矮泰引-3中半矮秆基因的分子定位

矮泰引-3的矮生性状受两对独立遗传的半矮秆基因控制,利用SSR标记将这两个矮秆基因分别定位到第1和第4染色体上。等位性测交的结果表明,位于第1染色体上的矮秆基因与sd1是等位的,所以仍然称其为sd1;而位于第4染色体上的矮秆基因是一个新基因,暂命名为sdt2。利用SSR标记将sd1定位于RM297、RM302和RM212的同一侧,而与OSR3共分离,它们之间的位置关系可能是RM297-RM302-RM212-OSR3-sd1,遗传距离分别为4．7cM、0cM、0．8cM和0cM,这与sd1在第1染色体长臂上的确切位置是基本一致的。利用已有的SSR标记和拓展的SSR标记将sdt2定位于SSR332、RM1305和RM5633、RM307、RM401之间,它们的排列位置可能是SSR332-RM1305-sdt2-RM5633-RM307-RM401,它们之间的遗传距离分别为11．6cM、3．8cM、0．4cM、0cM和0．4cM。     

Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp (Cyprinus carpio haematopterus)

To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (Cyprinus carpio haematopterus) using dynamic quantitative trait locus (QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 cM, 0.45 cM, and 1.00 cM. We identified 148 QTLs related to four growth traits that were located on 25 chromosomes from three growth stages of Yellow River carp. A total of 32, 36, 43, and 37 QTLs were associated with body length, height, width, and weight, respectively. Among them, 47 QTLs were detected for only one growth trait in one stage, but all of the other QTLs were co-localized. Of the 14 main QTLs, 13 were located on chromosome 12, which suggests the presence of growth-related genes on this chromosome. We then detected 17 candidate genes within 50 K upstream and downstream of the 14 main QTLs. This is the first report of the dynamic QTL mapping of growth traits of Yellow River carp, and the results can be used in future studies of growth, development, and molecular-assisted breeding of this species.     

Physical Mapping of Rice Chromosomes 4 and 7 Using YAC Clones

Physical maps of rice chromosomes 4 and 7 were constructed bylanding yeast artificial chromosomes (YACs) along our high-densitymolecular linkage map. Using 114 DNA markers, 258 individualYACs were located on chromosome 4. Sixty-two out of 258 YACscarried two or more DNA marker positions and formed 16 contigswhich covered a total length of 17.1 cM. The other YACs werearranged to 23 positions. On chromosome 7, 203 individual YACswere landed on 109 DNA markers. Sixty-four out of 203 YACs formed15 contigs which covered a total length of 21.8 cM and 139 YACswere localized to 26 positions. Chromosomes 4 and 7 were coveredwith minimum tiling paths of 45 and 48 YACs, respectively. Takingthe average size of YAC insert DNA to be 350 kb and the entiregenome size to be 430 Mb, about 16–18 Mb of each chromosomeor an estimated 50% of their total lengths have been coveredwith YACs. Physical maps of these 2 chromosomes should be ofgreat help in identifying useful trait genes and unravelinggenetic and biological characteristics in rice.     

易组"太谷核不育基因"(Ms2)基因定位的研究

将在远缘杂交中由普通小麦（AABBDD）4D染色体易组导入六倍体小黑麦（AABBRR）以及硬粒小麦（AABB）的太谷核不育基因Ms2（原位于普通小麦4D染色体短臂距着丝点31．2cM的显性雄性不育核基因）。重新异回普通小麦染色体组中,所获得携带易组Ms2基因的新型太谷核不育小麦其显性雄性不育特性表达正常,且雄性不育株的雌性可育机制正常,对不育株幼穗花粉母细胞减数分型期染色体构型的观察可见其为整倍体（2n=42),尚未发现回归普通小麦的易组太谷核不育与原位 的太谷核不育基因有不同的表型。采用系统的标志基因测交法对回归普通小麦的易组太谷不育基因进行测交定位,发现易组Ms2基因与普通小麦显性秆标志基因Rht3连锁,从而将其定位于普通小麦4B 色体虎Rht3基因9.7cM处,新位点被命名为Ms2（4BS）,对Ms2基因在六倍体小黑麦与原太谷核不育小麦远缘杂交中位时的走向,普通小麦4A与4B染色体的互换更名以及Ms2（4BS）新位点的开发利用进行了讨论,认为异源多倍体生物核基因的组间易位倾向于从供体染色体向进化亲缘关系较密切,且染色体序数与染色体臂相同的部分同源染色体易位;1988年第7届国际小麦遗传学会对普通小麦4A与4B染色体的互换更名是正确的;Ms2（4BS）作为一个新型的遗传标记,作为小麦族内所有携带B染色体组的物种的育种工具和在拓建各为小麦种质资源的基因库等方面均有广泛的用途。     

