↵​Genetic Diversity and Population Structure of Two Faba Bean Mutant Populations Based on AFLP Markers

2021 ◽  
Author(s):  
Nurmansyah . ◽  
Hussein M. Migdadi ◽  
Salem S. Alghamdi ◽  
Muhammad. A. Khan ◽  
M. Afzal
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gamma Radiation ◽  
Faba Bean ◽  
Fragment Length Polymorphism ◽  
Similar Response ◽  
Two Samples ◽  
Induced Mutagenesis ◽  
The Difference ◽  
Nei's Genetic Distance

Background: Although induced mutagenesis can rapidly generate genetic diversity, every genotype responds differently to different mutagen treatments in induceing genetic diversity. This study assesses and compares the genetic diversity of two mutant faba bean populations. Methods: Two genotypes representing landrace (Hassawi 2) and inbred variety (ILB4347) were exposed to gamma radiation and diethyl sulfate (DES). Two hundred eighty-two samples derived from individual 140 M2 mutant plants of Hassawi 2 and ILB 4347 and two parental lines were characterized using 11 Amplified Fragment Length Polymorphism (AFLP) primer combinations. Result: 89,820 bands within 2,083 polymorphic alleles were generated from the samples. Genetic diversity comparison of the mutant populations revealed that each genotype had varying responses to different treatments. The two genotypes had a relatively similar response to gamma radiation, while different responses were recorded in DES-derived mutant plants. Based on the Nei’s genetic distance, the populations were separated based on the genotypic origin. The population structure analyses showed that the Hassawi 2 and ILB4347 mutant populations were clustered into three and two groups, respectively. The difference in the number of clusters between the two mutant populations explains their breeding history. The present diversity considered as a valuable material used for breeding and conservation purposes.

scholarly journals AFLP-Based Analysis of Variation and Population Structure in Mutagenesis Induced Faba Bean

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 303
Author(s):  
Nurmansyah ◽  
Salem S. Alghamdi ◽  
Hussein M. Migdadi ◽  
Muhammad A. Khan ◽  
Muhammad Afzal
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Faba Bean ◽  
High Genetic Diversity ◽  
Banding Patterns ◽  
Wide Range ◽  
Induced Mutagenesis ◽  
Control Parent ◽  
Analysis Of Variation ◽  
Allele Count

Genetic diversity enrichment is urgently necessary to develop climate-resilient faba bean cultivars. The present study aimed to measure the enrichment of genetic diversity and changes in the population structure of faba bean, following induced mutagenesis. 120 samples, including 116 M2 mutant plants, generated by exposing the ILB4347 accession to four mutagen treatments (25 and 50 Gray gamma radiation and 0.01%, and 0.05% diethyl sulfate) and four reference genotypes were characterized using 11 amplified fragment length polymorphism (AFLP) primer combinations. The AFLP markers generated 1687 polymorphic alleles, including 756 alleles (45%) that were detected infrequently (f ≤ 0.1). The total allele count of the mutant plants ranged from 117 to 545. We observed a wide range of banding patterns and counts among the mutant plants, showing the high genetic diversity induced by mutation. Mutations also changed the population structure, by altering 31.78% of the total membership coefficient (Q). Although mutations changed the population structure, Nei’s genetic distance showed that the mutant population remained closely related to its control parent. This is the first report examining genetic diversity and population changes in faba bean mutant populations and, thus, could facilitate the application of induced mutagenesis during faba bean breeding.

scholarly journals First insights into the genetic diversity of Mycobacterium tuberculosis strains in Salvador, Bahia State, Brazil

2011 ◽  
Vol 27 (9) ◽  
pp. 1859-1863
Author(s):  
Aída Cristina do Nascimento Silva ◽  
Lucilaine Ferrazoli ◽  
Vera Simonsen ◽  
Joice Neves Reis ◽  
Susan Martins Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mycobacterium Tuberculosis ◽  
Population Structure ◽  
Restriction Fragment Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Genetic Population ◽  
Recent Transmission ◽  
Single Pattern ◽  
Study Population ◽  
Restriction Fragment Length

This study constitutes a first attempt to describe the genetic population structure of Mycobacterium tuberculosis circulating in Salvador, Bahia State, Brazil. A total of 56 confirmed cases of pulmonary tuberculosis, identified between March and June 2008, were analyzed using restriction fragment length polymorphism (IS6110-RFLP). The study population was characterized by a predominance of males (71.43%) over 30 years of age (68.75%). Forty-one isolates were found to belong to a single pattern (73.2%), while 15 (26.7%) were found in group patterns, forming six clusters. The higher level of diversity observed is much more suggestive of endogenous reactivation than recent transmission.

