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Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species 总被引:9,自引:0,他引:9
T. Ishii S. R. McCouch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(8):1257-1266
Primer pairs flanking ten chloroplast microsatellite loci, originally identified in Oryza
sativa cv Nipponbare, were evaluated for amplification and allelic diversity using a panel of 13 diverse cultivars of rice (O. sativa), 19 accessions of wild rice (three O. officinalis, five O. latifolia, five O.
minuta, four O. australiensis, one O. brachyantha and one O. ridleyi) and eight other Gramineae species (maize, teosinte, wheat, oat, barley, pearl millet, sorghum and sugarcane). Amplified
products were obtained for all samples at nine out of ten loci. Among the rice cultivars, the number of alleles per locus
ranged from one to four, with monomorphic patterns observed at five loci. The average polymorphism information content (PIC)
value at the other five (polymorphic) loci was 0.54 among the 13 cultivars. When wild rice and the other Gramineae species
were compared based on the proportion of shared alleles, their phylogenetic relationships were in agreement with previous
studies using different types of markers; however, the magnitude of the differences based on chloroplast microsatellites underestimated
the genetic distance separating these divergent species and genera. A sequence-based comparison of homologous regions of the
rice and maize chloroplast genomes revealed that, while a high level of microsynteny is evident, the occurrence of actively
evolving microsatellite motifs in specific regions of the rice chloroplast genome appears to be mainly a species or genome-specific
phenomenon. Thus the chloroplast primer pairs used in this study bracketed mutationally active microsatellite motifs in rice
but degenerate, interrupted motifs or highly conserved, mutationally inert motifs in distantly related genera.
Received: 17 March 1999 / Accepted: 11 November 1999 相似文献
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Application and functional study of dwarf and semi-dwarf genes are of great importance to both crop breeding and molecular biology. A new semi-dwarf gene, sd-t(t), non-allelic to sd-1, had been identified in an indica rice variety, Aitaiyin 2. In this study the gene was genetically mapped by using an F2 population, which consisted of 474 individuals developed from a cross between Aitaiyin 2 and B30. The sd-t(t) gene was located between the RFLP markers R514 and R1408B with a distance of 1.1 cM to R514, and 4.5 cM to R1408B on chromosome 4. A physical contig covering the sd-t(t) mapping region was further constructed by screening a BAG library with R514 and R1408B as probes, and the physical distance between R514 and R1408B was estimated at approximately 147 kb. This result will facilitate map-based cloning of the sd-t(t) gene. 相似文献
5.
Li Fengling Flanagan Catherine A. Zhao Yuju Ma Hong Huang Hai 《Plant Molecular Biology Reporter》1999,17(2):109-122
Transposon tagging is a useful tool for biological studies. Transposon insertions have been used to obtain new mutants which are extremely helpful in understanding gene function. These insertions immediately provide a means to isolate the corresponding genes. Transposon tagging has also been used to clone genes previously defined by point mutations. In addition, transposon insertions into cloned genes that lack mutations can be generated to facilitate functional analysis. The maize Ac/Ds transposon elements are known to transpose to local sites with high frequencies and have been shown to function in several dicots. To generate a collection of Ds elements for the purpose of targeted insertional mutagenesis of mapped genes in Arabidopsis, we have mapped 44 Ds insertions by simple sequence length polymorphism (SSLP). Because the Arabidopsis genome project is advancing rapidly, many genes will be discovered whose functions are unknown. The mapped 44 Ds insertions will be a useful resource for post-genome analysis of gene functions in Arabidopsis. 相似文献
6.
Although Slc:Wistar rats are used widely in biomedical research as outbred rats, close
similarities in growth curves, survival rates, and immunological and biochemical
phenotypes have been reported between Slc:Wistar and F344 inbred rats. We reported
previously that nine genetic variations that were fixed in Slc:Wistar rats had identical
genotypes in F344 rats. Here, we examined the genetic characteristics of Slc:Wistar rats
using 27 simple-sequence length polymorphism (SSLP) markers and compared them with other
Wistar stocks available in Japan and with some F344 strains. Among 27 SSLP loci, 23 (85%)
were fixed in the Slc:Wistar rats, which was the highest among the other Wistar stocks.
The 23 fixed loci shared identical genotypes with corresponding loci in F344 rats.
Further, the predominant allele types in the unfixed loci had allele frequencies as high
as 80%, and these alleles were identical in the F344 rats. When the nine genetic
variations reported previously are added, a total of 32 (89%) out of the 36 loci examined
were fixed and identical in the Slc:Wistar and F344 rat genomes. These findings indicate
the low genetic variation in Slc:Wistar rats and the high genetic similarity between the
Slc:Wistar and F344 inbred rats. This study demonstrates the importance of characterizing
outbred rats and the need to pay ample attention to the genetic characteristics the
Slc:Wistar rats for their proper use. 相似文献
7.
