Effects of the Photoperiod Genes Ppd1 and Ppd2 on Growth and Development of the Shoot Apex in Wheat

Two major genes influencing the photoperiod response in wheat,Ppd1 and Ppd2, have been identified on the group 2 chromosomes.Substitution lines, which had been characterized on the basisof time of ear emergence as carrying either the insensitiveor sensitive alleles of the two Ppd genes, were used to investigatethe effect of these genes on development. They were grown undershort photoperiods, and growth and development of the shootapex was measured. The primary influence of the Ppd genes was on ear growth. Inthe plants carrying the insensitive alleles, Ppd1 and Ppd2,the relative growth rate of the floral apex was faster thanthat of plants with the sensitive alleles, ppd1 and ppd2. Therewere no differences in the rate of spikelet initiation, butthe spikelets of the ppd lines grew and developed more slowly. The Ppd2 material segregated for another gene located on chromosome2B affecting duration of the life cycle. This gene also affectedthe relative growth rate of the ear. It was considered that the major effect of the Ppd1, Ppd2 andthe second genetic factor on chromosome 2B is on floral growthrate. Differences in apex morphology, stem growth and ear emergenceare thought to be due to the differences in floral apex growthand size. Wheat, photoperiod genes, shoot apex development, shoot apex growth     

Beginning and duration of expression of photoperiodic response genes in winter common wheat

The influence of various Ppd genes on the beginning and duration of photoperiodic responce has been investigated in near isogenic lines of winter bread wheat Mironovskaya 808. During ontogenesis the photoperiodic responce is ascertained from the middle 2nd stage of ontogenesis according to Kuperman (usually a week later after vernalization completion in winter genotypes) and it is completed to the late 5th stage (2-3 weeks before heading). Different Ppd alleles do not affect the photoreaction intensity however they have an influence on its duration through the rate of development. Ppd-A1a and Ppd-B1a genes manifest shorter duration of expression when compared to the recessive alleles in the initial Mironovskaya 808 cultivar. Effect of the Ppd-B1a gene is stronger and of the Ppd-A1a is weaker.     

Differences in the genetic systems controlling photoreaction and vernalization requirements in winter wheat]

Comparing of vernalization requirement and photoperiodic sensitivity in various winter genotypes and F4 lines was carried out. The results of genetic analysis of Ppd genotypes in the crosses of winter wheat cultivars differing in photosensitivity and duration of vernalization requirement are described. It has been shown that differences in duration of vernalization requirement are under control of independent genetic system, distinctive from Ppd gene system regulating level of photosensitivity. This independence does not deny the opposite possibility of Ppd genes to modify duration of vernalization requirement in winter wheat.     

Complete Nucleotide Sequence of a 43-Kilobase Genomic Island Associated with the Multidrug Resistance Region of Salmonella enterica Serovar Typhimurium DT104 and Its Identification in Phage Type DT120 and Serovar Agona

This study describes the characterization of the recently described Salmonella genomic island 1 (SGI1) (D. A. Boyd, G. A. Peters, L.-K. Ng, and M. R. Mulvey, FEMS Microbiol. Lett. 189:285-291, 2000), which harbors the genes associated with the ACSSuT phenotype in a Canadian isolate of Salmonella enterica serovar Typhimurium DT104. A 43-kb region has been completely sequenced and found to contain 44 predicted open reading frames (ORFs) which comprised approximately 87% of the total sequence. Fifteen ORFs did not show any significant homology to known gene sequences. A number of ORFs show significant homology to plasmid-related genes, suggesting, at least in part, a plasmid origin for the SGI1, although some with homology to phage-related genes were identified. The SGI1 was identified in a number of multidrug-resistant DT120 and S. enterica serovar Agona strains with similar antibiotic-resistant phenotypes. The G+C content suggests a potential mosaic structure for the SGI1. Emergence of the SGI1 in serovar Agona strains is discussed.     

