scholarly journals Development of microsatellite loci and population genetics in the bumblebee catfish species Pseudopimelodus atricaudus and Pseudopimelodus magnus (Siluriformes: Pseudopimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
José David Rangel-Medrano ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
High Genetic Diversity ◽  
The Family ◽  
The Mean

ABSTRACT The Neotropical freshwater catfish Pseudopimelodus atricaudus and Pseudopimelodus magnus are two recently discovered species endemic to the Colombian Magdalena-Cauca River basin. In this study, a set of 13 microsatellite loci were developed by using next generation sequence technology to assess the genetic diversity and population structure in P. atricaudus and test for cross-species amplification in P. magnus. Both species exhibited high genetic diversity (P. atricaudus: Na: 9.000 - 9.769 alleles/locus, Ho: 0.760 - 0.804, HE: 0.804 - 0.840; P. magnus: Na: 12.8 - 5.4 alleles/locus, Ho: 0.638 - 0.683, HE: 0.747 - 0.755) compared to the mean levels of genetic diversity reported for Neotropical Siluriformes, and lack of genetic differentiation among sampling sites within the Cauca River (P. atricaudus: F’ST=0.013 - 0.017, P > 0.05, D’est= -0.004 - 0.023, P > 0.05; P. magnus: F’ST= 0.031, P= 0.055; D’est= 0.045, P= 0.058). This work is the first insight on the diversity and the population genetics of species of the family Pseudopimelodidae and provides a framework to further population genetic and conservation analyses needed in this poorly studied family at the microevolutionary level.

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 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 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 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 (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.

Genetic diversity and population structure of Korean alder (Alnus japonica; Betulaceae)

1999 ◽  
Vol 29 (9) ◽  
pp. 1311-1316 ◽  
Author(s):  
Man Kyu Huh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Alnus Japonica ◽  
Alnus Crispa ◽  
The Mean ◽  
Fixation Indices

The genetic diversity and population genetic structure of Alnus japonica (Thunb.) Steudel in Korea were studied and compared with those of alder from Canada. Nineteen of the 25 loci studied (76.0%) showed detectable polymorphism. The mean genetic diversity within populations was 0.207, which was higher than that for two Canadian alder species (Alnus rugosa (Du Roi) Spreng. and Alnus crispa (Ait.) Pursh). Analysis of fixation indices, calculated for all polymorphic loci in each population, showed a substantial deficiency of heterozygotes relative to Hardy-Weinberg expectations. The mean population differentiation value of A. japonica in Korea (GST = 0.095) is similar to those of A. rugosa in Canada (GST = 0.052). These low values of GST in two countries, reflecting little spatial genetic differentiation, may indicate extensive gene flow (via pollen and (or) seeds) and (or) recent colonization.

Genetic diversity among four short stature cattle populations of India

2008 ◽  
Vol 43 ◽  
pp. 15-23
Author(s):  
M.S. Tantia ◽  
R.K. Vijh ◽  
B. Mishra ◽  
S.T. Bharani Kumar
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Short Stature ◽  
Correspondence Analysis ◽  
Microsatellite Loci ◽  
South India ◽  
Relative Magnitude ◽  
Expected Heterozygosity ◽  
The Mean

SummaryThe genetic diversity, genetic differentiation and relationship between four short stature cattle populations of south India - Punganur, Iduki, Kasargod and Vatakara - was studied, using 24 microsatellite loci. A total of 164 alleles were observed. The mean number of alleles per locus was 6.58 with mean observed and expected heterozygosity values of 0.70 and 0.75 respectively. The relative magnitude of gene differentiation (FST) was 6% and was significant except between the Iduki and Kasargod populations. The negative FIS values obtained for the majority of loci indicated a lack of population structure in the four populations. Both phylogenetic and correspondence analysis exhibited a closeness between Iduki and Kasargod animals. The results indicated that all four populations were outbred and Kasargod and Iduki animals should be considered as one even though these are reared for different purposes.

scholarly journals Genetic Diversity and Population Genetic Structure of Erythrophleum fordii Oliv., an Endangered Rosewood Species in South China

