Genetic diversity in common bean accessions evaluated by means of morpho-agronomical and RAPD data

Germplasm banks store genotype samples, improved varieties, landraces and wild species, all generically denominated accessions. The importance of characterizing germplasm banks is based on the identification and knowledge of relevant traits for genetic improvement and ex situ germplasm conservation. Thus, the present study had as aim the evaluation of the genetic diversity among 220 accessions of a Brazilian common bean germplasm bank of the "Instituto Agronômico de Campinas" (IAC) by means of 23 morpho-agronomical descriptors and 19 RAPD loci. These accessions correspond to genotypes from the Andean and Middle American gene pool as well as from cultivars derived from common bean improvement programs. The Middle American accessions and the improved cultivars were clustered into one group, distinct from the one formed by the Andean accessions. In relation to the molecular data, 47% of the genetic similarity was detected among the Middle American accessions, and similar results were observed for the improved cultivars (50%). The Andean accessions revealed 60% of genetic similarity. The cluster constituted by the improved cultivars and the Middle American genotypes differed, basically, in tegument color. Both molecular and morpho-agronomical data sets were equally effective to quantify and organize the genetic diversity of common bean accessions. This information may be useful to direct crosses and for the proper organization of the IAC germplasm bank.

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All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Diversity ◽

10.3390/d13040139 ◽

2021 ◽

Vol 13 (4) ◽

pp. 139

Author(s):

Marlien M. van der Merwe ◽

Jia-Yee S. Yap ◽

Peter D. Wilson ◽

Helen T. Murphy ◽

Andrew Ford

Keyword(s):

Genetic Diversity ◽

Allelic Variation ◽

Germplasm Conservation ◽

Snp Markers ◽

Genomic Diversity ◽

Ex Situ ◽

Spatial Distance ◽

Genetic Connectivity ◽

Conservation Genomics ◽

Modelling Framework

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

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Genetic diversity of common bean accessions in the germplasm bank of the Instituto Agronômico - IAC

Cropp Breeding and Applied Biotechnology ◽

10.12702/1984-7033.v05n01a01 ◽

2005 ◽

Vol 5 (1) ◽

pp. 1-9 ◽

Cited By ~ 7

Author(s):

A.F. Chiorato ◽

S.A.M. Carbonell ◽

C.A. Colombo ◽

L.A.S. Dias ◽

M.F. Ito

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Germplasm Bank

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

PLoS ONE ◽

10.1371/journal.pone.0255418 ◽

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.

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Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics

10.7287/peerj.preprints.2048 ◽

2016 ◽

Author(s):

Juan José Martínez ◽

Pablo Melgarejo ◽

Pilar Legua ◽

Francisco García ◽

Francisca Hernández

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Plant Material ◽

Phenotypic Variability ◽

Geographical Area ◽

Geographic Origin ◽

Germplasm Management ◽

Morphometric Characteristics ◽

Germplasm Bank ◽

Improvement Programs

Background . Miguel Hernandez University ( Spain ) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the juice’s acidity and pH had the highest power of discrimination, and were, therefore, the most useful for genetic characterization of this pomegranate germplasm banks. This is opposed to leaf and flower characteristics, which had a low power of discrimination. This germplasm bank, more specifically, was characterized by its considerable phenotypic (and presumably genetic) diversity among pomegranate accessions, with a greater proximity existing among the varieties from the same geographical area, suggesting that over time, there had not been an exchange of plant material among the different cultivation areas. In summary, knowledge on the extent of the genetic diversity of the collection is essential for germplasm management. In this study, these data may help in developing strategies for pomegranate germplasm management and may allow for more efficient use of this germplasm in future breeding programs for this species.

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Comparison of Genetic Diversity between Nuña and and Other Andean bean (Phaseolus vulgaris) Populations

HortScience ◽

10.21273/hortsci.32.3.544c ◽

1997 ◽

Vol 32 (3) ◽

pp. 544C-544

Author(s):

James Nienhuis ◽

Paul Skroch ◽

Steve Beebe

Keyword(s):

Genetic Diversity ◽

Energy Efficiency ◽

Phaseolus Vulgaris ◽

Common Bean ◽

Core Collection ◽

Rapd Markers ◽

Practical Consideration ◽

Common Beans ◽

Germplasm Bank ◽

Wide Range

Nuñas are a type of common bean (Phaseolus vulgaris) that possess the unusual characteristic of popping or expanding their cotyledonary tissue when heated. Numerous landraces of nuña beans were domesticated in the Andean region of South America (Peru, Bolivia, and Ecuador) and have been grown and consumed in this region since antiquity. The practical consideration in the domestication of nuñas in the high Andes was likely due to the greater energy efficiency in cooking toasted vs. boiled seeds.The Phaseolus germplasm bank at CIAT (Centro Internacional de Agricultura Tropical) has developed a core collection of Andean beans that includes numerous nuña landraces. Based on the wide range of phaseolin types observed among nuña landraces, it has been hypothesized that nuñas may represent a greater source of genetic diversity compared to other landraces and cultivars of common bean. Eighty nuña accessions and 120 nonpopping common bean accessions were randomly sampled from the CIAT Andean germplasm core collection. The 200 accessions were characterized for 140 mapped RAPD markers. The objectives of our research were to 1) understand the genetic structure of nuña bean accessions relative to other Andean common beans, and 2) to measure the genetic distance and genetic diversity between nuña and other Andean bean populations.

