Assessment of Genetic Diversity and Identification of Core Germplasm of Pueraria in Guangxi Using SSR Markers

Abstract Pueraria is not only one of the most important commercial crops, but a health supplement for human being. There are abundant Pueraria germplasm resources and a large planting scale in Guangxi. However, the genetic diversity and core germplasm of the Pueraria species in Guangxi are rarely understood. In this study, 272 individuals of Pueraria species in Guangxi combined with 23 pairs of simple sequence repeat primers were used to evaluate the genetic diversity and construct core germplasm. Ultimately, 118 alleles were identified and 112 alleles were polymorphic; the mean expected heterozygosity per locus is 0.1841, and the mean gene flow Nm is 1.7690. 272 individuals were divided into two main clusters, which is consistent with the results based on principal coordinate analysis and STRUCTURE cluster analysis. We proposed a core collection of 20 Pueraria accessions capturing 105 alleles. There was a non-significant relationship between genetic distance and geographical distance. The results could provide theoretical support for the scientific conversation of Pueraria genetic resources, which can serve as the basis for the breeding program of Pueraria.

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Selection of a core collection of Prunus sibirica L. germplasm by a stepwise clustering method using simple sequence repeat markers

PLoS ONE ◽

10.1371/journal.pone.0260097 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0260097

Author(s):

Yongqiang Sun ◽

Shengjun Dong ◽

Quangang Liu ◽

Jianhua Chen ◽

Jingjing Pan ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Core Collection ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Northern China ◽

Genetic Distances ◽

Germplasm Resources ◽

Sequence Repeat ◽

Simple Sequence

Prunus sibirica is an economically important tree species that occurs in arid and semi-arid regions of northern China. For this species, creation of a core collection is critical for future ecological and evolutionary studies, efficient economic utilization, and development and management of the broader collection of its germplasm resources. In this study, we sampled 158 accessions of P. sibirica from Russia and China using 30 pair of simple sequence repeat molecular markers and 30 different schemes to identify candidate core collections. The 30 schemes were based on combinations of two different sampling strategies, three genetic distances, and five different sample sizes of the complete germplasm resource. We determined the optimal core collection from among the 30 results based on maximization of genetic diversity among groups according to Number of observed alleles (Na), Number of effective alleles (Ne), Shannon’s information index (I), Polymorphic information content (PIC), Nei gene diversity (H) and compared to the initial collection of 158 accessions. We found that the optimal core collection resulted from preferred sampling at 25% with Nei & Li genetic distance these ratios of Na, Ne, I, PIC and H to the complete 158 germplasm resources were 73.0%, 113%, 102%, 100% and 103%, respectively, indicating that the core collection comprised a robust representation of genetic diversity in P. sibirica. The proposed core collection will be valuable for future molecular breeding of this species and management of its germplasm resources.

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Genetic Diversity and Characterization of a Core Collection of Malus Germplasm Using Simple Sequence Repeats (SSRs)

Plant Molecular Biology Reporter ◽

10.1007/s11105-011-0399-x ◽

2011 ◽

Vol 30 (4) ◽

pp. 827-837 ◽

Cited By ~ 35

Author(s):

Sarah M. Potts ◽

Yuepeng Han ◽

M. Awais Khan ◽

Mosbah M. Kushad ◽

A. Lane Rayburn ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Core Collection ◽

Simple Sequence

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A new set of microsatellite loci for Cattleya walkeriana Gardner, an endangered tropical orchid species and its transferability to Cattleya loddigesii Lindl. and Cattleya nobilior Reichenbach

Plant Genetic Resources ◽

10.1017/s1479262117000193 ◽

2017 ◽

Vol 16 (3) ◽

pp. 284-287

Author(s):

Bruno C. Rossini ◽

Mariá B. Kampa ◽

Celso L. Marino ◽

Fernanda Bortolanza Pereira ◽

Fábio M. Alves ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Loci ◽

Null Alleles ◽

Germplasm Resources ◽

Significant Linkage Disequilibrium ◽

Orchid Species ◽

Expected Heterozygosity ◽

Tropical Orchid ◽

Significant Linkage

AbstractIn this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

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Analysis of the polymorphism of expressed sequencetag-Simple sequence repeat in quail

