scholarly journals Population genetics of Hyphaene thebaica Mart., in Rabigh province, Saudi Arabia: Implications for conservation

2021 ◽  
Vol 17 (3) ◽  
pp. 153-159
Author(s):  
Hassan Mansour
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Saudi Arabia ◽  
Genetic Differentiation ◽  
Polymorphic Loci ◽  
Gene Migration ◽  
Perennial Plant ◽  
Severe Deficiency ◽  
Human Habitation ◽  
Simple Sequence

Hyphaene thebaica is a perennial plant distributed in desert and subtropical regions of the world. In Rabigh Province, western Saudi Arabia, the few persisting populations of this species are exposed to many threats, including overcutting and, recently, human habitation. These threats are predicted to be exacerbated with the advancement of aridification caused by climate change. The conservation and revival of the diminished populations of H. thebaica requires an assessment of their genetic diversity and genetic differentiation. To accomplish this objective, we applied 10 simple sequence repeat (SSR) primer pairs, with which all are polymorphic loci. These polymorphic loci were used to determine the population genetics of 60 plant accessions sampled from 5 populations of H. thebaica located in five sites in Rabigh Province: Wadi EL Khaneg, Wadi Al Johfa, Wadi Al Hakak and Wadi Khurieba and Wadi Kuliayah . Low to moderate levels of genetic diversity were found in all populations (the values of the PPL% ranged between 52.5% and 22.5%) along with a decreased value of HT (0.388) and a considerable inbreeding value (F= 0.4552), which verified an obvious shortage of heterozygotes. High genetic differentiation among the populations and a low level of gene flow suggest isolation among the H. thebaica populations, which caused a severe deficiency in gene migration. The data obtained herein will inspire several recommendations for conservation the existing populations, including seed preservation, and management of human activities. All of these actions are urgently needed to prevent imminent extinction.

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 Differentiation in Moroccan Opuntia ficus-indica Cultivars Using Simple Sequence Repeat (SSR) Markers

2016 ◽  
Vol 8 (3) ◽  
pp. 380-385 ◽  
Author(s):  
Aissam EL FINTI ◽  
Driss TALIBI ◽  
Mouhamed SIDKI ◽  
Abdelhamid E. MOUSADIK
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Opuntia Ficus Indica ◽  
Distance Analysis ◽  
Reference Collection ◽  
Ssr Loci ◽  
Set Up ◽  
Genetic Distance Analysis ◽  
Simple Sequence

Estimation of genetic parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources. In this study, 13 Opuntia ficus-indica cultivars were analyzed using 10 SSR markers selected for studying the genetic diversity among these chosen cultivars. Over the 10 SSR markers, a total of 45 reproducible bands were scored with an average of 4.5 alleles/locus, while the observed heterozygosity (Ho) values of amplified loci ranged from 0.15 (SSR1) to 0.92 (SSR2 and SSR 11). Genetic distance analysis of the 13 cultivars showed a large genetic differentiation (GST = 0.47) and high number of different groups. Most of the accessions were not found to be clustered according to their eco-geographical origin. In addition, each cultivar was characterized by its own multiallelic combination between loci. The results revealed the usefulness of SSR in understanding of genetic diversity in Moroccans Barbary fig cultivars, thus being helpful to set up rational decisions concerning the establishment of a national reference collection.

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

2019 ◽  
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 of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) ranged from 0.070 to 0.905, and the average locus polymorphic information content (PIC) was 0.5354. The provenance ‘Was’ had the lowest 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, clones distributed in 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 smaller gene flow and higher degree of genetic differentiation compared with the other provenances, and was classified into one group. There was no 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; however, the genetic variation among provenances has no clear correlation with their geographical locations. Clones reflecting population genetic information can be selected to build a core resource bank, which could provide effective protection and promote the scientific utilization of the P. deltoids resource, laying a solid foundation for poplar breeding.

scholarly journals Genetic diversity and population structure of Meretrix petechialis in China revealed by sequence-related amplified polymorphism markers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8723 ◽  
Author(s):  
Qiaoyue Xu ◽  
Junhong Zheng ◽  
Hongtao Nie ◽  
Qingzhi Wang ◽  
Xiwu Yan
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Scientific Basis ◽  
Germplasm Resources ◽  
Polymorphic Loci ◽  
Information Index ◽  
Geographical Populations ◽  
Meretrix Petechialis

