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1.
N. Diwan M. S. McIntosh G. R. Bauchan 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,90(6):755-761
A core collection is a subset of a large germplasm collection that contains accessions chosen to represent the genetic variability of the germplasm collection. The purpose of the core collection is to improve management and use of a germplasm collection. Core collections are usually assembled by grouping accessions and selecting from within these groups. The objective of this study was to compare 11 methods of assembling a core collection of the U.S. National collection of annual Medicago species. These methods differed in their use of passport and evaluation data as well as their selection strategy. Another objective was to compare core collections with sample sizes of 5%, 10% and 17% of the germplasm collection. Core collections assembled with evaluation data and cluster analysis better represented the germplasm collection than core collections assembled based solely on passport data and random selection of accessions, The Relative Diversity and the logarithm methods generated better core collections than the proportional method. The 5% and 10% sample size core collection were judged insufficient to represent the germplasm collection. 相似文献
2.
Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data 下载免费PDF全文
Gene banks have been established to conserve the genetic diversity of crop species. Large germplasm collections lead to management problems (space, maintenance costs, etc.), especially in collections involving species with recalcitrant seeds that must be maintained as growing plants. Core collections (CCs) are thus developed to reduce the size of large germplasm collections while keeping the maximum variability. This also facilitates fine phenotypic evaluation. In this study, several software packages (DARwin, PowerMarker and MSTRAT) and methods (Max length subtree, M strategy, simulated annealing and MinSD) were compared to define a mandarin (Citrus reticulata) CC. One hundred and sixty‐seven accessions were sampled from two germplasm collections, which were genotyped with 50 SSR, 24 InDel and 68 single nucleotide polymorphism markers. All the CC obtained were tested for the maintenance of the genetic variability parameters (Ho and He) of the initial collection, the level of linkage disequilibrium (LD) and the phenotypic diversity retention. The Max length subtree function from DARWin seemed to be the most appropriate method for establishing a CC in C. reticulata. It maintained 96.82% of the allelic richness and 17.96% of the size of the initial collection with only 30 accessions. Besides it did not increase the LD (r2 value) of the initial collection and retained the vast majority of the phenotypic variability. However, a CC with 70 accessions would be more helpful for genetic association studies. 相似文献
3.
Matthew W. Blair Lucy M. Díaz Hector F. Buendía Myriam C. Duque 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,119(6):955-972
Cultivated common bean germplasm is especially diverse due to the parallel domestication of two genepools in the Mesoamerican
and Andean centers of diversity and introgression between these gene pools. Classification into morphological races has helped
to provide a framework for utilization of this cultivated germplasm. Meanwhile, core collections along with molecular markers
are useful tools for organizing and analyzing representative sets of these genotypes. In this study, we evaluated 604 accessions
from the CIAT core germplasm collection representing wide genetic variability from both primary and secondary centers of diversity
with a newly developed, fluorescent microsatellite marker set of 36 genomic and gene-based SSRs to determine molecular diversity
and with seed protein analysis to determine phaseolin alleles. The entire collection could be divided into two genepools and
five predominant races with the division between the Mesoamerica race and the Durango–Jalisco group showing strong support
within the Mesoamerican genepool and the Nueva Granada and Peru races showing less diversity overall and some between-group
admixture within the Andean genepool. The Chile race could not be distinguished within the Andean genepool but there was support
for the Guatemala race within the Mesoamerican genepool and this race was unique in its high level of diversity and distance
from other Mesoamerican races. Based on this population structure, significant associations were found between SSR loci and
seed size characteristics, some on the same linkage group as the phaseolin locus, which previously had been associated with
seed size, or in other regions of the genome. In conclusion, this study has shown that common bean has very significant population
structure that can help guide the construction of genetic crosses that maximize diversity as well as serving as a basis for
additional association studies. 相似文献
4.
