scholarly journals Difference of genomic compartments is correlated with contrastive modes of functional losses of host specificity determinants during the course of pathotype differentiation in Pyricularia oryzae

2021 ◽  
Author(s):  
Soichiro Asuke ◽  
Nicole John Magculia ◽  
Yoshihiro Inoue ◽  
Trinh Thi Phuoug Vy ◽  
Yukio Tosa
Keyword(s):  
Host Specificity ◽  
Pyricularia Oryzae ◽  
Gene Interactions ◽  
Avirulence Genes ◽  
Loss Of Function ◽  
Genome Sequences ◽  
Nucleotide Substitutions ◽  
Rich Region ◽  
Poor Region ◽  
Specificity Determinants

The specificity between pathotypes of Pyricularia oryzae and genera of gramineous plants is governed by gene-for-gene interactions. Here, we show that avirulence genes involved in this host specificity have undergone different modes of functional losses dependent on, or affected by genomic compartments harboring them. The avirulence of an Eleusine pathotype on wheat is controlled by five genes including PWT3 which played a key role in the evolution of the Triticum pathotype (the wheat blast fungus). We cloned another gene using an association of its presence/absence with pathotypes, and designated it as PWT6. PWT6 was widely distributed in a lineage composed of Eleusine/Eragrostis isolates, but completely absent in a lineage composed of Lolium/Triticum isolates. On the other hand, PWT3 homologs were present in all isolates, and their loss of function in Triticum isolates was caused by insertions of transposable elements or nucleotide substitutions. Analyses of whole genome sequences of representative isolates revealed that these two genes were located in different genomic compartments; PWT6 was located in a repeat-rich region while PWT3 was located in a repeat-poor region. These results suggest that the course of differentiation of the pathotypes in P. oryzae appears to be illustrated as processes of functional losses of avirulence genes, but that modes of the losses are affected by genomic compartments in which they reside.

scholarly journals INAPPROPRIATE TECHNOLOGY What Is in It for the Rich?

2007 ◽  
Vol 11 (4) ◽  
pp. 487-518 ◽  
Author(s):  
ANA FERNANDES ◽  
KRISHNA B. KUMAR
Keyword(s):  
Green Revolution ◽  
Developed Countries ◽  
Welfare Effects ◽  
Luxury Good ◽  
Rich Region ◽  
The Poor ◽  
Poor Region ◽  
Inferior Good ◽  
The Rich ◽  
Local Use

In this paper, we investigate incentives, other than altruism, that developed countries have for improving developing country technologies. We propose a simple model of international trade between two regions, in which individuals have preferences over an inferior good and a luxury good. The poor region has a comparative advantage in the production of the inferior good. Even when costly adaptation of the technology to the poor region's characteristics is required—making the technology inappropriate for local use—there are parameter configurations for which the rich region has an incentive to incur this cost. It benefits from a terms-of-trade improvement and from greater specialization in the luxury good. Indeed, there are cases where the rich region would prefer to improve the poor region's technology for producing the inferior good rather than its own. We apply our model to the Green Revolution and provide a quantitative assessment of its welfare effects.

scholarly journals The efficacy of CRISPR-mediated cytosine base editing with the RPS5a promoter in Arabidopsis thaliana

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Minkyung Choi ◽  
Jae-Young Yun ◽  
Jun-Hyuk Kim ◽  
Jin-Soo Kim ◽  
Sang-Tae Kim
Keyword(s):  
Arabidopsis Thaliana ◽  
Cytidine Deaminase ◽  
Biological Research ◽  
Loss Of Function ◽  
Nucleotide Substitutions ◽  
Viral Origin ◽  
Nonsense Mutations ◽  
Base Editing ◽  
Low Efficiency ◽  
Viable System

