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1.
David N. Kuhn Antonio Figueira Uilson Lopes Juan Carlos Motamayor Alan W. Meerow Kathleen Cariaga Barbie Freeman Donald S. LivingstoneIII Raymond J. Schnell 《Tree Genetics & Genomes》2010,6(5):783-792
The seeds of Theobroma cacao (cacao) are the source of cocoa, the raw material for the multi-billion dollar chocolate industry. Cacao’s two most important
traits are its unique seed storage triglyceride (cocoa butter) and the flavor of its fermented beans (chocolate). The genome
of T. cacao is being sequenced, and to expand the utility of the genome sequence to the improvement of cacao, we are evaluating Theobroma grandiflorum, the closest economically important species of Theobroma for its potential use in a comparative genomic study. T. grandiflorum differs from cacao in important agronomic traits such as flavor of the fermented beans, disease resistance to witches’ broom
and abscission of mature fruits. By comparing genomic sequences and analyzing viable inter-specific hybrids, we hope to identify
the key genes that regulate cacao’s most important traits. We have investigated the utility in T. grandiflorum of three types of markers (microsatellite markers, single-strand conformational polymorphism markers and single nucleotide
polymorphism (SNP) markers) developed in cacao. Through sequencing of amplicons of 12 diverse individuals of both cacao and
T. grandiflorum, we have identified new intra- and inter-specific SNPs. Two markers which had no overlap of alleles between the species were
used to genotype putative inter-specific hybrid seedlings. Sequence conservation was significant and species-specific differences
numerous enough to suggest that comparative genomics of T. grandiflorum and T. cacao will be useful in elucidating the genetic differences that lead to a variety of important agronomic trait differences. 相似文献
2.
E. S. L. Santos C. B. M. Cerqueira-Silva G. M. Mori D. Ahnert R. X. Corrêa A. P. Souza 《Biologia Plantarum》2012,56(4):789-792
Seventeen polymorphic microsatellite markers were isolated from enriched genomic libraries for Theobroma cacao, providing additional tools for studying the genetic diversity and map saturation of this species. These markers were characterized in 32 accessions of the T. cacao germplasm collection from the Centro de Pesquisas do Cacau. The number of alleles at each locus varied from 2 to 8, with an average of 4.41 alleles per locus. The polymorphism information content varied from 0.060 to 0.695, with an average of 0.333. The markers characterized in this study will be employed in map saturation studies and diversity assessments of cacao genotypes. 相似文献
3.
Isolation and characterization of microsatellite markers for the endangered <Emphasis Type="Italic">Taxus yunnanensis</Emphasis> 总被引:1,自引:0,他引:1
Ying-Chun Miao Jian-Rong Su Zhi-Jun Zhang Hui Li Jing Luo Ya-Ping Zhang 《Conservation Genetics》2008,9(6):1683-1685
Eleven polymorphic microsatellite loci were characterized for the endangered conifer Taxus yunnanensis. Eight loci were isolated through SSR-anchored PCR, one locus was developed by cross-species amplification tests, while the
last two loci were obtained from cross-species microsatellite sequences available in GenBank. Variability of these markers
was tested in 48 individuals collected from its main distribution range in Southwest China. The number of alleles per locus
ranged from 2 to 9, and the observed and expected heterozygosity varied from 0.000 to 0.625 and from 0.062 to 0.853, respectively.
Ten of these eleven loci were significantly deviated from Hardy–Weinberg expectation, except TS07 which showed a distinct
heterozygote excess. The availability of these new polymorphic microsatellite markers will provide an ideal marker system
for detailed population genetics studies in T. yunnanensis and potentially also for closely related species. 相似文献
4.
Taxus sumatrana (Miq.) de Laub. (Taxaceae) is an endangered conifer with a scattered distribution in central Taiwan. In this study, we described
the development of 12 microsatellite loci in T. sumatrana for genetic studies. These new markers were tested in nine individuals of the rare species. The number of alleles ranged
from 3 to 13 and expected heterozygosity from 0.627 to 0.948. Eleven of twelve loci are significantly deviated from Hardy–Weinberg
expectations due to the heterozygote deficiency. 相似文献
5.
