scholarly journals A study on genetic diversity of bagrid catfish (Hemibagrus guttatus Lacepede, 1803) using microsatellite markers

2018 ◽  
Vol 16 (1) ◽  
pp. 59-65
Author(s):  
Bùi Hà My ◽  
Nguyễn Thị Hương ◽  
Nguyễn Hữu Đức ◽  
Trần Thị Thúy Hà
Keyword(s):  
Microsatellite Markers ◽  
Economic Value ◽  
Low Frequency ◽  
Wild Populations ◽  
Genetic Characteristics ◽  
Allele Number ◽  
Expected Heterozygosity ◽  
Artificial Breeding ◽  
The Mean ◽  
High Level

Bagrid catfish (Hemibagrus guttatus Lacepede, 1803) is a wild species of high economic value in Northern Vietnam. Artificial reproduction of bagrid catfish requires sources of quality fingerlings in terms of genetics. In fact, bagrid catfish is endangered due to overhunting. Until now, studying on bagrid catfish was mainly focused on biology characterictics and artificial breeding. In this study, three microsatellite markers were used to assess the genetic characteristics of four bagrid catfish populations (three wild populations collected in Tuyên Quang, Phu Tho, Ha Giang and a cultured population in Hai Duong). These markers were registed Genbwith the code of KJ873116, KJ873117 and NC 023976 for HM7, HM8 and SS1, respectively. All of the loci showed high level of polymorphism with 16 alleles in total which were 5 at locus HM7, 5 at locus HM8, and 6 at locus SS1. Total allele number in population collected in Ha Giang was higher than that of Tuyen Quang, Phu Tho and Hai Duong populations. The mean of number of observed alleles (Na = 3,83 ± 0,24) was higher than the mean number of effective alleles (Ne = 2,14 ± 0,13) and low frequency alleles (< 0,1) were observed in all loci. The value of the expected heterozygosity (He = 0,38- 0,63) was lower than that of the observed heterozygosity (Ho = 0,51-0,71). FIS value was low and the genetic differences between four populations was insignificant as FST < 0,05. The results provide useful information for breeding program and conservation of the bagrid catfish in the future.

The way of value of Correlation of genomic DNA microsatellite loci and live weight of Chukchi reindeer

2020 ◽  
pp. 27-32
Author(s):  
V. Dodokhov ◽  
N. Pavlova ◽  
T. Rumyantseva ◽  
L. Kalashnikova
Keyword(s):  
Microsatellite Markers ◽  
Agricultural Production ◽  
Live Weight ◽  
Biodiversity Loss ◽  
Tribal Community ◽  
High Germination ◽  
Wide Range ◽  
The Mean ◽  
High Level ◽  
Dna Microsatellite

The article presents the genetic characteristic of the Chukchi reindeer breed. The object of the study was of the Chukchi reindeer. In recent years, the number of reindeer of the Chukchi breed has declined sharply. Reduced reindeer numbers could lead to biodiversity loss. The Chukchi breed of deer has good meat qualities, has high germination viability and is adapted in adverse tundra conditions of Yakutia. Herding of the Chukchi breed of deer in Yakutia are engaged only in the Nizhnekolymsky district. There are four generic communities and the largest of which is the agricultural production cooperative of nomadic tribal community «Turvaurgin», which was chosen to assess the genetic processes of breed using microsatellite markers: Rt6, BMS1788, Rt 30, Rt1, Rt9, FCB193, Rt7, BMS745, C 143, Rt24, OheQ, C217, C32, NVHRT16, T40, C276. It was found that microsatellite markers have a wide range of alleles and generally have a high informative value for identifying of genetic differences between animals and groups of animal. The number of identified alleles is one of the indicators of the genetic diversity of the population. The total number of detected alleles was 127. The Chukchi breed of deer is characterized by a high level of heterozygosity, and the random crossing system prevails over inbreeding in the population. On average, there were 7.9 alleles (Na) per locus, and the mean number of effective alleles (Ne) was 4.1. The index of fixation averaged 0.001. The polymorphism index (PIC) ranged from 0.217 to 0.946, with an average of 0.695.

Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops

2014 ◽  
Vol 12 (S1) ◽  
pp. S125-S129
Author(s):  
Gi-An Lee ◽  
Sok-Young Lee ◽  
Ho-Sun Lee ◽  
Kyung-Ho Ma ◽  
Jae-Gyun Gwag ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Germplasm Management ◽  
Underutilized Crops ◽  
Crop Species ◽  
Closely Related Species ◽  
Polymorphic Loci ◽  
Allele Number ◽  
The Mean ◽  
Genetic Assessment

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.

scholarly journals Genetic diversity in Brazilian tall coconut populations by microsatellite markers

2013 ◽  
Vol 13 (4) ◽  
pp. 356-362 ◽  
Author(s):  
Francisco Elias Ribeiro ◽  
Luc Baudouin ◽  
Patricia Lebrun ◽  
Lázaro José Chaves ◽  
Claudio Brondani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Cape Verde ◽  
Coconut Palm ◽  
Different Populations ◽  
The Mean ◽  
High Level ◽  
Brazilian Populations

The tall coconut palm was introduced in Brazil in 1553, originating from the island of Cape Verde. The aim of the present study was to evaluate the genetic diversity of ten populations of Brazilian tall coconut by 13 microsatellite markers. Samples were collected from 195 individuals of 10 different populations. A total of 68 alleles were detected, with an average of 5.23 alleles per locus. The mean expected and observed heterozygosity value was 0.459 and 0.443, respectively. The number of alleles per population ranged from 36 to 48, with a mean of 40.9 alleles. We observed the formation of two groups, the first formed by the populations of Baía Formosa, Georgino Avelino and São José do Mipibu, and the second by the populations of Japoatã, Pacatuba and Praia do Forte. These results reveal a high level of genetic diversity in the Brazilian populations.

scholarly journals Microsatellites Cross-Species Amplification across Some African Cichlids

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Etienne Bezault ◽  
Xavier Rognon ◽  
Karim Gharbi ◽  
Jean-Francois Baroiller ◽  
Bernard Chevassus
Keyword(s):  
Microsatellite Markers ◽  
Oreochromis Niloticus ◽  
Molecular Genetic ◽  
Point Of View ◽  
Genetic Studies ◽  
African Cichlid ◽  
Wide Range ◽  
The Mean ◽  
High Level ◽  
African Cichlids

The transfer of the genomic resources developed in the Nile tilapia, Oreochromis niloticus, to other Tilapiines sensu lato and African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32 O. niloticus microsatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P95) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 within Oreochromis species to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids.

scholarly journals Genetic characterization of the Mirgorod pig breed, obtained by analysis of single nucleotide polymorphisms of genes

2019 ◽  
Vol 6 (2) ◽  
pp. 47-57
Author(s):  
P. Vashchenko ◽  
V. Balatsky ◽  
K. Pocherniaev ◽  
V. Voloshchuk ◽  
V. Tsybenko ◽  
...  
Keyword(s):  
Allelic Diversity ◽  
Low Frequency ◽  
Stress Sensitivity ◽  
Nucleotide Polymorphisms ◽  
Muscle Area ◽  
Eye Muscle ◽  
Genetic Characteristics ◽  
Productive Traits ◽  
High Level ◽  
Genetic Anomaly

Aim. To determine genetic characteristics of the Mirgorod pig breed by analysis of 25 SNPs of 22 genes and to conduct the associative analysis of genes MC4R (SNP c.1426 G > A), LEP (SNP g.2845 А ˃ Т), GH (BsuRI- polymorphism), CTSF (SNP g. 22 G > C) with productive traits of animals. Methods. Blood samples of pedigree Mirgorod pigs, bred at SI «Experimental farm named after Decemberists», Poltava region, were used for the studies. DNA genotyping was performed by PCR-RFLP and TaqMan. Results. Specifi c features of the breed were determined in terms of gene allele frequencies, high level of genetic variability (He – 0.326) and allelic diversity (mean number of alleles per locus – 1.96). The KPL2/m allele that causes genetic anomaly of ISTS is absent among investigated Mirgorod pigs, and the recessive RYR1 g.1843T allele, responsible for stress sensitivity of pigs, occurs at a low frequency (0.04). Unlike other breeds, a relatively high frequency of the minor allele g.15A (0.16) of CTSK and polymorphism of the LEP gene (SNP g.3996 T > C) (He – 0.455) was observed. Statistically signifi cant associations of polymorphisms have been established: MC4R (SNP c.1426 G > A) with age of gaining 100 kg, the thickness of backfat and the Eye Muscle Area, GH/BsuRI with the age of gaining 100 kg, and CTSF (SNP g. 22G > C) with Eye Muscle Area. There was a trend of statistically signifi cant differences between groups of pigs with different genotypes of LEP (SNP g.2845 А ˃ Т) and the thickness of the backfat (p = 0.09). Conclusions. It is reasonable to carry out the restoration of the gene pool of the Mirgorod pig breed, taking into account the SNPs of the studied genes and their associations with the productive traits. It is expedient to give preference to pigs with SNP genotypes с.1426 MC4R GA, MC4R AA, g. 22 CTSF CC, g.2845 LEP TT for breed reproduction.