AbstractCRISPR/Cas9-mediated genome editing is an important and versatile technology in modern biological research. Recent advancements include base-editing CRISPR tools that enable targeted nucleotide substitutions using a fusion protein comprising a nickase variant of Cas9 and a base deaminase. Improvements in base editing efficiencies and inheritable of edited loci need to be made to make CRISPR a viable system in plants. Here, we report efficiency of cytosine base editors (CBEs) in Arabidopsis thaliana by applying the strong endogenous RPS5a promoter to drive the expression of nickase Cas9 and either rAPOBEC1 from rat (BE3) or the PmCDA1 activation-induced cytidine deaminase from sea lamprey (AIDv2). Compared with the strong heterologous CaMV35S promoter of viral origin, the RPS5a promoter improved CBE efficiency by 32% points with the number of T1 plants showing over 50% conversion ratio when the LFY gene was targeted. CBE induced nonsense mutations in LFY via C-to-T conversion, which resulted in loss-of-function lfy phenotypes; defects in LFY function were associated with the targeted base substitutions. Our data suggest that optimal promoter choice for CBE expression may affect base-editing efficiencies in plants. The results provide a strategy to optimize low-efficiency base editors and demonstrate their applicability for functional assays and trait development in crop research.

scholarly journals When Coupled to Natural Transformation in Acinetobacter sp. Strain ADP1, PCR Mutagenesis Is Made Less Random by Mismatch Repair

2005 ◽  
Vol 71 (11) ◽  
pp. 7610-7612 ◽  
Author(s):  
Alison Buchan ◽  
L. Nicholas Ornston
Keyword(s):  
Structure Function ◽  
Mismatch Repair ◽  
Protein Function ◽  
Natural Transformation ◽  
Function Analysis ◽  
Repair System ◽  
Loss Of Function ◽  
Nucleotide Substitutions ◽  
Full Spectrum ◽  
Mismatch Repair System

ABSTRACT Random PCR mutagenesis is a powerful tool for structure-function analysis of targeted proteins, especially when coupled with DNA integration through natural transformation followed by selection for loss of function. The technique has been applied successfully to structure-function analysis of transcriptional regulators, enzymes, and transporters in Acinetobacter sp. strain ADP1. However, the mismatch repair system prevents the full spectrum of nucleotide substitutions that may be selected at the level of protein function from being recovered. This barrier may be overcome by introducing PCR-mutagenized genes into strains in which the corresponding genes have been deleted.

scholarly journals Life and Death of Selfish Genes: Comparative Genomics Reveals the Dynamic Evolution of Cytoplasmic Incompatibility

2020 ◽  
Vol 38 (1) ◽  
pp. 2-15 ◽  
Author(s):  
Julien Martinez ◽  
Lisa Klasson ◽  
John J Welch ◽  
Francis M Jiggins
Keyword(s):  
Cytoplasmic Incompatibility ◽  
Gene Gain ◽  
Evolutionary Models ◽  
Loss Of Function ◽  
Genome Sequences ◽  
Life And Death ◽  
Selfish Genes ◽  
Wolbachia Genome ◽  
The Cross ◽  
Gain Loss

Abstract Cytoplasmic incompatibility is a selfish reproductive manipulation induced by the endosymbiont Wolbachia in arthropods. In males Wolbachia modifies sperm, leading to embryonic mortality in crosses with Wolbachia-free females. In females, Wolbachia rescues the cross and allows development to proceed normally. This provides a reproductive advantage to infected females, allowing the maternally transmitted symbiont to spread rapidly through host populations. We identified homologs of the genes underlying this phenotype, cifA and cifB, in 52 of 71 new and published Wolbachia genome sequences. They are strongly associated with cytoplasmic incompatibility. There are up to seven copies of the genes in each genome, and phylogenetic analysis shows that Wolbachia frequently acquires new copies due to pervasive horizontal transfer between strains. In many cases, the genes have subsequently acquired loss-of-function mutations to become pseudogenes. As predicted by theory, this tends to occur first in cifB, whose sole function is to modify sperm, and then in cifA, which is required to rescue the cross in females. Although cif genes recombine, recombination is largely restricted to closely related homologs. This is predicted under a model of coevolution between sperm modification and embryonic rescue, where recombination between distantly related pairs of genes would create a self-incompatible strain. Together, these patterns of gene gain, loss, and recombination support evolutionary models of cytoplasmic incompatibility.