Transferability of olive microsatellite loci across the genus <Emphasis Type="Italic">Olea</Emphasis> 总被引:3,自引:0,他引:3
Rallo P Tenzer I Gessler C Baldoni L Dorado G Martín A 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2003,107(5):940-946
The transferability of microsatellite markers developed for olive cultivars (Olea europaea L.) has been tested and confirmed in the Olea complex. Thirty two genotypes, belonging to different taxa of the genus Olea, have been analyzed with four olive SSRs. Positive amplifications at all loci were obtained in 13 taxa (at least one accession per species). Sixty seven different alleles have been detected at the four loci analyzed. Polymorphic products have been observed at the inter- and intra-species level. Some SSR loci have shown multiple amplification products in some species. The high number of unique alleles has allowed the unambiguous discrimination of most accessions. Similarity coefficients and relationships among the Olea taxa have been calculated based on SSR amplification results. The reliability of SSRs as markers for intra-species variability evaluation has been confirmed while their use to explore relationships at the inter-species level is discussed, being dependent on the locus analyzed.Communicated by H.F. Linskens 相似文献
6.
Trichoderma theobromicola and T. paucisporum: two new species isolated from cacao in South America 总被引:3,自引:0,他引:3
Gary J. Samuels Carmen Suarez Karina Solis Keith A. Holmes Sarah E. Thomas Adnan Ismaiel Harry C. Evans 《Mycological Research》2006,110(4):381-392
Trichoderma theobromicola and T. paucisporum spp. nov. are described. Trichoderma theobromicola was isolated as an endophyte from the trunk of a healthy cacao tree (Theobroma cacao, Malvaceae) in Amazonian Peru; it sporulates profusely on common mycological media. Trichoderma paucisporum is represented by two cultures that were obtained in Ecuador from cacao pods partially infected with frosty pod rot, Moniliophthora roreri; it sporulates sporadically and most cultures remain sterile on common media and autoclaved rice. It sporulates more reliably on synthetic low-nutrient agar (SNA) but produces few conidia. Trichoderma theobromicola was reintroduced into cacao seedlings through shoot inoculation and was recovered from stems but not from leaves, indicating that it is an endophytic species. Both produced a volatile/diffusable antibiotic that inhibited development of M. roreri in vitro and on-pod trials. Neither species demonstrated significant direct in vitro mycoparasitic activity against M. roreri. 相似文献
7.
JAMES W. BORRONE J. STEVEN BROWN DAVID N. KUHN JUAN C. MOTAMAYOR RAYMOND J. SCHNELL 《Molecular ecology resources》2007,7(2):236-239
Theobroma cacao L. expressed sequence tags (ESTs) were converted into useful genetic markers for fingerprinting individuals and genetic linkage mapping. Primers were designed to microsatellite‐containing ESTs. Twenty‐two T. cacao accessions, parents of various mapping populations segregating for disease resistance and crop yield characteristics, were tested. Twenty‐seven informative loci were discovered with 26 primer pairs. The number of detected alleles ranged from two to 11 and averaged 4.4 per locus. All 27 markers could be mapped into at least one of the existing F1 or F2 populations segregating for agronomically important traits. 相似文献
8.
Lycopodium fordii Bak. (Lycopodiaceae, Pteridophyta) is a gardening plant with a native, fragmentary distribution in Taiwan. In this study,
we described the development of eleven microsatellite loci in L. fordii for genetic studies. These new markers were tested in 16 individuals of three populations. The number of alleles ranged from
1 to 5 and the expected heterozygosity from 0.41746 to 0.72222. Four of the nine polymorphic loci were significantly deviated
from Hardy-Weinberg expectations due to the heterozygote deficiency. The microsatellite markers have also been proved as informative
genetic markers for other 15 Lycopodium species. 相似文献
9.
Belén G. Pardo Almudena López Paulino Martínez Carmen Bouza 《Conservation Genetics》2007,8(5):1243-1245
The long-snouted seahorse Hippocampus guttulatus is one of the two European seahorse species. We describe the isolation of the first 12 microsatellite loci in this threatened
species. These new markers were tested in non-invasive samples of 32 seahorses from NW Spain. The number of alleles ranged
from 2 to 15 (mean: 6.3) and expected heterozygosity from 0.031 to 0.912 (mean: 0.500). All loci conformed to Hardy–Weinberg
expectations and no genotypic disequilibrium was observed between any pair of loci. The theoretical exclusion probabilities
for this set of loci, when no parental information exists or when one parent is known, were 0.973 and 0.998, respectively.
This study indicates the usefulness of these novel loci for population analysis and kinship studies in Hippocampus guttulatus. Their potential application is extended to the other European seahorse species, since all loci were successfully cross-amplified
in H. hippocampus. 相似文献
10.
