence tag-simple sequence repeat (EST-SSRs) were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which, 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used to analyze genetic diversity and structure of the natural populations. The obtained results revealed that the shows high levels of genetic diversity in populations, the average observed and expected heterozygosity were H O = 0.422 and H E = 0.479. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of bottleneck in all populations. Genetic differentiation among populations was moderate (F ST = 0.133) and indicating limited gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. These results showed a moderate genetic structure of P. vietnamensis. STRUCTURE analysis and the unweighted pair-group method with arithmetic means (UPGMA) tree revealed strong genetic structure and two genetic clusters related to geographical distances, as well. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species. Keywords: Conservation, EST-SSRs; Transcriptome; Panax vietnamensis ; Population genetics

Genetic Analysis of Chinese Cucumber Collections in the U.S. National Germplasm Collection

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 534e-534 ◽  
Author(s):  
J. Staub ◽  
Felix Sequen ◽  
Tom Horejsi ◽  
Jin Feng Chen
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Allelic Variation ◽  
Germplasm Collection ◽  
Principal Component ◽  
Isozyme Loci ◽  
National Plant Germplasm System ◽  
The U.S

Genetic variation in cucumber accessions from China was assessed by examining variation at 21 polymorphic isozyme loci. Principal component analysis of allelic variation allowed for the depiction of two distinct groupings of Chinese accessions collected in 1994 and 1996 (67 accessions). Six isozyme loci (Gpi, Gr, Mdh-2, Mpi-2, Pep-gl, and Pep-la) were important in elucidating these major groups. These groupings were different from a single grouping of Chinese 146 accessions acquired before 1994. Allelic variation in Chinese accessions allowed for comparisons with other accessions in the U.S. National Plant Germplasm System (U.S. NPGS) collection grouped by continent and sub-continent. When Chinese accessions taken collectively were compared with an array of 853 C. sativus U.S. NPGS accessions examined previously, relationships differed between accessions grouped by country or subcontinent. Data indicate that acquisition of additional Chinese and Indian cucumber accessions would be strategically important for increasing genetic diversity in the U.S. NPGS cucumber collection.

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