Mapping of avirulence genes in the rice blast fungus, Magnaporthe grisea, with RFLP and RAPD markers

Three genetically independent avirulence genes, AVR1-Irat7, AVRI-MedNoi; and AVR1-Ku86, were identified in a cross involving isolates Guy11 and 2/0/3 of the rice blast fungus, Magnaporthe grisea. Using 76 random progeny, we constructed a partial genetic map with restriction fragment length polymorphism (RFLP) markers revealed by probes such as the repeated sequences MGL/MGR583 and Pot3/MGR586, cosmids from the M. grisea genetic map, and a telomere sequence oligonucleotide. Avirulence genes AVR1-MedNoi and AVR1-Ku86 were closely linked to telomere RFLPs such as marker TelG (6 cM from AVR1-MedNoi) and TelF (4.5 cM from AVR1-Ku86). Avirulence gene AVR1-Irat7 was linked to a cosmid RFLP located on chromosome 1 and mapped at 20 cM from the avirulence gene AVR1-CO39. Using bulked segregant analysis, we identified 11 random amplified polymorphic DNA (RAPD) markers closely linked (0 to 10 cM) to the avirulence genes segregating in this cross. Most of these RAPD markers corresponded to junction fragments between known or new transposons and a single-copy sequence. Such junctions or the whole sequences of single-copy RAPD markers were frequently absent in one parental isolate. Single-copy sequences from RAPD markers tightly linked to avirulence genes will be used for positional cloning.     

Genetic Mapping in SCHIZOSACCHAROMYCES POMBE by Mitotic and Meiotic Analysis and Induced Haploidization

The genetic maps of the fission yeast Schizosaccharomyces pombe were extended through the use of haploidization (spontaneous or induced by m-fluorophenylalanine), as well as by tetrad, random spore and mitotic analysis. A new diploidization method utilizing a meiosis-deficient mutant and improved haploidization techniques was employed. As a result of these and previous studies, 118 genetic markers have been assigned to 3 linkage groups. Centromere markers for all 3 chromosomes were identified and genetic maps containing a total of 71 genes were constructed. Our experiments indicate that 3 is very likely to be the haploid chromosome number of S. pombe .     

基于元分析的抗玉米丝黑穗病QTL比较定位

以玉米遗传连锁图谱IBM2 2005 Neighbors为参考图谱,通过映射整合不同试验中的抗玉米丝黑穗病QTL,构建QTL综合图谱。在国内外种质中,共发现22个抗病QTL,分布在除第7染色体外的9条玉米染色体上。采用元分析技术,获得2个“一致性”抗病QTL,图距分别为8.79 cM和18.92cM。从MaizeGDB网站下载“一致性”QTL区间内基因和标记的原始序列;采用NCBI网站在线软件BLASTx通过同源比对在2个“一致性”QTL区间内初步获得4个抗病位置候选基因。借助比较基因电子定位策略,将69个水稻和玉米抗性基因定位于玉米IBM2图谱上,在2个“一致性”QTL区间内分别发现1个水稻抗性基因,初步推断为抗病位置候选基因。本文结果为抗玉米丝黑穗病QTL精细定位和分子育种提供了基础。     

Molecular genetic analysis of theripening-inhibitor andnon-ripening loci of tomato: A first step in genetic map-based cloning of fruit ripening genes

Ripening represents a complex developmental process unique to plants. We are using tomato fruit ripening mutants as tools to understand the regulatory components that control and coordinate the physiological and biochemical changes which collectively confer the ripe phenotype. We have genetically characterized two loci which result in significant inhibition of the ripening process in tomato,ripening-inhibitor (rin), andnon-ripening (nor), as a first step toward isolating genes likely to encode key regulators of this developmental process. A combination of pooled-sample mapping as well as classical restriction fragment length polymorphism (RFLP) analysis has permitted the construction of high-density genetic maps for the regions of chromosomes 5 and 10 spanning therin andnor loci, respectively. To assess the feasibility of initiating a chromosome walk, physical mapping of high molecular weight genomic DNA has been employed to estimate the relationship between physical distance (in kb) and genetic distance (in cM) around the targeted loci. Based on this analysis, the relationship in the region spanning therin locus is estimated to be 200–300 kb/cM, while thenor locus region ratio is approximately 200 kb/1 cM. Using RFLP markers tightly linked torin andnor, chromosome walks have been initiated to both loci in a yeast artificial chromosome (YAC) library of tomato genomic DNA. We have isolated and characterized several YAC clones linked to each of the targeted ripening loci and present genetic evidence that at least one YAC clone contains thenot locus.     

