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1.
Casa AM Mitchell SE Smith OS Register JC Wessler SR Kresovich S 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(1):104-110
Recently, a new type of molecular marker has been developed that is based on the presence or absence of the miniature inverted
repeat transposable element (MITE) family Heartbreaker (Hbr) in the maize genome. These so-called Hbr markers have been shown to be stable, highly polymorphic, easily mapped, and evenly distributed throughout the maize genome.
In this work, we used Hbr-derived markers for genetic characterization of a set of maize inbred lines belonging to Stiff Stalk (SS) and Non-Stiff Stalk
(NSS) heterotic groups. In total, 111 markers were evaluated across 62 SS and NSS lines. Seventy six markers (68%) were shared
between the two groups, and 25 of the common markers occurred at fairly low frequency (≤0.20). Only two markers (3%) were
monomorphic in all samples. Although DNA sequencing indicated that 5.5% of same-sized DNA fragments were non-homologous, this
result did not affect the cluster analyses (i.e., relationships obtained from the Hbr data were congruent with those derived from pedigree information). Distance matrices generated from Hbr markers were significantly correlated (p<0.001) with those obtained from pedigree (r=0.782), RFLPs (r=0.747), and SSRs (r=0.719). Overall, these results indicated that Hbr markers could be used in conjunction with other molecular markers for genotyping and relationship studies of related maize
inbred lines.
Received: 26 February 2001 / Accepted: 20 April 2001 相似文献
2.
Berchemiella wilsonii var. pubipetiolata (Rhamnaceae) is an endangered tree in eastern China. Habitat destruction has resulted in fragmentation of remnant populations
and extinction of local populations. AFLP and cpDNA markers were used to determine the population structure of remnant populations
of B. wilsonii var. pubipetiolata. Moderate nuclear genomic diversity was found within each of the four remnant populations (H
S = 0.141–0.172), while the cpDNA haplotype diversity in each population ranged from 0.356 to 0.681. Six haplotypes were identified
by a combined cpRFLP and cpSSR analysis in a total of 89 individuals. AMOVA revealed significantly AFLP genetic differentiation
within and between regions (ΦSC = 0.196, ΦCT = 0.396, respectively), and a high cpDNA haplotype differentiation between regions (ΦCT = 0.849). The results suggest low gene flow between populations of B. wilsonii var. pubipetiolata. Strong genetic divergence between two regional populations as revealed by both AFLP and cpDNA markers provided convincing
evidence that two distinct evolutionary lineages existed, and should be recognized as ‘evolutionary significant units’ (ESUs)
for conservation concerns. 相似文献
3.
Amine Zraidi Gertraud Stift Martin Pachner Abdolali Shojaeiyan Li Gong Tamas Lelley 《Molecular breeding : new strategies in plant improvement》2007,20(4):375-388
Using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR),
and morphological traits, the first genetic maps for Cucurbita pepo (2n=2x=40) were constructed and compared. The two mapping populations consisted of 92 F2 individuals each. One map was developed from a cross between an oil-seed pumpkin breeding line and a zucchini accession,
into which genes for resistance to Zucchini Yellow Mosaic Virus (ZYMV) from a related species, C. moschata, had been introgressed. The other map was developed from a cross between an oil-seed pumpkin and a crookneck variety. A total
of 332 and 323 markers were mapped in the two populations. Markers were distributed in each map over 21 linkage groups and
covered an average of 2,200 cM of the C. pepo genome. The two maps had 62 loci in common, which enabled identification of 14 homologous linkage groups. Polyacrylamide
gel analyses allowed detection of a high number of markers suitable for mapping, 10% of which were co-dominant RAPD loci.
In the Pumpkin-Zucchini population, bulked segregant analysis (BSA) identified seven markers less than 7 cM distant from the
locus n, affecting lignification of the seed coat. One of these markers, linked to the recessive hull-less allele (AW11-420), was
also found in the Pumpkin-Crookneck population, 4 cM from n. In the Pumpkin-Zucchini population, 24 RAPD markers, previously introduced into C. pepo from C. moschata, were mapped in two linkage groups (13 and 11 markers in LGpz1 and LGpz2, respectively), together with two sequence characterized
amplified region (SCAR) markers linked to genes for resistance to ZYMV. 相似文献
4.
