Simple Sequence Repeat (SSR) Polymorphisms and Population Genetics in Sichuan Wild Rhesus Macaques

2011 ◽  
Vol 343-344 ◽  
pp. 690-697
Author(s):  
Di Yan Li ◽  
Yong Fang Yao ◽  
Xiao Feng Huang ◽  
An Chun Cheng ◽  
Huai Liang Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Polymorphic Information Content ◽  
Rhesus Macaques ◽  
Genetic Management ◽  
Future Studies ◽  
Ssr Loci ◽  
Different Populations ◽  
Polymerase Chain ◽  
High Level ◽  
Simple Sequence

Cross-species amplification of twenty-five SSR loci from the DNA of five rhesus macaques of diverse regional origins was conducted using human primers for the polymerase chain reaction (PCR). Seven of these primer pairs, which consistently and unambiguously amplified polymorphic fragments from these five samples, were also used to amplify SSR loci for 111 Sichuan wild rhesus macaques of five different populations. The analysed microsatellite markers produced 109 alleles, varied from 4 to 16 alleles each locus. The number of alleles per population ranged from 6.79 to 11.38. Polymorphic information content showed that all seven loci were highly informative (mean = 0.9017±0.0166, >0.5). The average observed heterozygosity was less than the expected (mean = 0.6795 and mean = 0.8559, respectively). Genetic differentiation among the populations was considerably low with the overall and pairwise FST values (mean = 0.0375), and showed fairly low level of inbreeding (indicated by a mean FIS value of 0. 0.1991). Maintaining genetic diversity is a major issue in conservation biology. In comparison to other captive Macaca mulatta studies, these wild rhesus macaque populations showed a relatively high level of genetic diversity, and there was low gene flow among these populations. Careful genetic management is important for maintaining genetic variability levels. None of the seven informative loci are linked which screened in this study can be applied in future studies on population and conservation genetics of natural primate populations.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

scholarly journals Genetic diversity and phylogenetic analyses of 11 cohorts of captive rhesus macaques from Chinese zoos

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6957
Author(s):  
Qian Su ◽  
Yongfang Yao ◽  
Qin Zhao ◽  
Diyan Li ◽  
Meng Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rhesus Macaques ◽  
Phylogenetic Analyses ◽  
Genetic Management ◽  
Southeastern China ◽  
Mitochondrial Dna Control Region ◽  
Clade B ◽  
In Captivity ◽  
High Level ◽  
Major Haplogroups

Rhesus macaques are raised in almost every Chinese zoo due to their likeability and ease in feeding; however, little is yet known about the genetic diversity of rhesus macaques in captivity. In this study, a 475-base pair nucleotide sequence of the mitochondrial DNA control region was obtained from the fecal DNA of 210 rhesus macaque individuals in captivity. A total of 69 haplotypes were defined, 51 of which (73.9%) were newly identified. Of all haplotypes, seven were shared between two zoos, and 62 haplotypes (89.8%) appeared only in a specific zoo, indicating a low rate of animal exchange between Chinese zoos. Moreover, there was a relatively high level of genetic diversity among the rhesus macaques (Hd = 0.0623 ± 0.0009, Pi = 0.979 ± 0.003, K = 28.974). Phylogenetic analysis demonstrated that all haplotypes were clearly clustered into two major haplogroups—Clade A (southeastern China) and Clade B (southwestern China)—and each major clade contained several small sub-haplogroups. The haplotypes of rhesus macaques from the same zoo were not clustered together for the most part, but scattered among several subclades on the phylogenetic tree. This indicates that the rhesus macaques in most Chinese zoos may originat from a diverse collection of geographical areas. Our results demonstrate that zoos play an important role in the conservation of the genetic diversity of rhesus macaques, as well as provide useful information on the genetic management of captive rhesus macaques.

scholarly journals Distribution, Genetic Diversity and Population Structure of Aegilops tauschii Coss. in Major Wheat-Growing Regions in China

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 311
Author(s):  
Haiyan Yu ◽  
Juan Yang ◽  
Hailan Cui ◽  
Adeel Abbas ◽  
Shouhui Wei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Integrated Management ◽  
Aegilops Tauschii ◽  
Low Genetic Diversity ◽  
Limited Gene Flow ◽  
Different Populations ◽  
New Perspective ◽  
High Level ◽  
Grass Weed ◽  
Simple Sequence