小麦农家品种赤壳中一个主效抗条锈病基因的微卫星标记和定位

小麦农家品种赤壳(苏1900)对当前我国小麦条锈菌(Puccinia striiformis Westend.f.sp.tritici)多个流行小种均有较好抗性。遗传分析表明,该品种对条中32号小种的抗性是由一对显性基因控制。本文采用分离群体分析法(bulked segregant analysis,BSA)和微卫星多态性分析方法,对该基因进行了分子标记和定位研究。用Taichung29×赤壳的F2代分离群体建立抗、感DNA池,共筛选了400多对SSR引物,发现5个标记Xwmc44、Xgwm259、Xwmc367、Xcfa2292、Xbarc80在抗、感DNA池间与在抗、感亲本间同样具有多态性,它们均位于1BL染色体臂上。经用具有140株抗病株、60株感病株共200株植株的F2代分离群体进行的遗传连锁性检测,上述5个标记均与目的基因相连锁,遗传距离分别为8.3cM、9.1cM、17.2cM、20.6cM和31.6cM。用全套21个中国春缺-四体材料进行的检测进一步证实了这5个SSR标记均位于小麦1B染色体上。综合上述结果,将赤壳中的主效抗条锈病基因YrChk定位在1BL染色体臂上。与以前已定位于1B染色体上的抗条锈病基因的比较研究表明,YrChk基因可能是一个新的抗条锈病基因。小麦农家品种中抗病基因资源的发掘和利用将有助于提高我国小麦生产品种中的抗病基因丰富度,有助于改善长期以来小麦生产品种中抗病基因单一化的局面。     

Genetic regulation of the cytochrome P-450 system in Drosophila melanogaster. II. Localization of some genes regulating cytochrome P-450 activity

The localization of some genes determining the capacity for some cytochrome P-450 -dependent reactions have been studied in adult Drosophila. Strains with genetically determined high or low enzyme activities were crossed with strains carrying recessive visible markers on the chromosomes, and enzyme activities were measured in microsomes from recombinant F2 progeny. A dominantly inherited high p-nitroanisole (PNA) demethylation and biphenyl 3-hydroxylation in insecticide-resistant strains were both shown to be located around 65 cM on the second chromosome, regulated by one gene or closely linked genes. This localizes these activities to the same region as the gene responsible for the cross resistance to several classes of insecticides and a high metabolism of vinyl chloride in resistant strains. The occurrence of a regulatory gene mutation as a basis for the insecticide resistance is proposed. Hydroxylation of benzo[a]pyrene (BP) and deethylation of 7-ethoxy-coumarin seems to be determined by two third chromosome genes, at approx. 51 and 58 cM, respectively. The capacity for biphenyl 4-hydroxylation was shown to be determined by two genes on the second chromosome, one at or to the left of the gene black (48 cM) responsible for a low metabolism in strain Berlin K, and one at about 63 cM giving high formation of this metabolite in Oregon R. The latter could not be separated from the gene in insecticide-resistant strains at c:a 65 cM discussed above on the basis of the genetic localization, but observations supporting the occurrence of two closely linked genes regulating these different activities are available. In conclusion, 4-5 genes determining the capacity for several reactions, being a part of the genetic regulation of the cytochrome P-450 system in Drosophila melanogaster were indicated.     

