Molecular Markers for the agouti Coat Color Locus of the Mouse

The agouti (a) coat color locus of the mouse acts within the microenvironment of the hair follicle to control the relative amount and distribution of yellow and black pigment in the coat hairs. Over 18 different mutations with complex dominance relationships have been described at this locus. The lethal yellow (Ay) mutation is the top dominant of this series and is uniquely associated with an endogenous provirus, Emv-15, in three highly inbred strains. However, we report here that it is unlikely that the provirus itself causes the Ay-associated alteration in coat color, since one strain of mice (YBR-Ay/a) lacks the provirus but still retains a yellow coat color. Using single-copy mouse DNA sequences from the regions flanking Emv-15 we have detected three patterns of restriction fragment length polymorphisms (RFLPs) within this region that can be used as molecular markers for different agouti locus alleles: a wild-type agouti (A) pattern, a pattern which generally cosegregates with the nonagouti (a) mutation, and a pattern which is specific to Emv-15. We have used these RFLPs and a panel of 28 recombinant inbred mouse strains to determine the genetic linkage of these sequences with the agouti locus and have found complete concordance between the two (95% confidence limit of 0.00 to 3.79 centimorgans). We have also physically mapped these sequences by in situ hybridization to band H1 of chromosome 2, thus directly confirming previous assignments of the location of the agouti locus.     

A Genetic Linkage Map of Mouse Chromosome 10: Localization of Eighteen Molecular Markers Using a Single Interspecific Backcross

Interspecific mouse backcross analysis was used to generate a molecular genetic linkage map of mouse chromosome 10. The map locations of the Act-2, Ahi-1, Bcr, Braf, Cdc-2a, Col6a-1, Col6a-2, Cos-1, Esr, Fyn, Gli, Ifg, Igf-1, Myb, Pah, pgcha, Ros-1 and S100b loci were determined. These loci extend over 80% of the genetic length of the chromosome, providing molecular access to many regions of chromosome 10 for the first time. The locations of the genes mapped in this study extend the known regions of synteny between mouse chromosome 10 and human chromosomes 6, 10, 12 and 21, and reveal a novel homology segment between mouse chromosome 10 and human chromosome 22. Several loci may lie close to, or correspond to, known mutations. Preferential transmission of Mus spretus-derived alleles was observed for loci mapping to the central region of mouse chromosome 10.     

Molecular Genetic Characterization of Six Recessive Viable Alleles of the Mouse Agouti Locus

The agouti locus on mouse chromosome 2 encodes a secreted cysteine-rich protein of 131 amino acids that acts as a molecular switch to instruct the melanocyte to make either yellow pigment (phaeomelanin) or black pigment (eumelanin). Mutations that up-regulate agouti expression are dominant to those causing decreased expression and result in yellow coat color. Other associated effects are obesity, diabetes, and increased susceptibility to tumors. To try to define important functional domains of the agouti protein, we have analyzed the molecular defects present in a series of recessive viable agouti mutations. In total, six alleles (a(mJ), a(u), a(da), a(16H), a(18H), a(e)) were examined at both the RNA and DNA level. Two of the alleles, a(16H) and a(e), result from mutations in the agouti coding region. Four alleles (a(mJ), a(u), a(18H), and a(da)) appear to represent regulatory mutations that down-regulate agouti expression. Interestingly, one of these mutations, a(18H), also appears to cause an immunological defect in the homozygous condition. This immunological defect is somewhat analogous to that observed in motheaten (me) mutant mice. Short and long-range restriction enzyme analyses of homozygous a(18H) DNA are consistent with the hypothesis that a(18H) results from a paracentric inversion where one end of the inversion maps in the 5' regulatory region of agouti and the other end in or near a gene that is required for normal immunological function. Cloning the breakpoints of this putative inversion should allow us to identify the gene that confers this interesting immunological disorder.     

