Genetic Variation of Native Perilla Germplasms Collected from South Korea Using SSR Markers and Morphological Characteristics

Using morphological characteristics and SSR markers, we evaluated the morphological and genetic variation of 200 Perilla accessions collected from the five regions of South Korea and other region. In morphological characteristics analysis, particularly, leaf color, stem color, degree of pubescence, leaf size were found to be useful for distinguishing the characteristics of native Perilla accessions cultivated in South Korea. A total of 137 alleles were identified in the 20 simple sequence repeat (SSR) markers, and the number of alleles per locus ranged from 3 to 13, and the average number of alleles per locus was 6.85. The average gene diversity (GD) was 0.649, with a range of 0.290-0.828. From analysis of SSR markers, accessions from the Jeolla-do and Gyeongsang-do regions showed comparatively high genetic diversity values compared with those from other regions in South Korea. In the unweighted pair group method with arithmetic mean (UPGMA) analysis, the 200 Perilla accessions were found to cluster into three major groups and an outgroup with a genetic similarity of 42%, and did not showed a clear geographic structure from the five regions of South Korea. Therefore, it is believed that landrace Perilla seeds are frequently exchanged by farmers through various routes between the five regions of South Korea. The results of this study are expected to provide useful information for conservation of these genetic resources and selection of useful resources for the development of varieties for seeds and leafy vegetables of cultivated var. frutescens of Perilla crop in South Korea.

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Genetic diversity analysis of tropical sugar beet (Beta vulgaris L.) varieties in Bangladesh using RAPD markers

Genetika ◽

10.2298/gensr1601151s ◽

2016 ◽

Vol 48 (1) ◽

pp. 151-164

Author(s):

Saidin Saclain ◽

Abdul Latif ◽

Babul Bala ◽

Mithun Mallik ◽

Shahidul Islam

Keyword(s):

Genetic Variation ◽

Sugar Beet ◽

Genetic Distance ◽

Rapd Markers ◽

Gene Diversity ◽

Similarity Index ◽

Genetic Distances ◽

Group Method ◽

Pair Group ◽

Major Cluster

Knowledge on intra-specific genetic variation of an organism is important for its genetic improvement and conservation. In order to estimate genetic variation and relatedness in eleven tropical Sugar beet varieties we used randomly amplified polymorphic DNA (RAPD) markers. The RAPD analysis was performed using six decamer random primers, which amplified a total of 63 DNA fragments of which 43 (68.25%) were found polymorphic. The average polymorphic bands per primer was 7.17 and the overall gene diversity was 0.24. Among the 43 polymorphic loci studied, 2 were specific for 2K 310, 1 for Shubraha, 1 for Natura and 1 for HI-0473 varieties. Pair wise genetic distance and similarity indices were ranged from 0.12-0.51 and 66.73-92.91, respectively. Cauvery and 2K 310 were found to be the most distantly related with a higher genetic distance value (GD = 0.51) and lower similarity index (SI = 66.73), while Aranka and Serenada were the most closely related with their lower GD (0.12) and higher SI(92.91) values. In an unweighted pair group method of arithmetic mean dendrogram constructed on the basis of genetic distances, the eleven varieties grouped into two main clusters: 2K 310 alone was in one cluster whereas 10 other varieties grouped into a major cluster. This indicates that 2K 310 was distantly related with each of the other varieties. Distantly related varieties based on estimated genetic variation could be selected for future breeding program that could result in improvement of this crop.

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Construction of a Core Collection of Native Perilla Germplasm Collected From South Korea Based on SSR Markers and Morphological Characteristics

10.21203/rs.3.rs-855861/v1 ◽

2021 ◽

Author(s):

Kyu Jin Sa ◽

Dong Min Kim ◽

Jun Seok Oh ◽

Hyeon Park ◽

Do Yoon Hyun ◽

...

