Population structure and association analyses of the core collection of hexaploid accessions conserved <i>ex situ</i> in the Japanese gene bank NBRP-Wheat

Gene bank accessions are necessary for implementing many research and breeding projects. However, a great number of accessions are contaminated or confused. If such accessions are used, the results obtained from these projects are inaccurate and non-reproducible. There are methods that allow almost perfect genotype identification; nevertheless, they are relatively recent and results cannot be compared with the characteristics of the original accessions. Growing resistant cultivars is an environmentally safe and cheap way of disease management and knowledge of diverse resistance genes and their combinations can be used to identify varieties and verify their authenticity and homogeneity. For this purpose, all 172 accessions of the core collection (CC) of the Czech winter barley (Hordeum vulgare) gene bank, originating from 35 countries, were studied. For resistance tests, 51 reference isolates of Blumeria graminis f. sp. Hordei, collected in all nonpolar continents over a period of 63 years and representing the global virulence/avirulence diversity of the pathogen, were used. Only 25 barley accessions were homogeneous (genetically uniform), whereas 147 accessions were heterogeneous due to presence of different genotypes. In total, 17 resistance genes were found singly or in combinations; 76.3% of accessions with identified resistance genes carried alleles at the Mla locus. To purify the CC, progenies of individual plants must be multiplied and authenticity and homogeneity of the seed should be confirmed with resistance tests, and subsequently can be studied with more advanced methods.

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Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section

10.1101/2020.08.12.247718 ◽

2020 ◽

Author(s):

Liu Shuo ◽

Decroocq Stephane ◽

Harte Elodie ◽

Tricon David ◽

Chague Aurelie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Genetic Relationships ◽

Allelic Diversity ◽

Wild Relatives ◽

Ex Situ ◽

Conservation Measures ◽

Geographical Regions

AbstractIn-depth characterization of the genetic diversity and population structure of wild relatives of crops is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we therefore sampled the Alpine plum (Briançon apricot) Prunus brigantina Vill. across its natural distribution in the French Alps, where its populations are severely fragmented and its population size strongly impacted by humans. We analysed 71 wild P. brigantina samples with 34 nuclear markers and studied their genetic diversity and population structure, with the aim to inform in situ conservation measures and build a core collection for long-term ex-situ conservation. We also examined the genetic relationships of P. brigantina with other species in the Prunophora subgenus, encompassing the Prunus (Eurasian plums), Prunocerasus (North-American plums) and Armeniaca (apricots) sections, to check its current taxonomy. We detected a moderate genetic diversity in P. brigantina and a Bayesian model-based clustering approach revealed the existence of three genetically differentiated clusters, endemic to three geographical regions in the Alps, which will be important for in situ conservation measures. Based on genetic diversity and population structure analyses, a subset of 36 accessions were selected for ex-situ conservation in a core collection that encompasses the whole detected P. brigantina allelic diversity. Using a dataset of cultivated apricots and wild cherry plums (P. cerasifera) genotyped with the same markers, we detected gene flow neither with European P. armeniaca cultivars nor with diploid plums. In contrast with previous studies, dendrograms and networks placed P. brigantina closer to Armeniaca species than to Prunus species. Our results thus confirm the classification of P. brigantina within the Armeniaca section; it also illustrates the importance of the sampling size and design in phylogenetic studies.

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Development of a core collection for Sri Lankan cinnamon germplasm based on morphological characterization using an eco-geographic survey

Australian Journal of Crop Science ◽

10.21475/ajcs.19.13.09.p1561 ◽

2019 ◽

pp. 1473-1485

Author(s):

Rumana Azad ◽

L. Jayasekara ◽

R.A.A.K. Ranawaka ◽

Gamini Senanayake ◽

K.L. Wasantha Kumara ◽

...

Keyword(s):

Vegetative Propagation ◽

Core Collection ◽

Principal Component ◽

Hierarchical Cluster ◽

Morphological Characterization ◽

Leaf Length ◽

Ex Situ ◽

Germplasm Management ◽

Sri Lankan ◽

The Core

Cinnamomum verum is the most important spice produced by Sri Lanka. This study was carried out to fill the gap of knowledge on diversity of Sri Lankan cinnamon through morphological characterization. Therefore, an eco-geographic survey in major growing areas followed by the development of a core collection and vegetative propagation of the total collection for ex-situ conservation were carried out. Two hundred and sixty nine cinnamon accessions were collected. The average shoot regeneration frequency of 269 accessions was 47.76% after one month of vegetative propagation. The collection was established at Faculty of Agriculture, University of Ruhuna for further studies. The collection was characterized for 15 quantitative and qualitative characters of leaf, stem and inflorescence among which, a wide variation was detected for leaf characters mainly. Leaf length positively correlated with Leaf width (+0.643) and Petiole length (+0.483). Principal component analysis (PCA) revealed that there were 3 dimensions of PCA explaining 88.85% of total variance. In Hierarchical cluster analysis based on above characters, 269 accessions were grouped into five clusters at rescaled distance of 0.1. A representation of 10% accessions was randomly selected from each cluster to develop a core collection with 33 accessions. The core collection of 33 accessions was clustered into five groups according to the same method at rescaled distance of 0.075. The core collection is a representation of the total collection as clusters of the two dendograms could be overlapped. Morphological characterization and core collection development during this study will be useful for germplasm management, conservation and varietal improvement through breeding programmes.

