scholarly journals A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska

2019 ◽  
Author(s):  
Saurav Das ◽  
T. Plyler-Harveson ◽  
Dipak K. Santra ◽  
Kathy A. Nielson ◽  
Robert M. Harveson
Keyword(s):  
Genetic Diversity ◽  
Sugar Beet ◽  
Rhizoctonia Solani ◽  
Geographical Origin ◽  
Diversity Index ◽  
Statistical Significance ◽  
Issr Markers ◽  
Dry Bean ◽  
Amova Analysis ◽  
Color Marker

Abstract Root and stem rot caused by Rhizoctonia solani is a serious fungal disease of sugar beet and dry bean production in Nebraska. The objective of this study was to analyze morpho-genetic diversity of 38 Rhizoctonia solani isolates from sugar beet and dry bean fields in western Nebraska over 10 years. Morphological features and ISSR-based DNA markers were used to study the morphogenetic diversity. Fungal colonies were morphologically diverse in shapes, aerial hyphae formation, colony, and sclerotia color. Marker analysis using nineteen polymorphic ISSR markers showed polymorphic bands ranged from 15 - 28 with molecular weight of 100bp to 3kb. Polymorphic loci ranged from 43.26 – 92.88%. Nei genetic distance within the population ranged from 0.03 – 0.09 and Shannon diversity index varied from 0.24 – 0.28. AMOVA analysis based on ΦPT values showed 87% variation within and 13% among the population with statistical significance (p<0.05). Majority of the isolates from sugar beet showed nearby association within the population. A significant number of isolates showed similarity with isolates of both the crops suggesting their broad pathogenicity. Isolates were grouped into three different clusters in UPGMA based cluster analysis using marker information. Interestingly, there was no geographical correlation between the isolates. Principle component analysis showed randomized distribution of isolates from the same geographical origin. This information may help in molecular pathotyping of the pathogen for better disease management.

scholarly journals A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Saurav Das ◽  
T. Plyler-Harveson ◽  
Dipak K. Santra ◽  
Bijesh Maharjan ◽  
Kathy A. Nielson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sugar Beet ◽  
Rhizoctonia Solani ◽  
Diversity Index ◽  
Statistical Significance ◽  
Principal Component ◽  
Issr Markers ◽  
Crown Rot ◽  
Dry Beans ◽  
Dry Bean

Abstract Background Root and stem rot caused by Rhizoctonia solani is a serious fungal disease of sugar beet and dry bean production in Nebraska. Rhizoctonia root rot and crown rot in sugar beet and dry bean have reduced the yield significantly and has also created problems in storage. The objective of this study was to analyze morpho-genetic diversity of 38 Rhizoctonia solani isolates from sugar beet and dry bean fields in western Nebraska collected over 10 years. Morphological features and ISSR-based DNA markers were used to study the morphogenetic diversity. Results Fungal colonies were morphologically diverse in shapes, aerial hyphae formation, colony, and sclerotia color. Marker analysis using 19 polymorphic ISSR markers showed polymorphic bands ranged from 15 to 28 with molecular weight of 100 bp to 3 kb. Polymorphic loci ranged from 43.26–92.88%. Nei genetic distance within the population ranged from 0.03–0.09 and Shannon diversity index varied from 0.24–0.28. AMOVA analysis based on ΦPT values showed 87% variation within and 13% among the population with statistical significance (p < 0.05). Majority of the isolates from sugar beet showed nearby association within the population. A significant number of isolates showed similarity with isolates of both the crops suggesting their broad pathogenicity. Isolates were grouped into three different clusters in UPGMA based cluster analysis using marker information. Interestingly, there was no geographical correlation among the isolates. Principal component analysis showed randomized distribution of isolates from the same geographical origin. Identities of the isolates were confirmed by both ITS-rDNA sequences and pathogenicity tests. Conclusion Identification and categorization of the pathogen will be helpful in designing integrated disease management guidelines for sugar beet and dry beans of mid western America.

scholarly journals A longitudinal study on morphogenetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska

