scholarly journals Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 154 ◽  
Author(s):  
Lucia Lioi ◽  
Diana L. Zuluaga ◽  
Stefano Pavan ◽  
Gabriella Sonnante
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Genotyping By Sequencing ◽  
Fixation Index ◽  
Most Probable Number ◽  
Probable Number ◽  
Individual Snps ◽  
Starting Point ◽  
Genetic Diversity And Structure ◽  
The Common

The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.

scholarly journals GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

AGROFOR ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Veronika KUKUČKOVÁ ◽  
Nina MORAVČÍKOVÁ ◽  
Radovan KASARDA
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
The State ◽  
Most Probable Number ◽  
Pedigree Data ◽  
Probable Number ◽  
Expected Heterozygosity ◽  
High Level ◽  
The Bayesian Approach

The aim of this study was to assess genetic structure of Slovak Pinzgau populationbased on polymorphism at molecular markers using statistical methods. Femaleoffspring of 12 most frequently used bulls in Slovak Pinzgau breeding programmewere investigated. Pinzgau cattle were found to have a high level of diversity,supported by the number of alleles observed across loci (average 5.31, range 2-11)and by the high within-breed expected heterozygosity (average 0.66, range 0.64-0.73). The state of genetic diversity is satisfying and standard for local populations.Detection of 12 possible subpopulation structures provided us with detailedinformation of the genetic structure. The Bayesian approach was applied, detectingthree, as the most probable number of clusters. The similarity of eachsubpopulation using microsatellites was confirmed also by high-throughputmolecular data. The observed inbreeding (FROH=2.3%) was higher than thatexpected based on pedigree data (FPED=0.4%) due to the limited number ofavailable generations in pedigree data. One of the most important steps indevelopment of efficient autochthonous breed protection programs ischaracterization of genetic variability and assessment of the population structure.The chosen set of microsatellites confirmed the suitability in determination of thesubpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at moredetailed level was successfully performed using bovineSNP50 BeadChip.

scholarly journals Discovery of a spatially and temporally persistent core microbiome of the common bean rhizosphere

2020 ◽  
Author(s):  
Nejc Stopnisek ◽  
Ashley Shade
Keyword(s):  
Common Bean ◽  
Spatial Scales ◽  
The United States ◽  
Plant Health ◽  
Soil Conditions ◽  
Full Potential ◽  
Core Microbiome ◽  
Starting Point ◽  
The Common ◽  
Plant Microbiome

AbstractPlants recruit soil microbes that provide nutrients, promote growth and protect against pathogens1–3. However, the full potential of microbial communities for supporting plant health and agriculture is unrealized4–6, in part because rhizosphere members key for plant health are difficult to prioritize7. Microbes that ubiquitously associate with a plant species across large spatial scales and varied soil conditions provide a practical starting point for discovering beneficial members7. Here, we quantified the structures of bacterial/archaeal and fungal communities in the common bean rhizosphere (Phaseolus vulgaris), and assessed its core membership across space and time. To assess a spatial core, two divergent bean genotypes were grown in field conditions across five major growing regions in the United States, and then also compared to eight genotypes grown in Colombian soil. To assess a temporal core, we conducted a time course of rhizosphere and rhizoplane microbiome members over bean development in the field. Surprisingly, there were 48 persistent bacterial taxa that were detected in all samples, inclusive of U.S. and Colombian-grown beans and over plant development, suggesting cosmopolitan enrichment and time-independence. Neutral models of abundance-occupancy relationships and co-occurrence networks show that many of these core taxa are deterministically selected and likely in intimate relationships with the plant. Many of the core taxa were yet-uncultured and affiliated with Proteobacteria; these taxa are prime targets in support of translational plant-microbiome management. More generally, this work reveals that core members of the plant microbiome can have both broad ranges and temporal persistence with their host, suggesting intimate, albeit possibly opportunistic, interactions.