A. V. Semenova G. A. Rubtsova K. I. Afanas’ev S. D. Pavlov 《Russian Journal of Genetics》2010,46(7):894-897
The variation of a sample of rainbow trout (Parasalmo (Oncorhynchus) mykiss) from natural populations of several rivers of the Kamchatka Peninsula with respect to 43 microsatellite DNA loci has been
studied. These loci were earlier used for analysis of Asian populations of closely related salmonids. Ten of them may be regarded
as markers and seen promising for further studies on intraspecific relationships of rainbow trout of Kamchatka. Their use
in studies on more numerous samples from different localities and populations of Parasalmo (O.) mykiss in the Asian part of the species range will ensure efficient population genetic analysis of the Kamchatka population group
of this species. 相似文献
5.
Raghvendra Kumar Mishra Anil Kumar Swati Chaudhary Sushil Kumar 《Journal of genetics》2009,88(2):227-232
The multifoliate pinna (mfp) mutation alters the leaf-blade architecture of pea, such that simple tendril pinnae of distal domain are replaced by compound
pinna blades of tendrilled leaflets in mfp homozygotes. The MFP locus was mapped with reference to DNA markers using F2 and F2:5 RIL as mapping populations. Among 205 RAPD, 27 ISSR and 35 SSR markers that demonstrated polymorphism between the parents
of mapping populations, three RAPD markers were found linked to the MFP locus by bulk segregant analyses on mfp/mfp and MFP/MFP bulks assembled from the F2:5 population. The segregational analysis of mfp and 267 DNA markers on 96 F2 plants allowed placement of 26 DNA markers with reference to MFP on a linkage group. The existence of common markers on reference genetic maps and MFP linkage group developed here showed that MFP is located on linkage group IV of the consensus genetic map of pea. 相似文献
6.
Fuli Liu Xiuliang Wang Jianting Yao Wandong Fu Delin Duan 《Journal of applied phycology》2010,22(1):109-111
Expressed sequence tag-derived microsatellite markers (EST-SSR) were generated and characterized in Laminaria japonica using data mining from updated public EST databases and polymorphism testing. Fifty-eight of 578 ESTs (10.0%) containing
various repeat motifs were used to design polymerase chain reaction (PCR) amplification primers. A total of 12 pairs of primer
were generated and used in the PCR amplification. Alleles per locus ranged from two to ten (average of 5.7). The observed
heterozygosities and expected heterozygosities were from 0.045 to 0.543 and from 0.056 to 0.814, respectively. All loci were
in Hardy–Weinberg equilibrium and no linkage disequilibrium was detected. These robust, informative, and potentially transferable
polymorphic markers appear suitable for population, genetic, parentage, and mapping studies of L. japonica. 相似文献
7.
Kouichi Kawamura Masashi Kubota Miki Furukawa Yasushi Harada 《Conservation Genetics》2007,8(5):1163-1176
The amago salmon, Oncorhynchus masou ishikawae, is an endemic subspecies of O. masou in Japan. Owing to the extensive stocking of hatchery fish throughout Japan, indigenous populations of O. m. ishikawae are now on the verge of extinction. We examined the genetic effects of stocking hatchery fish on wild populations in the
River Koza, Japan, using microsatellite and mitochondrial DNA (mtDNA) markers. For mtDNA, haplotype mt1, which is common in
wild populations, was present exclusively in isolated wild populations assumed to be unaffected by previous stocking, while
it was never observed in hatchery fish. Genetic diversity was much higher in wild populations in the stocked area, which shared
many mtDNA haplotypes with hatchery fish, than in isolated wild populations with haplotype mt1. Pairwise F
ST estimates based on microsatellites showed significant differentiation among the isolated populations with many microsatellite
loci monomorphic. Significant deviation from Hardy–Weinberg equilibrium was observed in wild populations in the area subject
to stocking, where a Bayesian-based assignment test showed a high level of introgression with hatchery fish. These results
suggest that wild populations with haplotype mt1, which became isolated through anthropogenic environmental change in the
1950–1960s, represent indigenous populations of O. m. ishikawae in the River Koza. They have low genetic diversity, most likely caused by genetic bottlenecks following damming and environmental
deterioration, while stocking of hatchery fish over the past 30 years apparently had a large impact on the genetic structure
of wild populations in the main channel of the River Koza. 相似文献
8.