Assessing genetic variability among Brazilian strains ofXanthomonas axonopodispv.manihotisthrough restriction fragment length polymorphism and amplified fragment length polymorphism analyses

1999 ◽  
Vol 45 (9) ◽  
pp. 754-763 ◽  
Author(s):  
S Restrepo ◽  
T L Valle ◽  
M C Duque ◽  
V Verdier
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Bacterial Blight ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Restriction Fragment Length

Xanthomonas axonopodis pv.manihotis (Xam) causes bacterial blight, a major disease of cassava, which is a starchy root crop that feeds about 500 million people throughout the world. To better select resistant cassava germplasm, we examined the population structure of Xam in Brazil, Latin America's largest producer of cassava, and a major center of diversity for the crop. The 79 strains collected between 1941 and 1996 from three edaphoclimatic zones were analyzed by restriction fragment length polymorphism (RFLP), using a probe linked to a Xam pathogenicity gene (pthB). Thirty-eight haplotypes were identified, and geographical differentiation for the Xam strains was demonstrated. Strains from subtropical zone (ECZ 6) showed high genetic diversity in most of the sites from which they were collected. They also showed migration from site to site. RFLP and amplified fragment length polymorphism (AFLP) analyses were carried out on 37 Xam strains and compared; the AFLP assays were performed using eight primer combinations. A multiple correspondence analysis, used to assess genetic relatedness among strains and estimate genetic diversity, indicated that the Brazilian Xam population showed high diversity. No correlation was found between AFLP and RFLP data, but the two techniques provided complementary information on the genetic diversity of Xam. Most strains were highly aggressive on a susceptible cultivar. The genetic analysis presented here contributes to a better understanding of the Xam population structure in Brazil and will help select strains of the pathogen for screening cassava germplasm resistant to the disease.Key words: cassava bacterial blight, resistance, genetic diversity, molecular characterization.

Genetic diversity and population structure in a collection of roselle (Hibiscus sabdariffaL.) from Niger

2013 ◽  
Vol 12 (2) ◽  
pp. 207-214 ◽  
Author(s):  
Y. Bakasso ◽  
M. Zaman-Allah ◽  
C. Mariac ◽  
C. Billot ◽  
Y. Vigouroux ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Fragment Length Polymorphism ◽  
Genetic Groups ◽  
Diversity Assessment ◽  
Farmer Management ◽  
Morphological Differences ◽  
Close Relatives ◽  
The Impact ◽  
100 Seed Weight

Roselle (Hibiscus sabdariffaL.) is an economically important plant in Niger. Little is known about its genetic diversity and population structure. In this study, we performed the first diversity assessment of a collection of 124 roselle accessions and 16 accessions of its close relativesHibiscuscannabinusandAbelmoschusesculentus. Our study was based on ten agromorphological traits and 267 amplified fragment length polymorphism markers. We identified two major distinct groups inH. sabdariffausing a Bayesian method. These two genetic groups were associated with statistical differences for three phenological characteristics: number of days to flowering, 100-seed weight and calyx size. However, the calyx colour, i.e. a morphological characteristic often used to classify different local ecotypes, did not superimpose this separation. Our findings suggested that roselle diversity is genetically structured; the two different groups were clearly associated with morphological differences but were not commonly used by farmers for their classification. The impact of the perceived ecotype structure and its consequence on farmer management is discussed.

Evaluation of the genetic diversity and population structure of five indigenous and one introduced Chinese goose breeds using microsatellite markers

2012 ◽  
Vol 92 (4) ◽  
pp. 417-423 ◽  
Author(s):  
Jinjun Li ◽  
Qingyuan Yuan ◽  
Junda Shen ◽  
Zhengrong Tao ◽  
Guoqing Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Evolutionary Relationships ◽  
Distance Estimate ◽  
Cluster Analyses ◽  
Nei's Genetic Distance

Li, J., Yuan, Q., Shen, J., Tao, Z., Li, G., Tian, Y., Wang, D., Chen, L. and Lu, L. 2012. Evaluation of the genetic diversity and population structure of five indigenous and one introduced Chinese goose breeds using microsatellite markers. Can. J. Anim. Sci. 92: 417–423. The aim of this study was to determine the genetic diversity and evolutionary relationships among five indigenous Chinese goose breeds and one introduced goose breed using 29 microsatellite markers. A total of 334 distinct alleles were observed across the six breeds, and 45 of the 334 alleles (13.5%) were unique to only one breed. The indigenous geese showed higher diversity in terms of the observed number of alleles per locus (4.48–5.90) and observed heterozygosity (0.46–0.53) compared with the introduced breed (3.97 and 0.29, respectively). The pairwise genetic differentiation (FST) between the six goose breeds ranged from 0.04 between Panshi Grey goose (PS) and Yongkang Grey goose to 0.47 between PS and Landes goose; similarly, Nei's genetic distance varied between 0.25 and 0.75. However, the FST between the indigenous Chinese goose breeds was very small. In addition, genetic distance estimate, phylogenic, and cluster analyses of the genetic relationships and population structure revealed that some indigenous goose breeds had hybridized more frequently, resulting in a loss of genetic distinctiveness.

scholarly journals Rapid development of 56 novel microsatellite markers for the benthic freshwater bug Aphelocheirus aestivalis using Illumina paired-end sequencing data and M13-tailed primers

