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1.
Yoshida K Miyashita NT Ishii T 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,109(7):1406-1416
Nucleotide variation in the alcohol dehydrogenase (Adh1) locus region of the wild rice Oryza rufipogon and its related species was analysed to clarify the maintenance mechanism of DNA variation in Oryza species. The estimated nucleotide diversity in the Adh1 locus region of O. rufipogon was 0.002, which was one of the lowest values detected in nuclear loci of plant species investigated so far. Tests of neutrality detected significantly negative deviation from the neutral mutation model for the coding region, especially for replacement sites. When each of the ADH1 domains was considered, significance was detected only for the catalytic domain 1. These results suggest purifying selection in the Adh1 coding region. In the phylogenetic tree of Oryza species based on Adh1 variation, cultivated rice O. sativa subspp. japonica and indica were included in the cluster of O. rufipogon. The genetic distance of the Adh1 region between O. rufipogon and O. sativa was as low as the nucleotide diversity of O. rufipogon. These results imply that O. rufipogon and O. sativa cannot be classified based on the nucleotide variation of Adh1. No replacement divergence between O. rufipogon and the other three A-genome species (O. glumaepatula, O. barthii and O. meridionalis) were detected, indicating that ADH1 is conserved in the A-genome species. On the other hand, between O. rufipogon and the E-genome species O. australiensis, replacement changes were detected only in the catalytic domain 1. The difference in replacement substitutions between the A- and E-genome species may be related to adaptive changes in the ADH1 domains, reflecting environmental differences where the species encounter anaerobic stress. 相似文献
2.
Zhang S Gu YQ Singh J Coleman-Derr D Brar DS Jiang N Lemaux PG 《Plant molecular biology》2007,64(5):589-600
An ∼247-kb genomic region from FF genome of wild rice Oryza brachyantha, possessing the smallest Oryza genome, was compared to the orthologous ∼450-kb region from AA genome, O. sativa L. ssp. japonica. 37 of 38 genes in the orthologous regions are shared between japonica and O. brachyantha. Analyses of nucleotide substitution in coding regions suggest the two genomes diverged ∼10 million years ago. Comparisons
of transposable elements (TEs) reveal that the density of DNA TEs in O. brachyantha is comparable to O. sativa; however, the density of RNA TEs is dramatically lower. The genomic fraction of RNA TEs in japonica is two times greater than in O. brachyantha. Differences, particularly in RNA TEs, in this region and in BAC end sequences from five wild and two cultivated Oryza species explain major genome size differences between sativa and brachyantha. Gene expression analyses of three ObDREB1 genes in the sequenced region indicate orthologous genes retain similar expression patterns following cold stress. Our results
demonstrate that size and number of RNA TEs play a major role in genomic differentiation and evolution in Oryza. Additionally, distantly related O. brachyantha shares colinearity with O. sativa, offering opportunities to use comparative genomics to explore the genetic diversity of wild species to improve cultivated
rice.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Data deposition: Sequence data from this article were deposited with GenBank Library under accession number DQ810282.
Shibo Zhang and Yong Qiang Gu contributed equally to the work 相似文献
3.
Zhou HF Zheng XM Wei RX Second G Vaughan DA Ge S 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2008,117(7):1181-1189
The cross compatible wild relatives of crops have furnished valuable genes for crop improvement. Understanding the genetics
of these wild species may enhance their further use in breeding. In this study, sequence variation of the nuclear Lhs1 gene was used to investigate the population genetic structure and gene flow of Oryza rufipogon and O. nivara, two wild species most closely related to O. sativa. The two species diverge markedly in life history and mating system, with O. rufipogon being perennial and outcrossing and O. nivara being annual and predominantly inbreeding. Based on sequence data from 105 plants representing 11 wild populations covering
the entire geographic range of these wild species, we detected significantly higher nucleotide variation in O. rufipogon than in O. nivara at both the population and species levels. At the population level the diversity in O. rufipogon (Hd = 0.712; θ
sil = 0.0017) is 2–3 folds higher than that in O. nivara (Hd = 0.306; θ
sil = 0.0005). AMOVA partitioning indicated that genetic differentiation among O. nivara populations (78.2%) was much higher than that among O. rufipogon populations (52.3%). The different level of genetic diversity and contrasting population genetic structure between O. rufipogon and O. nivara might be explained by their distinct life histories and mating systems. Our simulation using IM models demonstrated significant
gene flow from O. nivara to O. rufipogon, indicating a directional introgression from the annual and selfing species into the perennial and outcrossing species. The
ongoing introgression has played an important role in shaping current patterns of genetic diversity of these two wild species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
4.
