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1.
KYUNG‐HO MA KWANG‐HO KIM ANUPAM DIXIT JAE‐WOONG YU JONG‐WOOK CHUNG JEONG‐HEUI LEE EUN‐GI CHO TAE SAN KIM YONG‐JIN PARK 《Molecular ecology resources》2006,6(3):689-691
A microsatellite‐enriched library of Job's tears (Coix lacryma‐jobi L. var. Ma‐yuen Stapf) was constructed using a modified biotin–streptavidin capture method. After screening, 17 polymorphic microsatellites were used for diversity analysis among 30 Job's tears accessions. The number of alleles ranged from one to five alleles per locus with an average of 2.8 alleles. Expected heterozygosity (HE) and polymorphism information content (PIC) ranged from 0 to 0.676 and from 0 to 0.666, respectively. The newly developed microsatellite markers are expected to be very valuable tools for evaluation of genetic diversity among large germplasm collection of Job's tears present in our Korean Gene Bank. 相似文献
2.
Xiu-Jie Xi Yun-Guo Zhu Ying-Peng Tong Xiao-Ling Yang Nan-Nan Tang Shu-Min Ma Shan Li Zhou Cheng 《PloS one》2016,11(4)
Job’s tears (Coix lachryma-jobi L.) is an important crop used as food and herbal medicine in Asian countries. A drug made of Job’s tears seed oil has been clinically applied to treat multiple cancers. In this study, the genetic diversity of Job’s tears accessions and the fatty acid composition, triglyceride composition, and anti-proliferative effect of Job’s tears seed oil were analyzed using morphological characteristics and ISSR markers, GC-MS, HPLC-ELSD, and the MTT method. ISSR analysis demonstrated low genetic diversity of Job’s tears at the species level (h = 0.21, I = 0.33) and the accession level (h = 0.07, I = 0.10), and strong genetic differentiation (GST = 0.6702) among all accessions. It also clustered the 11 accessions into three cultivated clades corresponding with geographical locations and two evidently divergent wild clades. The grouping patterns based on morphological characteristics and chemical profiles were in accordance with those clustered by ISSR analysis. Significant differences in morphological characteristics, fatty acid composition, triglyceride composition, and inhibition rates of seed oil were detected among different accessions, which showed a highly significant positive correlation with genetic variation. These results suggest that the seed morphological characteristics, fatty acid composition, and triglyceride composition may be mainly attributed to genetic factors. The proportion of palmitic acid and linoleic acid to oleic acid displayed a highly significant positive correlation with the inhibition rates of Job’s tears seed oil for T24 cells, and thus can be an important indicator for quality control for Job’s tears. 相似文献
3.
Camila Pinto da Cunha Francisco Vilela Resende Maria Imaculada Zucchi José Baldin Pinheiro 《Genetica》2014,142(5):419-431
Garlic is a spice and a medicinal plant; hence, there is an increasing interest in ‘developing’ new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide. 相似文献
4.
Weiguo Zhao Gi-An Lee Soon-Wook Kwon Kyung-Ho Ma Myung-Chul Lee Yong-Jin Park 《Genes & genomics.》2012,34(1):51-57
Italian millet is a commercially important grain crop. Nineteen polymorphic simple sequence repeat (SSR) markers, developed through construction of an SSR-enriched library from genomic DNA of Italian millet (Setaria italica L., P. Beauv.), were used for assessment of molecular genetic diversity against 40 accessions of S. italica. In total, 85 alleles were detected, with an average of 4.5 alleles per locus. The average gene diversity and polymorphism information content (PIC) values were 0.412 and 0.376, ranging from 0.02 to 0.88 and from 0.02 to 0.87, respectively. Values for observed (H O) and expected (H E) heterozygosities ranged from 0 to 0.73 and from 0.03 to 0.89, respectively. Nine loci deviated from Hardy-Weinberg equilibrium. The mean similarity coefficient among accessions was 0.6593. Based on the UPGMA algorithm, six different groups were successfully identified. In this clustering analysis, all Korean accessions grouped in one cluster, indicating that Korean accessions are genetically quite distinct from other introduced accessions. These newly developed microsatellite markers should be very useful tools for several genetic studies, including an assessment of diversity and population structure in Italian millet. 相似文献
5.