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552 Comparison of Genetic Diversity in between Two Germplasm Banks Containing Lycopersicon esculentum Accessions

HortScience ◽

10.21273/hortsci.35.3.491a ◽

2000 ◽

Vol 35 (3) ◽

pp. 491A-491

Author(s):

James Nienhuis ◽

Julie Rodriguez ◽

Wilber Phillips ◽

Peter Hanson ◽

Liliway Engle

Keyword(s):

Genetic Diversity ◽

Costa Rica ◽

Lycopersicon Esculentum ◽

Molecular Marker ◽

Research And Development ◽

Genetic Resources ◽

Core Collection ◽

Germplasm Bank ◽

Development Center ◽

Germplasm Banks

Worldwide, there are cuurently more than 60 germplasm banks that contain tomato (Lycopersicon esculentum) collections ranging is size from a few dozen to several thousands of accessions. In the utilization of these genetic resources sampling from only one germplasm bank may result in limiting available genetic diversity, whereas sampling from several germplasm banks may result in unnecessary redundancy. The current lack of knowledge regarding the relative magnitudes of genetic diversity contained within different collections makes it difficult to develop a core collection that maximizes genetic diversity. Two large tomato collections are housed at the Asian Vegetable Research and Development Center (AVRDC), Sanhua, Taiwan, R.O.C., and the Centro Agronomico Tropical de Investigacion y Enseoanza (CATIE), Turrialba, Costa Rica. Ninety-six accessions from CATIE and 102 accessions from AVRDC were randomly sampled from each base collection. The total of 198 accessions were charcterized for 103 polymorphic RAPD molecular marker bands. The results indicated that the two germplam banks sampled different genetic diversity. In addition, the magnitude of genetic diversity was greater in the AVRDC collection compared to CATIE.

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Improving the Conservation and Use of Traditional Germplasm through Breeding for Local Adaptation: The Case of the Castellfollit del Boix Common Bean (Phaseolus vulgaris L.) Landrace

Agronomy ◽

10.3390/agronomy9120889 ◽

2019 ◽

Vol 9 (12) ◽

pp. 889

Author(s):

Joan Casals ◽

Ana Rivera ◽

Aurora Rull ◽

Roser Romero del Castillo ◽

Josep Sabaté ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Negative Impact ◽

Genetic Erosion ◽

Ex Situ ◽

Phaseolus Vulgaris L ◽

Potential Index ◽

Local Environments ◽

Improvement Programs ◽

The Impact

The dramatic reduction in the diversity of crops in the last century is often attributed to the consolidation of scientific breeding, probably because the two processes have occurred at the same time. We carried out a breeding program to enhance the Castellfollit del Boix landrace of common bean (Phaseolus vulgaris L.) in a low-input environment to determine the effects of breeding on a landrace at risk of disappearing. The program increased the number of accessions conserved ex situ and obtained more efficient genotypes that are less likely to be abandoned by farmer without altering the characteristics that consumers appreciate most. As a result, the availability of the product, its promotion, and its use have increased. We propose a Conservation Potential Index to measure the impact of changes in the crop’s epiphenotype, and also apply it to a set of landraces from several crops. We argue that scientific breeding and information gathered in the context of genetic improvement programs can help to conserve biodiversity when they aim to adapt materials to different local environments, rather than having a negative impact on the biodiversity of crops. This approach contrasts with the genetic erosion that results from efforts to homogenize environments by increasing inputs, so that a few improved varieties adapted to these environments can be grown.

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The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections

BMC Plant Biology ◽

10.1186/s12870-019-2142-y ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Jorge Franco-Duran ◽

José Crossa ◽

Jiafa Chen ◽

Sarah Jane Hearne

Keyword(s):