Zining Wang Hui Guo Sylvie Cloutier 《Molecular breeding : new strategies in plant improvement》2017,37(1):3
Plant receptor-like kinase (Rlk) genes form a large family, each encoding a protein with a signal motif, a single transmembrane region, and a cytoplasmic kinase domain. Various gene duplications have contributed to the establishment and expansion of the family. Here, we characterized the formation and evolution of the Rlk gene family in cultivated rice and their possible progenitors. Using wheat Rlk gene sequences, we identified orthologs from the genomes of domesticated rice subspecies Oryza sativa ssp. japonica and ssp. indica and their putative progenitors O. glaberrima and O. rufipogon. The four chromosome 1 orthologous regions ranged from 103 to 281 kb comprising 181 syntenic blocks with 75 to 100% sequence identity. These regions contained 11–19 Triticum aestivum kinases (Taks) and 10–15 Lr10 receptor-like kinases (Lrks) organized in clusters and 3–12 transposable elements (TEs). Dot plot analyses showed that the 4 regions had 21–37 conserved catalytic domains, mainly in protein kinases (PKs) and tyrosine kinases (TyrKs) in coupling state. Over 50% of the sequences of glaberrima/rufipogon and japonica/indica pairs were colinear, while japonica/indica displayed a marked sequence expansion with duplicated genes and TEs. A total of 2312 single nucleotide polymorphisms (SNPs) and insertion-deletions (INDELs) were identified between japonica and indica. Duplication of the Rlk genes in O. glaberrima and O. rufipogon occurred after the grass species radiation and before the divergence of O. rufipogon from O. glaberrima; the orthologous Rlk genes from O. japonica and O. indica duplicated after O. sativa separated from O. rufipogon; paralogs, obtained through extensive duplication, happened after the separation of rice from maize. Tandem duplication was the major factor contributing to the gene copy number variation and genome size expansion. 相似文献
5.
Oryza rufipogon Griff. is the ancestor of Asian cultivated rice (O. sativa L.) and possesses valuable genes for rice breeding. Pollen abortion is one of the major causes of indica–japonica hybrid sterility in rice and it happens due to allelic interaction at the pollen sterility gene loci. A total of six loci
(Sa, Sb, Sc, Sd, Se, and Sf) have been found to be associated with F1 pollen sterility between indica and japonica rice, and five of them (all except Sf) have been mapped. Neutral alleles (S
n
) at each locus have the potential to overcome the pollen sterility associated with the respective locus. Therefore, exploitation
and utilization of neutral alleles have significant importance in overcoming indica–japonica hybrid sterility. In this study, an accession (IRW28) of O. rufipogon, native to China, was selected as paternal to cross with typical japonica (Taichung 65) and indica (Guanglu’ai 4) tester lines, and two F2 populations were developed. The simple sequence repeat markers tightly linked to five pollen sterility loci were applied
for genotyping the F2 populations. Chi-squared tests were applied to examine the normal segregation/distortion at each locus. The expected and
observed pollen sterility for each locus were estimated. As a result, the genotypes at five pollen sterility gene loci for
IRW28 were identified as: Sa
i−1/Sa
i−1, Sb
n
/Sb
n
, Sc
i−2/Sc
i−2, Sd
n
/Sd
n
and Se
n
/Se
n
. Our results suggest that IRW28 (O. rufipogon) has the neutral alleles for pollen fertility at the Sb, Sd and Se loci, and these alleles have a good affinity with indica and japonica rice. These neutral alleles provide valuable gene resources to overcome the inter-subspecific hybrid pollen sterility in
rice. 相似文献
6.
7.
