Genetic diversity of the azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) gene pool as assessed by SSR markers

Genome ◽  
2008 ◽  
Vol 51 (9) ◽  
pp. 728-738 ◽  
Author(s):  
H. X. Xu ◽  
T. Jing ◽  
N. Tomooka ◽  
A. Kaga ◽  
T. Isemura ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Allelic Variation ◽  
Gene Diversity ◽  
Azuki Bean ◽  
Himalayan Region ◽  
Null Alleles ◽  
Wild Germplasm ◽  
Ssr Analysis ◽  
River Region ◽  
Northeast Asian

To facilitate the wider use of genetic resources including newly collected cultivated and wild azuki bean germplasm, the genetic diversity of the azuki bean complex, based on 13 simple sequence repeat (SSR) primers, was evaluated and a core collection was developed using 616 accessions originating from 8 Asian countries. Wild germplasm from Japan was highly diverse and represented much of the allelic variation found in cultivated germplasm. The SSR results together with recent archaeobotanical evidence support the view that Japan is one center of domestication of azuki bean, at least for the northeast Asian azuki bean. Cultivated azuki beans from China, Korea, and Japan were the most diverse and were genetically distinct from each other, suggesting a long and relatively isolated history of cultivation in each country. Cultivated azuki beans from eastern Nepal and Bhutan were similar to each other and quite distinct from others. For two primers, most eastern Nepalese and Bhutanese cultivated accessions had null alleles. In addition, wild accessions from the Yangtze River region of China and the Himalayan region had a null allele for one or the other of these primers. Whether the distinct diversity of azuki bean in the Himalayan region is due to introgression or separate domestication events requires further study. In contrast, western Nepalese azuki beans showed an SSR profile similar to that of Chinese azuki beans. The genetic distinctness of cultivated azuki beans from Vietnam has been revealed for the first time. The specific alleles indicate that Vietnamese azuki beans have been cultivated in isolation from Chinese azuki beans for a long time. Wild germplasm from the Himalayan region showed the highest level of variation. Based on the results, Himalayan germplasm could be considered a novel gene source for azuki bean breeding. A comparison with mungbean SSR analysis revealed that the mean gene diversity of cultivated azuki bean (0.74) was much higher than that of cultivated mungbean (0.41). The reduction in gene diversity due to domestication, the domestication bottleneck, in azuki bean is not strong compared with that in mungbean.

scholarly journals SSR allelic diversity in relation to morphological traits and resistance to grain mould in sorghum

2010 ◽  
Vol 61 (3) ◽  
pp. 230 ◽  
Author(s):  
Rajan Sharma ◽  
S. P. Deshpande ◽  
S. Senthilvel ◽  
V. P. Rao ◽  
V. Rajaram ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Morphological Traits ◽  
Ssr Marker ◽  
Allelic Variation ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Average Score ◽  
Marker Loci

Allelic variation at 46 simple sequence repeat (SSR) marker loci well distributed across the sorghum genome was used to assess genetic diversity among 92 sorghum lines, 74 resistant and 18 susceptible to grain mould. Of the 46 SSR markers, 44 were polymorphic, with the number of alleles ranging from 2 to 20 with an average of 7.55 alleles per locus. Genetic diversity among the sorghum lines was high as indicated by polymorphic information content (PIC) and gene diversity values. PIC values of polymorphic SSR markers ranged from 0.16 to 0.90, with an average of 0.54. Gene diversity among the sorghum lines varied from 0.16 to 0.91, with an average score of 0.58 per SSR marker. AMOVA indicated that 12% of the total variation observed among the sorghum lines was accounted for between grain mould resistant and susceptible types. Diversity based on six morphological traits and grain mould scores indicated major roles of panicle type and glumes coverage, followed by grain colour, in clustering of the lines. Seven grain mould resistant/susceptible pairs with dissimilarity indices >0.50, but with similar flowering time, plant height, and panicle type/inflorescence within each pair, were selected for use in developing recombinant inbred line mapping populations to identify genomic regions (and quantitative trait loci) associated with sorghum grain mould resistance.

scholarly journals Genetic diversity analysis of soybean genotypes using SSR markers for salinity tolerance

2019 ◽  
Vol 30 (1) ◽  
pp. 1-9
Author(s):  
M Moniruzzaman ◽  
RM Saiem ◽  
RM Emon ◽  
MS Haque ◽  
NR Saha ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Dry Weight ◽  
Null Alleles ◽  
Root Weight ◽  
Root And Shoot Length ◽  
Soybean Genotypes ◽  
Ssr Loci