Genetic Analysis and Molecular Mapping of a Novel Gene Conferring Resistance to Rice Stripe Virus

Rice stripe virus (RSV) is one of the most damaging diseases affecting rice in East Asia. Rice variety 502 is highly resistant to RSV, while variety 5112 is extremely susceptible. Field statistical data revealed that all “502 × 5112” F₁ individuals were resistant to RSV and the ratio of resistant to susceptible plants was 3:1 in the F₂ population and 1:1 in the BC₁F₁ population. These results indicated that a dominant gene, designated RSV1, controlled the resistance. Simple sequence repeat (SSR) analysis was subsequently carried out in an F₂ population. Sixty SSR markers evenly distributed on the 12 rice chromosomes were screened and tested. Two markers, RM229 and RM206, showed linkage with RSV1. Based on this result, six SSR markers flanking RM229 and RM206 were further selected and tested. Results indicated that SSR markers RM457 and RM473E were linked to RSV1 with a genetic distance of 4.5 and 5.0 cM, respectively. All of the four SSR markers (RM229, RM473E, RM457 and RM206) linked to RSV1 were all located on chromosome 11, therefore RSV1 should be located on chromosome 11 also. In order to find some new markers more closely linked to the RSV1 gene, sequence-related amplified polymorphism (SRAP) analysis was performed. A total of 30 SRAP primer-pairs were analyzed, and one marker SR1 showed linkage with RSV1 at a genetic distance of 2.9 cM. Finally, RSV1 gene was mapped on chromosome 11 between SSR markers RM457 and SRAP marker SR1 with a genetic distance of 4.5 cM and 2.9 cM, respectively.     

Identification and mapping of a new powdery mildew resistance gene on chromosome 6D of common wheat

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most serious wheat diseases. The rapid evolution of the pathogen's virulence, due to the heavy use of resistance genes, necessitates the expansion of resistance gene diversity. The common wheat line D57 is highly resistant to powdery mildew. A genetic analysis using an F(2) population derived from the cross of D57 with the susceptible cultivar Yangmai 158 and the derived F(2:3) lines indicated that D57 carries two dominant powdery mildew resistance genes. Based on mapping information of polymorphic markers identified by bulk segregant analysis, these two genes were assigned to chromosomes 5DS and 6DS. Using the F(2:3) lines that segregated in a single-gene mode, closely linked PCR-based markers were identified for both genes, and their chromosome assignments were confirmed through linkage mapping. The gene on chromosome 5DS was flanked by Xgwm205 and Xmag6176, with a genetic distance of 8.3 cM and 2.8 cM, respectively. This gene was 3.3 cM from a locus mapped by the STS marker MAG6137, converted from the RFLP marker BCD1871, which was 3.5 cM from Pm2. An evaluation with 15 pathogen isolates indicated that this gene and Pm2 were similar in their resistance spectra. The gene on chromosome 6DS was flanked by co-segregating Xcfd80 and Xmag6139 on one side and Xmag6140 on the other, with a genetic distance of 0.7 cM and 2.7 cM, respectively. This is the first powdery mildew resistance gene identified on chromosome 6DS, and plants that carried this gene were highly resistant to all of the 15 tested pathogen isolates. This gene was designated Pm45. The new resistance gene in D57 could easily be transferred to elite cultivars due to its common wheat origin and the availability of closely linked molecular markers.     

Why Genes Evolve Faster on Secondary Chromosomes in Bacteria

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster evolution and reduced codon bias could in turn result from global effects of chromosome position, as genes on secondary chromosomes experience reduced dosage and expression due to their delayed replication, or selection on specific gene attributes. These alternatives were evaluated using orthologs common to genomes with multiple chromosomes and genomes with single chromosomes. Analysis of these ortholog sets suggested that inherently fast-evolving genes tend to be sorted to secondary chromosomes when they arise; however, prolonged evolution on a secondary chromosome further accelerated substitution rates. In summary, secondary chromosomes in bacteria are evolutionary test beds where genes are weakly preserved and evolve more rapidly, likely because they are used less frequently.     

Assembly of the Genome of the Disease Vector Aedes aegypti onto a Genetic Linkage Map Allows Mapping of Genes Affecting Disease Transmission

The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly assembled — there are 4,758 scaffolds, few of which have been assigned to a chromosome. To allow the mapping of genes affecting disease transmission, we have improved the genome assembly by scoring a large number of SNPs in recombinant progeny from a cross between two strains of Ae. aegypti, and used these to generate a genetic map. This revealed a high rate of misassemblies in the current genome, where, for example, sequences from different chromosomes were found on the same scaffold. Once these were corrected, we were able to assign 60% of the genome sequence to chromosomes and approximately order the scaffolds along the chromosome. We found that there are very large regions of suppressed recombination around the centromeres, which can extend to as much as 47% of the chromosome. To illustrate the utility of this new genome assembly, we mapped a gene that makes Ae. aegypti resistant to the human parasite Brugia malayi, and generated a list of candidate genes that could be affecting the trait.     