scholarly journals At Least Five Major Genes Are Involved in the Avirulence of an Eleusine Isolate of Pyricularia oryzae on Common Wheat

2020 ◽  
Vol 110 (2) ◽  
pp. 465-471 ◽  
Author(s):  
Soichiro Asuke ◽  
Shuko Nishimi ◽  
Yukio Tosa
Keyword(s):  
Molecular Markers ◽  
Common Wheat ◽  
Finger Millet ◽  
Segregation Ratio ◽  
Pyricularia Oryzae ◽  
Complementation Test ◽  
Wheat Cultivars ◽  
Avirulence Genes ◽  
The Third ◽  
Genetic Mechanisms

Pyricularia oryzae is composed of pathotypes that show host specificity at the plant genus level. To elucidate the genetic mechanisms of the incompatibility between the Eleusine pathotype (pathogenic on finger millet) and common wheat, an Eleusine isolate (MZ5-1-6) was crossed with a Triticum isolate (Br48) pathogenic on wheat, and resulting F1 cultures were sprayed onto common wheat cultivars Hope, Norin 4 (N4), and Chinese Spring (CS). On Hope, avirulent and virulent cultures segregated in a 3:1 ratio, suggesting that two avirulence genes are involved. They were tentatively designated as eA1 and eA2. On N4 and CS, the segregation ratio was not significantly deviated from the 7:1, 15:1, or 31:1 ratios, suggesting that three or more genes are involved. A comparative analysis of the segregation patterns suggested that two of these genes were eA1 and eA2. A complementation test indicated that the third gene (tentatively designated as eA3) was the Ao9 type of the PWT3 gene controlling the avirulence of Avena and Lolium isolates on wheat. The fourth gene (tentatively designated as eA4) was detected by backcrossing 200R72, an F1 culture lacking eA1, eA2, and eA3, with Br48. Comparative analyses of phenotypes and the presence and/or absence of molecular markers in the F1 population revealed that some cultures were avirulent on N4/CS in spite of lacking eA1, eA2, eA3, and eA4, indicating the presence of the fifth gene (tentatively designated as eA5). Taken together, we conclude that at least five avirulence genes are involved in the incompatibility between MZ5-1-6 and N4/CS.

scholarly journals Different Domains of Phytophthora sojae Effector Avr4/6 Are Recognized by Soybean Resistance Genes Rps4 and Rps6

2010 ◽  
Vol 23 (4) ◽  
pp. 425-435 ◽  
Author(s):  
Daolong Dou ◽  
Shiv D. Kale ◽  
Tingli Liu ◽  
Qinghua Tang ◽  
Xia Wang ◽  
...  
Keyword(s):  
Protein Translocation ◽  
Single Gene ◽  
Phytophthora Sojae ◽  
Avirulence Genes ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
C Terminus ◽  
Oomycete Pathogen ◽  
Soybean Leaves

At least 12 avirulence genes have been genetically identified and mapped in Phytophthora sojae, an oomycete pathogen causing root and stem rot of soybean. Previously, the Avr4 and Avr6 genes of P. sojae were genetically mapped within a 24 kb interval of the genome. Here, we identify Avr4 and Avr6 and show that they are actually a single gene, Avr4/6, located near the 24-kb region. Avr4/6 encodes a secreted protein of 123 amino acids with an RXLR-dEER protein translocation motif. Transient expression of Avr4/6 in soybean leaves revealed that its gene product could trigger a hypersensitive response (HR) in the presence of either Rps4 or Rps6. Silencing Avr4/6 in P. sojae stable transformants abolished the avirulence phenotype exhibited on both Rps4 and Rps6 soybean cultivars. The N terminus of Avr4/6, including the dEER motif, is sufficient to trigger Rps4-dependent HR while its C terminus is sufficient to trigger Rps6-mediated HR. Compared with alleles from avirulent races, alleles of Avr4/6 from virulent races possess nucleotide substitutions in the 5′ untranslated region of the gene but not in the protein-coding region.

scholarly journals The Solanum tuberosum GBSSI gene: a target for assessing gene and base editing in tetraploid potato