S. C. Hokanson A. K. Szewc-McFadden W. F. Lamboy J. R. McFerson 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(5-6):671-683
A collection of 66 Malus×domestica Borkh. accessions from the USDA-ARS Plant Genetic Resources Unit’s core collection was screened with a set of eight SSR (simple
sequence repeat) primers developed at the PGRU in order to determine genetic identities, estimate genetic diversity, and to
identify genetic relationships among these accessions. All eight primer pairs generated multiple fragments when used in amplification
reactions with DNA from these accessions. High levels of variation were detected with a mean of 12.1 alleles per locus and
a mean heterozygosity across all eight loci of 0.693. The eight primer pairs utilized in this study unambiguously differentiated
all but seven pairs of accessions in this collection of 66 M.×domestica Borkh. genotypes. The probability of matching any two genotypes at all eight loci in this study was approximately 1 in 1
billion. The markers detected two misnamed accessions in the collection. Genetic-identity data produced a genetic-relatedness
phenogram which was concordant with geographic origins and/or known pedigree information. These SSR markers show great promise
as tools for managing Malus ex situ germplasm collections as well as for collection and preservation strategies concerning wild Malus populations in situ.
Received: 28 March 1998 / Accepted: 29 April 1998 相似文献
5.
A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement 总被引:17,自引:0,他引:17
H. D. Upadhyaya R. Ortiz 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(8):1292-1298
A core collection is a chosen subset of large germplasm collection that generally contains about 10% of the total accessions
and represents the genetic variability of entire germplasm collection. The purpose of a core collection is to improve the
use of genetic resources in crop improvement programs. In many crops the number of accessions contained in the genebank are
several thousands, and a core subset consisting of 10% of total accessions would be an unwieldy proposition. In this article
we have suggested a two-stage strategy to select a chickpea mini core subset consisting of only about 1% of the entire collection
held in trust at ICRISAT’s genebank (16,991 accessions). This mini core subset still represents the diversity of the entire
core collection. The first stage involves developing a representative core subset (about 10%) from the entire collection using
all the available information on origin, geographical distribution, and characterization and evaluation data of accessions.
The second stage involves evaluation of the core subset for various morphological, agronomic, and quality traits, and selecting
a further subset of about 10% accessions from the core subset. At both stages standard clustering procedure was used to separate
groups of similar accessions. A mini core subset consisting 211 accessions from 1,956 core subset accessions, using data on
22 morphological and agronomic traits, was selected. Newman- Keuls’ test for means, Levene’s test for variances, the chi-square
test and Wilcoxon’s rank-sum non-parametric test for frequency distribution analysis for different traits indicated that the
variation available in the core collection has been preserved in the mini core subset. The most important phenotypic correlations
which may be under the control of coadapted gene complexes, were also preserved in the mini core. This mini core subset, due
to its drastically reduced size, will prove to be a point of entry to proper exploitation of chickpea genetic resources.
Received: 20 August 2000 / Accepted: 25 September 2000 相似文献
6.
Background
Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size. 相似文献7.
高粱种质资源的多样性和利用 总被引:2,自引:0,他引:2
全世界收集到的高粱种质资源168500份,其中国际热带半干旱地区作物研究所有36774份,占总数的21.8%,美国42221份,占25.1%,印度20812份,占12.4%,中国12836份,占7.6%,其他国家55857份,占33.1%。上述国际研究所和国家在对高粱种质资源进行收集、整理、登记的基础上,对其遗传的多样性和各种性状做了鉴定,从中筛选出许多具有优良农艺性状、品质性状、抗性性状的资源,满足了高粱遗传改良的需要,成为当代和未来人类有价值的资源。建立核心种质对种质资源的保存、维护和利用是一种经济、实用和有效的方法。 相似文献
8.