Soil salinity is a major constraint to soybean production. Five soybean genotypes were grown in pots with hydroponic culture under control and different salt stressed conditions to observe salt tolerance capacity on the basis of phenotypic screening and measure genetic diversity and relatedness among the genotypes. Minimum effects of salinity on root and shoot length was observed in Binasoyben-3, GC840 and Binasoyben-5at different salt stresses. Root dry weight and shoot dry weight of different soybean genotypes under different salt stresses were depicted. The highest reduction in root weight was noted in Binasoybean-1. The same genotypes were used to assess genetic diversity among them with simple sequence repeat (SSR) markers. A total of 33 alleles were detected among 5 soybean genotypes by using 10SSR markers. The number of alleles per locus ranged from 2 to 5, with an average of 3.33 alleles across the 10 loci. Rare alleles were observed at 10 SSR loci with an average of 2.8 alleles per locus. In this experiment, two SSR loci were found to be null alleles. The average values of null allele were 0.2. PIC values ranged from 0.27 in Satt184 to 0.77 in Satt339 with the average value of 0.56.The major allele frequency of the most common allele at each locus ranged from 0.80 in Satt184 to 0.20 in Satt339with a mean frequency of 0.48. The size of the different major alleles at different loci ranged from 173 bp for Satt509 to 407 bp for Satt339. The highest gene diversity (0.80) was observed in loci Satt339 and the lowest gene diversity (0.32) was observed in loci Satt184 with the mean diversity of 0.61. The lowest genetic distance (0.60) was observed in Asset vs Binasoybean-3 and Binasoybean-5 vs Binasoybean-3. The highest genetic distance (1.0) was observed between a numbers of genotype pairs with GC840 vs Asset. The UPGMA cluster analysis led to the grouping of the 5 genotypes into two major clusters. GC840, an advanced line identified to be salt tolerant, together with Binasoybean-5 and Binasoybean-3 clustered in the same sub group. The results from morphological and molecular study suggested that GC840 and Binasoybean-3 are moderately tolerant to salt stress. Progressive Agriculture 30 (1): 1-9, 2019

The genetic diversity of the Vigna angularis complex in Asia

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 647-658 ◽  
Author(s):  
Xu Xiao Zong ◽  
Akito Kaga ◽  
Norihiko Tomooka ◽  
Xin Wang Wang ◽  
Ouk Kyu Han ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Fragment Length Polymorphism ◽  
Geographic Origin ◽  
Northeast Asia ◽  
Azuki Bean ◽  
Himalayan Region ◽  
Vigna Angularis ◽  
Germplasm Collections ◽  
Close Relatives ◽  
Northeast Asian

A selected set of accessions of components of the azuki bean (Vigna angularis) complex comprising 123 cultivated accessions and 23 wild or weedy accessions from Bhutan, China (including Taiwan), India, Japan, Korea, and Nepal was analyzed using amplified fragment length polymorphism (AFLP) methodology. Using 12 AFLP primer pairs, 580 unambiguous bands were generated, 313 (53.9%) of which were polymorphic among azuki bean accessions. All 580 bands were used to assess phenotypic (band) and genetic (nucleotide) diversity among the 146 azuki bean accessions. The results indicate five major groups of azuki bean germplasm primarily associated with geographic origin of accessions and their status: wild, weedy, or cultivated. These five groups are (i) Himalayan wild, (ii) Nepal–Bhutan cultivated, (iii) Chinese wild, (iv) Taiwan wild – Bhutan cultivated, and (v) northeast Asian accessions. Within the northeast Asian accessions, three subgroups are present. These consist of (v1) Japanese complex – Korean cultivated, (v2) Japanese cultivated, and (v3) Chinese cultivated accessions. The results suggest domestication of azuki bean occurred at least twice, once in the Himalayan region of southern Asia and once in northeast Asia. The remarkable diversity of azuki bean germplasm in the Himalayan region compared with other regions suggests this is a rich source of germplasm for plant breeding. The results suggest there are important gaps in the germplasm collections of azuki bean and its close relatives from various parts of Asia and that specific collecting missions for Vigna germplasm related to azuki bean in the highlands of subtropical Asia are needed.Key words: AFLP markers, Asia, azuki bean, conservation, legume.

scholarly journals IMPROVED SSRs-BASED GENETIC DIVERSITY ASSESSMENT OF COCONUTS (COCOS NUCIFERA L) ALONG THE COAST OF KENYA