Keyword(s):

South Korea ◽

Ssr Markers ◽

Core Collection ◽

Morphological Traits ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Morphological Characteristics ◽

Diversity Indices ◽

The Core ◽

Long Time

Abstract The leaves and seed oil of Perilla crop (Perilla frutescens L.) have attracted interest as health foods in East Asia. This crop has been traditionally cultivated and used for a long time as a folk plant, especially in Korea. In our study, the 22 SSR markers and six morphological traits were used to assess the genetic diversity and population structure, to select a core collection of 400 Perilla accessions conserved in the RDA-Genebank of South Korea. A total of 173 alleles were detected and the number of alleles per locus ranged from 4 to 15 (average = 7.9). Gene diversity and polymorphic information content ranged from 0.138 to 0.868 (average = 0.567) and 0.134 to 0.853 (average = 0.522), respectively. The 400 accessions were not clearly distinguished geographically by STRUCTURE and UPGMA analyses. A core collection (44 accessions) was selected from the entire collection by using PowerCore. The core collection accounted for 11.0% of the entire Perilla collection, including 100% of the number of alleles maintained in the whole collection and with similar or greater Shannon-Weaver and Nei diversity indices than the whole collection. The core collection selected by SSR markers was evenly distributed in three clusters on a scatter plot by six morphological traits. The first core collection of Perilla accessions was constructed, and it maintained allelic richness. Further modiﬁcation of the core collection is expected with the continuous addition of new accessions of the two cultivated types of Perilla crop and their weedy types.

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Construction of a core collection of native Perilla germplasm collected from South Korea based on SSR markers and morphological characteristics

Scientific Reports ◽

10.1038/s41598-021-03362-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kyu Jin Sa ◽

Dong Min Kim ◽

Jun Seok Oh ◽

Hyeon Park ◽

Do Yoon Hyun ◽

...

Keyword(s):

South Korea ◽

Ssr Markers ◽

Core Collection ◽

Morphological Traits ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Morphological Characteristics ◽

Diversity Indices ◽

The Core ◽

Long Time

AbstractThe leaves and seed oil of Perilla crop (Perilla frutescens L.) have attracted interest as health foods in East Asia. This crop has been traditionally cultivated and used for a long time as a folk plant, especially in Korea. In our study, the 22 SSR markers and eight morphological traits were used to assess the genetic diversity and population structure, to select a core collection of 400 Perilla accessions conserved in the RDA-Genebank of South Korea. A total of 173 alleles were detected and the number of alleles per locus ranged from 4 to 15 (average = 7.9). Gene diversity and polymorphic information content ranged from 0.138 to 0.868 (average = 0.567) and 0.134 to 0.853 (average = 0.522), respectively. The 400 accessions were not clearly distinguished geographically by STRUCTURE and UPGMA analyses. A core collection (44 accessions) was selected from the entire collection by using PowerCore. The core collection accounted for 11.0% of the entire Perilla collection, including 100% of the number of alleles maintained in the whole collection and with similar or greater Shannon–Weaver and Nei diversity indices than the whole collection. The core collection selected by SSR markers was evenly distributed in three clusters on a scatter plot by eight morphological traits. The first core collection of Perilla accessions was constructed, and it maintained allelic richness. Further modification of the core collection is expected with the continuous addition of new accessions of the two cultivated types of Perilla crop and their weedy types.

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Genetic variation among Stipa grandis P. Smirn populations with different durations of fencing in the Inner Mongolian Steppe

The Rangeland Journal ◽

10.1071/rj09038 ◽

2010 ◽

Vol 32 (4) ◽

pp. 427 ◽

Cited By ~ 5

Author(s):

Jian-bo Wu ◽

Yu-bao Gao ◽

Xiao-ying Bao ◽

Hui Gao ◽

Mei-qing Jia ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Molecular Genetic ◽

