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 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.

Genetic diversity of fringed brome (Bromus ciliatus) as determined by amplified fragment length polymorphism

2005 ◽  
Vol 83 (10) ◽  
pp. 1322-1328 ◽  
Author(s):  
Yong-Bi Fu ◽  
Bruce E. Coulman ◽  
Yasas S.N. Ferdinandez ◽  
Jacques Cayouette ◽  
Paul M. Peterson
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Habitat Restoration ◽  
Fragment Length Polymorphism ◽  
Natural Populations ◽  
Germplasm Conservation ◽  
Amplified Fragment Length Polymorphism ◽  
Large Area ◽  
Geographic Origins

Fringed brome ( Bromus ciliatus L.) is found in native stands throughout a large area of North America. Little is known about the genetic diversity of this species. The amplified fragment length polymorphism (AFLP) technique was applied to assess the genetic diversity of 16 fringed brome populations sampled in Canada from the provinces of Alberta, British Columbia, Quebec, and Saskatchewan. Four AFLP primer pairs were employed to screen 82 samples with four to six samples per population and 83 polymorphic AFLP bands scored for each sample. The frequencies of the scored bands in all assayed samples ranged from 0.01 to 0.99 and averaged 0.53. Analysis of molecular variance revealed that 52.6% of the total AFLP variation resided among the 16 populations and 20.6% among the four provinces. The five Quebec populations appeared to be genetically the most diverse and distinct. The AFLP variability observed was significantly associated with the geographic origins of the fringed brome populations. These findings are useful for sampling fringed brome germplasm from natural populations for germplasm conservation and should facilitate the development of genetically diverse regional cultivars for habitat restoration and revegetation.

scholarly journals Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Cun Chen ◽  
Yanguang Chu ◽  
Changjun Ding ◽  
Xiaohua Su ◽  
Qinjun Huang
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Simple Sequence Repeat ◽  
Populus Deltoides ◽  
Sequence Repeat ◽  
Black Cottonwood ◽  
High Genetic Diversity ◽  
Simple Sequence

Abstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (Fst) and gene flow (Nm) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.

scholarly journals Genetic diversity in natural populations of Buriti (Mauritia flexuosa L. f.)

2011 ◽  
Vol 11 (3) ◽  
pp. 216-223 ◽  
Author(s):  
Liene Rocha Picanço Gomes ◽  
Maria Teresa Gomes Lopes ◽  
Jania Lilia da Silva Bentes ◽  
Willian Silva Barros ◽  
Pedro de Queiroz Costa Neto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Natural Populations ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Polymorphic Loci ◽  
Mauritia Flexuosa ◽  
Geographical Distances ◽  
Traditional Communities

This study aimed to characterize the genetic diversity of buriti populations by AFLP (Amplified Fragment Length Polymorphism) markers. The analysis was performed in four populations used by traditional communities in the state of Amazonia (Bom Jesus do Anamã, Lauro Sodré, Santa Luzia do Buiçuzinho, and Esperança II). From each population 30 plants were randomly selected. To obtain the markers four primer combinations were used. The percentage of polymorphic loci was estimated, the molecular variance among and within populations analyzed and a dendrogram constructed. The primers detected 339 polymorphic loci ranging from 81.1 % to 91.1 % among populations. Analysis of molecular variance attributed 77.18 % to variation within and 22.8 % to variation between populations. The dendrogram indicated the formation of two groups, showing that the populations of Bom Jesus do Anamã and Lauro Sodré are genetically most similar and thet the genetic and geographical distances are not correlated.

scholarly journals Analysis of Powdery Mildew-resistant Dogwood Accessions Using AFLP

HortScience ◽  
2007 ◽  
Vol 42 (1) ◽  
pp. 28-30 ◽  
Author(s):  
Margaret T. Mmbaga, ◽  
Roger J. Sauvé,
Keyword(s):  
Genetic Diversity ◽  
Powdery Mildew ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Breeding Program ◽  
High Genetic Diversity ◽  
Cornus Kousa

Twenty-five dogwood accessions (one Cornus kousa, three C. kousa × C. florida hybrids, and 21 C. florida) were characterized using amplified fragment length polymorphism. Among the C. florida accessions, four were named cultivars and 17 were selections from Tennessee State University's dogwood breeding program. Amplified fragment length polymorphism band profiles obtained from 13 EcoRI/MseI (+3/+3) primer pairs showed the presence of high genetic diversity between species and within the C. florida accessions. Each accession was distinctly different from each other, and the resistant clones clustered into distinct groups.

Assessing genetic variability among Brazilian strains ofXanthomonas axonopodispv.manihotisthrough restriction fragment length polymorphism and amplified fragment length polymorphism analyses

1999 ◽  
Vol 45 (9) ◽  
pp. 754-763 ◽  
Author(s):  
S Restrepo ◽  
T L Valle ◽  
M C Duque ◽  
V Verdier
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Bacterial Blight ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Restriction Fragment Length

Xanthomonas axonopodis pv.manihotis (Xam) causes bacterial blight, a major disease of cassava, which is a starchy root crop that feeds about 500 million people throughout the world. To better select resistant cassava germplasm, we examined the population structure of Xam in Brazil, Latin America's largest producer of cassava, and a major center of diversity for the crop. The 79 strains collected between 1941 and 1996 from three edaphoclimatic zones were analyzed by restriction fragment length polymorphism (RFLP), using a probe linked to a Xam pathogenicity gene (pthB). Thirty-eight haplotypes were identified, and geographical differentiation for the Xam strains was demonstrated. Strains from subtropical zone (ECZ 6) showed high genetic diversity in most of the sites from which they were collected. They also showed migration from site to site. RFLP and amplified fragment length polymorphism (AFLP) analyses were carried out on 37 Xam strains and compared; the AFLP assays were performed using eight primer combinations. A multiple correspondence analysis, used to assess genetic relatedness among strains and estimate genetic diversity, indicated that the Brazilian Xam population showed high diversity. No correlation was found between AFLP and RFLP data, but the two techniques provided complementary information on the genetic diversity of Xam. Most strains were highly aggressive on a susceptible cultivar. The genetic analysis presented here contributes to a better understanding of the Xam population structure in Brazil and will help select strains of the pathogen for screening cassava germplasm resistant to the disease.Key words: cassava bacterial blight, resistance, genetic diversity, molecular characterization.

Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

2008 ◽  
Vol 88 (1) ◽  
pp. 179-186 ◽  
Author(s):  
Chu-Chuan Fan ◽  
Nicola Pecchioni ◽  
Long-Qing Chen
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Population Level ◽  
Conservation Strategy ◽  
Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

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