2019 ◽  
Author(s):  
Saurav Das ◽  
Tammy Plyler-Harveson ◽  
Dipak K. Santra ◽  
Robert M. Harveson ◽  
Kathy A. Nielsen
Keyword(s):  
Genetic Diversity ◽  
Sugar Beet ◽  
Rhizoctonia Solani ◽  
Diversity Index ◽  
Statistical Significance ◽  
Morphological Characteristics ◽  
Distinct Group ◽  
Issr Marker ◽  
Dry Beans ◽  
Dry Bean

AbstractRoot and stem rot caused by Rhizoctonia solani is a serious fungal disease of sugar beet and dry bean production in Nebraska. Objective was to characterize morpho-genetic diversity of 38 Rhizoctonia solani isolated from sugar beet and dry beans fields in western Nebraska over 10 years. Classical morphological features and ISSR marker was used to study the morphogenetic diversity. Fungal colonies were morphologically diverse in shapes, aerial hyphae formation and colony, sclerotia color. Marker analysis using nineteen polymorphic ISSR marker showed polymorphic bands ranged from 15 - 28 with molecular weight 100bp to 3kb. Polymorphic loci ranged from 43.26 – 92.88%. Nei genetic distance within the population was ranged 0.03 –0.09 and Shannon diversity index varied from 0.24 – 0.28. AMOVA analysis based on ΦPT values showed 87% variation within and 13% among the population with statistical significance. Majority of the isolates from sugar beet showed nearby association within the population. There was significant number of cross crop clustering suggesting their broad pathogenicity. Isolates were grouped into three different clusters in UPGMA based cluster analysis using marker information. Interestingly, there was no specific geographical correlation between the isolates. PCA analysis showed randomized distribution among isolates from same geographical origin. Morphological characteristics showed crop-specific two distinct groups of isolates with few exceptions. While, genetic diversity showed two distinct group of isolates, one crop specific and one with wide pathogenicity. This information may help in molecular pathotyping of the pathogen for better disease management.

scholarly journals Low Divergence Among Natural Populations of Cornus kousa subsp. chinensis Revealed by ISSR Markers

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1082 ◽  
Author(s):  
Jia-Qiu Yuan ◽  
Qin Fang ◽  
Guo-Hua Liu ◽  
Xiang-Xiang Fu
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
In Situ Conservation ◽  
Geographic Distance ◽  
Natural Populations ◽  
Issr Markers ◽  
Mantel Test ◽  
Distribution Area ◽  
Genetic Characteristics ◽  
Cornus Kousa

Research Highlights: Taking Chinese dogwood (Cornus kousa subsp. chinensis) as an example, the genetic characteristics of natural populations collected from main a distribution area were evaluated using intersimple sequence repeat (ISSR) markers to reveal the genetic basis for further selection and breeding. Background and Objectives: Chinese dogwood is a small understory tree that is widely distributed in China. Chinese dogwood has attracted interest for its potential horticultural and ornamental values, and its natural resource potential urgently needs to be estimated. Materials and Methods: In this study, the genetic diversity of 12 natural populations collected from six provinces containing 223 individuals was evaluated based on ISSR markers. Results: Relatively high levels of genetic diversity were found at both the population and individual levels. The Shannon’s diversity index (I) among individuals (0.504) was higher than that among populations (0.338). Analysis of molecular variance (AMOVA) revealed that genetic variation mainly existed within populations (61.55%) rather than among populations (38.45%). According to the STRUCTURE analysis, 12 populations were assigned to two groups, i.e., the northern and southern ecological regions, which are separated by the Yangtze River. A Mantel test analysis showed that there was no significant correlation between genetic distance and geographic distance. Conclusions: Considering the breeding system of dogwoods, we speculated that the genetic characteristics of the natural populations of this species would be affected by the dispersal mode of its pollens and seeds; additionally, genetic drift could play an important role in its genetic differentiation. In conclusion, in situ conservation is recommended for Chinese dogwood based on our results.

scholarly journals Elucidation of genetic diversity among some accessions of sugar beet (Beta vulgaris L.) using inter-simple sequence repeats (ISSR) markers