S. Negrão M. M. Oliveira K. K. Jena D. Mackill 《Molecular breeding : new strategies in plant improvement》2008,22(2):159-168
The cultivated rice (Oryza sativa L.) has two subspecies, indica and japonica. The japonica rice germplasm has a narrower genetic diversity compared to the indica subspecies. Rice breeders aim to develop new varieties with a higher yield potential, with enhanced resistances to biotic
and abiotic stresses, and improved adaptation to environmental changes. In order to face some of these challenges, japonica rice germplasm will have to be diversified and new breeding strategies developed. Indica rice improvement could also profit from more “genepool mingling” for which japonica rice could play an important role. Interesting traits such as low-temperature tolerance, and wider climate adaptation could
be introgressed into the indica subspecies. In the past decade, huge developments in rice genomics have expanded our available knowledge on this crop and
it is now time to use these technologies for improving and accelerating rice breeding research. With the full sequence of
the rice genome, breeders may take advantage of new genes. Also new genes may be discovered from the genepool of wild relatives,
or landraces of the genus Oryza, and incorporated into elite japonica cultivars in a kind of “gene revolution” program. Expectedly, new technologies that are currently being optimized, aiming
for novel gene discovery or for tracking the regions under selection, will be suggested as new breeding approaches. This paper
revisits breeding strategies successfully employed in indica rice, and discusses their application in japonica rice improvement (e.g. ideotype breeding, wide hybridization and hybrid performance). 相似文献
8.
Soon-Jae Kwon Kyong-Cheul Park Jae-Han Son Thomas Bureau Cheul-Ho Park Nam-Soo Kim 《Molecules and cells》2009,27(4):459-465
MUG1 is a MULE transposon-related domesticated gene in plants. We assessed the sequence diversity, neutrality, expression, and
phylogenetics of the MUG1 gene among Oryza ssp. We found MUG1 expression in all tissues analyzed, with different levels in O. sativa. There were 408 variation sites in the 3886 bp of MUG1 locus. The nucleotide diversity of the MUG1 was higher than functionally known genes in rice. The nucleotide diversity (π) in the domains was lower than the average
nucleotide diversity in whole coding region. The π values in nonsynonymous sites were lower than those of synonymous sites.
Tajima D and Fu and Li D* values were mostly negative values, suggesting purifying selection in MUG1 sequences of Oryza ssp. Genome-specific variation and phylogenetic analyses show a general grouping of MUG1 sequences congruent with Oryza ssp. biogeography; however, our MUG1 phylogenetic results, in combination with separate B and D genome studies, might suggest an early divergence of the Oryza ssp. by continental drift of Gondwanaland. O. longistaminata MUG1 divergence from other AA diploids suggests that it might not be a direct ancestor of the African rice species.
These authors contributed equally to this work. 相似文献
9.
Liangming Chen Zhigang Zhao Xi Liu Linglong Liu Ling Jiang Shijia Liu Wenwei Zhang Yihua Wang Yuqiang Liu Jianmin Wan 《Molecular breeding : new strategies in plant improvement》2011,27(2):247-258
The incomplete fertility of japonica × indica rice hybrids has inhibited breeders’ access to the substantial heterotic potential of these hybrids. As hybrid sterility
is caused by an allelic interaction at a small number of loci, it is possible to overcome it by simple introgression at the
major sterility loci. Here we report the use of marker-assisted backcrossing to transfer into the elite japonica cv. Zhendao88 a photoperiod-sensitive male sterility gene from cv. Lunhui422S (indica) and the yellow leaf gene from line Yellow249 (indica). The microsatellite markers RM276, RM455, RM141 and RM185 were used to tag the fertility genes S5, S8, S7 and S9, respectively. Line 509S is a true-breeding photoperiod-sensitive male sterile plant, which morphologically closely resembles
the japonica type. Genotypic analysis showed that the genome of line 509S comprises about 92% japonica DNA. Nevertheless, hybrids between line 509S and japonica varieties suffer from a level of hybrid sterility, although the line is highly cross-compatible with indica types, with the resulting hybrids expressing a significant degree of heterosis. Together, these results suggest that segment
substitution on fertility loci based on known information and marker-assisted selection are an effective approach for utilizing
the heterosis of rice inter-subspecies. 相似文献
10.