Genetic analysis of anther culture response in wheat carrying alien translocations

A bread wheat cultivar, Saratovskaya 29, (S29), its nearly isogenic lines carrying alien translocations [Lr9 from Aegilops umbellulata (Eg29) and (Lr19) from Agropyron elongatum (Ps29)] and two F₁ hybrids between three nearly isogenic lines of S29 that differed by the Lr19+Rht1,Pro1+Pro2 and Ppd1+Ppd2 gene complexes, namely the S29 (Lr19+Rht1)/S29 (Ppd1+Ppd2) F₁ and the S29 (Pro1+Pro2)/S29 (Lr19+Rht1) F₁ were studied for their culture response with the following results. (1) Translocations with Lr9 and Lr19 decreased embryo frequency and green plant regeneration. (2) Both F₁ hybrids showed a decrease in embryo frequency. One of the F₁ hybrids, S29 (Lr19+Rht1)/S29 (Ppd1+Ppd2) showed a decrease, with respect to S29 for green plant regeneration; the other F₁ S29 (Pro1+Pro2)/S29 (Lr19+Rht1), equalled S29 for green plant regeneration. (3) The gene complex of the F₁ hybrid S29 (Pro1+Pro2)/S29 (Lr19+Rht1) was better than that of the F₁ hybrid S29 (Lr19+Rht1)/S29 (Ppd1+Ppd2) for embryo induction and green plant regeneration. This effect was possibly induced by interactions between the Pro1+Pro2 and Lr19+Rht1 genes or was the result of direct actions of the Pro1+Pro2 genes.     

Biallelic expression of Z-linked genes in male chickens

In birds, females are heterogametic (ZW), while males are homogametic (ZZ). It has been proposed that there is no dosage compensation for the expression of Z-linked genes in birds. In order to examine if the genes are inactivated on one of the two Z chromosomes, we analyzed the allelic expression of the B4GALT1 and CHD-Z genes on Z chromosomes in male chickens. One base substitution was detected among 15 chicken breeds and lines examined for each gene, and cross mating was made between the breeds or lines with polymorphism. cDNAs were synthesized from cultured cell colonies each derived from a single cell of an F1 male embryo. The allelic expression of the B4GALT1 gene was examined by restriction fragment length polymorphism analysis of the PCR products digested with RSAI, and that of the CHD-Z gene by the single nucleotide primer extension (SNuPE) method. Both of the genes displayed biallelic expression, suggesting that these Z-linked genes were not subject to inactivation in male chickens. Comparison between expression levels in males and females by real-time quantitative PCR suggested that expression was compensated for the CHD-Z gene but not for the B4GALT1 gene.     

Genetic analysis of the dwarfing gene Rht8 in wheat. Part II. The distribution and adaptive significance of allelic variants at the Rht8 locus of wheat as revealed by microsatellite screening

 Wheat microsatellite WMS 261 whose 192-bp allele has been shown to be diagnostic for the commercially important dwarfing gene Rht8 was used to screen over 100 wheat varieties to determine the worldwide spread of Rht8. The results showed Rht8 to be widespread in southern European wheats and to be present in many central European wheats including the Russian varieties ‘Avrora’, ‘Bezostaya’ and ‘Kavkaz’. Rht8 appears to be of importance to South European wheats as alternative giberellic acid (GA)-insensitive dwarfing genes do not appear to be adapted to this environment. The very successful semi-dwarf varieties bred by CIMMYT, Mexico, for distribution worldwide have been thought to carry Rht8 combined with GA-insensitive dwarfing genes. Additional height reduction would have been obtained from pleiotropic effects of the photoperiod-response gene Ppd1 that is essential to the adaptability of varieties bred for growing under short-winter days in tropical and sub-tropical areas. The microsatellite analysis showed that CIMMYT wheats lack Rht8 and carry a WMS 261 allelic variant of 165 bp that has been associated with promoting height. This presumably has adaptive significance in partly counteracting the effects of other dwarfing genes and preventing the plants being too short. Most UK, German and French wheats carry an allelic variant at the WMS 261 locus with 174 bp. This could be selected because of linkage with the recessive photoperiod-sensitive ppd1 allele that is thought to offer adaptive significance northern European wheats. Received: 17 October 1997 / Accepted: 12 November 1997     

