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1.
2.
Jerzy K. Kulski Atsuko Shigenari Takashi Shiina Kazuyoshi Hosomichi Makoto Yawata Hidetoshi Inoko 《Immunogenetics》2009,61(4):257-270
The study of the association of the Human Leukocyte Antigen (HLA) alleles and polymorphic retrotransposons such as Alu, HERV, and LTR at various loci within the Major Histocompatibility Complex allows for a better identification and stratification of disease associations and the origins of HLA haplotypes in different populations. This paper provides sequence and association data on two structurally polymorphic MER9-LTR retrotransposons that are located 54 kb apart and in close proximity to the multiallelic HLA-A gene involved in the regulation of the human immune system. Direct DNA sequencing and analysis of the PCR products identified DNA nucleotide variations between the MER9-LTR sequences at the two loci and their associations with HLA-A alleles as potential haplotype and evolutionary markers. All MER9-LTR sequences were haplotypic when associated with common HLA-A alleles. The number of SNP loci was 2.5 times greater for the solo LTR at the AK locus, which is located closer to the HLA-A gene than the solo or 3′ LTR at the HG locus. Our study shows that the nucleotide variations of the MER9-LTR DNA sequences are additional informative markers in fine mapping HLA-A genomic haplotypes for future population, evolutionary, and disease studies. 相似文献
3.
Jun J. Sato Akio Shinohara Nobumoto Miyashita Chihiro Koshimoto Kimiyuki Tsuchiya Ikuyo Nakahara Tetsuo Morita Hiromichi Yonekawa Kazuo Moriwaki Yasunori Yamaguchi 《Mammalian genome》2008,19(3):155-162
Genetic characterization of a wild-derived house mouse, Mus musculus, originally collected near Lake Balkhash in the Republic of Kazakhstan, was performed by examining protein polymorphisms
and nucleotide sequences for the hemoglobin beta chain (HBB) subunits. Protein electrophoresis, which was performed on a cellulose-acetate
plate, showed an independent mobility pattern representing a new, previously undiscovered haplotype. Neighbor-joining analyses
of the HBB adult genes, i.e., HBB-T1 and HBB-T2, and the intergenic spacer region showed that the Lake Balkhash mouse possessed
genomic components that were mixed from different haplotypes. Compared to the previously determined HBB haplotypes, d, p, and w1, the HBB-T1 gene and ca. 11 kb of the spacer region were most similar to the w1 haplotype; however, the remainder of the spacer region and the HBB-T2 gene were most similar to the d haplotype but may represent a still uncharacterized and divergent haplotype. The recombination event is predicted to have
occurred 2.5 kb upstream of the HBB-T2 gene and may have occurred through intersubspecific hybridization between mice of the
musculus subspecies group (with the w1 haplotype) and the castaneus subspecies group (with the d-like haplotype). Alternatively, an unknown subspecies group that is equidistantly divergent from each of these subspecies
groups may have been involved. Our findings suggest reticulate evolution among the subspecies groups during the evolution
of M. musculus. 相似文献
4.
A class of ribonucleases termed S-RNases, which control the pistil expression of self-incompatibility, represents the only known functional products encoded by the S locus in species from the Solanaceae, Scrophulariaceae and Rosaceae. Previously, we identified a pollen-specific F-box gene, AhSLF (S locus F-box)-S2, very similar to S2-RNase in Antirrhinum, a member of the Scrophulariaceae. In addition, AhSLF-S2 also detected the presence of its homologous DNA fragments. To identify these fragments, we constructed two genomic DNA libraries from Antirrhinum self-incompatible lines carrying alleles S1S5 and S2S4, respectively, using a transformation-competent artificial chromosome (TAC) vector. With AhSLF-S2-specific primers, TAC clones containing both AhSLF-S2 and its homologs were subsequently identified (S2TAC, S5TACa, S4TAC, and S1TACa). DNA blot hybridization, sequencing and segregation analyses revealed that they are organized as single allelic copies (AhSLF-S2, -S1, -S4 and -S5) tightly linked to the S-RNases. Furthermore, clusters of F-box genes similar to AhSLF-S2 were identified. In total, three F-box genes (AhSLF-S2, -S2A and -S2C) in S2TAC (51 kb), three (AhSLF-S4, -S4A and -S4D) in S4TAC (75 kb), two (AhSLF-S5 and -S5A) in S5TACa (55 kb), and two (AhSLF-S1 and -S1E) in S1TACa (71 kb), respectively, were identified. Paralogous copies of these genes show 38–54% identity, with allelic copies sharing 90% amino acid identity. Among these genes, three (AhSLF-S2C, -S4D and -S1E) were specifically expressed in pollen, similar to AhSLF-S2, implying that they likely play important roles in pollen, whereas three AhSLF-SA alleles showed no detectable expression. In addition, several types of retroelements and transposons were identified in the sequenced regions, revealing some detailed information on the structural diversity of the S locus region. Taken together, these results indicate that both single allelic and tandemly duplicated genes are associated with the S locus in Antirrhinum. The implications of these findings in evolution and possible roles of allelic AhSLF-S genes in the self-incompatible reaction are discussed in species like Antirrhinum.Sequence data from this article have been deposited with the EMBL/GenBank databases under accession numbers AJ300474, AJ515534, AJ515536 and AJ515535 相似文献
5.