Genetic diversity and structure of landrace accessions, elite lineages and cultivars of common bean estimated with SSR and SNP markers

2020 ◽  
Vol 47 (9) ◽  
pp. 6705-6715
Author(s):  
Marina Santos Carvalho ◽  
Cintia Machado de Oliveira Moulin Carias ◽  
Matheus Alves Silva ◽  
Marcia Flores da Silva Ferreira ◽  
Thiago Lívio Pessoa Oliveira de Souza ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Snp Markers ◽  
Genetic Diversity And Structure ◽  
Ssr And Snp Markers ◽  
Landrace Accessions

scholarly journals Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255418
Author(s):  
Siou Ting Gan ◽  
Chin Jit Teo ◽  
Shobana Manirasa ◽  
Wei Chee Wong ◽  
Choo Kien Wong
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Oil Palm ◽  
Core Collection ◽  
Elaeis Guineensis ◽  
Germplasm Conservation ◽  
Ex Situ ◽  
Fixation Index ◽  
Core Set ◽  
Genetic Diversity And Structure

Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright’s fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei’s genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.

scholarly journals Prevalence of Clostridium botulinum in Finnish Trout Farms: Pulsed-Field Gel Electrophoresis Typing Reveals Extensive Genetic Diversity among Type E Isolates

1998 ◽  
Vol 64 (11) ◽  
pp. 4161-4167 ◽  
Author(s):  
Sebastian Hielm ◽  
Johanna Björkroth ◽  
Eija Hyytiä ◽  
Hannu Korkeala
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
Clostridium Botulinum ◽  
Pulsed Field Gel Electrophoresis ◽  
Most Probable Number ◽  
Probable Number ◽  
Pulsed Field ◽  
Pfge Typing ◽  
Specific Pcr ◽  
Trout Farms

ABSTRACT The distribution of Clostridium botulinum serotypes A, B, E, and F in Finnish trout farms was examined. A total of 333 samples were tested with a neurotoxin-specific PCR assay. C. botulinum type E was found in 68% of the farm sediment samples, in 15% of the fish intestinal samples, and in 5% of the fish skin samples. No other serotypes were found. The spore counts determined by the most-probable-number method were considerably higher for the sediments than for the fish intestines and skin; the average values were 2,020, 166, and 310 C. botulinum type E spores kg−1, respectively. The contamination rates in traditional freshwater ponds and marine net cages were high, but in concrete ponds equipped with sediment suction devices the contamination rates were significantly lower. Pulsed-field gel electrophoresis (PFGE) typing of 42 isolates obtained in this survey and 12 North American reference strains generated 28 pulsotypes upon visual inspection, suggesting that there was extensive genetic diversity and that the discriminatory power of PFGE typing in C. botulinum type E was high. A numerical analysis of SmaI-XmaI macrorestriction profiles confirmed these findings, as it divided the 54 isolates into 15 clusters at a similarity level of 76%. For this material, this level of similarity corresponded to a three-band difference in the macrorestriction profiles, which indicated that there is no genotypic proof of a close epidemiological relationship among the clusters.

Genetic Diversity and Population Structure of Kerala Rice Landraces Using Genotyping-By-Sequencing

2021 ◽  
Author(s):  
Maya Peringottillam ◽  
Smitha Kunhiraman Vasumathy ◽  
Hari Krishna Kumar ◽  
Manickavelu Alagu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Genetic Purity ◽  
Next Generation Sequencing Technology ◽  
Distance Analysis ◽  
Rice Landraces ◽  
Genetic Diversity And Structure ◽  
Rice Landrace

Abstract Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for creating opportunities to guide more realistic and applicable strategies for the sustainable management of genetically diverse rice resources. This study is a pioneering effort where GBS-SNP markers were employed to assess the tremendous genetic diversity and structure of rice landrace collections from northern Kerala. Kerala holds an immense diversity of rice landraces that encountered selection pressures of environmental heterogeneity, biotic and abiotic stresses, however competent rather provide good yields, whereby drawing the attention of the rice breeding sector. The population structure and diversity analyses separated the accessions into three distinct subpopulations with a huge amount of genetic variation within subpopulations. Nei’s genetic distance analysis confirmed the existence of strong genetic differentiation among rice landrace populations. The values of FST and Nm established the farmers’ effort to preserve the genetic purity of rice landraces despite the extensive seed exchange programs across the states of India. Moreover, this low level of gene flow among subpopulations could provide the opportunity for well-adapted combinations of genes to be established by natural selection. The clustering pattern based on SNP markers furnished sufficient knowledge in identifying rice genotypes that eliminates the likelihood of duplication among indigenous cultivars. Similar clustering patterns of genotypes revealed shared genetic characters among them. Collectively these analyses can be used to completely understand the population of rice landraces in Kerala while contributing insights toward the evolution and selective pressures underlying these unique landraces.

scholarly journals Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv.

