Detailed Comparative Mapping of Cereal Chromosome Regions Corresponding to the Ph1 Locus in Wheat

Detailed physical mapping of markers from rice chromosome 9, and from syntenous (at the genetic level) regions of other cereal genomes, has resulted in rice yeast artificial chromosome (YAC) contigs spanning parts of rice 9. This physical mapping, together with comparative genetic mapping, has demonstrated that synteny has been largely maintained between the genomes of several cereals at the level of contiged YACs. Markers located in one region of rice chromosome 9 encompassed by the YAC contigs have exhibited restriction fragment length polymorphism (RFLP) using deletion lines for the Ph1 locus. This has allowed demarcation of the region of rice chromosome 9 syntenous with the ph1b and ph1c deletions in wheat chromosome 5B. A group of probes located in wheat homoeologous group 5 and barley chromosome 5H, however, have synteny with rice chromosomes other than 9. This suggests that the usefulness of comparative trait analysis and of the rice genome as a tool to facilitate gene isolation will differ from one region to the next, and implies that the rice genome is more ancestral in structure than those of the Triticeae.     

Cloning the Arabidopsis GA1 Locus by Genomic Subtraction

Arabidopsis thaliana ga1 mutants are gibberellin-responsive dwarfs. We used the genomic subtraction technique to clone DNA sequences that are present in wild-type Arabidopsis (ecotype Landsberg erecta, Ler) but are missing in a presumptive ga1 deletion mutant, ga1-3. The cloned sequences correspond to a 5.0-kb deletion in the ga1-3 genome. Three lines of evidence indicated that the 5.0-kb deletion in the ga1-3 mutant is located at the GA1 locus. First, restriction fragment length polymorphism mapping showed that DNA sequences within the 5.0-kb deletion map to the GA1 locus. Second, cosmid clones that contain wild-type DNA inserts spanning the deletion in ga1-3 complemented the dwarf phenotype when integrated into the ga1-3 genome by Agrobacterium tumefaciens-mediated transformation. Third, we identified molecular lesions in four additional ga1 alleles within the 5.0-kb region deleted in mutant ga1-3. One of these lesions is a large insertion or inversion located within the most distal intron encoded by the GA1 locus. The three other lesions are all single base changes located within the two most distal exons. RNA gel blot analysis indicated that the GA1 locus encodes a 2.8-kb mRNA. We calculated a recombination rate of 10-5 cM per nucleotide for the GA1 region of the Arabidopsis genome.     

Fine Physical Mapping of Ph1, a Chromosome Pairing Regulator Gene in Polyploid Wheat

The diploid-like chromosome pairing in polyploid wheat is controlled by the Ph1 (pairing homoeologous) gene that is located on chromosome arm 5BL. By using a combination of cytogenetic and molecular techniques, we report the physical location of the Ph1 gene to a submicroscopic chromosome region (Ph1 gene region) that is flanked by the breakpoints of two deletions (5BL-1 and ph1c) and is marked by a DNA probe (XksuS1). The Ph1 gene region is present distal to the breakpoint of deletion 5BL-1 but proximal to the C-band 5BL2.1. Two other DNA probes (Xpsr128 and Xksu75) flank the region-Xpsr128 being proximal and Xksu75 being distal. The estimated size of the region is less than 3 Mb. The chromosome region around the Ph1 gene is high in recombination as the genetic distance of the region between 5BL-1 breakpoint and C-band 5BL2.1 (not resolved by the microscope) is at least 9.3 cM.     

HLA－DRB1基因位点多态性的PCR－RFLP分析

设计并建立一套适合国内应用的改良ＰＣＲ－ＲＦＬＲ方法,分５组特异性扩增ＤＮＡ样品,随后进行酶切定型分析,准确检测了编码ＤＲ抗原特异性的ＨＬＡ－ＤＲＢ１基因位点的多态性,该法采用分组扩增,不发生与其它ＤＲＢ位点等位基因的交叉扩增,不仅适合纯合子的区分而且可以清楚准确地检测杂合子样品,已报道过的ＤＲＢ１位点编码的特异性组合都可以通过这个方法得到准确分析。所使用的Ⅱ类限制性内切酶均价格便宜、易购。     

