scholarly journals 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

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.

scholarly journals The Population Genetic Variation Analysis of Bitter Gourd Wilt Caused by Fusarium oxysporum f. sp. momordicae in China by Inter Simple Sequence Repeats (ISSR) Molecular Marker

2018 ◽  
Author(s):  
Rui Zang ◽  
Ying Zhao ◽  
Kangdi Guo ◽  
Kunqi Hong ◽  
Huijun Xi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Fusarium Oxysporum ◽  
Fusarium Wilt ◽  
Bitter Gourd ◽  
Economic Losses ◽  
Diseased Plant ◽  
Variation Analysis ◽  
Group I ◽  
Geographical Populations

AbstractThe bitter gourd fusarium wilt caused by Fusarium oxysporum f.sp. momordicae (FOM) was a devastating disease in China and leading to great economic losses every year. A total of 152 isolates, which have the typical Fusarium oxysporum characteristics with abundant microconidia and macroconidia on the white or ruby colonies, were obtained from diseased plant tissues with typical fusarium wilt symptoms. The BLASTn analysis of rDNA-ITS showed 99% identity with F.oxysporum species. Among the tested isolates, three isolates infected tower gourd, and five isolates were pathogenic to bottle gourd. However, they were all pathogenic to bitter gourd. Based on the molecular and morphologic results, the isolates were identified as FOM. For genetic variation analysis, forty ISSR primers were screened and eleven primers were used in PCR amplification. Totally, 121 loci were detected, of which 52 loci were polymorphic at rate of 42.98%. The POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.0902 and 0.1478, respectively, which indicated that the genetic diversity for the tested 152 isolates was relatively low. It also means that each geographical population was a relatively independent unit. While the value of coefficient of gene differentiation (Gst=0.4929 > 0.15) pointed to the genetic differentiation was mainly among populations. The strength of gene flow (Nm=0.5143<1.0) was weaker, indicating that gene exchanges were blocked to some degree. The dendrogram based on ISSR markers showed that the eight geographical populations were clustered into four groups at the threshold of genetic similar coefficient 0.96. Fujian, Jiangxi and Guangdong populations were clustered into Group I. Group II contained Hunan and Guangxi populations. Group III only had Hainan population. Group IV consisted Shandong and Henan populations. The geographical populations closer to each other grouped together, suggesting a correlationship between geographical origin and genetic differentiation. Two hybridization events were observed between Hainan and Hunan populations and between Guangdong and Guangxi by Structure analysis. Our findings enrich the knowledge on genetic variation characteristics of the FOM populations with helpful of development of effective disease management programs and disease resistance breeding.

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

Weed Science ◽  
2008 ◽  
Vol 56 (3) ◽  
pp. 394-399 ◽  
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.

scholarly journals A Short Tandem Repeat Assay for Studying Genetic Variation in Madurella mycetomatis (MmySTR)

2020 ◽  
Author(s):  
Bertrand Nyuykonge ◽  
Kimberly Eadie ◽  
Willemien H. A. Zandijk ◽  
Sarah A. Ahmed ◽  
Marie Desnos-Ollivier ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Tandem Repeats ◽  
Diversity Index ◽  
Clinical Manifestations ◽  
Pcr Amplification ◽  
Reference Database ◽  
Madurella Mycetomatis ◽  
Typing Technique ◽  
Short Tandem ◽  
D Value

Introduction: Madurella mycetomatis is the major causative agent of eumycetoma, a neglected tropical infection characterized by painless subcutaneous lesions, inflammation and grains draining from multiple sinuses. To study the epidemiology of mycetoma, a robust discriminatory typing technique is needed. We describe the use of a Short Tandem Repeats assay (MmySTR) for genotyping of M. mycetomatis isolates predominantly from Sudan. Methods: Eleven microsatellite markers (3 dinucleotides, 4 trinucleotide repeats and 4 tetranucleotide repeats) were selected from the M. mycetomatis MM55 genome using the Tandem Repeats Finder software. PCR amplification primers were designed for each microsatellite marker using primer3 software and amplified in a multicolor multiplex PCR approach. To establish the extent of genetic variation within the population, a collection of 120 clinical isolates from different regions was genotyped with this assay. Results: The 11 selected MmySTR markers showed a large genotypic heterogeneity. From a collection of 120 isolates, 108 different genotypes were obtained. The Simpsons’ diversity index (D) value for individual markers ranged from 0.081-0.881, the combined panel displayed an overall D value of 0.997. The MmySTR assay demonstrated high stability, reproducibility and specificity. Conclusion: The MmySTR assay is a promising new typing technique that can be used to genotype isolates of M. mycetomatis. Apart from the possible contribution of host factors, the genetic diversity observed among this group of isolates might contribute to the different clinical manifestations of mycetoma. We recommend the MmySTR assay to be used to establish a global reference database for future study of M. mycetomatis isolates.