The nucleotide sequences of ten SP11 and nine SRK alleles in Raphanus sativus were determined, and deduced amino acid sequences were compared with those of Brassica SP11 and SRK. The amino acid sequence identity of class-I SP11s in R. sativus was about 30% on average, the highest being 52.2%, while that of the S domain of class-I SRK was 77.0% on average and ranged from 70.8% to 83.9%. These values were comparable to those of SP11 and SRK in Brassica oleracea and B. rapa. SP11 of R. sativus S-21 was found to be highly similar to SP11 of B. rapa S-9 (89.5% amino acid identity), and SRK of R. sativus S-21 was similar to SRK of B. rapa S-9 (91.0%). SP11 and SRK of R. sativus S-19 were also similar to SP11 and SRK of B. oleracea S-20, respectively. These similarities of both SP11 and SRK alleles between R. sativus and Brassica suggest that these S haplotype pairs originated from the same ancestral S haplotypes. 相似文献
6.
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
7.
Xingguo Zhang Chaozhi Ma Tingdong Fu Yuanyuan Li Tonghua Wang Qingfang Chen Jinxing Tu Jinxiong Shen 《Molecular breeding : new strategies in plant improvement》2008,21(3):305-315
‘SI1300’ is a self-incompatible Brassica napus line generated by introgressing an S haplotype from B. rapa ‘Xishuibai’ into a rapeseed cultivar ‘Huayou No. 1’. Five S-locus specific primer pairs were employed to develop cleaved amplified polymorphic sequences (CAPS) markers linked the S haplotype of ‘SI1300’. Two segregating populations (F2 and BC1) from the cross between ‘SI1300’ and self-compatible European spring cultivar ‘Defender’, were generated to verify the molecular
markers. CAPS analysis revealed no desirable polymorphism between self-incompatible and self-compatible plants. Twenty primer
pairs were designed based on the homology-based candidate gene method, and six dominant sequence characterized amplified region
(SCAR) markers linked with the S-locus were developed. Of the six markers, three were derived from the SRK and SP11 alleles of class II B. rapa
S haplotypes and linked with S haplotype of ‘SI1300’. The other three markers were designed from the SLG-A10 and co-segregated with S haplotype of ‘Defender’. We successfully combined two pairs of them and characterized two multiplex PCR markers which could
discriminate the homozygous and heterozygous genotypes. These markers were further validated in 24 F3 and 22 BC1F2 lines of ‘SI1300 × Defender’ and another two segregating populations from the cross ‘SI1300 × Yu No. 9’. Nucleotide sequences
of fragments linked with S-locus of ‘SI1300’ showed 99% identity to B. rapa class II S-60 haplotype, and fragments from ‘Defender’ were 97% and 94% identical to SLG and SRK of B. rapa class I S-47 haplotype, respectively. ‘SI1300’ was considered to carry two class II S haplotypes and the S haplotype on the A-genome derived from B. rapa ‘Xishuibai’ determines the SI phenotype, while ‘Defender’ carry a class I S haplotype derived from B. rapa and a class II S haplotype from B. oleracea. SCAR markers developed in this study will be helpful for improving SI lines and accelerating marker-assisted selection process
in rapeseed SI hybrid breeding program. 相似文献
8.