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Almoataz Bellah Ali El-Mouhamady ◽  
Magdy Ahmad Al-Kordy ◽  
Tarik Abdel-Fatah Elewa
Keyword(s):  
Genetic Diversity ◽  
Sugar Beet ◽  
Genetic Improvement ◽  
Issr Markers ◽  
Sugar Yield ◽  
Genetic Progress ◽  
Improvement Program ◽  
Growing Seasons ◽  
Sugar Beet Crop ◽  
White Sugar

Abstract Background Sugar beet is considered a very important strategic economic crop, as it comes at the second place for white sugar production in Egypt after sugar cane and the sugar percentage in its roots is 20%. This work was conducted in Egypt as a direct response to bridge the gap which began to expand significantly between the production and consumption of white sugar and the desire for the genetic improvement process to increase the productivity of this crop. Further, as serious attempt to understand the nature of the genetic diversity among a group of sugar beet accessions with different origins, it constitutes an important source for establishing a program of breeding and improving sugar beet crop under Egyptian conditions. Results The process of verifying the existence of significant genetic variation between the eight sugar beet varieties with various origins was carried out through a set of genetic parameters through two growing seasons besides, the data of ISSR markers profile. Further, all the sugar beet varieties were superior in all the studied traits during their evaluation over two agricultural years, where the two sugar beet accessions Oscar Poly and Rass Poly are superior in TSS % and sucrose % traits, Mont Bianco and Sultan in apparent purity % trait, Blino and Sultan in root yield and top yield traits and Rass Poly and Blino in sugar yield trait, respectively. In addition, the values of heritability in broad sense were high in all studied traits except the two traits; sucrose % and sugar yield where their results were appeared medium during both growing seasons. In the same regard, expected genetic advance values showed significant genetic progress in all studied traits during the two growing seasons. As well, highly genetic diversity was obtained between the eight sugar beet accessions through generated 169 amplified fragments from the twelve ISSR primers, 122 of them were polymorphic with 72.18% polymorphism. Conclusions The eight sugar beet varieties achieved remarkable and distinctive results for all traits under study during two agricultural years. However, they were differentiated and various from each other. As they differed in their superiority in all estimated traits and they proved to be fertile material for studying in this investigation and very suitable for enriching the breeding and genetic improvement program to promote the sugar beet yield in order to increase the productivity of white sugar in Egypt.

scholarly journals Analysis of genetic diversity among different tomato genotypes using ISSR DNA marker

Genetika ◽  
2017 ◽  
Vol 49 (1) ◽  
pp. 31-42
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Mehraj Abbasov
Keyword(s):  
Genetic Diversity ◽  
Dna Marker ◽  
Diversity Index ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Variation Analysis ◽  
A Value ◽  
Polymorphic Bands ◽  
Simple Sequence

Inter simple sequence repeat (ISSR) markers were used for variation analysis among 41 tomato accessions. A total of 50 scorable bands were obtained, where 32 were polymorphic, representing 63.3% of all the amplified loci. Polymorphism percentage ranged from 50 to 90% and an average number of polymorphic bands of 4.0 were observed. An average genetic diversity index was 0.61. Primer UBC860 and UBC825 generated the greatest diversity index with a value of 0.89 and 0.85 respectively. The smallest diversity identified by primer UBC808, with an index of 0.34. The genetic similarity among studied genotypes ranged from 0.52 to 0.98. The cluster analysis based on Jaccard?s similarity coefficient divided genotypes into 6 distinct clusters on a value of 0.74. The lowest genetic distance was found between ?Gronastiy? and ?AG1224? (0.52), ?Orange? and ?AG1224? (0.54), and ?Evgeniya? and ?AG1224? (0.55) accessions. The highest similarity of 0.98 was determined between ?Zafar? and ?Azerbaijan-94?, ?Khachmaz-1? and ?Azerbaijan-94?, ?Khachmaz-1? and ?Severyanka?, and ?Shakar? and ?Absheron-1? accessions.