Saturated Molecular Map of the Rice Genome Based on an Interspecific Backcross Population

A molecular map has been constructed for the rice genome comprised of 726 markers (mainly restriction fragment length polymorphisms; RFLPs). The mapping population was derived from a backcross between cultivated rice, Oryza sativa, and its wild African relative, Oryza longistaminata. The very high level of polymorphism between these species, combined with the use of polymerase chain reaction-amplified cDNA libraries, contributed to mapping efficiency. A subset of the probes used in this study was previously used to construct an RFLP map derived from an inter subspecific cross, providing a basis for comparison of the two maps and of the relative mapping efficiencies in the two crosses. In addition to the previously described PstI genomic rice library, three cDNA libraries from rice (Oryza), oat (Avena) and barley (Hordeum) were used in this mapping project. Levels of polymorphism detected by each and the frequency of identifying heterologous sequences for use in rice mapping are discussed. Though strong reproductive barriers isolate O. sativa from O. longistaminata, the percentage of markers showing distorted segregation in this backcross population was not significantly different than that observed in an intraspecific F(2) population previously used for mapping. The map contains 1491 cM with an average interval size of 4.0 cM on the framework map, and 2.0 cM overall. A total of 238 markers from the previously described PstI genomic rice library, 250 markers from a cDNA library of rice (Oryza), 112 cDNA markers from oat (Avena), and 20 cDNA markers from a barley (Hordeum) library, two genomic clones from maize (Zea), 11 microsatellite markers, three telomere markers, eleven isozymes, 26 cloned genes, six RAPD, and 47 mutant phenotypes were used in this mapping project. Applications of a molecular map for plant improvement are discussed.     

大豆分子标记在RIL群体中的偏分离分析

利用栽培大豆与半野生大豆杂交得到的Ｆ８代重组自交系,对２３８个分子标记的偏分离现象进行了分析。结果表明,２９．４％的位点出现偏分离,并且有偏向母本“长农４号”的趋势。     

Polymorphism of the Goat Agouti Signaling Protein Gene and Its Relationship with Coat Color in Italian and Spanish Breeds

Agouti signaling protein (ASIP) is one of the key players in the modulation of hair pigmentation in mammals. Binding to the melanocortin 1 receptor, ASIP induces the synthesis of phaeomelanin, associated with reddish brown, red, tan, and yellow coats. We have sequenced 2.8?kb of the goat ASIP gene in 48 individuals and identified two missense (Cys126Gly and Val128Gly) and two intronic polymorphisms. In silico analysis revealed that the Cys126Gly substitution may cause a structural change by disrupting a highly conserved disulfide bond. We studied its segregation in 12 Spanish and Italian goat breeds (N?=?360) with different pigmentation patterns and found striking differences in the frequency of the putative loss-of-function Gly(126) allele (Italian 0.43, Spanish Peninsular 0.08), but we did not observe a clear association with coat color. This suggests that the frequency of this putative loss-of-function allele has evolved under the influence of demographic rather than selection factors in goats from these two geographical areas.     

Contrasting Mode of Evolution at a Coat Color Locus in Wild and Domestic Pigs

Despite having only begun ~10,000 years ago, the process of domestication has resulted in a degree of phenotypic variation within individual species normally associated with much deeper evolutionary time scales. Though many variable traits found in domestic animals are the result of relatively recent human-mediated selection, uncertainty remains as to whether the modern ubiquity of long-standing variable traits such as coat color results from selection or drift, and whether the underlying alleles were present in the wild ancestor or appeared after domestication began. Here, through an investigation of sequence diversity at the porcine melanocortin receptor 1 (MC1R) locus, we provide evidence that wild and domestic pig (Sus scrofa) haplotypes from China and Europe are the result of strikingly different selection pressures, and that coat color variation is the result of intentional selection for alleles that appeared after the advent of domestication. Asian and European wild boar (evolutionarily distinct subspecies) differed only by synonymous substitutions, demonstrating that camouflage coat color is maintained by purifying selection. In domestic pigs, however, each of nine unique mutations altered the amino acid sequence thus generating coat color diversity. Most domestic MC1R alleles differed by more than one mutation from the wild-type, implying a long history of strong positive selection for coat color variants, during which time humans have cherry-picked rare mutations that would be quickly eliminated in wild contexts. This pattern demonstrates that coat color phenotypes result from direct human selection and not via a simple relaxation of natural selective pressures.     