Genetic differentiation in populations of the cestode Bothriocephalus acheilognathi (Cestoda, Pseudophyllidea) as revealed by eight microsatellite markers

Parasitology ◽  
2003 ◽  
Vol 126 (5) ◽  
pp. 493-501 ◽  
Author(s):  
H. Y. LUO ◽  
P. NIE ◽  
Y. A. ZHANG ◽  
W. J. YAO ◽  
G. T. WANG
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Random Mating ◽  
Genetic Structure Of Populations ◽  
Bothriocephalus Acheilognathi ◽  
The Mean ◽  
High Level ◽  
Cross Fertilization

The genetic structure of populations of the fish cestode, Bothriocephalus acheilognathi collected from Bailianhe Reservoir (BLH), Changshou (CSH) and Liangzi (LZH) Lakes was investigated by using 8 microsatellite loci. A total of 108 adult worms were genotyped at each of the 8 loci. For the 3 populations, the mean number of alleles per locus ranged from 2·38 to 5·5, and the mean expected heterozygosity ranged from 0·432 to 0·559. The average polymorphic information content (PIC) was from 0·384 to 0·492. The significant Fis values indicated non-random mating within LZH and BLH populations. On the other hand, when samples were further classified into subpopulations at the level of host fish species, no or little heterozygote deficiency was detected at most loci, showing that cross-fertilization, predominantly, but not exclusively, must have occurred within the subpopulations. Microsatellite markers also revealed an unexpected high level of genetic differentiation, as measured by Rst and Nm values or by δu2 genetic distance among subpopulations from different hosts. Factors influencing the population genetic structure and the parasite host specificity are discussed.

Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

2021 ◽  
Author(s):  
Rafael Oliveira Moreira ◽  
Eduardo de Andrade Bressan ◽  
Horst Bremer Neto ◽  
Angelo Pedro Jacomino ◽  
Antonio Figueira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Native Species ◽  
Genetic Parameters ◽  
Genomic Library ◽  
Conservation Strategies ◽  
Paulo State ◽  
Allele Number ◽  
Expected Heterozygosity

Abstract Campomanesia phaea (Myrtaceae), known as cambuci, is a native species from the Brazilian Atlantic Forest with great potential to be developed as a new fruit crop. Microsatellite markers were developed for cambuci to characterize the genetic diversity and to investigate the genetic structure of a group of accessions originally collected at the presumed center of diversity of the species. The work involved the collection of 145 accessions from five regional groups (Juquitiba, Paraibuna, Mogi das Cruzes, Ribeirão Pires, and Salesópolis) in São Paulo state, Brazil. Fourteen loci were identified in an enriched genomic library developed from one of these accessions. Six out of 14 loci revealed to be polymorphic, disclosing 26 alleles. Based on the allele frequencies, the calculated genetic parameters of the five groups indicated an average allele number per loci (A) of 3.83, with the expected heterozygosity (He) of 0.57 and the observed heterozygosity (Ho) of 0.54. The analysis of the genetic structure indicated that most of the genetic diversity is found within each population (HS = 0.57), whereas the genetic diversity among populations was low (GST = 0.19). The genetic diversity parameter of Nei was considered low for the cambuci analyzed populations, with no evidence of inbreeding. Based on Darwin analysis, we chose 18 accessions from the five regional populations to compose a core collection that includes most of the genetic diversity found in this study. Our findings may contribute to define better conservation strategies and genetic breeding approaches for this native species in Brazil.