Genetic Relationship in Sainfoin (Onobrychis viciifolia) Landraces Cultivated East Anatolia by using RAPD and ISSR Markers

2021 ◽  
Author(s):  
Mehmet Macit Ertuş
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Calcareous Soils ◽  
Similarity Index ◽  
Issr Markers ◽  
High Genetic Diversity ◽  
Onobrychis Viciifolia ◽  
Young Leaves ◽  
Rapd And Issr ◽  
Issr Primers

Background: Sainfoin (Onobrychis viciifolia) is a forage crop that yields high in arid and calcareous soils and is cultivated in large areas. There aren’t many genetic diversity studies on the varieties of cultured sainfoin. This study was conducted to determine the genetic diversity and the degree of relationship between 23 cultivated landraces and one registered variety. Methods: To take samples from the populations, seeds were sown in the field in 2014. Samples were taken from the young leaves of the plants and preserved at -80oC in same year. RAPD and ISSR primers were used in the study. The bands obtained as a result of PCR were recorded and the data of both methods were also evaluated by combining them. Result: In the study, 5 RAPD and 4 ISSR primers were used and a total of 49 bands were obtained. Of 29 bands obtained using RAPD primers, 20 were found to be polymorphic and of 20 bands obtained using ISSR primers, 15 were found to be polymorphic. It was found that there was a very low correlation between the two methods. Using RAPD and ISSR markers and RAPD + ISSR combination, the similarity index among populations was found to be between 0.25-0.95, 0.5-1.00 and 0.45-0.91, respectively. The Nei’s genetic diversity index was found to be between 0.3365, 0.2656 and 0.3018 with RAPD, ISSR primers and RAPD + ISSR combination, respectively. Based on the dendrograms obtained using RAPD, ISSR primers and RAPD + ISSR combination, the populations under analysis were classified into 3, 3 and 5 groups, respectively. With this study, the closest populations were identified and a significantly high genetic diversity was detected.

Effect of habitat fragmentation on the genetic diversity of Stipa krylovii Reshov. in an agro-pastoral ecotone in northern China

2009 ◽  
Vol 89 (5) ◽  
pp. 875-882
Author(s):  
S Zheng ◽  
Z Cao ◽  
K Wang ◽  
M Zhao ◽  
J Mi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Northern China ◽  
Issr Markers ◽  
Inter Simple Sequence Repeats ◽  
Native Grassland ◽  
Stipa Krylovii ◽  
Fragmented Population ◽  
Two Populations ◽  
Amova Analysis

Native grassland in China have been fragmented due to the introduction of agriculture, which has the potential to reduce genetic diversity. In order to understand the potential effects of fragmentation, we conducted a study to examine the genetic diversity between two populations of Stipa krylovii in a typical steppe ecoregion, in northern China. One population was fragmented by farmland (PF) while the second was continuous steppe (PS). The populations were 30 km apart. Genetic diversity was assessed by sampling plants in four geographically similar subpopulations in each population and analyzed for their DNA using the inter-simple sequence repeats (ISSR) markers. Of 50 primers tested, 7 produced 122 amplified bands from 120 individuals, of which 92% (112) were polymorphic. According to the UPGMA dendogram, the four PF subpopulations were grouped separately from the four PS subpopulations. However, AMOVA analysis indicated that habitat fragmentation over the past 50 yr had not changed genetic diversity and variation among S. krylovii populations in an agro-pastoral ecotone in northern China. Therefore, the genetic diversity of this species can be maintained if agriculture disturbance is not increased. Key words: Genetic variation, gene flow, ISSR, fragmented population, non-fragmented population

Genetic diversity of wild and cultured swamp eel (Monopterus albus) populations from central China revealed by ISSR markers

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Wei Li ◽  
Wen-Xiu Sun ◽  
Jun Fan ◽  
Chao-Chao Zhang
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Gene Diversity ◽  
Issr Markers ◽  
Central China ◽  
Commercial Fish ◽  
Monopterus Albus ◽  
Information Index ◽  
Asian Swamp Eel ◽  
Swamp Eel

AbstractAsian swamp eel is a highly commercial fish, primarily for China and other Asian countries. The aim of this paper is to evaluate the genetic diversity of wild and cultured samples of Asian swamp eel Monopterus albus using ISSR markers. A total of 129 individuals belonging to three wild samples, Xiantao (XT), Huanggang (HG), Xinyang (XY) and three cultured samples, Wuhan (WH), Jingzhou (JZ) and Nanjing (NJ) were randomly selected for genetic analysis. Twelve ISSR primers were used for screening the six populations and 110 loci were obtained. The polymorphic loci were estimated to be 54%, 56.3%, 58.2%, 60.6%, 69.5% and 71% in NJ,WH, JZ, XT, HG and XY samples, respectively. Average heterozygosity value varied from 0.1956 to 0.2449. The three wild samples showed higher genetic diversity than the cultured samples (P < 0.05), including polymorphic bands (PPB), observed number of alleles per locus (to), effective number of alleles per locus (Ne), Nei’s gene diversity index (H) and Shannon’s information index (I).