Indian Journal of Animal Research ◽

10.18805/ijar.v0i0f.3803 ◽

2016 ◽

Author(s):

Jun Yan Bai ◽

You Zhi Pang ◽

Yan Xia Qi ◽

Xiao Hui Zhang ◽

Yin Xian Yun

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Improvement ◽

Melanin Synthesis ◽

Sequence Repeat ◽

Average Heterozygosity ◽

Information Contents ◽

The Mean ◽

Simple Sequence

Aiming at accelerating the application of molecular markers in the genetic improvement of quails, six EST-SSR markers were successfully developed using a bioinformatics method. Polymorphisms of three quail populations (Chinese yellow, China black and Korean quail) were detected. The results showed that there were 2-6 alleles in six EST-SSR markers. The mean polymorphism information contents of Chinese yellow , China blackand Korean quail were 0.5451, 0.4962 and 0.4937, respectively. The average heterozygosity values were 0.6134, 0.5759 and 0.5613. Among the six EST-SSR markers, three were highly polymorphicand the others were moderately polymorphic. The newly-developed six EST-SSR markers may be used to determine the genetic diversity of quails. The six EST-SSR markers identified were related to carbohydrate metabolism and melanin synthesis, but the specific mechanisms need to be further analyzed.

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Molecular characterization of almond accessions from the island of La Palma (Canary Islands, Spain) using SSR markers

Plant Genetic Resources ◽

10.1017/s1479262114000112 ◽

2014 ◽

Vol 12 (3) ◽

pp. 323-329 ◽

Cited By ~ 1

Author(s):

Guillermo Padilla ◽

Rafel Socias i Company ◽

Amando Ordás

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Average Value ◽

La Palma ◽

Expected Heterozygosity ◽

Commercial Cultivars ◽

Soft Shell ◽

Genetic Profiles ◽

Simple Sequence

In this study, 15 simple sequence repeat (SSR) markers were used for genetic diversity analysis of 45 almond accessions, which included 25 local cultivars from La Palma Island and three other commercial cultivars. A total of 110 amplification fragments were produced, with an average value of 7.9 alleles per locus. Twelve of the SSR markers can be considered as highly informative, with values of expected heterozygosity and power of discrimination above 0.5 and 0.8, respectively. Due to cases of synonymy and homonymy, 37 different genetic profiles were obtained, with the homonymy of the soft-shell varieties known as ‘Mollar’ being the most significant. Cluster analysis identified four groups within the accessions. One of these groups exclusively consisted of the two commercial cultivars ‘Guara’ and ‘Ferraduel’. The other commercial cultivar used in the study, ‘Desmayo Largueta’, was in a cluster with three cultivars from the same locality. The analysis of molecular variance revealed that the within-localities component accounts for most of the total variation, suggesting that La Palma almond cultivars did not originate independently in different parts of the island. The results of the study reveal the genetic singularity of La Palma almond cultivars and the genetic diversity among them.

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Comparison of the genetic diversity in two species of cycads

Australian Journal of Botany ◽

10.1071/bt04052 ◽

2005 ◽

Vol 53 (3) ◽

pp. 219 ◽

Cited By ~ 12

Author(s):

Longqian Xiao ◽

Xun Gong ◽

Gang Hao ◽

Xuejun Ge ◽

Bo Tian ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Mean Value ◽

The Mean ◽

The Difference ◽

General Opinion ◽

Simple Sequence ◽

Striking Contrast

Inter-simple sequence repeat (ISSR) markers were used to examine the level and distribution of genetic diversity in two cycad species: Cycas parvula S.L.Yang and C. balansae Warburg. The former is found in only two adjacent populations and the latter in a relatively wider distribution. Although genetic diversity in C. balansae (He = 0.1301) is higher than that in C. parvula (He = 0.0538), both are still low in comparison with the mean value (He = 0.169) in gymnosperms. This confirms the general opinion that cycads are genetic relics. The genetic differentiation in both species, however, presents a striking contrast: Gst is 0.0978 in C. parvula, but 0.4003 in C. balansae, which may be ascribed to the difference in distances between their populations.