Genes of the major histocompatibility complex (MHC) are exceptionally polymorphic due to the combined effects of natural and
sexual selection. Most research in wild populations has focused on the second exon of a single class II locus (DRB), but complete gene sequences can provide an illuminating backdrop for studies of intragenic selection, recombination, and
organization. To this end, we characterized class II loci in the banner-tailed kangaroo rat (Dipodomys spectabilis). Seven DRB-like sequences (provisionally named MhcDisp-DRB*01 through *07) were isolated from spleen cDNA and most likely comprise ≥5 loci; this multiformity is quite unlike the situation
in muroid rodents such as Mus, Rattus, and Peromyscus. In silico translation revealed the presence of important structural residues for glycosylation sites, salt bonds, and CD4+
T-cell recognition. Amino-acid distances varied widely among the seven sequences (2–34%). Nuclear DNA sequences from the Disp-DRB*07 locus (∼10 kb) revealed a conventional exon/intron structure as well as a number of microsatellites and short interspersed
nuclear elements (B4, Alu, and IDL-Geo subfamilies). Rates of nucleotide substitution at Disp-DRB*07 are similar in both exons and introns (π = 0.015 and 0.012, respectively), which suggests relaxed selection and may indicate that this locus is an expressed pseudogene.
Finally, we performed BLASTn searches against Dipodomys ordii genomic sequences (unassembled reads) and find 90–97% nucleotide similarity between the two kangaroo rat species. Collectively,
these data suggest that class II diversity in heteromyid rodents is based on polylocism and departs from the muroid architecture.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers EU817477–EU817485. 相似文献
11.
12.
The complementary sex determination (csd) gene is the primary gene determining the gender of honey bees (Apis spp). In this study we analyzed the polymorphism of csd gene in six Apis mellifera subspecies. The genomic region 3 of csd gene in these six A. mellifera was cloned, and identified. A total of 79 haplotypes were obtained from these six subspecies. Analysis showed that region
3 of csd gene has a high level of polymorphism in all the six A. mellifera subspecies. The A. m. anatolica subspecies has a slightly higher nucleotide diversity (π) than other subspecies, while the π values showed no significant
difference among the other five subspecies. The phylogenetic tree showed that all the csd haplotypes from different A. mellifera subspecies are scattered throughout the tree, without forming six different clades. Population differentiation analysis showed
that there are significant genetic differentiations among some of the subspecies. The NJ phylogenetic tree showed that the
A. m. caucasica and A. m. carnica have the closest relationship, followed by A. m. ssp, A. m. ligustica, A. m. carpatica and A. m. anatolica that were gathered in the tree in turn. 相似文献
13.
Selvaraj Michael Gomez N. Manikanda Boopathi S. Satheesh Kumar T. Ramasubramanian Zhu Chengsong P. Jeyaprakash A. Senthil R. Chandra Babu 《Acta Physiologiae Plantarum》2010,32(2):355-364
Drought is a major limitation for rice production in rainfed ecosystems. Identifying quantitative trait loci (QTLs) linked
to drought resistance provides opportunity to breed high yielding rice varieties suitable for drought-prone areas. Although
considerable efforts were made in mapping QTLs associated with drought-resistance traits in rice, most of the studies involved
indica × japonica crosses and hence, the drought-resistance alleles were contributed mostly by japonica ecotypes. It is desirable to look for genetic variation within indica ecotypes adapted to target environment (TE) as the alleles from japonica ecotype may not be expressed under lowland conditions. A subset of 250 recombinant inbred lines (RILs) of F8 generation derived from two indica rice lines (IR20 and Nootripathu) with contrasting drought-resistance traits were used to map the QTLs for morpho-physiological
and plant production traits under drought stress in the field in TE. A genetic linkage map was constructed using 101 polymorphic
PCR-based markers distributed over the 12 chromosomes covering a total length of 1,529 cM in 17 linkage groups with an average
distance of 15.1 cM. Composite interval mapping analysis identified 22 QTLs, which individually explained 4.8–32.2% of the
phenotypic variation. Consistent QTLs for drought-resistance traits were detected using locally adapted indica ecotypes, which may be useful for rainfed rice improvement. 相似文献
14.
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
15.