Critical Role ◽

Morphological Characteristics ◽

Group Method ◽

Scaling Analysis ◽

Pair Group ◽

Inner Mongolian Steppe

The genetic structure of a population should be carefully considered in ecological restoration because it may play a critical role in maintaining the persistence of a restored ecosystem. In the present study, we examined genetic diversity and genetic structure of Stipa grandis P. Smirn populations from fenced and grazed plots using amplified fragment length polymorphism markers. Molecular genetic variation showed that the genetic diversity of the fenced populations was greater compared with the overgrazed population. There was a significant variation among the populations (Fst = 0.3689, P < 0.001) by AMOVA analysis, and the gene flow was 0.4039 among the populations. The results from a comparison of limited morphological characteristics and from an unweighted pair group method with arithmetic mean cluster analysis and non-metric multi-dimensional scaling analysis suggested that genetic differentiation had occurred between the fenced populations and the grazed populations. The largest genetic diversity was in the moderately grazed population, which might be related to higher population density and greater sexual reproduction due to less disturbances in the plots. The genetic diversity of the long-term (24 years) fenced population was similar to that of a short-term fenced population (fenced for 11 years). These results suggested that the genetic diversity in the overgrazed population might be increased to some extent through fencing, but this effect did not occur beyond 11 years.

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Optimal use of SSR markers for varietal identification of upland cotton

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2015000700007 ◽

2015 ◽

Vol 50 (7) ◽

pp. 571-581 ◽

Cited By ~ 1

Author(s):

Guilherme da Silva Pereira ◽

Ana Luíza Ramos Cazé ◽

Michelle Garcia da Silva ◽

Vanessa Cavalcante Almeida ◽

Fernanda Oliveira da Cunha Magalhães ◽

...

Keyword(s):

Genetic Distance ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Group Method ◽

Discrimination Power ◽

Arithmetic Average ◽

Pair Group ◽

Varietal Identification ◽

The World ◽

The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

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Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

Forests ◽

10.3390/f10111019 ◽

2019 ◽

Vol 10 (11) ◽

pp. 1019 ◽

Cited By ~ 1

Author(s):

Zhong ◽

Yang ◽

Li ◽

Zhang ◽

Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

South China ◽

Expressed Sequence Tag ◽

Gene Diversity ◽

Jiangxi Province ◽

Group Method ◽

Cinnamomum Camphora ◽

Wild Populations ◽

Arithmetic Means

Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.

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Molecular Diversity Analysis of Lentil (Lens culinaris Medik.) through RAPD Markers

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v22i1.11260 ◽

2012 ◽

Vol 22 (1) ◽

pp. 51-58 ◽

Cited By ~ 2

Author(s):

M.E. Hoque ◽

M.M. Hasan

Keyword(s):

Genetic Distance ◽

Rapd Markers ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Molecular Genetic ◽

Group Method ◽

Diversity Analysis ◽

Pair Group ◽

Molecular Genetic Diversity

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular genetic diversity analysis among six BARI released lentil varieties viz. BARI masur-1, BARI masur-2, BARI masur-3, BARI masur-4, BARI masur-5 and BARI masur-6. PCR amplified products were visualized on 1.0% agarose gel and the band for each primer were scored. Ten RAPD markers were used in this study. Out of them 7 primers showed amplification of 53 DNA fragments with 60.37% of them being polymorphic. The highest number of polymorphic loci was noticed in the variety BARI masur-3. The same variety also showed maximum Neis gene diversity value (0.0552). The highest Neis genetic distance (0.5002) was observed in BARI masur-1 vs. BARI masur-5 whereas, the lowest genetic distance (0.0692) was found in BARI masur-1 vs. BARI masur-2. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Neis genetic distance grouped the six cultivars into two main clusters. BARI masur-1, BARI masur-2 and BARI masur-3 were in cluster I and BARI masur-4, BARI masur-5 and BARI masur-6 were in cluster II. The cultivar BARI masur-4 was closest to the cultivar BARI masur-6 with the lowest genetic distance (0.0972) and the highest genetic distance (0.5002) was found between BARI masur-1 and BARI masur-5. The RAPD markers were found to be useful in molecular characterization of lentil varieties which could be utilized by the breeders for the improvement of lentil cultivars. DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11260 Plant Tissue Cult. & Biotech. 22(1): 51-58, 2012 (June)

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Development of DNA fingerprinting keys for the identification of radish cultivars

Australian Journal of Experimental Agriculture ◽

10.1071/ea03031 ◽

2004 ◽

Vol 44 (1) ◽

pp. 95 ◽

Cited By ~ 11

Author(s):