Application and functional study of dwarf and semi-dwarf genes are of great importance to both crop breeding and molecular biology. A new semi-dwarf gene, sd-t(t), non-allelic to sd-1, had been identified in an indica rice variety, Aitaiyin 2. In this study the gene was genetically mapped by using an F2 population, which consisted of 474 individuals developed from a cross between Aitaiyin 2 and B30. The sd-t(t) gene was located between the RFLP markers R514 and R1408B with a distance of 1.1 cM to R514, and 4.5 cM to R1408B on chromosome 4. A physical contig covering the sd-t(t) mapping region was further constructed by screening a BAC library with R514 and R1408B as probes, and the physical distance between R514 and R1408B was estimated at approximately 147 kb. This result will facilitate map-based cloning of the sd-t(t) gene. 相似文献
8.
Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs) 总被引:14,自引:0,他引:14
M. R. Thomas N. S. Scott 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1993,86(8):985-990
Microsatellite repeat sequences were investigated as sequenced-tagged site (STS) DNA markers to determine the potential for genetic analysis of the grapevine genome. The PCR-generated markers detect codominant alleles at a single locus or site in the genome. The marker type is very informative detecting high heterozygosity (69%–88%) within individual grapevine cultivars and high genetic variation between cultivars, making it a useful marker type for plant genome mapping and genome typing. For five loci a screening of 26 V. vinifera cultivars found 13, 12, 8, 5, and 4 different length alleles respectively with some alleles more common than others. The genomic DNA sequences surrounding microsatellite sequences were conserved within the genus permitting STS primers to amplify STSs from other Vitis species. These Vitis species were found to have some unique alleles not present in V. vinifera. 相似文献
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Integrated map of AFLP, SSLP and RFLP markers using a recombinant inbred population of rice (Oryza sativa L.) 总被引:7,自引:0,他引:7
Y. G. Cho S. R. McCouch M. Kuiper M.-R. Kang J. Pot J. T. M. Groenen M. Y. Eun 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(3):370-380
A molecular map of rice consisting of 231 amplified fragment length polymorphisms (AFLPs), 212 restriction fragment length
polymorphisms (RFLPs), 86 simple-sequence length polymorphisms (SSLPs), five isozyme loci, and two morphological mutant loci
[phenol staining of grain (Ph), semi-dwarf habit (sd-1)] has been constructed using an F11 recombinant inbred (RI) population. The mapping population consisted of 164 RI lines and was developed via single-seed descent
from an intercross between the genetically divergent parents Milyang 23 (M) (tongil type) and Gihobyeo (G) ( japonica type). A subset of previously mapped RFLP and SSLP markers were used to construct the map framework. The AFLP markers were
derived from ten EcoRI(+2) and MseI(+3) primer combinations. All marker types were well distributed throughout the 12 chromosomes. The integrated map covered
1814 cM, with an average interval size of 3.4 cM. The MG map is a cornerstone of the Korean Rice Genome Research Program (KRGRP)
and is being continuously refined through the addition of partially sequenced cDNA markers derived from an immature-seed cDNA
library developed in Korea, and microsatellite markers developed at Cornell. The population is also being used for quantitative
trait locus (QTL) analysis and as the basis for marker-assisted variety development.
Received: 24 June 1997 / Accepted: 25 November 1997 相似文献
10.
Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.) 总被引:49,自引:0,他引:49
X. Chen S. Temnykh Y. Xu Y. G. Cho S. R. McCouch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(4):553-567
Ninety-four newly developed microsatellite markers were integrated into existing RFLP framework maps of four rice populations,
including two doubled haploid, a recombinant inbred, and an interspecific backcross population. These simple sequence repeats
(SSR) were predominantly poly(GA) motifs, targetted because of their abundance in rice. They were isolated from a previously
described sheared library and a newly constructed enzyme-digested library. Differences in the average length of poly(GA) tracts
were observed for clones isolated from the two libraries. The length of GA motifs averaged 21 repeat units for clones isolated
from the Tsp-509-digested library, while motifs averaged 17 units for clones from the sheared library. There was no evidence of clustering
of microsatellite markers near centromeres or telomeres. Mapping of the 94 newly developed markers as well as of 27 previously
reported microsatellites provided genome-wide coverage of the 12 chromosomes, with an average distance of 1 SSLP (simple sequence
repeat polymorphism) per 16–20 cM.
Received: 13 February 1997/Accepted: 28 February 1997 相似文献