中国春Ph1基因的分子标记及冬小麦ph1b代换系的获得

利用大麦 (HordeumvulgareL .)第 5染色体上RFLP探针衍生的 19个序列标志位点PCR(STS_PCR)引物对“中国春”小麦 (TriticumaestivumL .) (CS)及其ph1b突变体基因组总DNA进行PCR扩增 ,筛选出Ph1基因的一个连锁标记 ,再用“中国春”第 5部分同源群缺体_四体系和CS×ph1b突变体F2 群体证明并定位于离Ph1基因近着丝点端 5 .7cM (centiMorgan)处。然后将该标记转换成特异的序列特征扩增区 (SCAR)标记。以“阿勃”5B缺体为桥梁亲本 ,冬小麦“京 411”为受体亲本 ,“中国春”ph1b突变体为供体亲本 ,进行三轮杂交和一轮自交 ,每一轮经减数分裂分析和SCAR标记的辅助选择 ,快速地筛选出了ph1b基因型 ,并选得一个冬小麦“京 411”的ph1b中间代换系。     

Reversion at the HIS1 Locus of Yeast

The his1 gene (chromosome V) of Saccharomyces cerevisiae specifies phosphoribosyl transferase (E.C.2.4.2.17), the first enzyme of histidine biosynthesis. This hexameric enzyme has both catalytic and regulatory functions. The spontaneous reversion rates of seven his1 mutations were studied. The reversion rates of the alleles at the proximal end of the locus (relative to the centromere) were about 50-fold higher than distal alleles. Spontaneous reversion to prototrophy was studied in diploids homoallelic for each of the seven his1 mutations. Based on tetrad analysis, the prototrophy revertants could be assigned to three classes: (1) revertant tetrads that carried a prototrophic allele indistinguishable from wild type; (2) revertant tetrads that carried a prototrophic allele characterized by histidine excretion and feedback resistance; and (3) revertant tetrads that did not contain a prototrophic spore, but rather a newly derived allele that complemented the original allele intragenically. Four of the seven his1 mutations produced the excretor revertant class, and two mutations produced the complementer revertant class. The significance of these findings to our understanding of gene organization and the catalytic and regulatory functions of gene products are discussed.     

Molecular Markers of Ph1 Gene in Chinese Spring and Development of Winter Wheat New Line Harboring ph1b Gene

he genomic DNA of common wheat (Triticum aestivum L.) “Chinese Spring” (CS) and its ph1b mutant were analyzed by using 19 sequence tagged site PCR (STS-PCR) primers, which derived from RFLP probes from barley (Hordeum vulgare L.) chromosome 5H. One marker was identified on wheat chromosome 5BL, which is 5.7 cM (centiMorgan) proximal to Ph1 gene, using the CS homoeologous group 5 nullisomic-tetrasomic, ditelosomic 5BL line and an F2 population from CS×ph1b mutant. This linked PCR marker was converted into a more specific sequence characterized amplified region (SCAR) marker. To obtain a new winter wheat line containing ph1b gene, the authors used a nullisomic 5B line of “Abbodanza”as a bridge parent and crossed respectively with the CS ph1b mutant (donor) and a winter wheat variety, “Jing 411” (recipient). The meiotic chromosome pairing was checked in the progeny of each cross, as well as using the marker-assistant selection of the SCAR marker identified for ph1b gene. After three inter-crossing and one selfing, a relatively stable ph1b substitution line of winter wheat with “Jing 411” background was obtained.     

A DNA Fragment Mapped within the Submicroscopic Deletion of Ph1, a Chromosome Pairing Regulator Gene in Polyploid Wheat

Bread wheat is an allohexaploid consisting of three genetically related (homoeologous) genomes. The homoeologous chromosomes are capable of pairing but strict homologous pairing is observed at metaphase 1. The diploid-like pairing is regulated predominantly by Ph1, a gene mapped on long arm of chromosome 5B. We report direct evidence that a mutant of the gene (ph1b) arose from a submicroscopic deletion. A probe (XksuS1-5) detects the same missing fragment in two independent mutants ph1b and ph1c and a higher intensity fragment in a duplication of the Ph1 gene. It is likely that XksuS1-5 lies adjacent to Ph1 on the same chromosome fragment that is deleted in ph1b and ph1c. XksuS1-5 can be used to tag Ph1 gene to facilitate incorporation of genetic material from homoeologous genomes of the Triticeae. It may also be a useful marker in cloning Ph1 gene by chromosome walking.     