Aegilops tauschii Coss. is known as a noxious grass weed seriously affecting wheat quality and yield. To investigate its present occurrence in wheat fields and the potential genetic diversity of the grass weed in China, a filed survey covering major wheat production regions was conducted during 2017–2019. Seeds of different Ae. tauschii populations collected from the survey were analyzed with Simple Sequence Repeats (SSRs) technique. Results showed that Ae. tauschii was occurring in each of the provinces surveyed with varied occurrence frequency ranging from 0.91% in Sichuan Province to 92.85% in Henan Provinces. Eighty alleles with size ranging from 98 bp to 277 bp were detected from the 192 collected Ae. tauschii populations with 17 SSR markers. Ae. tauschii, in this study, exhibited a moderately high level of genetic diversity, high differentiation, deficient heterozygosity and limited gene flow. Compared with other provinces, Hubei populations possessed relatively low genetic diversity. Dendrogram analysis showed that genetic distance did not seem to be related to geographic distribution. Additionally, STRUCTURE analysis suggested that Ae. tauschii populations in wheat fields of China can be divided into three groups, which was further supported by cluster analysis. Among the three groups, solely 7% of the total variation was detected, whereas the majority variation (67%) occurred among different populations within same group. Undoubtedly, such information will help us to better understand population relationships and spread of Ae. tauschii in China and will provide a new perspective for its integrated management.

scholarly journals Genetic structure of populations of several endangered and endemic Dianthus species revealed by microsatellite markers

2018 ◽  
Vol 77 (2) ◽  
pp. 181-188 ◽  
Author(s):  
Anca Butiuc-Keul ◽  
Cornelia Crăciunaș ◽  
Irina Goia ◽  
Anca Farkas ◽  
Liliana Jarda ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Genetic Structure Of Populations ◽  
Ssr Loci ◽  
Different Populations ◽  
The Mean ◽  
Simple Sequence

Abstract In order to develop a proper conservation programme for several endangered, rare or endemic species of Dianhtus from Romania, molecular characterization by simple sequence repeat (SSR) markers has been accomplished. Amplification of SSR loci in individuals belonging to different populations of D. callizonus, D. glacialis ssp. gelidus, D. henteri, D. nardiformis and D. tenuifolius revealed 23 polymorphic alleles. D. callizonus and D. tenuifolius showed particular sets of SSR alleles. D. glacialis ssp. gelidus, D. henteri and D. nardiformis proved to share almost the same alleles in most of the loci. The highest genetic diversity was observed in D. glacialis ssp. gelidus and D. tenuifolius in locus MS-DINMADSBOX. Allelic patterns across Dianthus species indicate that the mean number of different alleles was highest in D. glacialis ssp. gelidus, while the number of effective alleles was highest in D. tenuifolius. There are no particular differences in individuals belonging to the same species. Genetic diversity is generally low, ranging from 0.18 (D. callizonus) to 0.44 (D. henteri). Regarding the genetic diversity within populations of the same species, no differences were revealed by the use of the SSR markers tested in the present study.

scholarly journals VALIDATION AND TRANSFERABILITY OF SIMPLE SEQUENCE REPEATS (SSR’S) FROM SOME SPECIES OF ACACIA GENUS TO ACACIA NILOTICA L.

2016 ◽  
Vol 8 (11) ◽  
pp. 95
Author(s):  
Amita Yadav ◽  
Manila Yadav ◽  
Sandeep Kumar ◽  
Dushyant Sharma ◽  
Jaya Parkash Yadav
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Climatic Conditions ◽  
Acacia Nilotica ◽  
Group Method ◽  
Acacia Species ◽  
Pair Group ◽  
High Level ◽  
Simple Sequence

Objective: In present study genetic transferability of SSR’s from related Acacia species to Acacia nilotica was evaluated along with its genetic diversity analysis from north Indian region. Methods: A total of 30 primers selected from 5 different Acacia species were screened for amplification and polymorphism. Dendrogram and 2 D Plot were constructed using NTSys PC version 2.02e. Different diversity parameters like Polymorphism information content (PIC), alleles per primer, number (no.) of amplicons were also calculated for each primer pair.Results: SSRs from Acacia tortilis, A. senegal and A. koa were highly transferable in A. nilotica. Out of 30, only twenty-two primers showed amplification with an average of 1.36 alleles per locus. Polymorphic information content (PIC) values ranged from 0.5 to 0.96 with an average of 0.81. Jaccard similarity coefficient (J) values ranged from 0.04 to 0.67 showing a high level of diversity. Un-weighted pair group method with arithmetic mean (UPGMA), based cluster analysis, divided all accessions into three main clusters.Conclusion: Geographical and climatic conditions showed a great impact on genetic diversity. The results indicated high transferability of genomic resources from related species and will facilitate more studies to characterize the relatively less studied Acacia niloticagenome. 

