SSR Marker-Based Genetic Resource Assessment of The Rainbow Clam Moerella Iridescens Along The Coasts of China: Implications for Strategy of Conservation Management

Abstract This study aims to determine the genetic structure and diversity of rainbow clam Moerella iridescens in different sea areas of China. Seventeen pairs of microsatellite primers (SSR) were used to amplify the SSRs of rainbow clam in Lianyungang of Haizhou Bay, Chongming of Shanghai, Ningde in Fujian, Cixi and Wenzhou in Zhejiang. A total of 1146 alleles were detected in 310 individuals from the 17 SSR loci. The average observed heterozygosity of six populations was 0.4381–0.6139, the average expected heterozygosity was 0.5897–0.7325, and the average Shannon diversity index was 1.2655–1.7998. The clams exhibited rich genetic diversity and the FST of the genetic differentiation index of the six populations was 0.0470, indicating low genetic differentiation amongst the populations. The results indictated that rainbow clam along China coasts exhibited high diversity and low population differentiation.

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Inter and intra population diversity analysis in toria (Brassica rapa L.) using SSR marker

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.80.1.14 ◽

2020 ◽

Vol 80 (01) ◽

Author(s):

Aradhana Phukan ◽

P. K. Barua ◽

R. N. Sarma ◽

N. Borah

Keyword(s):

Genetic Diversity ◽

Brassica Rapa ◽

Ssr Marker ◽

Population Diversity ◽

Population Variation ◽

High Yield ◽

High Genetic Diversity ◽

Information Index ◽

Expected Heterozygosity ◽

Ssr Loci

Six popular toria (Brassica rapa L.) lines of Assam were used to determine the intra and inter populations diversity using SSR markers. Application of 39, 28 loci SSR loci revealed a total of 80 alleles. The SSR marker BRMS-029 had the highest PIC value in each population. Genetic diversity within individuals was high and accounted for 86% of the total variation, while among population variation was accounting for 13%. So, intra population diversity was found higher than the inter population diversity. The population M27 showed the highest number of alleles (2.128), highest number of effective alleles (1.592), Shanon information index (0.463), expected heterozygosity (0.275) and unbiased expected heterozygosity (0.282) indicating the presence of more heterozygotes in the population. The dendogram showed three distinct populations (TS 36, TS 38 and Jeuti) among the six populations and other three populations are slightly overlapping indicating gene flow. The high genetic diversity within cultivars of B. rapa is required to avoid inbreeding and to enable high yield. This study provided a new insight into the exploitation of the genetically diverse toria lines as potential resources for future breeding programs.

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Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

Journal of Plant Pathology ◽

10.1007/s42161-021-00759-8 ◽

2021 ◽

Author(s):

Rui Zang ◽

Ying Zhao ◽

Kangdi Guo ◽

Kunqi Hong ◽

Huijun Xi ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Fusarium Oxysporum ◽

Diversity Index ◽

Gene Diversity ◽

Pcr Amplification ◽

Bitter Gourd ◽

Diseased Plant ◽

Variation Analysis ◽

Group I

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.

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Genetic Structure and Diversity among Species of Salacia: An Endangered Medicinal Herb of Western Ghats, India

South Asian Journal of Experimental Biology ◽

10.38150/sajeb.9(1).p23-33 ◽

2019 ◽

Vol 9 (1) ◽

pp. 23-33

Author(s):

Chandrashekhar G Patil ◽

Sheetal Ganapati Kamat ◽

R Vasudeva

Keyword(s):