Flowering in Pisum: Identification of a new ppd allele and its physiological action as revealed by grafting

The late flowering, quantitative long day habit of wild type pea ( Pisum sativum L.) is conferred by the joint presence of dominant genes Sn, Dne and Ppd. Grafting studies have shown that flowering in wild type plants is delayed under short days by formation of a graft-transmissible inhibitor and that the early flowering, day neutral mutants sn and dne are deficient in this inhibitor. However, the physiological action of the Ppd gene has not been examined by grafting and the possibility exists that the ppd mutation causes early flowering and a day neutral habit by blocking response to, rather than synthesis of, the inhibitor. We here identify a second, more severe (probably null) mutant allele ( ppd -2) at the Ppd locus and show that flowering was delayed by 4 nodes in a ppd -2 shoot grafted to a wild type stock, and promoted by 13 nodes in a wild type shoot grafted to a ppd -2 stock. Thus a ppd -2 shoot can respond to inhibitor donated by a wild type stock but a ppd -2 stock is unable to provide sufficient inhibitor to prevent early flower initiation in a wild type shoot. We conclude genes Sn, Dne and Ppd each control steps in the synthesis of the flower inhibitor. Grafts among the sn, dne and ppd mutants gave an indication that the three genes may act in the sequence Sn, Ppd, Dne , but possible cases of physiological complementation need to be tested using null mutants in the same genetic background.     

The genetics of Salmonella genomic island 1

Multidrug-resistant Salmonella enterica serovar Typhimurium phage type DT104, resistant to ampicillin, chloramphenicol/florfenicol, streptomycin, sulfonamides, and tetracycline, has disseminated worldwide. The resistance genes reside on the 43-kb Salmonella genomic island 1 (SGI1), which is transferable. Drug-resistant variants of SGI1 have been identified in numerous serotypes. Strains harboring SGI1 may be more virulent and have a tendency to rapidly disseminate.     

Large-scale profiling and identification of potential regulatory mechanisms for allelic gene expression in colorectal cancer cells

Allelic variation in gene expression is common in humans and this variation is associated with phenotypic variation. In this study, we employed high-density single nucleotide polymorphism (SNP) chips containing 13,900 exonic SNPs to identify genes with allelic gene expression in cells from colorectal cancer cell lines. We found 2 monoallelically expressed genes (ERAP2 and MYLK4), 32 genes with an allelic imbalance in their expression, and 13 genes showing allele substitution by RNA editing. Among a total of 34 allelically expressed genes in colorectal cancer cells, 15 genes (44.1%) were associated with cis-acting eQTL, indicating that large portions of allelically expressed genes are regulated by cis-acting mechanisms of gene expression. In addition, potential regulatory variants present in the proximal promoter regions of genes showing either monoallelic expression or allelic imbalance were not tightly linked with coding SNPs, which were detected with allelic gene expression. These results suggest that multiple rare variants could be involved in the cis-acting regulatory mechanism of allelic gene expression. In the comparison with allelic gene expression data from Centre d'Etude du Polymorphisme Humain (CEPH) family B cells, 12 genes showed B-cell specific allelic imbalance and 1 noncoding SNP showed colorectal cancer cell-specific allelic imbalance. In addition, different patterns of allele substitution were observed between B cells and colorectal cancer cells. Overall, our study not only indicates that allelic gene expression is common in colorectal cancer cells, but our study also provides a better understanding of allele-specific gene expression in colorectal cancer cells.     