Forests ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 636 ◽  
Author(s):  
Jing Tan ◽  
Zhi-Gang Zhao ◽  
Jun-Jie Guo ◽  
Chun-Sheng Wang ◽  
Jie Zeng
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Endangered Species ◽  
Genetic Differentiation ◽  
South China ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
The Mean ◽  
Erythrophleum Fordii ◽  
Private Alleles

Erythrophleum fordii Oliv. is a valuable rosewood species indigenous to the tropical and warm sub-tropical zones of Vietnam, Laos, and South China. The natural forests have been heavily fragmented mostly due to over-exploitation and over-utilization, and alteration to croplands and fast-growing plantations. Therefore, it has been included in the IUCN Red List of Endangered Species as an endangered species. In the present study, genetic diversity and population genetic structure of 11 populations were estimated by SSR makers in South China. Five high polymorphic loci were studied with a total of 34 alleles, among which, seven were private alleles. The mean number of alleles per locus (A), the mean number of efficient alleles per locus (Ae), the observed (Ho) and expected (He) heterozygosity, and Shannon’s index (I) of the 11 populations were 3.40, 2.31, 0.52, 0.56, and 0.90, respectively. Correlation analysis between genetic parameters and geographical factors showed that He and I were in significant negative correlation with longitude, indicating that genetic diversity of E. fordii reduced gradually from West to East in south China. FIS of eight populations with above five samples was on average 0.01, most loci conformed to Hardy-Weinberg equilibrium in these populations; their genetic differentiation coefficient (FST) was 0.18, indicating that genetic differentiation among populations was relatively low and there existed 18% genetic variation among populations. Gene flow (Nm) between these populations was 1.28. The Mantel test showed that genetic distance was not significantly correlated with geographical distance (p > 0.05). It was concluded that populations with high genetic diversity or private alleles, especially Longmen, Wuming and Pingxiang populations should be a priority for in situ conservations, meanwhile more populations and as many families as possible in each population should be collected for ex situ conservations of germplasm resources of this species in the future.

The Breeding System, Genetic Diversity and Pollen Sterility in Eucalyptus pulverulenta, a Rare Species With Small Disjunct Populations

1990 ◽  
Vol 38 (6) ◽  
pp. 559 ◽  
Author(s):  
GB Peters ◽  
JS Lonie ◽  
GF Moran
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Rare Species ◽  
Population Genetic ◽  
Pollen Sterility ◽  
Species Range ◽  
Disjunct Distribution ◽  
Eastern Australia ◽  
The Mean ◽  
Allozyme Loci

There are eight known populations of E. pulverulenta, which has a disjunct distribution in south-eastern Australia. Levels of genetic variation were studied in four populations of about 5000 plants in all. Of a total of 16 allozyme loci examined eight were polymorphic, but the level of polymorphism was generally low. Within populations there was a mean 1.42 alleles per locus. Both the total species and mean population genetic diversities were low for a tree species (0.10 and 0.07 respectively), while the between-population genetic diversity was high at 30%. These data are consistent with the effects expected of genetic drift. Population structure may thus have been critical in determining levels of genetic diversity throughout the species' range. Analysis of half-sib arrays in three populations showed that the mean outcrossing rate (t) was 70%, comparable to values from other Eucalyptus species. The mean level of inbreeding (Wright's F) was 0.19, although both F and t varied considerably between populations. Significant levels of pollen sterility have been reported in this species, and data presented here show that this trait extends through much of the species' range. Overall, these data suggest that neither its disjunct population structure nor its tendency to male sterility caused the species' detectable level of outcrossing to differ markedly from levels reported in other eucalypt species. However, it remains possible that pollen sterility may have had some effect in at least one population. Strategies for conservation of this rare species are also considered.

scholarly journals Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Zulfahmi Zulfahmi ◽  
Parjanto Parjanto ◽  
Edi Purwanto ◽  
Ahmad Yunus
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Genetic Material ◽  
Ex Situ ◽  
Breeding Programs ◽  
The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

scholarly journals Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Cristhian Danilo Joya ◽  
Ricardo Marcel Landínez-García ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Anthropogenic Activities ◽  
Lower Section ◽  
Habitat Disturbances ◽  
Genetic Groups ◽  
Lack Of Information ◽  
Species Specific

ABSTRACT Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.

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