Genetic variation in nine stocks of Meretrix petechialis collected from China was analyzed using sequence-related amplified polymorphism (SRAP) markers. Eight primer pairs produced 132 polymorphic loci with an average of 16.5 loci per primer pair. A population from Jiangsu had the highest percentage of polymorphic loci at 27.27%, suggesting that these resources had a rich genetic diversity. The Nei’s gene diversity of the nine populations ranged from 0.0647 to 0.0793; a population from Shandong was the lowest and a population from North Korea the highest. The Shannon’s information index was between 0.1023 and 0.1202, with the lowest in the Shandong population and the highest in the Jiangsu population. The Nei’s unbiased genetic distance between the nine populations was 0.0243–0.0570 and the genetic similarity was 0.9446–0.9760; the genetic distance between Guangxi and Shandong populations was the furthest (0.0570) and the genetic distance between Shandong and Jiangsu populations was the closest (0.0243). Nei’s gene diversity analysis indicated that the genetic variance was mainly found within individual geographical populations, and the analysis of molecular variance revealed low but significant genetic differentiation among local and regional populations. The limited gene flow (Nm = 0.555) was inferred as a major reason for the extent of genetic differentiation in M. petechialis. The results obtained here indicated that M. petechialis have high degree of genetic diversity and the potential of further breeding with excellent germplasm resources. This study provides a scientific basis for the protection of germplasm resources and the breeding of M. petechialis.

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

2019 ◽  
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 of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) ranged from 0.070 to 0.905, and the average locus polymorphic information content (PIC) was 0.5354. The provenance ‘Was’ had the lowest 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, clones distributed in 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 smaller gene flow and higher degree of genetic differentiation compared with the other provenances, and was classified into one group. There was no 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; however, the genetic variation among provenances has no clear correlation with their geographical locations. Clones reflecting population genetic information can be selected to build a core resource bank, which could provide effective protection and promote the scientific utilization of the P. deltoids resource, laying a solid foundation for poplar breeding.

scholarly journals Population genetics of the Chilean frog Batrachyla Leptopus (Leptodactylidae)

2000 ◽  
Vol 23 (1) ◽  
pp. 43-48 ◽  
Author(s):  
J.R. Formas ◽  
L.M. Brieva
Keyword(s):  
Population Genetics ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Inbreeding Coefficient ◽  
Genetic Identity ◽  
Electrophoretic Variation ◽  
Polymorphic Loci ◽  
Continental Group ◽  
Insular Populations ◽  
F Statistics

Electrophoretic variation of proteins encoded by 14 loci was analyzed in eight (five continental and three insular) populations of the Chilean leptodactylid frog Batrachyla leptopus. The overall proportion of polymorphic loci was estimated to be 18.7% and the average number of alleles per locus, 1.2, while observed and expected heterozygosities were 1.7 and 5.1%, respectively. The estimated coefficient of genetic identity was 0.940; the corresponding figure for genetic distance was 0.063. F-statistics analysis showed a total inbreeding coefficient (Fit) of 0.855 and high levels of genetic subdivision (Fst = 0.596) as well as of inbreeding within populations (Fis = 0.640). However, there was only a moderate level of genetic differentiation (Fst = 0.181) between the insular group of populations and the continental group.

scholarly journals Genetic variations in Turkey cultivar and ecotype Medicago sativa species: cytological, total protein profile, and molecular characterization

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Büşra Yazıcılar ◽  
Gholamreza Jannati ◽  
Ismail Bezirganoglu
Keyword(s):  
Genetic Diversity ◽  
Flow Cytometry ◽  
Medicago Sativa ◽  
Cytogenetic Analysis ◽  
Nutritional Value ◽  
Protein Profile ◽  
Control Plant ◽  
Perennial Plant ◽  
Sds Page ◽  
Simple Sequence

Abstract Background Alfalfa(Medicago sativa L.) is a perennial plant, which is high in nutritional value and resistant to environmental conditions, and it is one of most frequently preferred feed crop among the leguminous family. In this study, it was aimed to determine the genetic diversity of some alfalfa ecotypes and their varieties by DNA, protein, nucleus, and chromosome counts. The genetic distance between the populations of control (M. truncatula), five different cultivars (Alsancak, Bilensoy, Iside, Plato, Bilensoy82), and three different ecotypes (Erzurum, Muş, and Konya) was investigated by cytogenetic analysis, flow cytometry, simple sequence repeats (SSR), and SDS PAGE techniques. Results Cytogenetic analysis of these tested plants has verified the existence of expected levels such as diploid, triploid, and tetraploid as well as aneuploid (2n = 4x = 30) plants. Flow cytometry analysis have displayed that all of tested plants were tetraploid, whereas cytological analysis had either diploid, triploid, or tetraploid. Genetic diversity dendrogram was created using Erzurum, Muş, Konya, Bilensoy82, Alsancak, and Plato varieties. The Iside and Bilensoy were found to be morphogenetic in relationship. Our control plant, M. truncatula, did not have a similarity relationship with other ecotypes and cultivars. The total numbers of protein bands differed among tested plants from 140 kDA to 25 kDa. Conclusions This paper first reports on the genetic variation of Turkish alfalfa plants by using detailed analysis techniques. This work provides important findings for the classification, conservation, and innovation of alfalfa germplasm resources.

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