Analysis of inheritance of morphological and biochemical characters introgressed into common wheat from Aegilops speltoides Tausch

Genetic control of some morphological traits and the gliadin composition were examined in plants of two lines of common wheat carrying genes introgressed from the wild diploid cereal Aegilops speltoides. Leaf hairiness was shown to be controlled by a single introgressed dominant gene that was not allelic to the known common wheat gene Hl1. Waxlessness of the whole plant is controlled by the introgressed from Ae. speltoides inhibitor gene allelic to gene W1 located on chromosome 2B. This gene was epistatic to the introgressed gene controlling spike waxlessness. The introgressed gene of spike color was shown to be allelic to Rg1 located on chromosome 1B of common wheat. However, the former gene proved to be linked to an allele of the Gli-B1 locus other than in wheat.     

The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae

High-throughput elucidation of synthetic genetic interactions (SGIs) has contributed to a systems-level understanding of genetic robustness and fault-tolerance encoded in the genome. Pathway targets of various compounds have been predicted by comparing chemical-genetic synthetic interactions to a network of SGIs. We demonstrate that the SGI network can also be used in a powerful reverse pathway-to-drug approach for identifying compounds that target specific pathways of interest. Using the SGI network, the method identifies an indicator gene that may serve as a good candidate for screening a library of compounds. The indicator gene is selected so that compounds found to produce sensitivity in mutants deleted for the indicator gene are likely to abrogate the target pathway. We tested the utility of the SGI network for pathway-to-drug discovery using the DNA damage checkpoint as the target pathway. An analysis of the compendium of synthetic lethal interactions in yeast showed that superoxide dismutase 1 (SOD1) has significant SGI connectivity with a large subset of DNA damage checkpoint and repair (DDCR) genes in Saccharomyces cerevisiae, and minimal SGIs with non-DDCR genes. We screened a sod1Δ strain against three National Cancer Institute (NCI) compound libraries using a soft agar high-throughput halo assay. Fifteen compounds out of ～3100 screened showed selective toxicity toward sod1Δ relative to the isogenic wild type (wt) strain. One of these, 1A08, caused a transient increase in growth in the presence of sublethal doses of DNA damaging agents, suggesting that 1A08 inhibits DDCR signaling in yeast. Genome-wide screening of 1A08 against the library of viable homozygous deletion mutants further supported DDCR as the relevant targeted pathway of 1A08. When assayed in human HCT-116 colorectal cancer cells, 1A08 caused DNA-damage resistant DNA synthesis and blocked the DNA-damage checkpoint selectively in S-phase.     

Allelic exclusion of a T cell receptor-beta minilocus.

A TCR-beta minilocus in germline configuration (beta M) has previously been shown to undergo rearrangement and expression in transgenic mice. To study allelic exclusion of TCR miniloci, several beta M transgenic mouse lines were generated and crossed with mice transgenic for a functionally rearranged TCR V beta 2 gene (beta R). PCR analysis of beta M beta R double transgenic mice revealed almost complete suppression of endogenous TCR V beta gene rearrangements, but blockage of minilocus V beta rearrangements was achieved with only one of five minilocus transgenic lines. This result cannot be explained by copy number or arrangement of the multiple miniloci integrated. It appears that the minilocus is not autonomously regulated which suggests that sequences flanking the integration sites influence accessibility of the minilocus for rearrangement and allelic exclusion. However, although productively rearranged genes were formed in double transgenic mice, surface expression of minilocus-encoded beta chains was not detected. This indicates that allelic exclusion may operate at a level after gene rearrangement.     