Interaction of the Murine Dilute Suppressor Gene (Dsu) with Fourteen Coat Color Mutations

The murine dilute suppressor gene, dsu, was previously shown to suppress the dilute coat color phenotypes of mice homozygous for the dilute (d), leaden (ln), and ashen (ash) mutations. Each of these mutations produce adendritic melanocytes, which results in an abnormal transportation of pigment granules into the hair shaft and a diluted coat color. The suppression of each mutation is associated with the restoration of near normal melanocyte morphology, indicating that dsu can compensate for the absence of normal d, ln and ash gene products. In experiments described here, we have determined whether dsu can suppress the coat color phenotype of 14 additional mutations, at 11 loci, that affect coat color by mechanisms other than alterations in melanocyte morphology. In no case was dsu able to suppress the coat color phenotype of these 14 mutations. This suggests that dsu acts specifically on coat color mutations that result from an abnormal melanocyte morphology. Unexpectedly, dsu suppressed the ruby eye color of ruby-eye (ru) and ruby-eye-2 (ru-2) mice, to black. The exact nature of the defect producing these two mutant phenotypes is unknown. Histological examination of the pigmented tissues of the eyes of these mice indicated that dsu suppresses the eye color by increasing the overall level of pigmentation in the choroid but not the retinal pigmented epithelium. Choroid melanocytes, like those in the skin, are derived from the neural crest while melanocytes in the retinal pigmented epithelium are derived from the optic cup. This suggests that dsu may act specifically on neural crest-derived melanocytes. These studies have thus identified a second group of genes whose phenotypes are suppressed by dsu and have provided new insights into the mechanism of action of dsu.     

Fine Structure Mapping and Deletion Analysis of the Murine Piebald Locus

piebald (s) is a recessive mutation that affects the development of two cell types of neural crest origin: the melanocytes, responsible for pigment synthesis in the skin, and enteric ganglia, which innervate the lower bowel. As a result, mice carrying piebald mutations exhibit white spotting in the coat and aganglionic megacolon. Previously the gene had been localized to the distal half of mouse chromosome 14. To determine its precise location relative to molecular markers, an intersubspecific backcross was generated. Two anchor loci of chromosome 14, slaty and hypogonadal, in addition to simple sequence length repeat markers, were used to localize s to a 2-cM interval defined by the markers D14Mit38 and D14Mit42. The molecular markers were also used to characterize nine induced s alleles. Three of these mutations exhibited no deletions or rearrangements of the flanking markers, whereas the other six had two or more of these markers deleted. The extent of the deletions was found to be consistent with the severity of the homozygous phenotype. The location of deletion breakpoints in the induced alleles, coupled with the recombination breakpoints in the backcross progeny, provide useful molecular landmarks to define the location of the piebald gene.     

实验红鲫C1HD系的生化遗传标记

目的 建立实验红鲫C1HD系生化遗传标记.方法 采用聚丙烯酰胺梯度凝胶垂直电泳法,分析实验红鲫C1HD系与普通红鲫的苹果酸脱氢酶(MDH)和超氧化物歧化酶(SOD)等同工酶.结果 实验红鲫C1HD系和普通红鲫血清蛋白电泳可分离出25条以上蛋白带,分为A、B、C等3个区段.在A、B区段,实验红鲫C1HD系分别具有SP-A1谱带和SP-B1、SP-B3～8谱带,但缺少SP-A2、SP-A3和SP-B2谱带.实验红鲫C1HD系具有8条SOD同工酶电泳谱带,比普通红鲫多出SOD-3、SOD-8两条特征带.两种红鲫均具备MDH-1、MDH-2和MDH-3电泳谱带,且带型一致;普通红鲫额外具备MDH-4和MDH-5两条电泳谱带.结论 血清蛋白SP-A1和超氧化物歧化酶SOD-3、SOD-8电泳谱带可以作为实验红鲫C1HD系的生化遗传标记.     