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Analysis of genetic diversity and association of seed and mucilage yields with inter simple sequence repeats (ISSR) polymorphism in a collection of Plantgao species

10.1101/2020.07.06.189266 ◽

2020 ◽

Author(s):

Bagheri Motahareh ◽

Bahram Heidrai ◽

Zolfaghar Shahriari ◽

Ali Dadkhodaie ◽

Zahra Heidari ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Phylogenetic Network ◽

Germplasm Conservation ◽

Inter Simple Sequence Repeats ◽

Geographical Regions ◽

The Mean ◽

Polymorphic Bands ◽

Simple Sequence ◽

Issr Primers

AbstractAnalysis of genetic diversity in medicinal plants assists germplasm conservation and selection for use in breeding schemes. The aims of the present study were to assess genetic diversity and differentiation of several Plantago species using Inter Simple Sequence Repeats (ISSR) markers and identify marker-trait associations (MTAs). Thirty-one Plantago accessions belonging to eight species with various mating system and chromosome number were collected from geographical regions of Iran environments. Polymorphism in the DNA of Plantago accessions were analyzed using polymerase chain reaction (PCR) of 25 ISSR primers. The data for number of polymorphic bands were analyzed on the basis of several genetic diversity parameters. The results of gel analysis indicated that the ISSR primers amplified 5 to 21 polymorphic bands with 100 to 3000 bp size. The mean polymorphism was 83.83% and five primers showed 100% polymorphism among Plantago accessions. The Polymorphism Information Content (PIC) for ISSR as a dominant marker ranged from 0.1103 to 0.3829 with the mean 0.2727 in the species tested. Accessions in P. amplexicaulis and P. pysillum species represented the highest Nei’s and Shannon’s genetic diversity whilst the lowest obtained for P. lagopus. Analysis of phylogenetic network generated by the Neighbor-Net Algorithm showed moderate split of the eight species tested and the network depicted moderate conflict. The principal coordinate analysis (PCoA) results showed lower conflict in separation of accessions of the eight species. Fifty-six significant MTAs were detected for the traits tested in Plantago accessions, of which six were shared between three seed and mucilage traits and 24 were common between two traits. The coefficient of determination (R2) for the identified MTAs varied between 32 and 73%. In conclusion, the results of genetic diversity analysis suggested that ISSR marker could efficiently differentiate Plantago species and the information of genetic diversity might assist Plantago improvement and conservation.

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Is it possible to obtain zero estimates of genetic diversity? A case study of the Nigerian indigeneous goat breeds at the β-lactoglobulin gene locus

Biotechnology in Animal Husbandry ◽

10.2298/bah1704375e ◽

2017 ◽

Vol 33 (4) ◽

pp. 375-388

Author(s):

Emeka Ezewudo ◽

Geka Abubakar ◽

Sunday Egena ◽

Olushola Alabi

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Gene Locus ◽

Polymorphic Locus ◽

Information Index ◽

Expected Heterozygosity ◽

Goat Population ◽

The Mean ◽

Β Lactoglobulin

The current investigation was conducted to appraise the genetic diversity and genetic distance of three goat populations namely; Red Sokoto, Sahel and West African Dwarf (WAD), in Nigeria, making use of blood samples collected from 20, 20 and 20 individual from which blood DNAs were extraction, respectively. The DNAs extracted were used to study polymorphism at the ?-lactoglobulin gene locus using RLFP-PCR process. Results revealed that the mean total number of alleles was 1 while the effective number of alleles was also 1. The percentage of polymorphic locus was 0% while Shannon?s information index, observed homozygousity, expected heterozygosity, unbiased expected heterozygosity and inbreeding coefficient (F) were all observed to be 0.000. The pairwise Fst was 0.000 between all the breeds of goats. Variation within and between the populations of goats was 0% at p>0.05. The genetic distance between the goat breeds was 0.000. The present study revealed that RLFP-PCR may not be a powerful tool for the study of the ?-lactoglobulin gene locus and hence other methodologies should be employed for a broader judgment on the genetic status of the goat population at the locus.