Selection of international molecular standards for DNA fingerprinting of <Emphasis Type="Italic">Theobroma cacao</Emphasis> 总被引:1,自引:0,他引:1
Saunders JA Mischke S Leamy EA Hemeida AA 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,110(1):41-47
A collaborative international program was initiated to identify and describe the genetic diversity of living germplasm collections of Theobroma cacao genotypes that are maintained in several international collections scattered throughout tropical cacao growing countries of the world. Simple sequence repeat (SSR) DNA analysis was identified as the most appropriate molecular tool for DNA fingerprinting these collections during an international forum representing academic, government and industry scientists in the cacao community. Twenty-five SSR primers, which had been previously described, were evaluated as potential candidates to define an efficient, standardized, molecular fingerprinting protocol for T. cacao accessions. These primers have been evaluated for reliability, widespread distribution across the cacao genome, number of alleles produced by the SSR primers in cacao and their ability to discriminate between cacao accessions. Approximately 690 cacao accessions were used to evaluate the utility of these SSR primers as international molecular standards, and a small number of test samples of T. cacao were sent to two other independent laboratories for verification. DNA fragments were selectively amplified by PCR, using the SSR primers labeled with fluorescent dyes, and separated by capillary electrophoresis. Based on this study, the 15 SSR primers that had the highest reproducibility and consistency within a common genotype, while allowing the differentiation of separate divergent genotypes, were selected as international molecular standards for DNA fingerprinting of T. cacao. 相似文献
11.
Cupressus chenggiana S. Y. Hu (Cupressaceae) is an endemic and endangered conifer species in southwest China. In order to study the population
genetics and design the effective conservation methods, we aimed to develop microsatellite primers for this species in the
present study. We developed eight new microsatellite loci for this species through biotin capture method. Polymorphism of
each locus was further assessed in 18 individuals from three geographically distant populations. The number of alleles per
locus ranged from 6 to 11 with an average of 8.13. The observed and expected heterozygosities ranged from 0.219 to 0.296 and
from 0.374 to 0.470, with averages of 0.254 and 0.417, respectively. We further found that three of nine microsatellite loci
developed previously for another congeneric species showed polymorphic banding patters. We performed primer-crossing tests
of these loci in the other two congeneric species which are closely related to C. chenggiana (C. gigantea and C. duclouxiana). These microsatellite markers would be effective for analyzing genetic diversity and population genetic structure of this
species and its morphological differentiation with the close relatives. 相似文献
12.
Hung-Du Lin Teh-Wang Lee Fang-Jiao Lin Chung-Jian Lin Tzen-Yuh Chiang 《Conservation Genetics》2008,9(4):945-947
Pararasbora moltrechti (Cyprinidae) is an endangered freshwater fish with a scattered distribution in the central Taiwan. In order to undertake
a conservation program for this species in Taiwan, it is essential to evaluate its genetic diversity and population structure.
For this purpose, we described the development of eight microsatellite loci in P. moltrechti for genetic studies. These new molecular markers were tested in 36 individuals of the rare species. The number of alleles
per locus ranged from 8 to 14. As the expected heterozygosity varied from 0.770 to 0.932, all microsatellite loci, however,
were significantly deviated from Hardy–Weinberg expectations due to the heterozygote deficiency.
Hung-Du Lin and Teh-Wang Lee contributed equally. 相似文献
13.
Dahai Gao Qian Wang Yuxia Wu Haiyan Xu Qiushi Yu Jianquan Liu 《Conservation Genetics》2008,9(4):953-955
Thellungiella
salsuginea (Brassiaceae) is a typical halophyte which can tolerate extreme cold, drought, and salinity. In order to understand the adaptive
evolution of this species in the arid habitats, it is important to know its genetic structure. In this study, 17 polymorphic
microsatellite loci were isolated and characterized from an enrichment genomic library of this species. We further assessed
the polymorphisms of each locus in 18 individuals from nine geographically distant populations. The number of alleles per
locus ranged from six to fourteen. The observed and expected heterozygosity ranged from 0.17 to 0.28 and 0.32 to 0.45, respectively.
These markers have been crossly checked in another congeneric species, T. halophila. These microsatellite markers will be useful for investigating population genetics and adaptive evolution of this species
and morphological divergence between and it and the closely related species. 相似文献
14.
Chi-Chun Huang Kuo-Hsiang Hung Tsai-Wen Hsu Kuo-Hsiung Wang Chi-Yung Lin Tzen-Yuh Chiang 《Conservation Genetics》2008,9(5):1333-1335
Fatsia polycarpa Hayata (Araliaceae) is an element of evergreen forests at middle elevations in Taiwan, also representing the southern limitation
in distribution of the genus. In this study, we described the development of 11 microsatellite loci from F. polycarpa in Taiwan for genetic studies. These new markers were tested in 20 individuals of 5 populations of the woody species. The
number of alleles ranged from 9 to 18. The expected (H
E
) and observed (H
O
) heterozygosities were 0.80–0.95 and 0.10–0.75, respectively. Six of the 11 microsatellite loci are significantly deviated
from Hardy–Weinberg expectations likely due to the population structure within samples. No linkage disequilibrium were observed
from pairwise comparisons of loci.