Genetic Diversity ◽

Southern China ◽

Issr Marker ◽

Group Method ◽

Population Genetic Differentiation ◽

Expected Heterozygosity ◽

Marker Analysis ◽

Endangered Medicinal Herb ◽

High Level ◽

Genetic Structure And Diversity

Salacia is one of the medicinally valuable genus, distributed throughout tropical areas which include India, Sri Lanka, Southern China and other Southern Asian Countries. The genus Salacia is represented by 21 species in India, among them eight species are recorded from the state of Karnataka in the Southern part of India. Despite its pharmaceutical importance, very little information exists about the genetic diversity of Salacia at molecular level. Hence the present study was carried out to evaluate the genetic among six species of Salacia namely S. chinensis, S. malabarica, S. oblonga, S. macrosperma, S. reticulata and S. gambleana with the help of ISSR marker analysis. Dendrogram and genetic distance were generated adopting Unweighted Paired Group Method with Arithmetic mean (UPGMA) in the NTSYS-pc software. Basic genetic parameters were calculated by analysing the genetic data with Pop gene 1.32 and GenAlEx 6.2 software. The overall polymorphism across the ten primers screened revealed 26 % polymorphism. A 60% polymorphism was scored for the primer UBC 841, whereas, no polymorphism was observed for primer UBC 840 and ISSR 6. The average observed heterozygosity was more than expected heterozygosity. Observed heterozygosity (Ho) ranged from 0.15 (UBC 841) to 0.38 (ISSR 6) with an average of 0.25, whereas expected heterozygosity (He) ranged from 0.10 (UBC 843) to 0.35 (ISSR 6) with an average of 0.23 for Salacia species. The higher heterozygosity pointed towards increased genetic diversity amongst the species. ISSR marker analysis showed high level of inter and intra population genetic differentiation.

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Development and characterization of microsatellite loci for Cedrela fissilis Vell (Meliaceae), an endangered tropical tree species

Silvae Genetica ◽

10.1515/sg-2014-0031 ◽

2014 ◽

Vol 63 (1-6) ◽

pp. 240-243 ◽

Cited By ~ 4

Author(s):

F. B. Gandara ◽

E. V. Tambarussi ◽

Alexandre Magno Sebbenn ◽

E. M. Ferraz ◽

M. A. Moreno ◽

...

Keyword(s):

Genomic Library ◽

Population Level ◽

Fixation Index ◽

Allele Number ◽

Neotropical Tree ◽

Expected Heterozygosity ◽

Adult Trees ◽

Ssr Loci ◽

Polymorphic Microsatellite

Abstract The timber of the Neotropical tree Cedrela fissilis is used in construction, shipbuilding, carpentry and for medical purposes. In this study, polymorphic microsatellite (SSR) markers derived from an enriched genomic library were characterized using 120 adult trees from four different C. fissilis populations. No substantial genotypic linkage disequilibrium was detected among all possible pairs of SSR loci. The number of alleles per locus ranged from 2 to 20, the average allele number ranged from 8 to 9.7, depending on the population. The observed heterozygosity among the different SSR loci varied from 0.0 to 1.00 , the expected heterozygosity varied from 0.07 to 0.95 On the population level, the average observed and expected heterozygosities ranged from 0.50 to 0.63 and from 0.64 to 0.70, respectively. The average fixation index among populations ranged from 0.09 to 0.24. Thus, the SSR loci revealed high poly - morphism rates and can be used to study the genetic diversity,structure, mating system, and gene flow in C. fissilis.

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New insights on the genetic basis of Portuguese grapevine and on grapevine domestication

Genome ◽

10.1139/g09-048 ◽

2009 ◽

Vol 52 (9) ◽

pp. 790-800 ◽

Cited By ~ 29

Author(s):

M. S. Lopes ◽

D. Mendonça ◽

M. Rodrigues dos Santos ◽

J. E. Eiras-Dias ◽

A. da Câmara Machado

Keyword(s):

Gene Flow ◽

Genetic Differentiation ◽

Vitis Vinifera ◽

Ssr Markers ◽

Genetic Basis ◽

Genetic Resource ◽

Putative Parent ◽

Last Glaciation ◽

Wild Grapevine ◽

Nuclear Ssr

As the ancestor of cultivated grape, Vitis vinifera subsp. sylvestris represents a unique, invaluable genetic resource for the improvement of cultivated grapevines. Recently, five populations of wild grapevines were identified in Portugal. Sixty vines were characterized with 11 nuclear SSR markers and further compared with 70 genotypes of Portuguese Vitis vinifera subsp. sativa. The obtained data demonstrate moderate genetic differentiation between wild grapevine populations and moderate to high genetic differentiation between wild and cultivated grapevines. However, the identification of high degrees of similarity between wild and cultivated grapes (up to 87%) and a putative parent–progeny relationship between wild and cultivated grapes with 17 additional SSR markers is indicative of gene flow between local wild grapevine populations and Portuguese domesticated vines. Also, the ancestry of some Azorean cultivars was ascertained. The obtained data further support the hypothesis of several domestication centres, with Portugal, Spain, and Italy playing a particular role after the last glaciation, giving rise to many of the Western European cultivars.