Forests ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1282
Author(s):  
Yu Wang ◽  
Zhongyi Jiao ◽  
Jiwei Zheng ◽  
Jie Zhou ◽  
Baosong Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Management Strategies ◽  
Natural Populations ◽  
Snp Markers ◽  
Fixation Index ◽  
Landscape Genomics ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure ◽  
Chosenia Arbutifolia

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

scholarly journals Phenotypic and Genetic Diversity in Strains of Common Blight Bacteria (Xanthomonas campestris pv. phaseoli and X. campestris pv. phaseoli var. fuscans) in a Secondary Center of Diversity of the Common Bean Host Suggests Multiple Introduction Events

2006 ◽  
Vol 96 (11) ◽  
pp. 1204-1213 ◽  
Author(s):  
Ruth López ◽  
Carmen Asensio ◽  
Robert L. Gilbertson
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Xanthomonas Campestris ◽  
New World ◽  
Gene Pools ◽  
East African ◽  
Highly Pathogenic ◽  
Castilla Y Leon ◽  
Secondary Center ◽  
The Common

Common bacterial blight (CBB) disease of the common bean (Phaseolus vulgaris) is caused by Xanthomonas campestris pv. phaseoli and the brown-pigmented variant X. campestris pv. phaseoli var. fuscans. CBB first was described in Castilla y León County, Spain, in 1940, and is now a major constraint on common bean production. In this secondary center of diversity of the common bean, large-seeded Andean cultivars predominate, although medium-seeded Middle American cultivars also are grown. Xanthomonad-like bacteria associated with CBB in Castilla y León were characterized on the basis of carbohydrate metabolism, brown pigment production, genetic analyses (repetitive-element polymerase chain reaction [rep-PCR] and random amplified polymorphic DNA [RAPD]) and pathogenicity on cultivars representing the two common bean gene pools (Andean and Middle American). X. campestris pv. phaseoli was more prevalent (80%) than X. campestris pv. phaseoli var. fuscans (20%). Patterns of carbohydrate metabolism of Spanish CBB bacteria were similar to those of known strains; and only X. campestris pv. phaseoli var. fuscans strains utilized mannitol as a sole carbon source. rep-PCR and RAPD analyses revealed relatively little genetic diversity among Spanish X. campestris pv. phaseoli strains, and these strains were placed together with New World strains into a large cluster. Similar to other New World strains, representative Spanish X. campestris pv. phaseoli strains were highly pathogenic on bean cultivars of both gene pools, showing no gene pool specialization such as that found in certain East African strains. Genetic analyses and pathogenicity tests confirmed and extended previous results, indicating that these East African strains represent distinct xanthomonads that independently evolved to be pathogenic on common bean. X. campestris pv. phaseoli var. fuscans strains were more closely related and genetically distinct from X. campestris pv. phaseoli strains. However, two distinct clusters of X. campestris pv. phaseoli var. fuscans strains were identified, one having the most New World strains and the other having the most African strains. Spanish strains were placed in both clusters, but all strains tested were highly pathogenic on bean cultivars of both gene pools. Together, our results are consistent with multiple introductions of CBB bacteria into Spain. These findings are discussed in terms of breeding for CBB resistance and the overall understanding of the genetic diversity and evolution of CBB bacteria.

scholarly journals Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 518 ◽  
Author(s):  
Ana Campa ◽  
Ester Murube ◽  
Juan José Ferreira
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Association Studies ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Gene Pools ◽  
Genome Wide Association Studies ◽  
Snap Bean ◽  
Diversity Panel ◽  
Main Gene

A common bean (Phaseolus vulgaris) diversity panel of 308 lines was established from local Spanish germplasm, as well as old and elite cultivars mainly used for snap consumption. Most of the landraces included derived from the Spanish common bean core collection, so this panel can be considered to be representative of the Spanish diversity for this species. The panel was characterized by 3099 single-nucleotide polymorphism markers obtained through genotyping-by-sequencing, which revealed a wide genetic diversity and a low level of redundant material within the panel. Structure, cluster, and principal component analyses revealed the presence of two main subpopulations corresponding to the two main gene pools identified in common bean, the Andean and Mesoamerican pools, although most lines (70%) were associated with the Andean gene pool. Lines showing recombination between the two gene pools were also observed, most of them showing useful for snap bean consumption, which suggests that both gene pools were probably used in the breeding of snap bean cultivars. The usefulness of this panel for genome-wide association studies was tested by conducting association mapping for determinacy. Significant marker–trait associations were found on chromosome Pv01, involving the gene Phvul.001G189200, which was identified as a candidate gene for determinacy in the common bean.

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