Bremia lactucae Regel (Chromista, Peronosporaceae) is an economically destructive pathogen, which causes downy mildew disease on lettuce
(Lactuca sativa L.) worldwide. The ribosomal internal transcribed spacer (ITS) of Bremia lactucae isolates was analyzed for the first time. The ITS region of lettuce downy mildew was observed to have a size of 2458 bp;
thereby, having one of the longest ITS sizes recorded to date. The majority of the extremely large sized ITS2 length of 2086
was attributed to the additional presences of nine repetitive elements with lengths of 179–194 bp, which between them shared
the low homology of 48–69%. Comparison of the ITS2 sequences with the B. lactucae isolates from other host plants showed that isolates present on Lactuca sativa were distinct from those on L. indica var. laciniata, as well as Hemistepta and Youngia. We suggest the high degree of sequence heterogeneity exhibited in the ITS2 region of B. lactucae may warrant the specific detection and diagnosis of this destructive pathogen or its division into several distinct species. 相似文献
16.
Conservation of 16 nuclear microsatellite loci, originally developed for Quercus macrocarpa (section Albae), Q. petraea, Q. robur (section Robur), and Q. myrsinifolia, (subgenus Cyclobalanopsis) was tested in a Q. infectoria ssp. veneris population from Cyprus. All loci could be amplified successfully and displayed allele size and diversity patterns that match
those of oak species belonging to the section Robur. At least in one case, limited amplification and high levels of homozygosity support the occurrence of “null alleles” caused
by a possible mutation in the highly conserved primer areas, thus hindering PCR. The sampled population exhibited high levels
of diversity despite the very limited distribution of this species in Cyprus and extended population fragmentation. Allele
sizes of Q. infectoria at locus QpZAG9 partially match those of Q. alnifolia and Q. coccifera from neighboring populations. However, sequencing showed homoplasy, excluding a case of interspecific introgression with
the latter, phylogenetically remote species. Q. infectoria ssp. veneris sequences at this locus were concordant to those of other species of section Robur, while sequences of Quercus alnifolia and Quercus coccifera were almost identical to Q. cerris. 相似文献
17.
Virgilio C. Andaya Thomas H. Tai 《Molecular breeding : new strategies in plant improvement》2007,20(4):349-358
Rice seedlings are sensitive to low temperatures (≤15°C) and under prolonged or repeated exposure, yellowing and stunting
are commonly observed. Damage to seedlings results in poor stand establishment and delayed maturation, which can cause significant
reductions in yield. In general, japonica rice varieties exhibit more cold tolerance than indica varieties. Earlier genetic analysis of the California rice variety M202 revealed several quantitative trait loci (QTL) that
contribute to its tolerance to low temperatures in comparison to the indica rice variety IR50. Among these QTL, qCTS4 is associated with tolerance to yellowing and stunting of rice seedlings and accounts for 40% of the phenotypic variation.
Here we report on the fine mapping of qCTS4 to a 128 kb region of chromosome 4, which is highly suppressed for recombination in our mapping populations. Our results
provide the necessary foundation for identifying the gene(s) underlying qCTS4 and the markers developed here may be used to introgress this region into indica varieties to improve seedling tolerance to low temperatures.
The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information
and does not imply recommendation or endorsement by the U.S. Department of Agriculture. 相似文献
18.
Mikami I Uwatoko N Ikeda Y Yamaguchi J Hirano HY Suzuki Y Sano Y 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2008,116(7):979-989
To examine continuous variation of amylose levels in Asian rice (Oryza sativa) landraces, the five putative alleles (Wx
a
, Wx
in
, Wx
b
, Wx
op
, and wx) at the wx locus were investigated in near-isogenic lines (NILs). Apparent amylose levels ranged from 0.5 to 29.9% in the NILs, showing
a positive relation with the levels of Wx gene product, granule-bound starch synthase (GBSS) as well as the enzymatic activity per milligram starch granule. Only opaque
(Wx
op
) accessions had an enzymatic activity per GBSS that was reduced to half the level of the others. Nucleotide sequences in the Wx gene were compared among 18 accessions harboring the five different alleles. Each of the Wx alleles had a unique replacement, frame-shift or splice donor site mutation, suggesting that these nucleotide changes could
be reflected in phenotype alterations. A molecular phylogenetic tree constructed using the Wx gene indicated that ssp. japonica forms a distinct clade, whereas ssp. indica forms different clades together with the wild progenitor. Unexpectedly, the wx allele of 160 (indica from Taiwan) joined the japonica lineage; however, comparisons using linked genes for two Taiwanese accessions revealed that the wx gene was the product of gene flow from japonica to indica. Therefore, the japonica lineage frequently included Wx
in
, Wx
b
and wx, while Wx
a
and Wx
op
were found in the other lineages, strongly suggesting that allelic diversification occurred after divergence of the two subspecies.