The Doublesex Locus of Drosophila Melanogaster and Its Flanking Regions: A Cytogenetic Analysis

The region of the third chromosome (84D-F) of Drosophila melanogaster that contains the doublesex (dsx) locus has been cytogenetically analyzed. Twenty nine newly induced, and 42 preexisting rearrangements broken in dsx and the regions flanking dsx have been cytologically and genetically characterized. These studies established that the dsx locus is in salivary chromosome band 84E1-2. In addition, these observations provide strong evidence that the dsx locus functions only to regulate sexual differentiation and does not encode a vital function. To obtain new alleles at the dsx locus and to begin to analyze the genes flanking dsx, 59 lethal and visible mutations in a region encompassing dsx were induced. These mutations together with preexisting mutations in the region were deficiency mapped and placed into complementation groups. Among the mutations we isolated, four new mutations affecting sexual differentiation were identified. All proved to be alleles of dsx, suggesting that dsx is the only gene in this region involved in regulating sexual differentiation. All but one of the new dsx alleles have equivalent effects in males and females. The exception, dsxEFH55, strongly affects female sexual differentiation, but only weakly affects male sexual differentiation. The interactions of dsxEFH55 with mutations in other genes affecting sexual differentiation are described. These results are discussed in terms of the recent molecular findings that the dsx locus encodes sex-specific proteins that share in common their amino termini but have different carboxyl termini. The 72 mutations in this region that do not affect sexual differentiation identify 25 complementation groups. A translocation, T(2;3)Es that is associated with a lethal allele in one of these complementation groups is also broken at the engrailed (en) locus on the second chromosome and has a dominant phenotype that may be due to the expression of en in the anterior portion of the abdominal tergites where en is not normally expressed. The essential genes found in the 84D-F region are not evenly distributed throughout this region; most strikingly the 84D1-11 region appears to be devoid of essential genes. It is suggested that the lack of essential genes in this region is due to the region (1) containing genes with nonessential functions and (2) being duplicated, possibly both internally and elsewhere in the genome.     

Exploring the Genetic Characteristics of Two Recombinant Inbred Line Populations via High-Density SNP Markers in Maize

Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43–11.50 cM/Mb while the minimum was 0.08–0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop.     

Genetic Recombination at the Buff Spore Color Locus in SORDARIA BREVICOLLIS. II. Analysis of Flanking Marker Behavior in Crosses between Buff Mutants

Aberrant asci containing one or more wild-type spores were selected from crosses between pairs of alleles of the buff locus in the presence of closely linked flanking markers. Data were obtained relating to the site of aberrant segregation and the position of any associated crossover giving recombination of flanking markers. Aberrant segregation at a proximal site within the buff gene may be associated with a crossover proximal to the site of aberrant segregation or, with equal frequency, with a crossover distal to the site of the second mutant present in the cross. Similarly, segregation at a distal site may be associated with a crossover distal to the site or, with lower frequency, with a crossover proximal to the site of the proximal mutant present in the cross. Crossovers between the alleles were rare. This evidence for the relationship between hybrid DNA and crossing over is discussed in terms of current models for the mechanism of recombination.     

基于转录组数据的杜仲红叶性状SSR分子标记分析

对‘华仲12号’杜仲的幼嫩叶片（绿色）和成熟叶片（红色）及‘华仲11号’杜仲成熟叶片（绿色）进行转录组测序,进行测序数据的拼接和组装,且对转录组获得的基因（Unigenes）进行SSR分析。研究得到54 517条平均长度为806.90 bp的Unigenes,其中25 993条Unigenes在Nr、Swiss-Prot、KEGG和COG蛋白数据库获得功能注释,占所有Unigenes的47.68%。参照KEGG数据库,可将注释到的6 910条Unigenes划分到122个代谢途径分支,其中花色苷代谢途径相关酶基因39个,类黄酮代谢途径38个,类胡萝卜素合成途径34个。54 517条Unigenes中共包含17 010个完整型SSR位点,占总SSR位点的96.28%。完整型SSR位点共包含67种重复基元,其中出现频率最高的重复基元类型为单核苷酸重复中的A/T （7 747个）,其次是AG/CT （5 039个）和AT/AT （850个）从花色苷代谢途径、类黄酮代谢途径及类胡萝卜素代谢途径中共找到13个SSR位点。为今后杜仲遗传多样性分析、遗传图谱构建及杜仲红叶性状分子标记开发等方面奠定了分子基础。     