Identification of the Molecular Markers Linked to the Salt-resistance Locus in the Wheat Using RAPD-BSA Technique

Calli from mature embryo of “Jimai-24” wheat ( Triticum aestivum L.) were induced on medium containing Zhengdingmycin then continuously cultured on medium containing 0.5% NaCl till to regenerate plants named 8901-17 salt-tolerant mutant. “Jimai-24” was compared with 8901-17 by using the technique of RAPD. Thirty-five out of 280 random primers could detect DNA polymorphism. The similarity index was 0.978, indicating that they were NILs (near-isogenic lines). Two F2 populations (“Jimai-24”×8901-17 and 8901-17דZhongmai-9”) had been constructed using the method of half-division. The two relative DNA pools (salt tolerant DNA pool and susceptible DNA pool) which come from the two F2 populations, respectively, had been made according to the method of BSA (bulked segregant analysis). RAPD analysis between the two DNA relative pools was carried on with above 35 random primers which could detect DNA polymorphism definitely. The identical polymorphism between the two sets of DNA pools come from the two F2 populations could be determined only by OperonQ4 primer. This result implied that the polymorphic fragment amplified by OperonQ4 primer was the molecular marker of RAPD closely linked to the salt tolerant mutation locus.     

Copy Number Variation at the APOL1 Locus

Two coding variants in the APOL1 gene (G1 and G2) explain most of the high rate of kidney disease in African Americans. APOL1-associated kidney disease risk inheritance follows an autosomal recessive pattern: The relative risk of kidney disease associated with inheritance of two high-risk variants is 7–30 fold, depending on the specific kidney phenotype. We wished to determine if the variability in phenotype might in part reflect structural differences in APOL1 gene. We analyzed sequence coverage from 1000 Genomes Project Phase 3 samples as well as exome sequencing data from African American kidney disease cases for copy number variation. 8 samples sequenced in the 1000 Genomes Project showed increased coverage over a ~100kb region that includes APOL2, APOL1 and part of MYH9, suggesting the presence of APOL1 copy number greater than 2. We reasoned that such duplications should be enriched in apparent G1 heterozygotes with kidney disease. Using a PCR-based assay, we observed the presence of this duplication in additional samples from apparent G0G1 or G0G2 individuals. The frequency of this APOL1 duplication was compared among cases (n = 123) and controls (n = 255) with apparent G0G1 heterozygosity. The presence of APOL1 duplication was observed in 4.06% of cases and 0.78% controls, preliminary evidence that this APOL1 duplication may alter susceptibility to kidney disease (p = 0.03). Taqman-based copy number assays confirmed the presence of 3 APOL1 copies in individuals positive for this specific duplication by PCR assay, but also identified a small number of individuals with additional APOL1 copies of presumably different structure. These observations motivate further studies to better assess the contribution of APOL1 copy number on kidney disease risk and on APOL1 function. Investigators and clinicians genotyping APOL1 should also consider whether the particular genotyping platform used is subject to technical errors when more than two copies of APOL1 are present.     

Regulatory Mutants at the his1 Locus of Yeast

The his1 gene in Saccharomyces cerevisiae codes for phosphoribosyl transferase, an allosteric enzyme that catalyzes the initial step in histidine biosynthesis. Mutants that specifically alter the feedback regulatory function were isolated by selecting his1 prototrophic revertants that overproduce and excrete histidine. The prototrophs were obtained from diploids homoallelic for his1--7 and heterozygous for the flanking markers thr3 and arg6. Among six independently derived mutant isolates, three distinct levels of histidine excretion were detected. The mutants were shown to be second-site alterations mapping at the his1 locus by recovery of the original auxotrophic parental alleles. The double mutants, HIS1--7e, are dominant with respect to catalytic function but recessive in regulatory function. When removed from this his1--7 background, the mutant regulatory site (HIS1-e) still confers prototrophy but not histidine excretion. To yield the excretion phenotype, the primary and altered secondary sites are required in cis array. Differences in histidine excretion levels correlate with resistance to the histidine analogue, triazoalanine.     