Ryu Osaka Masayoshi Watada Daisuke Kageyama Masashi Nomura 《Symbiosis (Philadelphia, Pa.)》2010,52(1):41-45
A maternally-inherited spiroplasma endosymbiont of Drosophila hydei does not exert apparent phenotypes on both sexes of its host and is prevalent in natural populations of D. hydei. Our previous experiments using a laboratory stock of D. hydei revealed that low temperatures (such as 15°C and 18°C) dramatically lower the vertical transmission rates of this spiroplasma.
Therefore, we hypothesized that, in temperate regions, the infection frequencies may decrease in cool seasons but increase
in the summer season. To clarify the temporal population dynamics of the spiroplasma infection, D. hydei were collected from two Japanese populations in 2006–2008 from May to early August, representing the only period when a number
of D. hydei are collectable in Japan, and examined for spiroplasma infection. Within each year, the frequency of spiroplasma infection
fluctuated considerably in both populations. Consistent with our hypothesis, the infection frequency showed an increasing
trend in both populations in 2007. However, the data in 2006 and 2008 did not show consistent patterns of increase. The population
dynamics of spiroplasma infection may be affected but not critically determined by temperature. Moreover, despite the fluctuation
within each year, the infection frequencies seemed to be stable across the years. The frequencies of spiroplasma infection
in D. hydei populations may be stabilized by multiple factors. One of these factors may involve a context-dependent positive effect of
spiroplasma on the fitness of D. hydei, as was recently observed in laboratory experiments. 相似文献
9.
M. N. Melnikova S. D. Pavlov A. A. Kolesnikov N. B. Petrov 《Russian Journal of Genetics》2010,46(6):699-704
Using AP-PCR, the genome of Kamchatka mykiss (Parasalmo (O.) mykiss) was examined. Polymorphic fragments, implying geographic differences among the samples, were selected, cloned, and sequenced.
Based on these sequences, longer, specific SCAR primers were selected and constructed. Using the BLAST software program, the
sequences were analyzed for analogy to those from the GenBank database. It seemed likely that all sequences obtained belonged
to earlier unexamined repeated sequences, variable in the populations of the species of interest. A total of seven SCAR markers,
characterized by population-significant variability of the DNA products in Kamchatka geographic group of rainbow trout were
constructed. These markers can be used for further investigation of the species Parasalmo (O.) mykiss. The SCAR marker sequences were deposited in GenBank under the accession numbers EU805500 to EU805506. 相似文献
10.
In vitro culture is an important aid for ex situ conservation of rare, endemic or threatened plants. In this work, we establish an efficient method for the seed germination,
seedling development, and axillary shoot propagation of Centaurea zeybekii Wagenitz. The seeds, collected from a wild population, were surface sterilised and cultured on various in vitro germination media. The effects of photoperiod and temperature on seed germination were also investigated. Germinations were
obtained after 6 weeks in culture and the radicle emergence was evaluated as a main indicator. A high frequency of germination
was obtained on distilled water supplemented with vitamines and 1 mg/L GA3. Although the seed germination frequencies were not affected by photoperiod, the highest germination frequency was obtained
at 24 ± 2°C. A high frequency of axillary shoot proliferation was produced on MS medium supplemented with 1 mg/L BA. Then,
the axillary shoots were separated and transferred to MS medium with or without plant growth regulators for rooting. Rhizogenezis
was promoted after 6 weeks only in MS and 1/2 MS media containing 0.5 mg/L IBA. The rooting process was very slow and the
percentage of shoot rooting was also very low (15%).
The present study not only enables reinforcement of wild plant populations using ex situ growth of individuals, but it also helps to large number of aseptic seedling to use it in clonaly micropropagation studies. 相似文献
11.