The present results were discussed in relation to the maintenance of agronomically valuable genes in various landraces. 相似文献
19.
Honggen Zhang Lijia Zhang Hua Si Yongshen Ge Guohua Liang Minghong Gu Shuzhu Tang 《Molecular breeding : new strategies in plant improvement》2016,36(7):102
Three-line japonica hybrids have been developed mainly on Chinsurah Boro II (BT)-type cytoplasmic male sterile (CMS) lines of Oryza sativa L., but the unstable sterility of some BT-type CMS lines, and the threat of genetic vulnerability when using a single cytoplasm source, have inhibited their use in rice cultivation. Previously, the sterility of Honglian (HL)-type japonica CMS lines derived from common red-awned wild rice (Oryza rufipogon) has been proven to be more stable than that of BT-type japonica CMS lines. Here, we genetically characterized HL-type japonica CMS lines and the restorer-of-fertility (Rf) gene for breeding HL-type japonica hybrids. HL-type japonica CMS lines displayed stained abortive pollen grains, unlike HL-type indica CMS lines. The BT-type japonica restorer lines, which contain Rf, had different capabilities to restore HL-LiuqianxinA (HL-LqxA), an HL-type japonica CMS line, and the restorers for the HL-type japonica CMS lines could be selected from the preexisting BT-type japonica restorers in rice production. A genetic analysis showed that the restoration of normal fertility to HL-LqxA was controlled by a major gene and was affected by minor effector genes and/or modifiers. The major Rf in SiR2982, a BT-type japonica restorer, was mapped to a ~100-kb physical region on chromosome 10, and was demonstrated to be Rf5 (Rf1a) by sequencing. Furthermore, Rf5 partially restored fertility and had a dosage effect on HL-type japonica CMS lines. These results will be helpful for the development of HL-type japonica hybrids. 相似文献
20.
Xifeng Chen Jianwei Pan Jing Cheng Guanghuai Jiang Yang Jin Zhimin Gu Qian Qian Wenxue Zhai Bojun Ma 《Molecular breeding : new strategies in plant improvement》2009,24(4):387-395
Spotted leaf 5 (spl5), a lesion mimic mutant, was first identified in rice (Oryza sativa L.) japonica cv. Norin8 in 1978. This mutant exhibits spontaneous disease-like lesions in the absence of any pathogens and resistance
to rice blast and bacterial blight; however, the target gene has not yet been isolated. In the present study, we employed
a map-based cloning strategy to finely map the spl5 gene. In an initial mapping with 100 F2 individuals (spl5/spl5) derived from a cross between the spl5 mutant and indica cv. 93-11, the spl5 gene was located in a 3.3-cM region on chromosome 7 using six simple sequence repeat (SSR) markers. In a high-resolution
genetic mapping, two F2 populations with 3,149 individuals (spl5/spl5) were derived from two crosses between spl5 mutant and two indica cvs. 93-11 and Zhefu802 and six sequence-tagged site (STS) markers were newly developed. Finally, the spl5 gene was mapped to a region of 0.048 cM between two markers SSR7 and RM7121. One BAC/PAC contig map covering these markers’
loci and the spl5 gene was constructed through Pairwise BLAST analysis. Our bioinformatics analysis shows that the spl5 gene is located in the 80-kb region between two markers SSR7 and RM7121 with a high average ratio of physical to genetic
distance (1.67 Mb/cM) and eighteen candidate genes. The analysis of these candidate genes indicates that the spl5 gene represents a novel class of regulators controlling cell death and resistance response in plants. 相似文献