Kyung-Ho Ma Anupam Dixit Young-Chang Kim Dong-Yun Lee Tae-San Kim Eun-Gi Cho Yong-Jin Park 《Conservation Genetics》2007,8(6):1507-1509
Panax ginseng C.A. Meyer, commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. Its roots are highly
prized for several medicinal properties. The present study describes development and characterization of twenty-two polymorphic
microsatellite markers for this species. A total of 99 alleles were detected with an average of 4.5 alleles per locus across
20 accessions. Values for observed (H
O
) and expected (H
E
) heterozygosities ranged from 0.05 to 1.00 and from 0.18 to 0.73, respectively. Eleven loci deviated from Hardy–Weinberg
equilibrium (P < 0.001). Significant (P < 0.05) heterozygote deficiency was observed at 13 loci. Exact test for linkage disequilibrium showed significant values
(P < 0.05) between 12 pairs of loci. These microsatellite markers provide powerful tools for understanding population and conservation
genetics of this species and also for genetic differentiation and authentication of different Panax species being used in commercial ginseng products. 相似文献
6.
Genetic diversity in spring bread wheat (T.␣aestivum L.) was studied in a total of 69 accessions. For this purpose, 52 microsatellite (SSR) markers were used and a total of 406
alleles were detected, of which 182 (44.8%) occurred at a frequency of <5% (rare alleles). The number of alleles per locus
ranged from 2 to 14 with an average of 7.81. The largest number of alleles per locus occurred in the B genome (8.65) as␣compared
to the A (8.43) and D (5.93) genomes, respectively. The polymorphism index content (PIC) value varied from 0.24 to 0.89 with
an average of 0.68. The highest PIC for all accessions was found in the B␣genome (0.71) as compared to the A (0.68) and D␣genomes
(0.63). Genetic distance-based method (standard UPGMA clustering) and a model-based method (structure analysis) were used for cluster analysis. The two methods led to analogical results. Analysis of molecular variance (AMOVA)
showed that 80.6% of the total variation could be explained by the variance within the geographical groups. In comparison
to the diversity detected for all accessions (H
e
= 0.68), genetic diversity among European spring bread wheats was H
e
= 0.65. A comparatively higher diversity was observed between wheat varieties from Southern European countries (Austria/Switzerland,
Portugal/Spain) corresponding to those from other regions. 相似文献
7.
S. Suresh J. -W. Chung G. -T. Cho J. -S. Sung J. -H. Park J. -G. Gwag 《Plant biosystems》2013,147(4):635-644
We assessed the molecular genetic diversity and population structure of Amaranthus species accessions using 11 simple sequence repeat markers. A total of 122 alleles were detected, and the number of alleles per marker (NA) ranged from 6 to 21 with an average of 11.1 alleles. The frequency of major alleles per locus ranged from 0.148 to 0.695, with an average value of 0.496 per marker. The overall polymorphic information content values were 0.436–0.898, with an average value of 0.657. The observed heterozygosity (HO) and expected heterozygosity (HE) ranged from 0.056 to 0.876 and from 0.480 to 0.907, with average values of 0.287 and 0.698, respectively. The average HO (0.240) was lower than the HE and gene flow (Nm), and showed substantial genetic variability among all populations of amaranth accessions. The sample groupings did not strictly follow the geographic affiliations of the accessions. A similar pattern was obtained using model-based structure analysis without grouping by species type. Knowledge of the genetic diversity and population structure of amaranth can be used to select representative genotypes and manage Amaranthus germplasm breeding programs. 相似文献
8.