The clonal diversity of Clintonia udensis Trautv. et Mey. was detected by ISSR markers among 16 populations, and its correlation with ecological factors was analyzed as well
in this work. Results showed that individuals (clonal ramets) per genotype were 1.12 and 1.149 at population and species levels,
respectively, and that the 16 populations were all multiclonal. The detected genotypes were localized, without exception,
within populations but demonstrated relatively high clonal differentiation among populations. The clonal diversity of the
studied populations was high, with the average Simpson’s index of 0.975, while the genets showed a clonal architecture of
“guerilla”. The population genetic diversities revealed by genet were consistent with those by ramet, further confirming their
genetic differentiation among populations. And its genotype diversity within populations probably resulted largely from the
frequent seedling regeneration and self-compatibility. In addition, the correlation analysis further revealed that, among
the ecological factors, Simpson’s index of C. udensis had a significant positive correlation (P<0.05) with pH values in the soil but not others. 相似文献
12.
An understanding of the variation pattern in disease resistance (R) genes is essential for its use in breeding programs aimed at neutralizing the threat of pathogens. Although the variation
between populations is well known, there is little research about R-gene variation patterns within populations. Here, we investigate the polymorphism at three R-gene loci of 39 individual plants from nine populations of Arabidopsis thaliana. Our data suggest that alleles of each locus from individuals within a local population were either nearly identical, or
highly diverse as ones between populations. The vast majority (92.5%) of within-population variation was shared globally,
with high levels of allelic diversity (up to 11.7%) and abundant diverse-alleles. This unique pattern of within-population
variation at R-loci suggests that individual plants within a population had the great potential to maintain a high level of globally-shared
polymorphisms, and that the diversifying selection was the major force maintaining such polymorphisms. Consequently, the shared-polymorphism
became recyclable for new R-genes, as the corresponding avirulence re-emerges in pathogen populations.
Nucleotide sequence data reported are available in the GenBank databases under the accession numbers EF368054-EF368158. 相似文献
13.
Genetic variation and clonal diversity of nine populations of Bromus ircutensis Kom. from the Otingdag sandy land were investigated using Inter Simple Sequence Repeat (ISSR) markers. A total of 102 bands were amplified by using 11 ISSR primers chosen for the study. Among those 99% were polymorphic indicating high level of genetic variation at the species
level with a mean genetic diversity (H) of 0.292 and Shannon information index (I) of 0.450. Percentage of polymorphic loci (PPL) of nine populations was 76.48% on average, which provides more evidence of considerable genetic variation at the population
level. AMOVA analysis revealed that total genetic variation was higher within populations (87.06%) than between populations (12.94%),
which is mainly the result of the extensive gene flow (Nm = 1.682) among B. ircutensis populations. UPGMA cluster analysis divided the nine populations into two groups. There was significant or moderate negative correlations between
genetic diversity parameters (PPL, H, I) and longitude or latitude. Mantel test also showed a significant correlation between geographical distance and genetic distance
(r = 0.681, p = 0.002). Our findings indicated that distribution of B. ircutensis populations was influenced by geographical and ecological factors. Clonal diversity was also high with 108 individuals identified
by 11 ISSR primers being all of different genets. Our results provide a molecular basis for sustainable management and conservation
of B. ircutensis in the study area. 相似文献
14.
LV Dos Santos MV de Queiroz MF Santana MA Soares EG de Barros EF de Araújo T Langin 《World journal of microbiology & biotechnology》2012,28(3):1087-1095
A nonautonomous element of 624 bp, called RetroCl1 (Retroelement Colletotrichum lindemuthianum 1), was identified in the plant pathogenic fungus Colletotrichum lindemuthianum. RetroCl1 contains terminal direct repeats (223 bp) that are surrounded by CTAGT sequences. It has a short internal domain of 178 bp
and shows characteristics of terminal-repeat retrotransposon in miniature (TRIM) family. We used RetroCl1 sequence to develop molecular markers for the Colletotrichum genus. IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism)
markers were used to analyze the genetic diversity of C. lindemuthianum. Fifty-four isolates belonging to different races were used. A total of 45 loci were amplified. The Nei index showed significant
differences among the populations divided according to race, indicating that they are structured according to pathotype. No
clear correlation between IRAP and REMAP markers with pathogenic characterization was found. C. lindemuthianum has high genetic diversity, and the analysis of molecular variance showed that 51% of variability is found among the populations
of different races. The markers were also tested in different Colletotrichum species. In every case, multiple bands were amplified, indicating that these markers can be successfully used in different
species belonging to the Colletotrichum genus. 相似文献
15.