2021 ◽  
Author(s):  
Justus C. Masha ◽  
Najya Muhammed ◽  
Vincent Njung’e ◽  
Maurice E. Oyoo ◽  
Manfred Miheso
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Cocos Nucifera ◽  
Marker Gene ◽  
Ex Situ ◽  
Ssr Analysis ◽  
Diversity Assessment ◽  
Ssrs Markers ◽  
Important Cash Crop

ABSTRACTCoconut is the most important cash crop along the Coast of Kenya, yet its genetic diversity has not been fully established. A genetic diversity study of 48 coconut genotypes that were collected along the Coast of Kenya was conducted with 13 polymorphic short sequence repeats (SSRs) markers. SSR analysis was performed using GeneMapper while data analysis was done with PowerMarker and DARwin softwares.The results revealed a total of 68 alleles ranging from 2 to 11 per locus with a mean of 5.23 per marker. Gene diversity and polymorphic information content (PIC) ranged between 0.41 to 0.83 and 0.33 to 0.79, respectively. A neighbour-joining dendrogram grouped the genotypes into three major clusters containing distinct sub-clusters. This study underscored that capillary electrophoresis is a more accurate and informative technique for SSRs allele scoring than agarose gels, which was reported in a previous study with the same SSRs markers and coconut genotypes in Kenya. The clusters observed forms the basis to isolate conservation blocks, which are the key to establishing a genebank, since there is no documented coconut genebank for ex-situ conservation in Kenya.

Genetic diversity of the rice bean (Vigna umbellata) genepool as assessed by SSR markers

Genome ◽  
2013 ◽  
Vol 56 (12) ◽  
pp. 717-727 ◽  
Author(s):  
J. Tian ◽  
T. Isemura ◽  
A. Kaga ◽  
D.A. Vaughan ◽  
N. Tomooka
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Genetic Profile ◽  
Rice Bean ◽  
Ssr Analysis ◽  
Asian Rice ◽  
Cultivated Populations ◽  
Wild Accessions ◽  
Simple Sequence

The genetic diversity of 472 rice bean accessions (388 cultivated and 84 wild) from 16 Asian countries was evaluated by 13 simple sequence repeat (SSR) markers. In total, 168 alleles were detected, and the numbers of alleles in cultivated and wild accessions were 129 and 132, respectively. The gene diversity in cultivated populations (0.565) was about 83% of that for wild (0.678) populations. Cultivated populations from Vietnam, Myanmar, Nepal, and India had the highest gene diversity (>0.5). East Asian accessions formed a distinct genepool. Indonesian cultivated accessions showed high genetic divergence from other cultivated populations and had the most similar genetic structure to wild accessions. In Nepalese cultivated accessions, many accessions from western regions were quite distinct from others and formed a specific group. These Nepalese accessions could be considered a unique gene source for rice bean breeding. In contrast, eastern Nepalese accessions showed an SSR profile similar to that of Southeast Asian rice beans. The present study represents the first comprehensive SSR analysis in cultivated and wild rice bean germplasm and clarifies geographical distribution of genetic profile that might be used to broaden the genetic base of currently grown rice bean cultivars.

Genetic Analysis of Chinese Cucumber Collections in the U.S. National Germplasm Collection

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 534e-534 ◽  
Author(s):  
J. Staub ◽  
Felix Sequen ◽  
Tom Horejsi ◽  
Jin Feng Chen
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Allelic Variation ◽  
Germplasm Collection ◽  
Principal Component ◽  
Isozyme Loci ◽  
National Plant Germplasm System ◽  
The U.S

Genetic variation in cucumber accessions from China was assessed by examining variation at 21 polymorphic isozyme loci. Principal component analysis of allelic variation allowed for the depiction of two distinct groupings of Chinese accessions collected in 1994 and 1996 (67 accessions). Six isozyme loci (Gpi, Gr, Mdh-2, Mpi-2, Pep-gl, and Pep-la) were important in elucidating these major groups. These groupings were different from a single grouping of Chinese 146 accessions acquired before 1994. Allelic variation in Chinese accessions allowed for comparisons with other accessions in the U.S. National Plant Germplasm System (U.S. NPGS) collection grouped by continent and sub-continent. When Chinese accessions taken collectively were compared with an array of 853 C. sativus U.S. NPGS accessions examined previously, relationships differed between accessions grouped by country or subcontinent. Data indicate that acquisition of additional Chinese and Indian cucumber accessions would be strategically important for increasing genetic diversity in the U.S. NPGS cucumber collection.