Liu X Yang Q Lin F Hua L Wang C Wang L Pan Q 《Molecular genetics and genomics : MGG》2007,278(4):403-410
Blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most devastating diseases of rice worldwide. The Chinese native cultivar (cv.) Q15 expresses the broad-spectrum
resistance to most of the isolates collected from China. To effectively utilize the resistance, three rounds of linkage analysis
were performed in an F2 population derived from a cross of Q15 and a susceptible cv. Tsuyuake, which segregated into 3:1 (resistant/susceptible)
ratio. The first round of linkage analysis employing simple sequence repeat (SSR) markers was carried out in the F2 population through bulked-segregant assay. A total of 180 SSR markers selected from each chromosome equally were surveyed.
The results revealed that only two polymorphic markers, RM247 and RM463, located on chromosome 12, were linked to the resistance
(R) gene. To further define the chromosomal location of the R gene locus, the second round of linkage analysis was performed using additional five SSR markers, which located in the region
anchored by markers RM247 and RM463. The locus was further mapped to a 0.27 cM region bounded by markers RM27933 and RM27940
in the pericentromeric region towards the short arm. For fine mapping of the R locus, seven new markers were developed in the smaller region for the third round of linkage analysis, based on the reference
sequences. The R locus was further mapped to a 0.18 cM region flanked by marker clusters 39M11 and 39M22, which is closest to, but away from
the Pita/Pita
2 locus by 0.09 cM. To physically map the locus, all the linked markers were landed on the respective bacterial artificial
chromosome clones of the reference cv. Nipponbare. Sequence information of these clones was used to construct a physical map
of the locus, in silico, by bioinformatics analysis. The locus was physically defined to an interval of ≈37 kb. To further
characterize the R gene, five R genes mapped near the locus, as well as 10 main R genes those might be exploited in the resistance breeding programs, were selected for differential tests with 475 Chinese
isolates. The R gene carrier Q15 conveys resistances distinct from those conditioned by the carriers of the 15 R genes. Together, this valuable R gene was, therefore, designated as Pi39(t). The sequence information of the R gene locus could be used for further marker-based selection and cloning.
Xinqiong Liu and Qinzhong Yang contributed equally to this work. 相似文献
9.
We previously identified both self-incompatible and self-compatible plants in a natural population of self-incompatible Petunia axillaris subsp. axillaris, and found that all the self-compatible plants studied carried either SC1- or SC2-haplotype. Genetic crosses showed that SC2 was identical to S17 identified from another natural population of P. axillaris, except that its pollen function was defective, and that the pollen-part mutation in SC2 was tightly linked to the S-locus. Recent identification of the S-locus F-box gene (SLF) as the gene that controls pollen specificity in S-RNase-based self-incompatibility has prompted us to examine the molecular basis of this pollen-part mutation. We cloned and sequenced the S17-allele of SLF of P.axillaris, named PaSLF17, and found that SC2 SC2 plants contained extra restriction fragments that hybridized to PaSLF17 in addition to all of those observed in S17 S17 plants. Moreover, these additional fragments co-segregated with SC2. We used the SC2-specific restriction fragments as templates to clone an allele of PaSLF by PCR. To determine the identity of this allele, named PaSLFx, primers based on its sequence were used to amplify PaSLFalleles from genomic DNA of 40 S-homozygotes of P. axillaris, S1 S1 through S40 S40. Sequence comparison revealed that PaSLFx was completely identical with PaSLF19 obtained from S19 S19. We conclude that the S-locus of SC2 contained both S17-allele and the duplicated S19-allele of PaSLF. SC2 is the first naturally occurring pollen-part mutation of a solanaceous species that was shown to be associated with duplication of the pollen S. This finding lends support to the proposal, based on studies of irradiation-generated pollen-part mutants of solanaceous species, that duplication, but not deletion, of the pollen S, causes breakdown of pollen function. 相似文献
10.