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Genetic Differentiation in Moroccan Opuntia ficus-indica Cultivars Using Simple Sequence Repeat (SSR) Markers

Notulae Scientia Biologicae ◽

10.15835/nsb839864 ◽

2016 ◽

Vol 8 (3) ◽

pp. 380-385 ◽

Cited By ~ 1

Author(s):

Aissam EL FINTI ◽

Driss TALIBI ◽

Mouhamed SIDKI ◽

Abdelhamid E. MOUSADIK

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Ssr Markers ◽

Opuntia Ficus Indica ◽

Distance Analysis ◽

Reference Collection ◽

Ssr Loci ◽

Set Up ◽

Genetic Distance Analysis ◽

Simple Sequence

Estimation of genetic parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources. In this study, 13 Opuntia ficus-indica cultivars were analyzed using 10 SSR markers selected for studying the genetic diversity among these chosen cultivars. Over the 10 SSR markers, a total of 45 reproducible bands were scored with an average of 4.5 alleles/locus, while the observed heterozygosity (Ho) values of amplified loci ranged from 0.15 (SSR1) to 0.92 (SSR2 and SSR 11). Genetic distance analysis of the 13 cultivars showed a large genetic differentiation (GST = 0.47) and high number of different groups. Most of the accessions were not found to be clustered according to their eco-geographical origin. In addition, each cultivar was characterized by its own multiallelic combination between loci. The results revealed the usefulness of SSR in understanding of genetic diversity in Moroccans Barbary fig cultivars, thus being helpful to set up rational decisions concerning the establishment of a national reference collection.

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Contrasting evolutionary processes drive morphological and genetic differentiation in a subtropical fir (Abies, Pinaceae) species complex

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz077 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jorge Cruz-Nicolás ◽

Gustavo Giles-Pérez ◽

Eréndira González-Linares ◽

Julia Múgica-Gallart ◽

Andrés Lira-Noriega ◽

...

Keyword(s):

Genetic Differentiation ◽

Population Size ◽

Species Complex ◽

Isolation By Distance ◽

Morphological Differentiation ◽

Resin Duct ◽

Evolutionary Force ◽

Ssr Loci ◽

Selective Forces ◽

Species Descriptions

Abstract Interacting stochastic and selective forces drive population and species divergence. Such interaction may generate contrasting clines between genetic and phenotypic factors, which can be related to either geographical or environmental variation depending on the predominant evolutionary force (which in its turn is partly determined by population size). Here, we investigated whether the morphological and genetic differentiation across a species complex in Abies in central Mexico fits isolation by distance (IBD) or isolation-by-adaptation (IBA) frameworks. This complex includes two species (A. religiosa and A. flinckii) with discernible morphological and environmental differences and dissimilar range sizes. After comparing variation at nuclear SSR loci and diagnostic morphological traits of needles with the climate variables contributing to ecological differentiation, we found that the widely distributed A. religiosa has more genetic diversity and is morphologically more heterogeneous than the geographically restricted A. flinckii. Morphological differentiation at three physiologically important traits (needle thickness, number of stomata rows and location of the resin duct) is significantly correlated with geography in A. flinckii (indicative of IBD), but is significantly associated with climate variation in A. religiosa (suggesting IBA). In agreement with quantitative genetics theory, PST (phenotypic differentiation)-G’ST (genetic differentiation) comparisons indicate contrasting contributions of putatively adaptive (A. religiosa) and stochastic (A. flinckii) factors to the morphological differentiation of species related to their population size. The integration of such quantitative genetic/evolutionary aspects may reinforce species descriptions and help in disentangling resilient taxonomic discordance.

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Genome-wide development of lncRNA-derived-SSR markers for Dongxiang wild rice (Oryza rufipogon Griff.)

10.1101/2021.08.23.457289 ◽

2021 ◽

Cited By ~ 1

Author(s):

Wanling Yang ◽

Yuanwei Fan ◽

Yong Chen ◽

Gumu Ding ◽

Hu Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Stress Responses ◽

Wild Rice ◽

Diversity Index ◽

Oryza Rufipogon ◽

Coding Sequences ◽

Genome Wide ◽

Ssr Loci ◽

Dongxiang Wild Rice

AbstractDongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost distributed common wild rice found in the world. It contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in crop breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice materials. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content (PIC) values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research, including genetic diversity analysis, QTL mapping, and molecular breeding programs, to make good use of the elite lncRNA genes from DXWR.

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