Genetic Diversity ◽

Crop Improvement ◽

Sample Selection ◽

Cost Effective ◽

Fixed Number ◽

Sample Sizes ◽

Germplasm Bank ◽

Selection Strategies ◽

The Impact ◽

Germplasm Banks

Abstract Background Germplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of samples representing as broadly as possible the diversity present in the wider collection. A relevant question is whether it is necessary to develop completely independent germplasm samples or it is possible to select nested sets from a pre-defined core set panel not from the whole collection. We used data from 15,384, maize landraces stored in the CIMMYT germplasm bank to study the impact on 8 diversity criteria and the sample representativeness of: (1) two core selection strategies, a statistical sampling (DM), or a numerical maximization method (CH); (2) selecting samples of varying sizes; and (3) selecting samples of different sizes independently of each other or in a nested manner. Results Sample sizes greater than 10% of the whole population size retained more than 75% of the polymorphic markers for all selection strategies and types of sample; lower sample sizes showed more variability (instability) among repetitions; the strongest effect of sample size was observed on the CH-independent combination. Independent and nested samples showed similar performance for all the criteria for the DM method, but there were differences between them for the CH method. The DM method achieved better approximations to the known values in the population than the CH method; 2-d multidimensional scaling plots of the collection and samples highlighted tendency of sample selection towards the extremes of diversity in the CH method, compared with sampling more representative of the overall genotypic distribution of diversity under the DM method. Conclusions The use of core subsets of size greater than or equal to 10% of the whole collection satisfied well the requirement of representativeness and diversity. Nested samples showed similar diversity and representativeness characteristics as independent samples offering a cost effective method of sample definition for germplasm banks. For most criteria assessed the DM method achieved better approximations to the known values in the whole population than the CH method, that is, it generated more statistically representative samples from collections.

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Examination of Genetic Diversity of Common Bean from the Western Balkans

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.140.4.308 ◽

2015 ◽

Vol 140 (4) ◽

pp. 308-316 ◽

Cited By ~ 14

Author(s):

Marko Maras ◽

Barbara Pipan ◽

Jelka Šuštar-Vozlič ◽

Vida Todorović ◽

Gordana Đurić ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Common Bean ◽

Gene Pool ◽

Molecular Data ◽

Gene Pools ◽

Western Balkans ◽

Mesoamerican Gene Pool ◽

Information Index ◽

Large Clusters

In this study, genetic diversity of 119 accessions of common bean (Phaseolus vulgaris) from five former Yugoslav republics constituting the western Balkans was assessed by 13 microsatellite markers. This set of markers has proven before to efficiently distinguish between bean genotypes and assign them to either the Andean or the Mesoamerican gene pool of origin. In this study, 118 alleles were detected or 9.1 per locus on average. Four groups (i.e., Slovene, Croatian, Bosnian, and Serbian) showed similarly high levels of genetic diversity as estimated by the number of different alleles, number of effective alleles, Shannon’s information index, and expected heterozygosity. Mildly narrower genetic diversity was identified within a group of Macedonian accessions; however, this germplasm yielded the highest number of private alleles. All five germplasms share a great portion of genetic diversity as indicated by the analysis of molecular variance (AMOVA). On the basis of the scored number of migrants, we concluded that the most intensive gene flow in the region exists in Bosnia and Herzegovina. Cluster analysis based on collected molecular data classified the accessions into two large clusters that corresponded to two gene pools of origin (i.e., Andean and Mesoamerican). We found that Andean genotypes are more prevalent than Mesoamerican in all studied countries, except Macedonia, where the two gene pools are represented evenly. This could indicate that common bean was introduced into the western Balkans mainly from the Mediterranean Basin. Bayesian cluster analysis revealed that in the area studied an additional variation exists which is related to the Andean gene pool. Different scenarios of the origin of this variation are discussed in the article.

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Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm

PLoS ONE ◽

10.1371/journal.pone.0260651 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0260651

Author(s):

Sintayehu Admas ◽

Kassahun Tesfaye ◽

Teklehaimanot Haileselassie ◽

Eleni Shiferaw ◽

K. Colton Flynn

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Germplasm Conservation ◽

Genetic Distances ◽

Geographic Region ◽

Ex Situ ◽

Conservation Strategies ◽

Breeding Programs

Evaluation of the genetic diversity and an understanding of the genetic structure and relationships of chickpea genotypes are valuable to design efficient germplasm conservation strategies and crop breeding programs. Information is limited, in these regards, for Ethiopian chickpea germplasms. Therefore, the present study was carried out to estimate the genetic diversity, population structure, and relationships of 152 chickpea genotypes using simple sequence repeats (SSR) markers. Twenty three SSR markers exhibited polymorphism producing a total of 133 alleles, with a mean of 5.8 alleles per locus. Analyses utilizing various genetic-based statistics included pairwise population Nei’s genetic distance, heterozygosity, Shannon’s information index, polymorphic information content, and percent polymorphism. These analyses exemplified the existence of high genetic variation within and among chickpea genotypes. The 152 genotypes were divided into two major clusters based on Nei’s genetic distances. The exotic genotypes were grouped in one cluster exclusively showing that these genotypes are distinct to Ethiopian genotypes, while the patterns of clustering of Ethiopian chickpea genotypes based on their geographic region were not consistent because of the seed exchange across regions. Model-based population structure clustering identified two discrete populations. These finding provides useful insight for chickpea collections and ex-situ conservation and national breeding programs for widening the genetic base of chickpea.

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