Katsuyuki Kakeda 《Plant cell reports》2009,28(9):1453-1460
Diploid Hordeum bulbosum (a wild relative of cultivated barley) exhibits a two-locus self-incompatibility (SI) system gametophytically controlled
by the unlinked multiallelic loci S and Z. This unique SI system is observed in the grasses (Poaceae) including the tribe Triticeae. This paper describes the identification
and characterization of two F-box genes cosegregating with the S locus in H. bulbosum, named Hordeum
S locus-linked F-box 1 (HSLF1) and HSLF2, which were derived from an S
3 haplotype-specific clone (HAS175) obtained by previous AMF (AFLP-based mRNA fingerprinting) analysis. Sequence analysis showed
that both genes encode similar F-box proteins with a C-terminal leucine-rich repeat (LRR) domain, which are distinct from
S locus (or S haplotype-specific) F-box protein (SLF/SFB), a class of F-box proteins identified as the pollen S determinant in S-RNase-based gametophytic SI systems. A number of homologous F-box genes with an LRR domain were found in
the rice genome, although the functions of the gene family are unknown. One allele of the HSLF1 gene (HSLF1-S
3) was expressed specifically in mature anthers, whereas no expression was detected from the other two alleles examined. Although
the degree of sequence polymorphism among the three HSLF1 alleles was low, a frameshift mutation was found in one of the unexpressed alleles. The HSLF2 gene showed a low level of expression with no tissue specificity as well as little sequence polymorphism among the three
alleles. The multiplicity of S locus-linked F-box genes is discussed in comparison with those found in the S-RNase-based SI system.
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 AB511822–AB511825
and AB511859–AB511862. 相似文献
11.
Marjan Khalili Mahani Nobuyuki Inomata Alireza Saboori Baraldin Ebrahim Sayed Tabatabaei Hiroko Ishiyama Ardeshir Ariana Alfred E. Szmidt 《Experimental & applied acarology》2009,48(4):273-289
Allothrombium
pulvinum Ewing is a common natural enemy of aphids and some other arthropods. So far, there are no studies that have addressed genetic
variation of this predatory mite. We investigated genetic variation of A. pulvinum across its whole known range in Iran. A 410 bp portion of the mitochondrial cytochrome c oxidase subunit I gene (coxI) and 797–802 bp portion of the internal transcribed spacer 2 of rDNA (ITS2) were sequenced for 55 individuals from 11 populations, resulting in 12 and 26 haplotypes, respectively. In the coxI region, haplotype and nucleotide diversities varied among populations from 0.00 to 0.90 and from 0.0000 to 0.0110, respectively.
In the ITS2 region they varied from 0.20 to 0.91 and from 0.0006 to 0.0023, respectively. For both gene regions the highest haplotype
and nucleotide diversities were detected in population Mahmoud Abad from northern Iran. Statistically significant population
differentiation (F
ST) was detected in most pair-wise population comparisons. The results of population differentiation for both gene regions were
generally congruent indicating that A. pulvinum from Iran consists of genetically different populations. This suggests that A. pulvinum comprises at least two geographically distinct populations or even more than one species. This study is an initial step towards
understanding genetic variation of A. pulvinum, a taxon for which little molecular information is available. More intensive sampling and analysis of additional DNA regions
are necessary for more detailed classification of this taxon. 相似文献
12.
Finkers-Tomczak A Bakker E de Boer J van der Vossen E Achenbach U Golas T Suryaningrat S Smant G Bakker J Goverse A 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,122(3):595-608
The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146–152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming
from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16
(S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of
a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding
for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation
in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping
the H1 locus and will facilitate the map-based cloning of the H1 resistance gene. 相似文献
13.