2020 ◽  
Vol 47 (12) ◽  
pp. 9995-10003
Author(s):  
Agnieszka Kaczmarczyk-Ziemba
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rapid Development ◽  
Whole Genome ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Two Samples

AbstractThe freshwater true bug Aphelocheirus aestivalis (Aphelocheiridae) is widely distributed in Europe but occurs rather locally and often in isolated populations. Moreover, it is threatened with extinction in parts of its range. Unfortunately, little is known about the genetic diversity and population structure due to the lack of molecular tools for this species. Thus, to overcome the limitations, a whole-genome sequencing has been performed to identify polymorphic microsatellite markers for A. aestivalis. The whole-genome sequencing has been performed with the Illumina MiSeq platform. Obtained paired-end reads were processed and overlapped into 2,378,426 sequences, and the subset of 267 sequences containing microsatellite motifs were then used for in silico primer designing. Finally, 56 microsatellite markers were determined and 34 of them were polymorphic. Analyses performed in two samples (collected from Drawa and Gowienica rivers, respectively) showed that the number of alleles per locus ranged from 2 to 21, and the observed and expected heterozygosity varied from 0 to 0.933 and 0.064 to 0.931, respectively. The microsatellite markers developed in the present study provide new suitable tools available for the scientific community to study A. aestivalis population dynamics. The assessment of its genetic diversity and population structure will provide important data, that can be used in population management and conservation efforts, elucidating the broad- and fine-scale population genetic structure of A. aestivalis.

scholarly journals Analysis of Genetic Diversity and Population Structure of Orobanche foetida Populations From Tunisia Using RADseq

2021 ◽  
Vol 12 ◽  
Author(s):  
Amal Boukteb ◽  
Shota Sakaguchi ◽  
Yasunori Ichihashi ◽  
Mohamed Kharrat ◽  
Atsushi J. Nagano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Faba Bean ◽  
Isolation By Distance ◽  
Distance Effect ◽  
Wild Plant ◽  
Clustering Methods ◽  
North West ◽  
North East ◽  
The North

Orobanche foetida Poiret is a holoparasitic plant that lacks chlorophyll and totally depending on its host for its growth. Orobanche foetida parasitizes host plant roots and extract nutrient and water via a haustorium. Although O. foetida distributes in the Mediterranean region as a wild plant parasite, it parasitizes faba bean causing serious damages which may reach 90% yield losses in Tunisia. Analysis of genetic diversity of the parasite is important to better understand its evolution and spread, remained largely unknown. In this work, we present the first study on genetic diversity and population structure using the robust technique Restriction-site-Associated DNA sequencing (RADseq) for Orobanche spp. We collected 244 samples of O. foetida from 18 faba bean fields in the north of Tunisia including 17 populations from the north-west and one population form the north-east. To overcome the difficulty of SNP discovery in O. foetida genome as a non-model and tetraploid plant, we utilized three different informatics pipelines, namely UNEAK, pyRAD and Stacks. This study showed that genetic differentiation occurred in the Tunisian O. foetida emphasizing the isolation by distance effect. However, no strong population clustering was detected in this work basing on the three data sets and clustering methods used. The present study shed the light on the current distribution and the genetic variation situation of the fetid broomrape in Tunisia, highlighting the importance of understanding the evolution of this parasite and its genetic background. This will aid in developing efficient strategies to control this parasite and its expansion in Tunisia and worldwide.

scholarly journals Genetic Diversity and Population Structure of Faba Bean (Vicia faba) from Turkey

HortScience ◽  
2016 ◽  
Vol 51 (8) ◽  
pp. 980-983
Author(s):  
Şurhan Göl ◽  
Sami Doğanlar ◽  
Anne Frary
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Vicia Faba ◽  
Ssr Markers ◽  
Faba Bean ◽  
High Efficiency ◽  
Starch Content ◽  
Molecular Genetic ◽  
Distance Matrix ◽  
High Genetic Diversity

Faba bean (Vicia faba L.) is an important food and feed legume because of the nutritional value of its seed protein and starch content, good biomass, and high efficiency nitrogen fixation. This study analyzed the molecular genetic diversity and population structure of 101 Turkish faba bean accessions using simple sequence repeat (SSR) markers. A total of 32 SSR markers yielded 281 loci of which 277 (98.6%) were polymorphic. Mean dissimilarity between genotypes was 0.355, a relatively high value which was expected given faba bean’s large genome and limited breeding history. According to the results, faba bean individuals grouped into three main clusters based on both distance matrix (neighbor-joining algorithm) and model-based (population structure) clustering analyses. Clustering was not correlated with seed size or origin within Turkey. Six cultivars were included in the analysis and showed high genetic diversity compared with the landraces, as expected, given the fact that at least some of the cultivars were bred by hybridization. A total of 47 individuals were selected for the core collection to represent the diversity of Turkish faba bean germplasm. This core set encompasses material adapted to all growing regions and should be a priority for morphological characterization.

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