scholarly journals Genetic diversity and spatial genetic structure within a population of an aromatic shrub, Lippia origanoides (Verbenaceae), in the Chicamocha Canyon, northeastern Colombia

2008 ◽  
Vol 90 (6) ◽  
pp. 455-465 ◽  
Author(s):  
ADRIANA SUÁREZ G. ◽  
GENIS CASTILLO ◽  
MARIA I. CHACÓN S.
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Diversity Index ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Classical Model ◽  
Issr Markers ◽  
Breeding Systems ◽  
Group Method ◽  
Pair Group

SummaryThe geographical scale of genetic structure in a continuous population is highly dependent on its breeding system and dispersion capabilities, and this knowledge is important for the study of population dynamics as well as for conservation purposes. In the present study, spatial autocorrelation statistics and intersimple sequence repeat (ISSR) markers were used to describe the genetic structure of a natural population of a prominent aromatic plant, Lippia origanoides, native to the Chicamocha Canyon in northeastern Colombia. For this purpose, individuals were sampled from two localities within the Chicamocha Canyon, where the species is abundant and continuously distributed. Cluster (principal coordinate analysis (PCO) and unweighted pair group method using arithmetic averages (UPGMA)), analysis of molecular variance (AMOVA) and Bayesian analyses revealed a low level of genetic differentiation among the two localities, suggesting that they belong to a single population. Genetic diversity levels in this population, described as the percentage of polymorphic loci (P=86·21%) and quantified using Shannon's diversity index (I=0·453) and the average panmictic heterozygosity (HB=0·484), were shown to be comparable to or higher than that in other plant species with allogamous breeding systems and to other related Verbenaceae species. Fine-scale autocorrelation analyses showed a pattern consistent with the classical model of isolation by distance with moderate but significant levels of local spatial structure. Our results suggest that sampling individuals at distances greater than ~1·2 km may result in the collection of different genotypes, which could help preserve the levels of genetic diversity in a propagation programme. The causes of this spatial pattern are currently unknown and could be influenced by many contemporary factors such as restricted seed dispersal and/or short-distance pollen movement, among others.

Genetic diversity of biennial wormwood

Weed Science ◽  
2004 ◽  
Vol 52 (1) ◽  
pp. 53-60 ◽  
Author(s):  
Lemma W. Mengistu ◽  
Michael J. Christoffers ◽  
George O. Kegode
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Gene Diversity ◽  
Morphological Diversity ◽  
The United States ◽  
Issr Markers ◽  
Dry Bean ◽  
Morphological Studies ◽  
Low Levels ◽  
Its1 And Its2

Biennial wormwood is native to North America and has become an important weed problem in soybean and dry bean fields of North Dakota, South Dakota, and Minnesota in the United States and in the prairie provinces of Canada. Intersimple sequence repeat (ISSR) markers were used to study the genetic diversity among six biennial wormwood and one annual wormwood populations. Deoxyribonucleic acid (DNA) sequences from internal transcribed spacer (ITS1 and ITS2) regions of ribosomal DNA and morphological diversity among the biennial and annual wormwood populations were also studied. High levels of genetic diversity were evident with Nei's gene diversity statistic (h) = 0.40 for biennial wormwood and h = 0.36 for annual wormwood. Total diversity of six biennial wormwood populations was HT = 0.40, and 22% of this diversity was among populations (GST = 0.22). Estimated gene flow among biennial wormwood populations was low (Nm = 0.9), and high levels of differentiation may be due in part to low levels of genetic exchange among biennial wormwood populations. Although biennial wormwood behaves more like an annual than a biennial, the ISSR, ITS, and morphological studies show that the two species are dissimilar.

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