一个柱穗山羊草（Aegilops cylindrica）系统中的类Ph1基因

第一次在一个Ａｅ．ｃｙｌｉｎｄｒｉｃａ系统中发现了Ｐｈ１－ｌｉｋｅ基因,但它的作用略小于Ｐｈ１。同时证明了Ａｅ,ｃｙｌｉｎｄｒｉｃａ在控制染色体配对基因方面存在多态现象。ｐｈ１ｂ基因可以诱导普通小麦与Ａｅ．ｃｙｌｉｎｄｒｉｃａ间的部分同源染色体配对,同时用普通小麦对（中国春ｐｈ１ｂ突变体×Ａｅ．ｃｙｌｉｎｄｒｉｃａ）Ｆ_１回交获得了成功。表明利用ｐｈ１ｂ基因通过诱导部分同源染色体配对可以把Ａｅ．ｃｙｌｉｎｄｒｉｃａ中的有益基因导入到普通小麦中。     

A New Variant of the Mouse Akp1 Locus

A new electrophoretic migration type of alkaline phosphatase 1 (Akp1) was found on the cellulose acetate electrophoresis for kidney and liver homogenates of KWHM mouse, a newly established inbred strain derived from the Korean wild mouse (Mus musculus molossinus). This new type of alkaline phosphatase 1 was distinguished from previously reported AKP1A and AKP1B types in the mouse, and tentatively named AKP1C. In genetic analysis by mating experiments between KWHM and C57BL/6J (AKP1A) or BALB/cA (AKP1B), the phenotypic segregation ratios of AKP1A : AKP1AC : AKP1C or AKP1B : AKP1BC : AKP1C were 1 : 2 : 1 in both groups of F2 generations. It was therefore concluded that AKP1C type is controlled by Akp1c allele which is codominant with Akp1a and Akp1b alleles.     

Recognition of phytotropins by the receptor for 1-N-naphthylphthalamic acid

The structure requirements for phytotropin activity and receptor binding are expressed in terms of a recognition site on the receptor with which phytotropins, including 1-N-naphthylphthalamic acid, interact. It is postulated that the site can be represented by a large region which accepts planar molecules, and is possibly electrophilic in nature. A second area is also postulated which may be lipophilic or electrophilic, together with a carboxyl acceptor. It is suggested that if the requirements of the carboxyl acceptor and adjacent area are met, then phytotropin activity will result if the candidate molecule has a configuration, or can adopt a configuration, such that a conjugated portion of the molecule can interact with the larger area. It is argued that the close relationship observed between receptor binding and effect on the gravitropic response implies that the receptors may be directly involved in the gravitropic response mechanism.     

Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain

Recent discovery of 5-hydroxymethylcytosine (5hmC) in genomic DNA raises the question how this sixth base is recognized by cellular proteins. In contrast to the methyl-CpG binding domain (MBD) of MeCP2, we found that the SRA domain of Uhrf1, an essential factor in DNA maintenance methylation, binds 5hmC and 5-methylcytosine containing substrates with similar affinity. Based on the co-crystal structure, we performed molecular dynamics simulations of the SRA:DNA complex with the flipped cytosine base carrying either of these epigenetic modifications. Our data indicate that the SRA binding pocket can accommodate 5hmC and stabilizes the flipped base by hydrogen bond formation with the hydroxyl group.     

Novel Interallelic Complementation at the his1 Locus of Yeast

In yeast, 17 histidine-requiring mutants derived from and interallelically complementary to his1-7 were analyzed. The genetic basis of the complementation response was elucidated by mitotic and meiotic gene conversion. Each allele probably carries an unaltered 7-site mutation and a unique second-site alteration. The second-site alterations appear to be clustered within the proximal and distal segments of the his1 structural gene. Models of intraalelic complementation are reviewed in light of the unique complementational response between a single-site mutant and a double mutant including the identical altered base sequence.