A. Pradhan ◽

G. Yan ◽

J. A. Plummer

Keyword(s):

Dna Fingerprinting ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Morphological Characteristics ◽

Group Method ◽

Base Pairs ◽

Difference Matrix ◽

Pair Group ◽

Young Leaves ◽

Polymerase Chain

Identification of cultivars is extremely important both for cultivation and breeding of crop plants. Cultivar identification based on morphological characteristics can be difficult and complicated. Polymerase chain reaction technologies, such as random amplified polymorphic DNA (RAPD) analysis, can readily and quickly identify cultivars using seeds and young leaves. Sixty individuals representing 7 radish cultivars were examined for RAPD marker polymorphism. Based on the polymorphism generated, 5 primers were selected, out of the 14��examined, to fingerprint the cultivars. The 5 primers produced a total of 52 fragments, 6 monomorphic and 46�polymorphic fragments, ranging in size from 206 to 2258 base pairs. A total and mean character difference matrix was calculated based on the RAPD data and a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA). Three DNA fingerprinting keys were developed for the 7 cultivars and 5 markers derived from 3 primers was the minimum required to distinguish cultivars. Results demonstrated that RAPD markers could be effectively used for the identification of radish cultivars.

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Genetic Variation in Invasive Populations of Yellow Toadflax (Linaria vulgaris) in the Western United States

Weed Science ◽

10.1614/ws-07-157.1 ◽

2008 ◽

Vol 56 (3) ◽

pp. 394-399 ◽

Cited By ~ 24

Author(s):

Sarah M. Ward ◽

Scott D. Reid ◽

Judy Harrington ◽

Jason Sutton ◽

K George Beck

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Recombination ◽

Diversity Index ◽

Gene Diversity ◽

Group Method ◽

Restricted Gene Flow ◽

Genetic Structuring ◽

Invasive Weed ◽

Yellow Toadflax

Intraspecific genetic variation may contribute significantly to invasiveness and control problems, but has been characterized to date in relatively few invasive weed species. We examined 56 intersimple sequence repeat (ISSR) loci in 220 individuals from 11 invading populations of yellow toadflax sampled across five western states. All populations showed high levels of genetic diversity. Estimated values for Shannon's diversity measure ranged from 0.217 to 0.388, and for expected heterozygosity from 0.178 to 0.260. Nei's total gene diversity index (HT), on the basis of all individuals across all populations, was 0.267. Partitioning of genetic variance using analysis of molecular variance revealed 1.7% of genetic variation among regional population groups, 29.1% among populations within groups, and 69.2% within populations, consistent with expectations for an outcrossing species but suggesting little geographic differentiation. Pairs of adjacent individuals identical at all ISSR loci that appeared to be ramets of a single clone were detected in only one population. This indicates that patch expansion in yellow toadflax is driven more by sexual reproduction via seed than by rhizomatous clonal spread, at least at the spatial scale of sampling for this study. Eight populations had significant values for Mantel's R at P = 0.05, suggesting some fine-scale positive genetic structuring, possibly from restricted gene flow. Population clustering on the basis of Nei's genetic distance between populations and unweighted pair group method with arithmetic mean did not reflect geographic location. It is likely that multiple introductions of this species have occurred across the Intermountain West, followed by extensive genetic recombination. High levels of genetic diversity within yellow toadflax populations pose management challenges, as already seen in reports of variable response to herbicide application and limited impacts of biocontrol agent releases.

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Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus

BioMed Research International ◽

10.1155/2015/941357 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Yuejin Zhang ◽

Yuanyuan Chen ◽

Ruihong Wang ◽

Ailin Zeng ◽

Michael K. Deyholos ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Large Scale ◽

Gene Diversity ◽

High Genetic Diversity ◽

Information Index ◽

Polyporus Umbellatus ◽

Ssr Primers ◽

Expressed Sequence

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 naturalPolyporus umbellatusaccessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13P.umbellatusaccessions showed relatively high genetic diversity. The expected heterozygosity, Nei’s gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.

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