Stojałowski SA Milczarski P Hanek M Bolibok-Brągoszewska H Myśków B Kilian A Rakoczy-Trojanowska M 《Journal of applied genetics》2011,52(3):313-318
The Rfc1 gene controls restoration of male fertility in rye (Secale cereale L.) with sterility-inducing cytoplasm CMS-C. Two populations of recombinant inbred lines (RIL) were used in this study to
identify DArT markers located on the 4RL chromosome, in the close vicinity of the Rfc1 gene. In the population developed from the 541×2020LM intercross, numerous markers tightly linked with the restorer gene
were identified. This group contained 91 DArT markers and three SCARs additionally analyzed in the study. All these markers
were mapped in the distance not exceeding 6 cM from the gene of interest. In the second mapping population (541×Ot1-3 intercross),
only 9 DArT markers located closely to the Rfc1 gene were identified. Five of these DArT markers were polymorphic in both populations. 相似文献
16.
S. D. Pavlov A. A. Kolesnikov M. N. Melnikova M. V. Ushakova 《Russian Journal of Genetics》2004,40(12):1407-1412
The populations of mykizha Parasalmo (O.) mykiss from western and eastern coasts of Kamchatka were studied by restriction analysis of a fragment of fish mitochondrial genome that included the control region and the region of the cytochrome b gene ( cytb). The restriction patterns obtained with five enzymes ( MspI; Tru1I; RsaI; BsuRI; DdeI) were identical in all studied individuals. Sequencing of the cytb gene showed high similarity between all samples (99.6–100%). In general, the geographical group of mykiss from Kamchatka is monophyletic with low genetic divergence at the population level. Shantarian mykiss originates most likely from that native to Kamchatka.Translated from Genetika, Vol. 40, No. 12, 2004, pp. 1695–1701.Original Russian Text Copyright © 2004 by Pavlov, Kolesnikov, Melnikova, Ushakova. 相似文献
17.
Wang J Raman H Zhou M Ryan PR Delhaize E Hebb DM Coombes N Mendham N 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2007,115(2):265-276
Aluminium (Al) tolerance in barley is conditioned by the Alp locus on the long arm of chromosome 4H, which is associated with Al-activated release of citrate from roots. We developed
a high-resolution map of the Alp locus using 132 doubled haploid (DH) lines from a cross between Dayton (Al-tolerant) and Zhepi 2 (Al-sensitive) and 2,070
F2 individuals from a cross between Dayton and Gairdner (Al-sensitive). The Al-activated efflux of citrate from the root apices
of Al-tolerant Dayton was 10-fold greater than from the Al-sensitive parents Zhepi 2 and Gairdner. A suite of markers (ABG715,
Bmag353, GBM1071, GWM165, HvMATE and HvGABP) exhibited complete linkage with the Alp locus in the DH population accounting 72% of the variation for Al tolerance evaluated as relative root elongation. These
markers were used to map this genomic region in the Dayton/Gairdner population in more detail. Flanking markers HvGABP and
ABG715 delineated the Alp locus to a 0.2 cM interval. Since the HvMATE marker was not polymorphic in the Dayton/Gairdner population we instead investigated
the expression of the HvMATE gene. Relative expression of the HvMATE gene was 30-fold greater in Dayton than Gardiner. Furthermore, HvMATE expression in the F2:3 families tested, including all the informative recombinant lines identified between HvGABP and ABG715 was significantly correlated
with Al tolerance and Al-activated citrate efflux. These results identify HvMATE, a gene encoding a multidrug and toxic compound extrusion protein, as a candidate controlling Al tolerance in barley. 相似文献
18.