Juliana Morini Küpper Cardoso Perseguini Gliciane Micaele Borges Silva Jo?o Ricardo Bachega Feijó Rosa Rodrigo Gazaffi Jéssica Fernanda Mar?al Sérgio Augusto Morais Carbonell Alisson Fernando Chiorato Maria Imaculada Zucchi Antonio Augusto Franco Garcia Luciana Lasry Benchimol-Reis 《Genetics and molecular biology》2015,38(1):67-78
Because of the continuous introduction of germplasm from abroad, some collections
have a high number of accessions, making it difficult to explore the genetic
variability present in a germplasm bank for conservation and breeding purposes.
Therefore, the aim of this study was to quantify and analyze the structure of genetic
variability among 500 common bean accessions to construct a core collection. A total
of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in
the 180 common bean accessions selected to compose the core collection ranged from
0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500
accessions were clustered into 15 distinct groups and the 180 accessions into four
distinct groups in the Structure analysis. According to analysis of molecular
variance, the most divergent accessions comprised 97.2% of the observed genetic
variability present within the base collection, confirming the efficiency of the
selection criterion. The 180 selected accessions will be used for association mapping
in future studies and could be potentially used by breeders to direct new crosses and
generate elite cultivars that meet current and future global market needs. 相似文献
9.
Thomas C. de Bang Adebola A. Raji Ivan L. Ingelbrecht 《Plant Molecular Biology Reporter》2011,29(3):655-662
Current methods for molecular fingerprinting of cassava (Manihot esculenta Crantz) have limited throughput or are costly, thus preventing the characterization of large germplasm collections such as
those held by the International Agricultural Research Centers or National Research Institutions, which comprise hundreds to
thousands of accessions. Here, we report the development of a fluorescence-based multiplex simple sequence repeat (SSR) marker
kit that enables accurate and cost-effective cassava fingerprinting. The kit comprises 16 SSR markers assembled into five
multiplex panels and was tested on 21 cassava cultivars alongside one accession of Manihot epruinosa, a wild relative. A total of 68 alleles were detected with, on average, 4.25 alleles per locus and a polymorphism information
content of 0.53. The marker kit reported here is comparable to previously published amplified fragment length polymorphism
and SSR marker systems in terms of discriminating power and informativeness while offering significant advantages in speed
and cost of marker analysis. Previous molecular genetic diversity studies have suggested that cassava germplasm collections
contain duplicate entries based on the occurrence of identical genetic profiles. Using the newly developed microsatellite
kit, three out of six putative duplicate accessions could be readily differentiated, showing that these are distinct genotypes.
The relevance of these findings with respect to the characterization and management of large cassava germplasm collections
is discussed. 相似文献
10.
Bianca Baccili Zanotto Vigna Letícia Jungmann Patrícia Mara Francisco Maria Imaculada Zucchi Cacilda Borges do Valle Anete Pereira de Souza 《Tropical plant biology》2011,4(3-4):157-169
Brachiaria brizantha (Hochst. ex A. Rich.) Stapf. (syn. Urochloa brizantha (Hochst. ex A. Rich.) R.D. Webster) is a species used primarily as forage in tropical America and Southeast Asia. B. brizantha has been extensively researched since the 1980s with the initiation of the Tropical Forages Breeding Program conducted by the Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária; EMBRAPA), holding one of the largest germplasm collections in the world. This work has identified 15 new microsatellite markers for this species, which have been used in addition to five previously reported markers, to estimate the genetic similarities among 172 accessions and six cultivars of this species. Similarity index values ranged from 0.40 to 1.00. Two duplications were found in the germplasm. A Bayesian analysis performed using the STRUCTURE 2.3.3 program revealed the presence of three clusters with different allelic pools. This analysis is valuable for the performance of crosses to explore heterosis; however, the mode of reproduction of the accessions and ploidy barriers must be observed for effective exploration. A grouping analysis using the neighbor-joining method was consistent with the STRUCTURE analysis, and a combination approach suggested that this germplasm collection does not exhibit considerable genetic variability despite the presence of three distinct allelic pools. The lack of correlation between the genetic and geographic distances is also discussed. 相似文献