ANUPAM DIXIT MING‐HUA JIN JONG‐WOOK CHUNG JAE‐WOONG YU HUN‐KI CHUNG KYUNG‐HO MA YONG‐JIN PARK EUN‐GI CHO 《Molecular ecology resources》2005,5(4):736-738
Fifty microsatellite sequences (SSRs) were isolated from an enriched library of sesame (Sesamum indicum L.) using a modified protocol. After screening, 10 polymorphic microsatellites were used to determine their usefulness in diversity analysis among 16 sesame accessions. The number of alleles ranged from three to six alleles per locus with an average of 4.6 alleles. The fragment size varied from 150 bp to 307 bp. Expected heterozygosites (HE) and polymorphism information contents (PICs) ranged from 0.437 to 0.858 and 0.34 to 0.80, respectively, which indicates the highly informative nature of the microsatellites reported here. These microsatellite markers will be very useful in diversity analysis among a large germplasm collection of sesame present in our Korean gene bank and also in the establishment of its core collection. 相似文献
9.
Rang-Jin Xie Jian Zhou Guo-Yun Wang Shui-Ming Zhang Lin Chen Zhong-Shan Gao 《Plant Molecular Biology Reporter》2011,29(3):554-562
A collection of 122 Chinese bayberry accessions and one wax myrtle (Myrica cerifera L.) were analyzed with 14 polymorphic simple sequence repeats (SSRs). The average number of alleles per locus was 9.3, and
polymorphism information content varied from 0.07 to 0.83, with a mean value of 0.62. The genetic relationships among the
123 accessions were analyzed using the unweighted pair-group method with arithmetic mean (UPGMA). The similarity among all
the accessions, based on Dice’s coefficient, varied from 0.78 to 0.99, and 0.74 between the Chinese bayberries and wax myrtle.
A set of 122 Chinese bayberries clustered into four groups, with the first group further divided into six subgroups. The accessions
originating from the same geographical region were more closely related than those from different regions, although extensive
gene flow has taken place. The Mantel test, used to compare similarity matrices calculated from AFLP and SSR data, showed
that their combination could provide information on the genetic relationship among the Chinese bayberry accessions. Ten selected
SSR markers were able to distinguish most accessions, and multiplex PCR systems were developed. In addition, we found that
SSRs developed from Chinese bayberry are transferable to M. cerifera. 相似文献
10.
11.
Peter O. Aikpokpodion Juan C. Motamayor Victor O. Adetimirin Yaw Adu-Ampomah Ivan Ingelbrecht Albertus B. Eskes Raymond J. Schnell Maria Kolesnikova-Allen 《Tree Genetics & Genomes》2009,5(4):699-711
Knowledge of genebank and on-farm genetic diversity, particularly in an introduced crop species, is crucial to the management
and utilization of the genetic resources available. Microsatellite markers were used to determine genetic diversity in 574
accessions of cacao, Theobroma cacao L., representing eight groups covering parental populations in West Africa, genebank, and farmers’ populations in Nigeria.
From the 12 microsatellite markers used, a total of 144 alleles were detected with a mean allelic richness of 4.39 alleles/locus.
The largest genetic diversity was found in the Upper Amazon parent population (H
nb
= 0.730), followed by the 1944 Posnette’s Introduction (H
nb
= 0.704), and was lowest in the Local parent population (H
nb
= 0.471). Gene diversity was appreciably high in the farmers’ populations (H
nb
= 0.563–0.624); however, the effective number of alleles was lower than that found in the genebank’s Posnette’s population.
Fixation index estimates indicated deficiency of heterozygotes in the Upper Amazon and the Local parent populations (F
is
= 0.209 and 0.160, respectively), and excess of heterozygotes in the Trinitario parent population (F
is
= −0.341). The presence of inbreeding in the Local parent populations and substructure (Wahlund effect) in the Upper Amazon
were suggested for the deficiency of heterozygotes observed. Non-significant genetic differentiation observed between the
genebank’s and farmers’ populations indicated significant impact of national breeding programs on varieties grown in farmers’
plantations. From this study, we showed that appreciable genetic diversity was present in on-farm and field genebank collections
of cacao that can be exploited for crop improvement in West Africa. Suggestions for future conservation of on-farm genetic
diversity and local landraces are further discussed. 相似文献
12.