Arctophila fulva var. pendulina is a rare endemic perennial grass confined to seashore and riverbank meadows around the Bothnian Bay, the northernmost part
of the Baltic Sea. The number of A. fulva populations has decreased during the last few decades in Finland and Sweden, and nowadays there are only eight populations
left in the drainage area of the Bothnian Bay. We investigated the distribution of genetic variation within and between six
subpopulations in the largest remaining population at Liminka Bay, Finland, using amplified fragment length polymorphism (AFLP)
markers. Relatively high amounts of variation were found in the subpopulations, the mean Nei’s expected heterozygosity being
typical (0.267) for an outcrossing species. Despite the fact that no seedlings or viable seeds of A. fulva have been found in the previous field studies, the observed high genotypic diversity suggested that sexual reproduction has
played an important role at some time during the history of the studied A. fulva population. Analysis of population structure revealed a low level of genotypic differentiation (ΦST=0.046) between subpopulations, and also significant sub-structuring within subpopulations. Isolation-by-distance between
subpopulations was present on scales larger than 1 km. The overall pattern of genetic variation within and between subpopulations
suggest that the population has characters of both stepping-stone and metapopulation models. Because our results suggested
that subpopulations are more or less ephemeral, the conservation and management effort in this species should be targeted
to conservation of the required habitat of the species instead of extant subpopulations. 相似文献
19.
Laetitia Mahé Marie-Christine Combes Vitor M. P. Várzea Claire Guilhaumon Philippe Lashermes 《Molecular breeding : new strategies in plant improvement》2008,21(1):105-113
Coffee leaf rust due to Hemileia vastatrix is one of the most serious diseases in Arabica coffee (Coffea arabica). A resistance gene (SH3) has been transferred from C. liberica into C. arabica. The present work aimed at developing sequence-characterized genetic markers for leaf rust resistance. Linkage between markers
and leaf rust resistance was tested by analysing two segregating populations, one F2 population of 101 individuals and one backcross (BC2) population of 43 individuals, derived from a cross between a susceptible and a SH3-introgressed resistant genotype. A total
of ten sequence-characterized genetic markers closely associated with the SH3 leaf rust resistance gene were generated. These included simple sequence repeats (SSR) markers, sequence-characterised amplified
regions (SCAR) markers resulting from the conversion of amplified fragment length polymorphism (AFLP) markers previously identified
and SCAR markers derived from end-sequences of bacterial artificial chromosome (BAC) clones. Those BAC clones were identified
by screening of C. arabica genomic BAC library using a cloned AFLP-marker as probe. The markers we developed are easy and inexpensive to run, requiring
one PCR step followed by gel separation. While three markers were linked in repulsion with the SH3 gene, seven markers were clustered in coupling around the SH3 gene. Notably, two markers appeared to co-segregate perfectly with the SH3 gene in the two plant populations analyzed. These markers are suitable for marker-assisted selection for leaf rust resistance
and to facilitate pyramiding of the SH3 gene with other leaf rust resistance genes. 相似文献
20.
Cool-season grasses often harbor obligate fungal symbionts from the genus Neotyphodium, and these symbiota can function as a single ecological unit. Previous studies have shown that gene flow in Neotyphodium in Festuca arizonica is low enough such that populations could diverge and form local adaptations. A reciprocal transplant experiment was performed
between two F. arizonica/Neotyphodium populations in Arizona, Clint’s Well and Flagstaff, using symbiota with the most common Neotyphodium genotypes in each population, to test for local adaptations. The genetic difference between populations is potentially large
as Neotyphodium from Clint’s Well are of hybrid origin. Local environmental variation was the most important source of variation for F. arizonica/Neotyphodium symbiota growth, with individuals at Flagstaff growing larger and individuals at Clint’s Well not reproducing. Local environment
and the source population of the symbiota interacted to affect vegetative growth. Symbiota from Clint’s Well, which harbor
hybrid Neotyphodium, had higher volume/wet mass and volume/dry mass ratios but only in the marginal Clint’s Well habitat. The local environment
also affected F. arizonica/Neotyphodium reproduction because only symbiota transplanted to Flagstaff reproduced. Symbiota from Clint’s Well produced more panicles,
whereas symbiota from Flagstaff with nonhybrid Neotyphodium produced greater seed mass per panicle. Overall seed mass production was not different, suggesting that the two strategies
are functionally equivalent. We find that F. arizonica/Neotyphodium symbiota vary geographically, but potential local adaptations are only apparent in marginal habitats and may be related to
the evolutionary history of the Neotyphodium part of the symbiota. 相似文献