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Analysis of genetic diversity of Ficus carica L. (Moraceae) collection using simple sequence repeat (SSR) markers

Acta Scientiarum Polonorum Hortorum Cultus ◽

10.24326/asphc.2019.4.9 ◽

2019 ◽

Vol 18 (4) ◽

pp. 93-109

Author(s):

Ilaria Marcotuli ◽

Andrea Mazzeo ◽

Domenica Nigro ◽

Stefania Lucia Giove ◽

Angelica Giancaspro ◽

...

Keyword(s):

Genetic Diversity ◽

Ficus Carica ◽

Accurate Information ◽

Main Crop ◽

Polymorphic Pattern ◽

Genetic Diversity And Structure ◽

The Mean ◽

High Level ◽

Simple Sequence ◽

Modern Technologies

Modern technologies and accurate information on genetic diversity and structure are contributing to improve the plant breeding, in particular for all the minor species with a lack of data. Genetic diversity of 139 different Ficus carica L. genotypes collected from Italy and Croatia, and divided into two subgroups: uniferous (only main crop) and biferous (breba and main crop), was investigated using 49 microsatellite markers. A total of 70 alleles were generated, of which 64 (91.4%) showed a polymorphic pattern indicating high level of genetic diversity within the studied collection. The mean heterozygosity over the 64 single locus microsatellites was 0.33 and the expected and observed averaged variance were 16.50 and 184.08, respectively. The 139 fig genotypes formed two clusters in the PCoA analysis, suggesting a division between Italian and Croatian genotypes. Moreover, the fig accessions could be divided into two main clusters based on the STRUCTURE analysis according to the biological type, uniferous or biferous, with partly overlapping varieties. In conclusion, our results demonstrated that molecular markers were able to discriminate among genotypes and useful for the authentication of fig tree varieties (homonymies and synonymies).

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Comparing the efficiency of sampling strategies to establish a representative in the phenotypic-based genetic diversity core collection of orchardgrass (Dactylis glomerata L.)

Czech Journal of Genetics and Plant Breeding ◽

10.17221/9/2012-cjgpb ◽

2013 ◽

Vol 49 (No. 1) ◽

pp. 36-47 ◽

Cited By ~ 4

Author(s):

M. Studnicki ◽

W. Mądry ◽

J. Schmidt

Keyword(s):

Genetic Diversity ◽

Core Collection ◽

Dactylis Glomerata ◽

Sampling Strategy ◽

Sampling Strategies ◽

Core Collections ◽

The Core ◽

Entire Collection ◽

The Mean ◽

Dactylis Glomerata L

Establishing a core collection that represents the genetic diversity of the entire collection with a minimum loss of its original diversity and minimal redundancies is an important problem for gene bank curators and crop breeders. In this paper, we assess the representativeness of the original genetic diversity in core collections consisting of one-tenth of the entire collection obtained according to 23 sampling strategies. The study was performed using the Polish orchardgrass Dactylis glomerata L. germplasm collection as a model. The representativeness of the core collections was validated by the difference of means (MD%) and difference of mean squared Euclidean distance (d‒D%) for the studied traits in the core subsets and the entire collection. In this way, we compared the efficiency of a simple random and 22 (20 cluster-based and 2 direct cluster-based) stratified sampling strategies. Each cluster-based stratified sampling strategy is a combination of 2 clusterings, 5 allocations and 2 methods of sampling in a group. We used the accession genotypic predicted values for 8 quantitative traits tested in field trials. A sampling strategy is considered more effective for establishing core collections if the means of the traits in a core are maintained at the same level as the means in the entire collection (i.e., the mean of MD% in the simulated samples is close to zero) and, simultaneously, when the overall variation in a core collection is greater than in the entire collection (i.e., the mean of d‒D% in the simulated samples is greater than that obtained for the simple random sampling strategy). Both cluster analyses (unweighted pair group method with arithmetic mean UPGMA and Ward) were similarly useful in constructing those sampling strategies capable of establishing representative core collections. Among the allocation methods that are relatively most useful for constructing efficient samplings were proportional and D2 (including variation). Within the Ward clusters, the random sampling was better than the cluster-based sampling, but not within the UPGMA clusters.

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