Adoukonou-Sagbadja H Wagner C Dansi A Ahlemeyer J Daïnou O Akpagana K Ordon F Friedt W 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2007,115(7):917-931
Fonio millets (Digitaria exilis Stapf, D. iburua Stapf) are valuable indigenous staple food crops in West Africa. In order to investigate the genetic diversity and population
differentiation in these millets, a total of 122 accessions from five countries (Benin, Burkina Faso, Guinea, Mali and Togo)
were analysed by Amplified Fragment Length Polymorphisms (AFLPs). Genetic distance-based UPGMA clustering and principal coordinate
analysis revealed a clear-cut differentiation between the two species and a clustering of D. exilis accessions in three major genetic groups fitting to their geographical origins. Shannon’s diversity index detected in D. iburua was low (H = 0.02). In D. exilis, the most widespread cultivated species, moderate levels of genetic diversity (Shannon’s diversity H = 0.267; Nei’s gene diversity H′ = 0.355) were detected. This genetic diversity is unequally distributed with the essential part observed in the Upper Niger
River basin while a very low diversity is present in the Atacora mountain zone. Analysis of molecular variance (AMOVA) revealed
that a large part of the genetic variation resides among the genetic groups (70%) and the country of origin (56%), indicating
a clear genetic differentiation within D. exilis. Influence of mating system (inbreeding or apomixis), agricultural selection and ecological adaptations as well as founding
effects in the genetic make-up of the landraces were visible and seemed to jointly contribute to the genetic structure detected
in this species. The genetic variability found between the analysed accessions was weakly correlated with their phenotypic
attributes. However, the genetic groups identified differed significantly in their mean performance for some agro-morphologic
traits. The results obtained are relevant for fonio millets breeding, conservation and management of their genetic resources
in West Africa. 相似文献
13.
Jung-Ro Lee Gi-Yun Hong Anupam Dixit Jong-Wook Chung Kyung-Ho Ma Jae-Hak Lee Hee-Kyoung Kang Yang-Hee Cho Jae-Gyun Gwag Yong-Jin Park 《Conservation Genetics》2008,9(1):243-246
The present study reports isolation and characterization of 12 polymorphic microsatellite markers for Amaranthus hypochondriacus. A total of 92 alleles were detected across the 20 accessions, with an average of 7.7 alleles per locus. The observed (H
O
) and expected (H
E
) heterozygosity values ranged from 0 to 0.95 and from 0.49 to 0.92, respectively. At significance threshold (P < 0.05), nine loci deviated from Hardy-Weinberg equilibrium (HWE), whereas significant linkage disequilibria (LD) were observed
between five pairs of loci. The 12 loci were successfully amplified in 18 other amaranth species representing cultivated grain
and vegetable species, their putative progenitors and wild species. These results demonstrate wide potential applicability
of these markers for the study of intra- and inter-specific genetic diversity as well as evolutionary relationships among
cultivated and wild amaranths. 相似文献
14.
Xiao-Li Peng Chang-Ming Zhao Gui-Li Wu Jian-Quan Liu 《Trees - Structure and Function》2007,21(4):457-464
Repeated cycles of retreat and recolonization during the Quaternary ice ages are thought to have greatly influenced current
species distributions and their genetic diversity. It remains unclear how this climatic oscillation has affected the distribution
of genetic diversity between populations of wind-pollinated conifers in the Qinghai-Tibetan region. In this study, we investigated
the within-species genetic diversity and phylogenetic relationships of Picea likiangensis, a dominant forest species in this region using polymorphic DNA (RAPD) markers. Our results suggest that this species has
high overall genetic diversity, with 85.42% of loci being polymorphic and an average expected heterozygosity (H
E) of 0.239. However, there were relatively low levels of polymorphism at population levels and the differences between populations
were not significant, with percentages of polymorphic bands (PPB) ranging from 46.88 to 69.76%, Nei’s gene diversity (H
E) from 0.179 to 0.289 and Shannon’s indices (Hpop) from 0.267 to 0.421. In accordance with our proposed hypothesis, a high level of genetic differentiation among populations
was detected based on Nei’s genetic diversity (G
ST = 0.256) and AMOVA analysis (Phi
st = 0.236). Gene flow between populations was found to be limited (Nm = 1.4532) and far lower than reported for other conifer species with wide distribution ranges from other regions. No clusters
corresponding to three morphological varieties found in the south, north and west, respectively, were detected in either UPGMA
or PCO analyses. Our results suggest that this species may have had different refugia during the glacial stages in the southern
region and that the northern variety may have multiple origins from these different refugia. 相似文献
15.