RAPD analysis on genetic diversity of typical tea populations in Hunan Province

2008 ◽  
Vol 5 (1) ◽  
pp. 67-72
Author(s):  
Shen Cheng-Wen ◽  
Huang Yi-Huan ◽  
Huang Jian-An ◽  
Luo Jun-Wu ◽  
Liu Chun-Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Genetic ◽  
Diversity Index ◽  
Gene Diversity ◽  
Population Variation ◽  
Hunan Province ◽  
Rapid Amplification ◽  
Population Genetic Variation ◽  
Shannon’S Diversity Index

AbstractGenetic diversity and genetic variation of 240 adult plants of four tea populations in Hunan – Camellia sinensis var. sinensis, C. sinensis var. assamica cv. Duntsa, C. ptilophylla and C. sinensis var. assamica cv. Jianghua – were studied by rapid amplification of polymorphic DNA (RAPD) markers. The results showed 226 loci using 21 random primers (10 bp), of which 201 (88.9%) were polymorphic. The genetic diversity analysis indicated that Shannon's index was 0.43; 74.7% of which was within-population genetic diversity while 25.3% was among-population variation. The gene diversity indexes of total populations (HT), within populations (HS) and among populations (HST) were, respectively, 0.37, 0.28 and 0.09. The coefficient of gene differentiation (GST) among populations was 0.23, indicating a 76.7% variation within populations and 23.3% among populations. These results displayed a rich within-population genetic variation, as in Shannon's diversity index. Interpopulation gene flow (Nm) was 0.74, which indicates the limited genetic exchange between populations.

scholarly journals Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Zulfahmi Zulfahmi ◽  
Parjanto Parjanto ◽  
Edi Purwanto ◽  
Ahmad Yunus
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Genetic Material ◽  
Ex Situ ◽  
Breeding Programs ◽  
The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

scholarly journals DNA barcode reference libraryconstruction and population genetic diversity and structure analysis of Amomum villosum Lour. in Daodi production area

2020 ◽  
Author(s):  
Zhang Danchun ◽  
Xiaoxia Ding ◽  
Wan Guan ◽  
Juan Huang ◽  
He Su ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Diversity Index ◽  
Gene Diversity ◽  
Dna Barcode ◽  
Guangdong Province ◽  
Shannon Index ◽  
Success Rates ◽  
Genetic Diversity And Structure ◽  
Amomum Villosum

Abstract Background: The Amomum villosum has the situation that it is inferior and other other varieties are used as A. villosum in the market. In order to develop and utilize the genuine medicinal materials A. villosum, this experiment aims to carry out the identification and research of variety of the A. villosum and analyze its genetic diversity, constructing the DNA barcode database of the genuine medicinal materials A. villosum in Guangdong Province and providing recommendations for populations planting, which will be critical to the further research of A. villosum. (2) Methods: A total of 141 samples of A. villosum were analyzed by DNA barcoding to construct DNA barcode database. The genetic diversity of A. villosum sampled from 7 populations in Guangdong Province was detected based on ISSR molecular marker technology. (3) Results: The success rates of PCR amplification and sequencing of five barcodes of A. villosumwas rbcL> ITS > ITS2 >psbA-trnH>matK. 141 samples of A. villosum from 7 populations in Guangdong Province were used to construct a reference DNA barcode database containing 531 sequences. The results of genetic diversity were as follow, the number of alleles Na ranged from 1.2879 to 1.7121, the effective number of alleles Ne ranged from 1.1848 to 1.4240, the gene diversity index (H) ranged from 0.2536 to 0.1117, and the Shannon index (I) ranged from 0.3816 to 0.1658, whichindicatedthegenetic diversity of A.Villosum was rich. The total genetic diversity among the 7 populations (Ht) was 0.3299, the genetic diversity within the populations (Hs) was 0.1819, and the gene differentiation coefficient (Gst) was 0.4487. AMOVA showed that the genetic variation within the populations and the genetic variation between the populations accounted for 68.74% (P<0.05) and 31.26% (P<0.05) respectively, indicating that the genetic variation of A. villosum was mainly within the populations. The gene flow Nm was 0.6143.The genetic distance of the 7 populations was 0.0844 - 0.3347, and the genetic identity was 0.7156 - 0.9191, confirming that the genetic relationship of each population was relatively close. The 7 populations were significantly grouped in the cluster analysis and the genetic level of each population from high to low was as follow: ZY (National Highway Roadside) > ZJD (Zhongjiaodong) > GY (Geopark) >MM (Dianbai) > YC (Dadong Village) > XFC (Xingfu Village) > TK (Tankui Village). There was no correlation between the geographic distance and the degree of genetic differentiation among populations. Conclusion: By amplifying and sequencing five barcodes of ITS2, psbA-trnH, ITS, matK and rbcL, a reference DNA barcode database of A. villosum with 531 sequences was constructed. The results of genetic diversity showed that it is necessary to take appropriate in situ protection measures for the populations of A. villosum in Yangchun City and increase the genetic exchange between populations to improve the genetic diversity of A. villosum.