SNP-based large-scale identification of allele-specific gene expression in human B cells

Polymorphism and variations in gene expression provide the genetic basis for human variation. Allelic variation of gene expression, in particular, may play a crucial role in phenotypic variation and disease susceptibility. To identify genes with allelic expression in human cells, we genotyped genomic DNA and cDNA isolated from 31 immortalized B cell lines from three Centre d'Etude du Polymorphisme Humain (CEPH) families using high-density single-nucleotide polymorphism (SNP) chips containing 13,900 exonic SNPs. We identified seven SNPs in five genes with monoallelic expression, 146 SNPs in 125 genes with allelic imbalance in expression with preferentially higher expression of one allele in a heterozygous individual. The monoallelically expressed genes (ERAP2, MDGA1, LOC644422, SDCCAG3P1 and CLTCL1) were regulated by cis-acting, non-imprinted differential allelic control. In addition, all monoallelic gene expression patterns and allelic imbalances in gene expression in B cells were transmitted from parents to offspring in the pedigree, indicating genetic transmission of allelic gene expression. Furthermore, frequent allele substitution, probably due to RNA editing, was also observed in 21 genes in 23 SNPs as well as in 48 SNPs located in regions containing no known genes. In this study, we demonstrated that allelic gene expression is frequently observed in human B cells, and SNP chips are very useful tools for detecting allelic gene expression. Overall, our data provide a valuable framework for better understanding allelic gene expression in human B cells.     

In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches

We report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar Nipponbare of rice (Oryza sativa L.), called Oryza Tag Line (OTL). Sixteen thousand eight hundred and fourteen T-DNA and 12,410 Tos17 discrete insertion sites have been characterized in these lines. We estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence-indexed T-DNA (6563 genes) and/or Tos17 (2755 genes) inserts. Six hundred and forty-three genes are interrupted by both T-DNA and Tos17 inserts. High quality of the sequence indexation of the T2 seed samples was ascertained by several approaches. Field evaluation under agronomic conditions of 27,832 OTL has revealed that 18.2% exhibit at least one morphophysiological alteration in the T1 progeny plants. Screening 10,000 lines for altered response to inoculation by the fungal pathogen Magnaporthe oryzae allowed to observe 71 lines (0.7%) developing spontaneous lesions simulating disease mutants and 43 lines (0.4%) exhibiting an enhanced disease resistance or susceptibility. We show here that at least 3.5% (four of 114) of these alterations are tagged by the mutagens. The presence of allelic series of sequence-indexed mutations in a gene among OTL that exhibit a convergent phenotype clearly increases the chance of establishing a linkage between alterations and inserts. This convergence approach is illustrated by the identification of the rice ortholog of AtPHO2, the disruption of which causes a lesion-mimic phenotype owing to an over-accumulation of phosphate, in nine lines bearing allelic insertions.     

Comparative genetic analysis: the utility of mouse genetic systems for studying human monogenic disease

One of the long-term goals of mutagenesis programs in the mouse has been to generate mutant lines to facilitate the functional study of every mammalian gene. With a combination of complementary genetic approaches and advances in technology, this aim is slowly becoming a reality. One of the most important features of this strategy is the ability to identify and compare a number of mutations in the same gene, an allelic series. With the advent of gene-driven screening of mutant archives, the search for a specific series of interest is now a practical option. This review focuses on the analysis of multiple mutations from chemical mutagenesis projects in a wide variety of genes and the valuable functional information that has been obtained from these studies. Although gene knockouts and transgenics will continue to be an important resource to ascertain gene function, with a significant proportion of human diseases caused by point mutations, identifying an allelic series is becoming an equally efficient route to generating clinically relevant and functionally important mouse models.     

Analysis of allelic state of genes responsible for baking properties in allocytoplasmic wheat hybrids

A collection of allocytoplasmic hybrids of common wheat (AWH) was screened for the allelic state of genes responsible for baking properties (high-molecular glutenins, puroindolines, and Waxy). The possibility of the introgression of the Waxy gene of T. timopheevii into the wheat genome was demonstrated in several AWH lines using the set of molecular markers. Allelic gene variants responsible for the bread-making quality were revealed in 22 AWH lines, which make it possible to detect the most superior lines for both molecular-genetic analysis and applied research.