Precise Mapping of the Homothallism Genes HML and HMR in SACCHAROMYCES CEREVISIAE

The HML and HMR loci carry unexpressed copies of MATa and MATα information, and a replica of that information is transposed to MAT during mating-type interchange in Saccharomyces yeasts. A negative control mechanism keeps silent the information located at the HML and HMR loci. We mapped these loci by constructing strains in which these loci are expressed. In these strains, the mating type of the segregants is dependent upon the allele at HML and HMR. This novel approach is independent of their switching function. HML is located on the left arm of chromosome III distal to his4 by about 26.8 centimorgans (cM). HMR maps on the right arm of the same chromosome distal to thr4 by about 39.8 cM and proximal to MAL2 by about 1.0 cM. The results allow the exact placement of these loci and are in accord with the observations made by Harashima and Oshima (1976).     

Mapping of meiotic genes in rye (Secale cereale L.): Localization of sy19 mutation, impairing homologous synapsis, by means of isozyme and microsatellite markers

The sy19 mutation, which impairs the homology of meiotic chromosome synapsis in rye, were mapped using a specially created F₂ population by means of isozyme Acph1 locus and microsatellite (SSR) markers. The sy19 gene was localized in the chromosome 7R in the pericentromeric region of long arm based on the linked inheritance with the Acph1 locus. The locus was linked with five rye SSR markers, with the Xrems1234 locus being located closest to the sy19 gene (6.4 cM). The genetic map of the analyzed chromosome 7R region includes ten markers and the sy19 locus. A possible function of the Sy1 and Sy19 genes based on the data on comparative genomics is discussed.     

Neuropeptide Y Receptor Genes on Human Chromosome 4q31–q32 Map to Conserved Linkage Groups on Mouse Chromosomes 3 and 8

Npy1randNpy2r,the genes encoding mouse type 1 and type 2 neuropeptide Y receptors, have been mapped by interspecific backcross analysis. Previous studies have localized the human genes encoding these receptors to chromosome 4q31–q32. We have now assignedNpy1randNpy2rto conserved linkage groups on mouse Chr 8 and Chr 3, respectively, which correspond to the distal region of human chromosome 4q. Using yeast artificial chromosomes, we have estimated the distance between the human genes to be approximately 6 cM. Although ancient tandem duplication events may account for some closely spaced G-protein-coupled receptor genes, the large genetic distance between the human type 1 and type 2 neuropeptide Y receptor genes raises questions about whether this mechanism accounts for their proximity.     

Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 5 of Wheat

The distribution of genes and recombination in the wheat genome was studied by comparing physical maps with the genetic linkage maps. The physical maps were generated by mapping 80 DNA and two phenotypic markers on an array of 65 deletion lines for homoeologous group 5 chromosomes. The genetic maps were constructed for chromosome 5B in wheat and 5D in Triticum tauschii. No marker mapped in the proximal 20% chromosome region surrounding the centromere. More than 60% of the long arm markers were present in three major clusters that physically encompassed <18% of the arm. Because 48% of the markers were cDNA clones and the distributions of the cDNA and genomic clones were similar, the marker distribution may represent the distribution of genes. The gene clusters were identified and allocated to very small chromosome regions because of a higher number of deletions in their surrounding regions. The recombination was suppressed in the centromeric regions and mainly occurred in the gene-rich regions. The bp/cM estimates varied from 118 kb for gene-rich regions to 22 Mb for gene-poor regions. The wheat genes present in these clusters are, therefore, amenable to molecular manipulations parallel to the plants with smaller genomes like rice.     

Cytogenetic Mapping of Enzyme Loci on Chromosomes J and U of DROSOPHILA SUBOBSCURA

Enzyme loci located on chromosome J and U were mapped cytologically by means of a Y translocation technique. A linkage map of the two chromosomes was established in a parallel experiment and the recombination frequency in different regions of the chromosomes determined. A comparison of the cytogenetic localization of the enzyme genes in D. subobscura and D. melanogaster indicates that many paracentric inversions must have taken place in the course of divergent evolution. However, no displacements of genes from one element to another due to pericentric inversions, reciprocal translocations or transposing elements can be observed. In spite of the large number of structural rearrangements that have occurred in the phylogeny of the genus Drosophila, gross similarities of banding pattern in homologous regions of the chromosomes of the two species become apparent.