Molecular Markers Useful for Intraspecies Subtyping and Strain Differentiation of Dermatophytes

Dermatophytosis is a very common skin disorder and the most frequent infection encountered by practicing dermatologists. The identification, pathogenicity, biology, and epidemiology of dermatophytes, the causative agents of dermatophytosis, are of interest for both dermatologists and medical mycologists. Recent advances in molecular methods have provided new techniques for identifying dermatophytes, including intraspecies variations. Intraspecies subtyping and strain differentiation have made possible the tracking of infections, the identification of common sources of infections, recurrence or reinfection after treatment, and analysis of strain virulence and drug resistance. This review describes molecular methods of intraspecies subtyping and strain differentiation, including analyses of mitochondrial DNA and non-transcribed spacer regions of ribosomal RNA genes, random amplification of polymorphic DNA, and microsatellite markers, along with their advantages and limitations.     

重组甘蔗花叶病毒E株系外壳蛋白的纯化及其多克隆抗体制备

目的：制备可用于甘蔗花叶病毒（ScMV）E株系（ScMV-E）检测用多克隆抗体。方法：将ScMV-E外壳蛋白（CP）基因连接到pET29a（＋）上,经PCR检测、酶切及测序鉴定获得重组质粒pET29a-CP,在大肠杆菌BL21（DE3）中诱导表达重组ScMV-E外壳蛋白;采用His Trap Kit纯化目的蛋白,作为抗原免疫新西兰大白兔,制备特异性抗体;通过间接ELISA、Western blot和组织印迹法检测所制备抗体的特异性。结果：SDS-PAGE分析表明,重组融合蛋白含6个组氨酸标记,相对分子质量约43000;Western blot检测显示所获得的抗体特异性良好,间接ELISA法测得血清的效价为1：81 920;甘蔗叶片的组织印迹检测结果显示杂交效果良好。结论：制备的多克隆抗体可直接用于ScMV-E检测,并有望用于制备ScMV-E检测试剂盒。     

Opposite Orientations of an Inverted Duplication and Allelic Variation at the Mouse Agouti Locus

The mouse agouti protein is a paracrine signaling molecule that causes yellow pigment synthesis. A pale ventral coloration distinguishes the light-bellied agouti (A(w)) from the agouti (A) allele, and is caused by expression of ventral-specific mRNA isoforms with a unique 5' untranslated exon. Molecular cloning demonstrates this ventral-specific exon lies within a 3.1-kb element that is duplicated in the opposite orientation 15-kb upstream to produce an interrupted palindrome and that similarity between the duplicated elements has been maintained by gene conversion. Orientation of the palindrome is reversed in A compared to A(w), which suggests that mutation from one allele to the other is caused by intrachromosomal homologous recombination mediated by sequences within the duplicated elements. Analysis of 15 inbred strains of laboratory and wild-derived mice with Southern hybridization probes and closely linked microsatellite markers suggests six haplotype groups: one typical for most strains that carry A(w) (129/SvJ, LP/J, CE/J, CAST/Ei), one typical for most strains that carry A (Balb/cJ, CBA/J, FVB/N, PERA/Rk, RBB/Dn); and four that are atypical (MOLC/Rk, MOLG/Dn, PERA/Ei, PERC/Ei, SPRET/Ei, RBA/Dn). Our results suggest a model for molecular evolution of the agouti locus in which homologous recombination can produce a reversible switch in allelic identity.     

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.