scholarly journals Genetic diversity of high and low molecular weight glutenin subunits in Saharan bread and durum wheats from Algerian oases

2012 ◽  
Vol 48 (No. 1) ◽  
pp. 23-32 ◽  
Author(s):  
I. Bellil ◽  
M. Chekara Bouziani ◽  
D. Khelifi
Keyword(s):  
Genetic Diversity ◽  
Molecular Weight ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Allelic Variation ◽  
Low Molecular Weight ◽  
Glutenin Subunits ◽  
Lmw Glutenin Subunits ◽  
Genotypic Identification ◽  
Diversity Studies

Saharan wheats have been studied particularly from a botanical viewpoint. Genotypic identification, classification and genetic diversity studies to date were essentially based on the morphology of the spike and grain. For this, the allelic variation at the glutenin loci was studied in a set of Saharan bread and durum wheats from Algerian oases where this crop has been traditionally cultivated. The high molecular weight and low molecular weight glutenin subunit composition of 40 Saharan bread and 30 durum wheats was determined by SDS-PAGE. In Saharan bread wheats 32 alleles at the six glutenin loci were detected, which in combination resulted in 36 different patterns including 17 for HMW and 23 for LMW glutenin subunits. For the Saharan durum wheats, 29 different alleles were identified for the five glutenin loci studied. Altogether, 29 glutenin patterns were detected, including 13 for HMW-GS and 20 for LMW-GS. Three new alleles were found in Saharan wheats, two in durum wheat at the Glu-B1 and Glu-B3 loci, and one in bread wheat at the Glu-B1 locus. The mean indices of genetic variation at the six loci in bread wheat and at the five loci in durum wheat were 0.59 and 0.63, respectively, showing that Saharan wheats were more diverse. This information could be useful to select Saharan varieties with improved quality and also as a source of genes to develop new lines when breeding for quality.

scholarly journals Phenotypic Characterisation for Growth and Nut Characteristics Revealed the Extent of Genetic Diversity in Wild Macadamia Germplasm

Agriculture ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 680
Author(s):  
Thuy T. P. Mai ◽  
Craig M. Hardner ◽  
Mobashwer M. Alam ◽  
Robert J. Henry ◽  
Bruce L. Topp
Keyword(s):  
Genetic Diversity ◽  
Growth Traits ◽  
Principal Component ◽  
Conservation Strategies ◽  
Wild Germplasm ◽  
Phenotypic Characterisation ◽  
Wide Range ◽  
Genetic And Environmental Factors ◽  
Positive Correlations ◽  
Wild Accessions

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.

scholarly journals Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ghazal Ghobadi ◽  
Alireza Etminan ◽  
Ali Mehras Mehrabi ◽  
Lia Shooshtari
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Wild Relatives ◽  
Resolving Power ◽  
Start Codon ◽  
Aegilops Cylindrica ◽  
Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

scholarly journals Gene diversity explains variation in biological features of insect killing fungus, Beauveria bassiana

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Laila Gasmi ◽  
Sehyeon Baek ◽  
Jong Cheol Kim ◽  
Sihyeon Kim ◽  
Mi Rong Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beauveria Bassiana ◽  
Gene Diversity ◽  
Dna Photolyase ◽  
Cyclophilin B ◽  
Biological Features ◽  
Number Variation ◽  
Potential Impact ◽  
Chitinase Genes ◽  
Fungus Beauveria Bassiana

AbstractBeauveria bassiana is a species complex whose isolates show considerable natural genetic variability. However, little is known about how this genetic diversity affects the fungus performance. Herein, we characterized the diversity of genes involved in various mechanisms of the infective cycle of 42 isolates that have different growth rates, thermotolerance and virulence. The analysed genes showed general genetic diversity measured as non-synonymous changes (NSC) and copy number variation (CNV), with most of them being subjected to positive episodic diversifying selection. Correlation analyses between NSC or CNV and the isolate virulence, thermotolerance and growth rate revealed that various genes shaped the biological features of the fungus. Lectin-like, mucin signalling, Biotrophy associated and chitinase genes NSCs correlated with the three biological features of B. bassiana. In addition, other genes (i.e. DNA photolyase and cyclophilin B) that had relatively conserved sequences, had variable CNs across the isolates which were correlated with the variability of either virulence or thermotolerance of B. bassiana isolates. The data obtained is important for a better understanding of population structure, ecological and potential impact when isolates are used as mycoinsecticides and can justify industrialization of new isolates.

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