Assessment of genetic diversity in Narbon vetch (Vicia narbonensis L.) germplasm using morphological and molecular markers

2018 ◽  
Vol 69 (9) ◽  
pp. 904 ◽  
Author(s):  
Siwar Bouabid ◽  
H. Chennaoui Kourda ◽  
A. Boussaha ◽  
M. Ben Naceur ◽  
A. Zoghlami Khélil
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Morphological Traits ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Germplasm Management ◽  
Vicia Narbonensis ◽  
High Level ◽  
Differentiation Index ◽  
Simple Sequence

Narbon vetch (Vicia narbonensis L.) is a promising forage legume with good resistance to cold and drought. The assessment of genetic diversity of Narbon vetch is an essential component in germplasm management. In this study, we analysed the genetic diversity of 13 local and introduced Narbon vetch accessions from three continents using 27 morphological traits and 13 simple sequence repeat (SSR) markers. Significant differences among accessions for morphological and phenological traits were observed. The SSR markers showed a total of 126 alleles with a mean number of two alleles per locus. Polymorphic information content values were in the range of 0.772–0.915 with an average of 0.858. A high level of diversity (Nei’s genetic differentiation index of 59) was observed among accessions. Analysis of genetic distances separated the studied accessions into three groups based on both morphological and SSR markers. Cluster analysis of the SSR markers separated the accessions into three groups according to geographical origin. The Tunisian populations shared the same morphological traits but differed genetically from each other and were similar to those from Lebanon. A significant correlation was detected between morphological traits and SSR markers. The results suggested that SSR markers can be used to efficiently distinguish Narbon vetch accessions and estimate their genetic diversity.

scholarly journals Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

2021 ◽  
Author(s):  
Júlia Halász ◽  
Noémi Makovics-Zsohár ◽  
Ferenc Szőke ◽  
Sezai Ercisli ◽  
Attila Hegedűs
Keyword(s):  
Simple Sequence Repeat ◽  
Principal Component ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Allele Number ◽  
Genetic Potential ◽  
Ssr Loci ◽  
High Level ◽  
Diversity Studies ◽  
Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

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 Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose
Keyword(s):  
Simple Sequence Repeats ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
High Level ◽  
Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

scholarly journals Evaluation of Genetic Diversity and Pedigree within Crapemyrtle Cultivars Using Simple Sequence Repeat Markers

2011 ◽  
Vol 136 (2) ◽  
pp. 116-128 ◽  
Author(s):  
Xinwang Wang ◽  
Phillip A. Wadl ◽  
Cecil Pounders ◽  
Robert N. Trigiano ◽  
Raul I. Cabrera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Interspecific Hybrids ◽  
Size Variation ◽  
Sequence Repeat ◽  
Allele Size ◽  
Low Genetic Diversity ◽  
Ssr Loci ◽  
Diversity Estimates ◽  
Simple Sequence

Genetic diversity was estimated for 51 Lagerstroemia indica L. cultivars, five Lagerstroemia fauriei Koehne cultivars, and 37 interspecific hybrids using 78 simple sequence repeat (SSR) markers. SSR loci were highly variable among the cultivars, detecting an average of 6.6 alleles (amplicons) per locus. Each locus detected 13.6 genotypes on average. Cluster analysis identified three main groups that consisted of individual cultivars from L. indica, L. fauriei, and their interspecific hybrids. However, only 18.1% of the overall variation was the result of differences between these groups, which may be attributable to pedigree-based breeding strategies that use current cultivars as parents for future selections. Clustering within each group generally reflected breeding pedigrees but was not supported by bootstrap replicates. Low statistical support was likely the result of low genetic diversity estimates, which indicated that only 25.5% of the total allele size variation was attributable to differences between the species L. indica and L. fauriei. Most allele size variation, or 74.5%, was common to L. indica and L. fauriei. Thus, introgression of other Lagestroemia species such as Lagestroemia limii Merr. (L. chekiangensis Cheng), Lagestroemia speciosa (L.) Pers., and Lagestroemia subcostata Koehne may significantly expand crapemyrtle breeding programs. This study verified relationships between existing cultivars and identified potentially untapped sources of germplasm.

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