Chi-Chun Huang, Kuo-Hsiang Hung, and Tsai-Wen Hsu contributed equally to this article. 相似文献
15.
Ashley MV Wilk JA Styan SM Craft KJ Jones KL Feldheim KA Lewers KS Ashman TL 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2003,107(7):1201-1207
The objectives of the present study were to develop microsatellite markers for the wild strawberry, Fragaria virginiana, to evaluate segregation patterns of microsatellite alleles in this octoploid species, and assess genetic variability at microsatellite loci in a wild population. A genomic library was screened for microsatellite repeats and several PCR primers were designed and tested. We also tested the use of heterologous primers and found that F. virginiana primers amplified products in cultivated strawberry, Fragaria × ananassa Duch. and Fragaria chiloensis. Similarly, microsatellite loci developed from cultivated strawberry also successfully amplified F. virginiana loci. We investigated four microsatellite loci in detail, three developed from F. virginiana and one from cultivated strawberry. A survey of 100 individuals from a population of F. virginiana in Pennsylvania demonstrated high heterozygosities (He or gene diversity ranged from 0.80 to 0.88 per locus) and allelic diversity (12–17 alleles per locus), but individual plants had no more than two alleles per locus. Segregation patterns in parents and progeny of two controlled crosses at these four loci were consistent with disomic Mendelian inheritance. Together these findings suggest that the genome of F. virginiana is "highly diploidized" and at least a subset of microsatellite loci can be treated as codominant, diploid markers. Significant heterozygote deficiencies were found at three of the four loci for hermaphroditic individuals but for only one locus among females in this gynodioecious species.Communicated by J. Dvorak 相似文献
16.
Maria L. Sereno Paulo S. B. Albuquerque Roland Vencovsky Antonio Figueira 《Conservation Genetics》2006,7(1):13-24
A sample of 94 accessions of Theobroma cacao L. (cacao), representing four populations from the Brazilian Amazon (Acre, Rondônia, lower Amazon and upper Amazon) were analyzed using microsatellite markers to assess the genetic diversity and the natural population structure. From the 19 microsatellite loci tested, 11 amplified scorable products, revealing a total of 49 alleles, including two monomorphic loci. The Brazilian upper Amazon population contained the largest genetic diversity, with the most polymorphic loci, the highest observed heterozygosity; and the majority of rare alleles, thereby this region might be considered part of the center of diversity of the species. The observed heterozygosity for all the Brazilian populations (H o = 0.347) was comparable with values reported for other similar upper Amazon Forastero cacao populations, with the Acre and Rondônia displaying the lowest values. The lower Amazon population, traditionally defined as highly homozygous, presented an unexpectedly high observed heterozygosity (H o = 0.372), disclosing rare and distinct alleles, with large identity with the upper Amazon population. It was hypothesized that part of the lower Amazon population might derive from successive natural or intentional introduction of planting material from other provenances, mainly upper Amazon. Most of the loci exhibited a lower observed heterozygosity than expected, suggesting that self-pollination might be more common than usually assumed in cacao, but excess of homozygotes might also derive from sub-grouping (Wahlund effect) or from sampling related individuals. Most of the gene diversity was found to occur within groups, with small differentiation between the four Brazilian Amazon populations, typical of species with high gene flow. 相似文献
17.
Dong-Yuan Zhang Na Chen Yan-Zhuo Yang Qian Zhang Jian-Quan Liu 《Conservation Genetics》2008,9(2):475-477
Rhubarb is an important Traditional Chinese Medicine. However, the wild resource has been declining. In order to design appropriate
conservation methods for the official species across their natural distributions, it is important to characterize their genetic
diversity. Here, we describe the development of 10 new microsatellite loci for AC/TG/CCA in Rheum tanguticum. The microsatellites were enriched using the combined biotin capture method. The polymorphism of each locus was further assessed
in 12 individuals from four geographically distinct populations of this species. The number of alleles ranged from three to
seven and the expected heterozygosity ranged from 0.53 to 0.73. All markers have been checked in the other three species in
the genus and two of them together comprise the official medicinal rhubarb resource with R. tanguticum. These microsatellite markers could provide a useful tool for genetic and conservation studies of the rhubarb species. 相似文献
18.