We describe a novel extension of the Genomic Matching Technique (GMT) that defines haplotypes of the mannose binding lectin
(MBL) region in Zebrafish (D. rerio). Four ancestral haplotypes have been identified to date, with at least one of these demonstrating a significant increase
in resistance to L. anguillarum. MBL activates the lectin pathway of the complement system and stimulates the development of the complement cascade and the Membrane
Attack Complex. Polymorphisms in humans have been associated with increased susceptibility and severity to a number of pathogenic
organisms. As teleosts have a relatively immature acquired immune system, polymorphisms within MBL and other innate defence genes are likely to be critical in defining their susceptibility/resistance to various pathogenic
organisms. We report multiple copies of MBL-like genes in D. rerio, with up to three copies tightly linked within a cluster spanning ∼15 kb on chromosome 2. Genomic analysis suggests that
duplication, retroviral insertion and possibly gene mutation and/or deletion have been key factors in the evolution of this
cluster. Molecular analysis has revealed extensive polymorphism, including at least five distinct amplicons and haplospecific
gene copy number variation. This study demonstrates polymorphism within a critical component of the teleost innate immune
system. The polymorphisms and the haplotypes encoding the unique variants are likely to be informative in defining susceptibility/resistance
to infectious agents commonly encountered within aquatic environments. Future investigations will define other important haplotypes
and transfer the knowledge to other finfish species, thereby enabling selection of broodstock for the aquaculture industry.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
14.
15.
Eriko Oikawa Shohei Takuno Atsushi Izumita Koji Sakamoto Hideaki Hanzawa Hiroyasu Kitashiba Takeshi Nishio 《Molecular breeding : new strategies in plant improvement》2011,28(1):1-12
In F1 hybrid breeding of Brassica vegetables utilizing the self-incompatibility system, identification of S genotypes in breeding lines is required. In the present study, we developed S-tester lines of 87 S haplotypes, i.e., 42 S haplotypes in B. rapa and 45 S haplotypes in B. oleracea. With these materials, we established a simple, efficient, and reliable dot-blot technique for S genotyping for 40 S haplotypes of B. rapa and and 33 of B. oleracea using allele-specific oligonucleotide probes and allele-specific primer pairs designed from sequences of each SP11 allele. In this method, DNA fragments amplified using multiplex primer pairs with digoxigenin-dUTP were hybridized with dot-blotted
allele-specific oligonucleotide probes with distinct signals. In addition, we developed a screening method for identification
of plants harboring a particular S haplotype using a labeled allele-specific oligonucleotide probe. This method is considered to be useful for purity testing
of F1 hybrid seeds. 相似文献
16.
Xin Xu N. Hayashi C. T. Wang H. Kato T. Fujimura S. Kawasaki 《Molecular breeding : new strategies in plant improvement》2008,22(2):289-299
The Pik-h gene in rice confers resistance to several races of rice blast fungus (Magnaporthe oryzae), and has been classified as a member of the Pik cluster, one of the most resistance (R) gene-dense regions in the rice genome. However, the loss of a key mutant isolate has long made it difficult to differentiate
Pik-h from other Pik group genes especially from Pik-m. We identified new natural isolates enabling the differentiation between Pik-h and Pik-m genes, and first confirmed the authenticity of the International Rice Research Institute (IRRI) “monogenic” line IRBLkh-K3,
and then fine-mapped the Pik-h gene in the Pik cluster. Using 701 susceptible individuals among 3,060 siblings from a cross of IRBLkh-K3×CO39, the Pik-h region was delimited to 270 kb, the narrowest interval among the Pik group genes reported to date, in the cv. Nipponbare genome. Annotation of this genome region first revealed 6 NBS-LRR type
R-gene analogs (RGAs), clustered within the central 120 kb, as possible counterparts of Pik-h and 6 other Pik group R genes. Interestingly, the Pik-h region and the cluster of RGAs were shown to be located 130 kb and 230 kb apart from Xa4 and Xa2 bacterial blight resistance genes, respectively, once classified as belonging to the Pik cluster. The closest recombination events were limited to the margins of the Pik-h region, and recombination was suppressed in the core interval with the RGA cluster. This fine-mapping, performed in a short
time using an HEGS system, will facilitate utilization of the cluster’s genetic resources and help to elucidate the mechanism
of evolution of R-genes. The presence of natural isolates also confirmed that evolution of Pik-h corresponds to pathogen evolution. 相似文献
17.
Self-incompatibility has been studied extensively at the molecular level in Solanaceae, Rosaceae and Scrophulariaceae, all
of which exhibit gametophytic self-incompatibility controlled by a single polymorphic locus containing at least two linked
genes, i.e., the S-RNase gene and the pollen-expressed SFB/SLF (S-haplotype-specific F-box/S-locus F-box) gene. However, the SFB gene in Japanese plum (Prunus salicina Lindl.) has not yet been identified. We determined eight novel sequences homologous to the SFB genes of other Prunus species and named these sequences PsSFB. The gene structure of the SFB genes and the characteristic domains in deduced amino acid sequences were conserved. Three sequences from 410 to 2,800 bp
of the intergenic region between the PsSFB sequences and the S-RNase alleles were obtained. The eight identified PsSFB sequences showed S-haplotype-specific polymorphism, with 74–83% amino acid identity. These alleles were exclusively expressed in the pollen.