Identification and structure analysis of three tilapia species using microsatellite markers

2009 ◽  
Vol 6 (2) ◽  
pp. 119-125
Author(s):  
Song Hong-Mei ◽  
Bai Jun-Jie ◽  
Quan Ying-Chun ◽  
Li Sheng-Jie
Keyword(s):  
Microsatellite Markers ◽  
Clustering Analysis ◽  
Phylogenetic Trees ◽  
Mean Value ◽  
Group Method ◽  
Oreochromis Aureus ◽  
Arithmetic Average ◽  
Pair Group ◽  
Expected Heterozygosity ◽  
The Mean

AbstractSeventeen special loci were selected from 77 microsatellite markers to distinguish three varieties of tilapias, including the six differential loci UNH636, UNH117, UNH172, UNH738, UNH878 and UNH896 in Oreochromis aureus; five differential loci UNH913, UNH907, UNH222, UNH980 and UNH880 in O. niloticus; and six differential loci of UNH876, UNH899, UNH853, UNH932, UNH933 and UNH773 in O. mossambicus. Any one of the 17 loci could amplify particular bands to distinguish one tilapia from the other two. The genetic structure of O. aureus, O. niloticus and O. mossambicus stocks and their phylogenetic relationships were also analysed using these 17 loci. In total 142 alleles were detected, and the average number of alleles per locus was 8.35. Additionally, a clustering analysis was performed based on the result of the Popgen32 software package and phylogenetic trees were constructed by MEGA4 using the unweighted pair group method using arithmetic average (UPGMA). The results showed that the mean value of observed heterozygosity was 0.0941, 0.5490 and 0.2588, the mean value of expected heterozygosity was 0.1089, 0.7230 and 0.1965, and the polymorphism information content was 0.0869, 0.7149 and 0.1643, in O. aureus, O. niloticus and O. mossambicus, respectively. The UPGMA tree demonstrated that O. aureus was more closely related to O. mossambicus than to O. niloticus.

Genetic relatedness and cultivar identification in a valuable garden species, Hesperantha coccinea ( Schizostylis coccinea)

2009 ◽  
Vol 7 (03) ◽  
pp. 281-290
Author(s):  
Kirsten Wolff ◽  
Sabina Knees ◽  
Suzanne Cubey
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Dna Fingerprinting ◽  
Genetic Relatedness ◽  
Cultivar Identification ◽  
Wild Populations ◽  
Multilocus Genotypes ◽  
Expected Heterozygosity ◽  
Garden Plants ◽  
Garden Plant

DNA fingerprinting using microsatellites is a useful aid in cultivar identification, but has rarely been applied to garden plants. Eleven microsatellite markers were developed for the valuable garden plantHesperanthacoccinea(Schizostylis coccinea), and used to determine relatedness of accessions. Several accessions, described as separate cultivars, appeared to have identical genotypes. Among the 53 accessions tested, there were 34 unique multilocus genotypes. The level of polymorphism detected in the cultivars was high, with on average seven alleles per locus and an average expected heterozygosity of 0.72 across loci. It is clear from the genotypes that a large proportion of the cultivars are closely related to each other. The resulting markers can now be used to generate a complete database of all known cultivars of the species and to detect essentially derived cultivars. As an extension of this study, the markers identified here could also inform us about the genetic diversity in wild populations.

Development and characterization of polymorphic microsatellite markers for Spathoglottis plicata (Orchidaceae)

2018 ◽  
Vol 16 (6) ◽  
pp. 572-575
Author(s):  
Chiuan-Yu Li ◽  
Chi-Chun Huang ◽  
Chaur-Tzuhn Chen ◽  
Kuo-Hsiang Hung
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Primers ◽  
Wild Populations ◽  
Terrestrial Orchid ◽  
Chain Reaction ◽  
Expected Heterozygosity ◽  
Genetic Patterns ◽  
Polymerase Chain ◽  
Polymorphic Microsatellite

AbstractWe developed novel and polymorphic microsatellite primers for Spathoglottis plicata, a tropical and subtropical terrestrial orchid, to investigate the genetic patterns and population structure among wild populations, and also to identify the varieties and hybrids of S. plicata in horticultural industry. The 12 novel microsatellites from S. plicata were developed by using polymerase chain reaction (PCR)-based isolation of microsatellite arrays. These markers that were successfully PCR amplified exhibited polymorphisms in S. plicata. The number of alleles, observed heterozygosity, expected heterozygosity and polymorphism information content values across loci ranged from 2.000 to 8.000, 0.000 to 0.756, 0.208 to 0.813 and 0.405 to 0.805 in total populations, respectively. The newly developed microsatellite markers exhibited variation in S. plicata. These markers can be used as a tool to further investigate the genetic diversity, conservation genetics and variety/hybrid identification of S. plicata.

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