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Development of the core collection through advanced maximization strategy with heuristic approach in cashew (Anacardium occidentale L.)

Plant Genetic Resources ◽

10.1017/s1479262118000035 ◽

2018 ◽

Vol 16 (4) ◽

pp. 367-377 ◽

Cited By ~ 1

Author(s):

G. S. Mohana ◽

M. G. Nayak

Keyword(s):

Core Collection ◽

Heuristic Approach ◽

Gene Bank ◽

Morphometric Characters ◽

The Core ◽

Efficient Management ◽

Entire Collection ◽

Validation Parameters ◽

Separate Block ◽

Clustering Approach

AbstractICAR-Directorate of Cashew Research is the nodal agency for conducting cashew research and manages the largest field gene bank in India. Cashew is a perennial tree and needs more land and other resources to maintain accessions. Conservation through seeds is not feasible because of cross-pollination. Tissue culture efforts to regenerate plants from mature explants are not successful. Therefore, efficient management of the filed gene bank particularly utilization requires designation of the core collection representing the spectrum of diversity present in the entire collection. In this study, a relatively new technique, the advanced M strategy with heuristic approach was deployed to develop the core collection. Sixty-eight morphometric characters of 478 accessions were subjected to analysis resulting in the core collection of 49 accessions. Further, another core collection of same number was constituted by K-Means clustering to compare the efficiency of two approaches. The validation parameters like mean difference, variance difference, coincidence rate, variable rate and class coverage among others were employed for comparative analysis. The results of these parameters revealed that the core collection designated by heuristic approach was better able to efficiently represent and retain the diversity of the entire collection compared with the core identified by clustering approach. Future conservation and breeding efforts will be focused on establishing a separate block in the field gene bank having 49 accessions of cashew core collection.

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Assessment of molecular genetic diversity and population structure of sesame (Sesamum indicum L.) core collection accessions using simple sequence repeat markers

Plant Genetic Resources ◽

10.1017/s1479262113000373 ◽

2013 ◽

Vol 12 (1) ◽

pp. 112-119 ◽

Cited By ~ 6

Author(s):

Jong-Hyun Park ◽

Sundan Suresh ◽

Gyu-Taek Cho ◽

Nag-Gor Choi ◽

Hyung-Jin Baek ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Simple Sequence Repeat ◽

Core Collection ◽

Sesamum Indicum ◽

Group Method ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

The Core ◽

Simple Sequence

Sesame (Sesamum indicum L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.

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Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

Frontiers in Genetics ◽

10.3389/fgene.2021.726152 ◽

2021 ◽

Vol 12 ◽

Author(s):

Debjani Roy Choudhury ◽

Ramesh Kumar ◽

Vimala Devi S ◽

Kuldeep Singh ◽

N. K. Singh ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Tamil Nadu ◽

East Coast ◽

Snp Markers ◽

The Core ◽

Core Set ◽

Population Structure Analysis ◽

The Mean

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.

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Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03775-5 ◽

2021 ◽

Vol 134 (5) ◽

pp. 1343-1362

Author(s):

Alex C. Ogbonna ◽

Luciano Rogerio Braatz de Andrade ◽

Lukas A. Mueller ◽

Eder Jorge de Oliveira ◽

Guillaume J. Bauchet

Keyword(s):

Population Genetics ◽

Population Structure ◽

Manihot Esculenta ◽

Ex Situ ◽

Germplasm Bank ◽

Effective Population ◽

Manihot Esculenta Crantz ◽

Genetic Groups ◽

Population Structure Analysis ◽

Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

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Port Governance and Cruise Tourism

Sustainability ◽

10.3390/su13094877 ◽

2021 ◽

Vol 13 (9) ◽

pp. 4877

Author(s):

Alejandro Vega-Muñoz ◽

Guido Salazar-Sepúlveda ◽

Nicolás Contreras-Barraza ◽

Lorena Araya-Silva

Keyword(s):

Core Collection ◽

Web Of Science ◽

Selection Process ◽

Meta Analysis ◽

Eligibility Criteria ◽

The Core ◽

Cruise Ships ◽

Governance Model ◽

Cruise Tourism ◽

Governance Models

Cruise activities, until 2020, have presented a significant increase in revenue, as well as number of cruises and passengers transported, and it has become a challenge for ports to respond to this demand for services. In response to this, the world’s ports have implemented different governance models. In this context, in this paper, we aim to review the different governance models, as well as port cooperation, competition, and stakeholders. For this purpose, using science metric meta-analysis, an article set is extracted that strictly refers to the governance model of two databases integrated into the Core Collection Web of Science, whose selection process is polished with the PRISMA guidelines, establishing the eligibility criteria of studies using PICOS tool, to which a qualitative meta-analysis is applied. A limited studies set is identified, that includes governance model implementations, private strategies and internalization patterns in the port sector and cruise ships, patterns of port cooperation and governance, governance models in cruise ports, structures and strategies, and changes in the cruise market. Finally, various governance model forms are determined, all documented in the scientific research worldwide, discussing the various components of study topics.

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