scholarly journals The reasons for low intrapopulation genetic variation in Lamium incisum Willd

2011 ◽  
Vol 60 (1) ◽  
pp. 79-84
Author(s):  
Katarzyna Wąsowicz ◽  
Monika Szczecińska ◽  
Jakub Sawicki
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Diversity Index ◽  
Gene Diversity ◽  
Weed Species ◽  
Preliminary Screening ◽  
Low Genetic Diversity ◽  
The Mean ◽  
Intrapopulation Genetic Variation ◽  
Issr Primers

The reasons for low intrapopulation genetic variation in Lamium incisum Willd The paper presents results of a study which aim was preliminary screening of intrapopulation genetic variability in Lamium incisum Willd. This weed species is rarely distributed in Poland and lessening its count during the last years. As a plant inhabiting anthropogenic sites it is exposed to extreme conditions and disturbances caused mostly by the progressive intensification of agriculture. In order to investigate the genetic variability of the selected population markers of ISSR category were used. The analysis of chosen individuals with use of three ISSR primers revealed total of 49 loci, of which only 15 were polymorphic. Nei's gene diversity index (HE=0.099) and the mean number of alleles per locus (AE=1.160) indicated low genetic diversity within the examined population. The research presented in this paper allows for a better learning of the genetic variability of the investigated species and considers probable factors influencing its level.

scholarly journals ISSR Marker Based Population Genetic Study of Melocanna baccifera (Roxb.) Kurz: A Commercially Important Bamboo of Manipur, North-East India

Scientifica ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Heikrujam Nilkanta ◽  
Thoungamba Amom ◽  
Leimapokpam Tikendra ◽  
Hamidur Rahaman ◽  
Potshangbam Nongdam
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Diversity Index ◽  
Species Level ◽  
Issr Marker ◽  
Polymorphic Band ◽  
North East India ◽  
North East ◽  
Shannon’S Diversity Index

Melocanna baccifera (Roxb.) Kurz is an economically important bamboo of North-East India experiencing population depletion in its natural habitats. Genetic variation studies were conducted in 7 populations sampled from 5 districts of Manipur using ISSR molecular markers. The investigation was carried out as a primary step towards developing effective conservation strategies for the protection of bamboo germplasm. ISSR marker analysis showed significant level of genetic variation within the populations as revealed by moderately high average values of Nei’s genetic diversity (H 0.1639), Shannon’s diversity index (I 0.2563), percentage of polymorphic bands (PPB 59.18), total genetic variation (Ht 0.1961), and genetic diversity within population (Hs 0.1639). The study also divulged a high genetic variation at species level with Shannon’s diversity index (I), Nei’s genetic diversity (H), and percentage of polymorphic band (PPB%) recorded at 0.3218, 0.1939, and 88.37, respectively. Genetic differentiation among the populations (Gst) was merely 19.42% leaving 80.58% of genetic variation exhibited within the populations. The low genetic diversity between populations was consistent with AMOVA. The low genetic differentiation among populations coupled with existence of significantly high genetic diversity at species level indicated the urgent necessity of preserving and protecting all the existing natural bamboo populations in the region.

scholarly journals Genetic Diversity of the Relict Plant Taiwania cryptomerioides Hayata (Cupressaceae) in Mainland China

2008 ◽  
Vol 57 (1-6) ◽  
pp. 242-249 ◽  
Author(s):  
Zhong-Chao Li ◽  
Xiao-Lan Wang ◽  
Xue-Jun Ge
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Gene Diversity ◽  
Mainland China ◽  
Small Population ◽  
Conservation Strategies ◽  
Biogeographic History ◽  
Inter Simple Sequence Repeats ◽  
Taiwania Cryptomerioides

Abstract The genetic diversity and differentiation of five populations of Taiwania cryptomerioides Hayata in mainland China were investigated using inter-simple sequence repeats (ISSR). In comparison with other coniferous species, T. cryptomerioides from mainland China possesses little genetic variation, particularly at the level of individual populations (the percentage of polymorphic loci, Nei’s gene diversity and Shannon’s indices of diversity at the species and population levels are 38.02%, 0.1326, 0.1986 and 9.27%, 0.035, 0.0518 respectively). In contrast, the level of population differentiation is much higher (GST: 0.7269; Shannon’s genetic differentiation: 0.7392; Hickory è B: 0.668; AMOVA genetic differentiation: 72.37%). The genetic divergence of pairs of populations was not significantly correlated with the geographical distance separating them. Current patterns of genetic variation were related to biogeographic history and the small population size. On the basis of these findings, we discuss the development of conservation strategies for this endangered species.

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