These results suggest that the PsSFB alleles are the pollen S-determinants of GSI in Japanese plum.
Nucleotide sequence data reported are available in the NCBI database under the accession numbers DQ849084–DQ849090 and DQ849118. 相似文献
18.
Franc-Christophe Baurens Stéphanie Bocs Mathieu Rouard Takashi Matsumoto Robert NG Miller Marguerite Rodier-Goud Didier MBéguié-A-MBéguié Nabila Yahiaoui 《BMC plant biology》2010,10(1):149
Background
Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). 相似文献19.
Kang H Weng Y Yang Y Zhang Z Zhang S Mao Z Cheng G Gu X Huang S Xie B 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,122(4):795-803
Scab, caused by Cladosporium cucumerinum, is an important disease of cucumber, Cucumis sativus. In this study, we conducted fine genetic mapping of the single dominant scab resistance gene, Ccu, with 148 F9 recombinant inbred lines (RILs) and 1,944 F2 plants derived from the resistant cucumber inbred line 9110Gt and the susceptible line 9930, whose draft genome sequence
is now available. A framework linkage map was first constructed with simple sequence repeat markers placing Ccu into the terminal 670 kb region of cucumber Chromosome 2. The 9110Gt genome was sequenced at 5× genome coverage with the
Solexa next-generation sequencing technology. Sequence analysis of the assembled 9110Gt contigs and the Ccu region of the 9930 genome identified three insertion/deletion (Indel) markers, Indel01, Indel02, and Indel03 that were closely
linked with the Ccu locus. On the high-resolution map developed with the F2 population, the two closest flanking markers, Indel01 and Indel02, were 0.14 and 0.15 cM away from the target gene Ccu, respectively, and the physical distance between the two markers was approximately 140 kb. Detailed annotation of the 180 kb
region harboring the Ccu locus identified a cluster of six resistance gene analogs (RGAs) that belong to the nucleotide binding site (NBS) type R
genes. Four RGAs were in the region delimited by markers Indel01 and Indel02, and thus were possible candidates of Ccu. Comparative DNA analysis of this cucumber Ccu gene region with a melon (C. melo) bacterial artificial chromosome (BAC) clone revealed a high degree of micro-synteny and conservation of the RGA tandem repeats
in this region. 相似文献
20.
Hiroyasu Kitashiba Shao Ling Zhang Jun Wu Kenta Shirasawa Takeshi Nishio 《Molecular breeding : new strategies in plant improvement》2008,21(3):339-349
Most Rosaceae fruit trees such as Japanese plum and sweet cherry have a gametophytic self-incompatibility (GSI) system controlled
by a single S locus containing at least two linked genes with multiple alleles, i.e., S-RNase as a pistil determinant and SFB (S-haplotype-specific F-box gene) as a candidate for the pollen S determinant. For identification of S genotypes, many methods based on polymerase chain reaction (PCR) utilizing polymorphism in length of the S-RNase and SFB gene have been developed. In this study, we developed two dot-blot analysis methods for S-haplotype identification utilizing allele-specific oligonucleotides based on the SFB-HVa region, which has high sequence polymorphism. Dot-blotting of allele-specific oligonucleotides hybridized with digoxigenin-labeled
PCR products allowed S genotyping of plants with nine S haplotypes (S-a, S-b, S-c, S-e, S-f, S-h, S-k, S-7 and S-10) in Japanese plum and ten S haplotypes (S-1, S-2, S-3, S-4, S-4′, S-5, S-6, S-7, S-9 and S-16) in sweet cherry (dot-blot-S-genotyping). In addition, dot-blotting of PCR products of SFB probed with the allele-specific oligonucleotides, occasionally utilizing competitive hybridization, was successful in screening
for a desirable S haplotype in sweet cherry (dot-blot-S-screening). 相似文献