E. J. OLIVEIRA J. G. PDUA M. I. ZUCCHI L. E. A. CAMARGO M. H. P. FUNGARO M. L. C. VIEIRA 《Molecular ecology resources》2005,5(2):331-333
Here we described the development of the first set of Passiflora microsatellite loci isolated from an enriched genomic library. A sample of 43 individuals from 12 accessions of the yellow passion fruit was used to characterize those loci, which revealed up to 20 alleles per locus. Two loci were monomorphic. The observed (HO) and expected (HE) heterozygosities were very similar, as expected for a self‐incompatible species. Allelic diversity (HT) was 0.444. This set of markers will permit genetic structure analyses of cultivated and wild populations of Passiflora, and contribute for integrating genetic maps based on dominant markers, as they can provide bridge alleles. 相似文献
16.
Yun-Sun Lee Sung-Kyoung Choi Junghwa An Han-Chan Park Sang-In Kim Mi-Sook Min Kyung-Seok Kim Hang Lee 《Genes & genomics.》2011,33(5):535-540
The main goals of this study were to isolate microsatellites markers of Korean water deer (Hydropotes inermis argyropus) and understand the genetic status of the species in South Korea. Twelve new microsatellite loci were isolated and characterized to establish basic population genetic parameters for 45 H. i. argyropus specimens in South Korea. There were no significant regional or genetic structure differences between the mid-eastern and southwestern populations in South Korea according to the population genetic analyses. The number of alleles per locus ranged from two to 13 with an average of 6.08. Mean expected (H E) and observed heterozygosity (H O) were 0.622 and 0.533, respectively. Microsatellite variability was also not significant between the two regions (F ST=0.012). These new markers should facilitate the future population genetics studies of Korean water deer and other closely related species. 相似文献
17.
Fourteen microsatellite markers were used to describe genetic diversity in a sample of 128 common bean (Phaseolus vulgaris L.) accessions cultivated within the territory of Slovenia and its nearby regions between 1800 and 2000. The accessions were
grouped into three periods: period I comprising accessions from the beginning of the 19th century, while the other two periods
included accessions from the middle (period II) and the end of the 20th century (period III). Seven control accessions of
known Mesoamerican and Andean origin were also included in the study. A total of 130 alleles were generated. Allelic richness,
in terms of number of alleles per locus, was 6.07 for period I, 6.71 for period II, and 6.07 for period III. In the UPGMA
dendrogram, all studied accessions were intermixed in three main clusters, indicating that the diversity in the time periods
overlapped. Two clusters consisted of accessions of Andean and Mesoamerican origin, while the third represents additional
variation, which existed in this area already 200 years ago. The analysis of molecular variance showed that a great part of
genetic diversity has been preserved till today, confirming the results of cluster analysis. The calculation of number of
alleles per locus revealed no significant quantitative change in genetic diversity over the last 200 years of common bean
cultivation. However, the calculation of genetic distances indicated slight qualitative shifts in genetic diversity of common
bean germplasm over time, while the calculations of allelic frequency variation and polymorphic information content revealed
recent decline of some alleles’ frequencies. These findings should stress the need for establishing an appropriate strategy
of genetic resources management.
The text was submitted by the authors in English. 相似文献
18.
Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers 总被引:9,自引:1,他引:8
Six polymorphic microsatellites (eight loci) were used to study the genetic diversity and population structure of common carp
from Dongting Lake (DTC), Poyang Lake (PYC), and the Yangtze River (YZC) in China. The gene diversity was high among populations
with values close to 1. The number of alleles per locus ranged from 2 to 11, and the average number of alleles among 3 populations
ranged from 6.5 to 7.9. The mean observed (H
O) and expected (H
E) heterozygosity ranged from 0.4888 to 0.5162 and from 0.7679 to 0.7708, respectively. Significant deviations from Hardy–Weinberg
Equilibrium expectation were found at majority of the loci and in all three populations in which heterozygote deficits were
apparent. The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within populations
were 3.03 and 96.97, respectively. The Fst values between populations indicated that there were significant genetic differentiations for the common carp populations
from the Yangtze River and two largest Chinese freshwater lakes. The factors that may result in genetic divergence and significant
reduction of the observed heterozygosity were discussed. 相似文献
19.
One hundred ninety-four germplasm accessions of fig representing the four fig types, Common, Smyrna, San Pedro, and Caprifig
were analyzed for genetic diversity, structure, and differentiation using genetic polymorphism at 15 microsatellite loci.
The collection showed considerable polymorphism with observed number of alleles per locus ranging from four for five different
loci, MFC4, LMFC14, LMFC22, LMFC31 and LMFC35 to nine for LMFC30 with an average of 4.9 alleles per locus. Seven of the 15 loci included in the genetic structure analyses exhibited significant
deviation from panmixia, of which two showed excess and five showed deficiency of heterozygote. The cluster analysis (CA)
revealed ten groups with 32 instances of synonymy among cultivars and groups differed significantly for frequency and composition
of alleles for different loci. The principal components analysis (PCA) confirmed the results of CA with some groups more differentiated
than the others. Further, the model based Bayesian approach clustering suggested a subtle population structure with mixed
ancestry for most figs. The gene diversity analysis indicated that much of the total variation is found within groups (H
G
/H
T = 0.853; 85.3%) and the among groups within total component (G
GT = 0.147) accounted for the remaining 14.7%, of which ~64% accounted for among groups within clusters (G
GC = 0.094) and ~36% among clusters (G
CT = 0.053). The analysis of molecular variance (AMOVA) showed approximately similar results with nearly 87% of variation within
groups and ~10% among groups within clusters, and ~3% among clusters. Overall, the gene pool of cultivated fig analyzed possesses
substantial genetic polymorphism but exhibits narrow differentiation. It is evident that fig accessions from Turkmenistan
are somewhat genetically different from the rest of the Mediterranean and the Caucasus figs. The long history of domestication
and cultivation with widespread dispersal of cultivars with many synonyms has resulted in a great deal of confusion in the
identification and classification of cultivars in fig. 相似文献
20.
I. I. Korshikov L. A. Kalafat A. N. Lisnichuk T. I. Velicoridko E. A. Mudrik 《Russian Journal of Genetics》2011,47(7):829-835
Allozyme variation at ten polymorphic loci and mating system was studied in three small isolated relict populations (4.4 to
22 ha) and in three artificial stands of Pinus sylvestris from the Kremenets Hill Ridge and Maloe Poles’e. It was established that the mean heterozygosity of 130 to 140 year-old trees
from natural populations (H
O = 0.288; H
E = 0.277) was substantially lower, compared to 30 to 40 year-old trees from artificial stands (H
O = 0.358; H
E = 0.330). The observed heterozygosity of seed embryos (H
O = 0.169 and 0.180) was substantially lower than of the mature trees from populations and artificial stands, respectively.
In the embryo samples, irrespectively of the forest stand origin, substantial hetedrozygote deficiency was observed (at six
to eight loci), compared to the Hardy-Weinberg expectations. The proportion of cross pollination in the populations and artificial
stands was low, t
m = 0.588 to 0.721; and t
m = 0.455 to 0.837, respectively. 相似文献