2019 ◽  
Author(s):  
Florian Veillet ◽  
Laura Chauvin ◽  
Marie-Paule Kermarrec ◽  
François Sevestre ◽  
Mathilde Merrer ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Genome Editing ◽  
Genome Engineering ◽  
Basic Research ◽  
Loss Of Function ◽  
Dna Breaks ◽  
Nucleotide Substitutions ◽  
Discrete Variation ◽  
Tetraploid Potato ◽  
Base Editing

AbstractGenome editing has recently become a method of choice for basic research and functional genomics, and holds great potential for molecular plant breeding applications. The powerful CRISPR-Cas9 system that typically produces double-strand DNA breaks is mainly used to generate knockout mutants. Recently, the development of base editors has broadened the scope of genome editing, allowing precise and efficient nucleotide substitutions. In this study, we produced mutants in two cultivated elite cultivars of the tetraploid potato (Solanum tuberosum) using stable or transient expression of the CRISPR-Cas9 components to knockout the amylose-producing StGBSSI gene. We set up a rapid, highly sensitive and cost-effective screening strategy based on high-resolution melting analysis followed by direct Sanger sequencing and trace chromatogram analysis. Most mutations consisted of small indels, but unwanted insertions of plasmid DNA were also observed. We successfully created tetra-allelic mutants with impaired amylose biosynthesis, confirming the loss-of-function of the StGBSSI protein. The second main objective of this work was to demonstrate the proof of concept of CRISPR-Cas9 base editing in the tetraploid potato by targeting two loci encoding catalytic motifs of the StGBSSI enzyme. Using a cytidine base editor (CBE), we efficiently and precisely induced DNA substitutions in the KTGGL-encoding locus, leading to discrete variation in the amino acid sequence and generating a loss-of-function allele. The successful application of base editing in the tetraploid potato opens up new avenues for genome engineering in this species.Key MessageThe StGBSSI gene was successfully and precisely edited in the tetraploid potato using gene and base editing strategies, leading to plants with impaired amylose biosynthesis.

scholarly journals Molecular structure of soybean E-genes and their functional mutations

2020 ◽  
pp. 3-13
Author(s):  
O. Okhrymovych ◽  
◽  
S. Chebotar ◽  
G. Chebotar ◽  
D. Zharikova ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Genetic Network ◽  
Structural Features ◽  
Loss Of Function ◽  
Nucleotide Substitutions ◽  
Early Maturity ◽  
E Gene ◽  
Wide Range

In this review, we discuss features of the molecular structure of known E-loci (early maturity) and their involvement in signaling to plant flowering, depending on the sensitivity of soybean genotypes to the photoperiod. These loci contribute to the adaptation of plants to a wide range of natural conditions due to mutations in genes and QTL that control flowering time. At the molecular level, E-genes are significantly different in structural features, origin and function. The lenghth of the identified genes range from one exon to 525 bp encoding the transcription factor (E1), up to 14 exons and about 20 kb for the GmGIa gene (E2). Among the functional mutations that in most cases lead to partial or complete loss of function, there are single-nucleotide substitutions or deletions, insertions of transposon-like sequences that can lead to amino acid substitutions in the protein, shift of the reading frame, appearance of the premature stop-codon. E-gene products are receptors of signals coming from the environment and they participate in signaling pathways that control the photoperiod. The overall impact and interactions between E-genes have not been fully studied yet, the molecular structure was investigated only for E1-E4, for which a genetic network of interactions was proposed, while at the same time five loci (E6-E9 and E11) were only mapped on soybean chromosomes, and the existence of a separate E5 locus has not yet been established. In eight of the 11 E-loci, the dominant allele causes late flowering. Also there is a pleiotropic effect of E-gene alleles on yield, plant height, stress resistance, and response to low temperatures. Knowledge of the allelic state of only some of the 11 genes is not sufficient. A comprehensive understanding of the functioning of the photoperiodic genetic response network is needed. E-genes are genetic determinants that can be used during selection and creation of new varieties with programmed rates of development.

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