Development of nuclear microsatellite markers for the Japanese conifers Tsuga diversifolia and T. sieboldii (Pinaceae)
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James R.P. Worth Jong‐Cheol Yang Seiichi Kanetani Satoshi Kikuchi Shota Sakaguchi Tokuko Ihara‐Udino 《Plant Species Biology》2018,33(1):67-71
Nuclear microsatellite markers were developed for the two Tsuga species native to the Japanese Archipelago, Tsuga diversifolia and T. sieboldii, and a population with genetic affinities to T. diversifolia on Ulleung Island, Korea. Tsuga diversifolia and T. sieboldii are widespread dominant trees of temperate and subalpine forests in Japan but to date no genetic markers have been developed for these species. Fifteen polymorphic loci were developed and characterized, of which 14 are reliably amplified in each taxon. Across both species and the Ulleung Island population, the number of alleles per locus ranged from 3 to 26 (average = 13.93) and observed heterozygosity ranged from 0.005 to 0.935 (average = 0.535). In addition, all 15 loci were successfully amplified in a single accession of the Chinese species, T. chinensis. These markers will be useful for investigating the species’ biogeography, range‐wide genetic diversity, conservation genetic issues and potential for hybridisation. 相似文献
19.
A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers 总被引:1,自引:0,他引:1
Pugh T Fouet O Risterucci AM Brottier P Abouladze M Deletrez C Courtois B Clement D Larmande P N'Goran JA Lanaud C 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,108(6):1151-1161
A linkage map of cacao based on codominant markers has been constructed by integrating 201 new simple sequence repeats (SSR) developed in this study with a number of isoenzymes, restriction fragment length polymorphisms (RFLP), microsatellite markers and resistance and defence gene analogs (Rgenes-RFLP) previously mapped in cacao. A genomic library enriched for (GA)n and (CA)n was constructed, and 201 new microsatellite loci were mapped on 135 individuals from the same mapping population used to establish the first reference maps. This progeny resulted from a cross between two heterozygous cacao clones: an Upper-Amazon Forastero (UPA 402) and a Trinitario (UF 676). The new map contains 465 markers (268 SSRs, 176 RFLPs, five isoenzymes and 16 Rgenes-RFLP) arranged in ten linkage groups corresponding to the haploid chromosome number of cacao. Its length is 782.8 cM, with an average interval distance between markers of 1.7 cM. The new microsatellite markers were distributed throughout all linkage groups of the map, but their distribution was not random. The length of the map established with only SSRs was 769.6 cM, representing 94.8% of the total map. The current level of genome coverage is approximately one microsatellite every 3 cM. This new reference map provides a set of useful markers that is transferable across different mapping populations and will allow the identification and comparison of the most important regions involved in the variation of the traits of interest and the development of marker-assisted selection strategies.Communicated by H. Nybom 相似文献
20.
Trichoderma species are usually considered soil organisms that colonize plant roots, sometimes forming a symbiotic relationship. Recent studies demonstrate that Trichoderma species are also capable of colonizing the above ground tissues of Theobroma cacao (cacao) in what has been characterized as an endophytic relationship. Trichoderma species can be re-isolated from surface sterilized cacao stem tissue, including the bark and xylem, the apical meristem, and to a lesser degree from leaves. SEM analysis of cacao stems colonized by strains of four Trichoderma species (Trichoderma ovalisporum-DIS 70a, Trichoderma hamatum-DIS 219b, Trichoderma koningiopsis-DIS 172ai, or Trichoderma harzianum-DIS 219f) showed a preference for surface colonization of glandular trichomes versus non-glandular trichomes. The Trichoderma strains colonized the glandular trichome tips and formed swellings resembling appresoria. Hyphae were observed emerging from the glandular trichomes on surface sterilized stems from cacao seedlings that had been inoculated with each of the four Trichoderma strains. Fungal hyphae were observed under the microscope emerging from the trichomes as soon as 6 h after their isolation from surface sterilized cacao seedling stems. Hyphae were also observed, in some cases, emerging from stalk cells opposite the trichome head. Repeated single trichome/hyphae isolations verified that the emerging hyphae were the Trichoderma strains with which the cacao seedlings had been inoculated. Strains of four Trichoderma species were able to enter glandular trichomes during the colonization of cacao stems where they survived surface sterilization and could be re-isolated. The penetration of cacao trichomes may provide the entry point for Trichoderma species into the cacao stem allowing systemic colonization of this tissue. 相似文献