An AFLP marker tightly linked to apomixis reveals hemizygosity in a portion of the apomixis-controlling locus in Paspalum simplex

Genome ◽  
2002 ◽  
Vol 45 (3) ◽  
pp. 513-519 ◽  
Author(s):  
Paola Labombarda ◽  
Alessandra Busti ◽  
Maria Eugenia Caceres ◽  
Fulvio Pupilli ◽  
Sergio Arcioni
Keyword(s):  
Mapping Population ◽  
Chromosome Region ◽  
Sequence Divergence ◽  
Chromosome Segment ◽  
Large Chromosome ◽  
Aflp Data ◽  
Specific Sequence ◽  
Physical Isolation ◽  
Fragment Libraries ◽  
Paspalum Simplex

A mapping population of Paspalum simplex segregating for apomixis (asexual reproduction through seeds) was screened with AFLPs to find apomixis-linked markers. Four AFLPs linked to apomixis in coupling phase were found. Three of them did not show recombinants among the 87 individuals of the mapping population, whereas the other was more loosely linked. Integrating the AFLP data with those obtained previously with rice RFLP anchor markers, a map was drawn for the chromosome region of P. simplex encompassing apomixis. We cloned the three AFLPs tightly linked with apomixis into plasmid vectors and used them as probes to hybridize the restriction digested DNA of the mapping population. Two of them revealed RFLP bands linked to apomixis together with other alleles, whereas one was proven to belong to a hemizygous portion of the apomixis locus. The total picture resulting from AFLP and RFLP analyses was that a cluster of markers tightly linked with apomixis was detected in P. simplex together with two other markers that were more loosely linked. These two markers enclosed a relatively large chromosome segment characterized by strong repression of recombination. The block of recombination may have caused sequence divergence and, therefore, hemizygosity of some regions belonging to the apomixis-controlling chromosome segment of P. simplex. The potential of developing an apomixis-specific sequence for screening large-fragment libraries for the physical isolation of the locus encompassing apomixis is discussed.Key-words: AFLP, apomixis, hemizygosity.

scholarly journals A Portion of the Apomixis Locus of Paspalum Simplex is Microsyntenic with an Unstable Chromosome Segment Highly Conserved Among Poaceae

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Giulio Galla ◽  
Lorena A. Siena ◽  
Juan Pablo A. Ortiz ◽  
Helmut Baumlein ◽  
Gianni Barcaccia ◽  
...  
Keyword(s):  
Chromosome Segment ◽  
Paspalum Simplex

GENETIC METHODS FOR ANALYSIS AND MANIPULATION OF INVERSION MUTATIONS IN BACTERIA

Genetics ◽  
1983 ◽  
Vol 105 (3) ◽  
pp. 517-537
Author(s):  
Molly B Schmid ◽  
John R Roth
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Recipient Cell ◽  
Chromosome Segment ◽  
Large Chromosome ◽  
Good Resolution ◽  
Wild Type ◽  
Chromosomal Inversions ◽  
Inversion Breakpoints ◽  
Generalized Transduction

ABSTRACT A number of genetic methods for the isolation, characterization and manipulation of large chromosomal inversions in Salmonella typhimurium are described. One inversion-carrying mutant is characterized in detail and used to demonstrate a number of unique genetic properties of bacterial inversions.—Contrary to expectation, it was found that large inversion mutations can be repaired by generalized transduction. The repair results from the simultaneous introduction of two wild-type transduced fragments into a single recipient cell. Homologous recombination between the two transduced fragments and the two inversion breakpoints causes the inverted segment to be reinverted. This results in regeneration of the wild-type orientation of this chromosome segment. Similar recombination events allow a large inversion mutation to be introduced into a wild-type strain; two transduced fragments from an inversion strain cause recombination events resulting in inversion of a large chromosome segment.—Genetic methods for mapping the extent of a large inversion mutation by generalized transduction are described and tested. The methods are operationally simple and allow good resolution of the two inversion breakpoints.

Molecular and morphological diagnostic markers for the Himalayan Ips DeGeer species (Coleoptera: Curculionidae: Scolytinae)

Zootaxa ◽  
2011 ◽  
Vol 3128 (1) ◽  
pp. 47 ◽  
Author(s):  
ABDUL A. BUHROO ◽  
FERENC LAKATOS
Keyword(s):  
Dna Sequences ◽  
Bark Beetles ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Morphological Characters ◽  
The Body ◽  
Specific Sequence ◽  
Haplotype Variation ◽  
Mitochondrial Cytochrome Oxidase ◽  
I Gene

Morphological and molecular analyses of Ips bark beetles collected in the eastern and northwestern Himalayan area resulted in the diagnosis of three species—Ips stebbingi, I. longifolia and I. schmutzenhoferi. These three species can be distinguished by morphological characters, including the frontal setae, the body size and the shape and position of the spines on the elytral declivity. DNA sequences of the mitochondrial Cytochrome Oxidase I gene were analyzed to detect haplotype variation within each of the species. A phylogenetic analysis was performed on our data plus data from GenBank. Considerable amount of intra-specific sequence divergence was found in I. longifolia, ranging between 0.2%−2.5%. Intra-specific sequence divergence in I. stebbingi ranged from 0.2%−1.1% and in I. schmutzenhoferi it varied by 0.2%. Interspecific sequence divergence was high among the three species: 7.4−8.6% between I. longifolia and I. stebbingi, 11.9−12.2% between I. stebbingi and I. schmutzenhoferi, and 11.5−12.6% between I. longifolia and I. schmutzenhoferi. Phylogenetic analyses revealed Himalayan Ips species to be monophyletic and unrelated to other Asian species. Ips stebbingi and I. longifolia were sister taxa and I. schmutzenhoferi was distinguished from I. stebbingi.

scholarly journals Characterization of a rice variety with high hydraulic conductance and identification of the chromosome region responsible using chromosome segment substitution lines

2010 ◽  
Vol 106 (5) ◽  
pp. 803-811 ◽  
Author(s):  
Shunsuke Adachi ◽  
Yukiko Tsuru ◽  
Motohiko Kondo ◽  
Toshio Yamamoto ◽  
Yumiko Arai-Sanoh ◽  
...  
Keyword(s):  
Chromosome Region ◽  
Rice Variety ◽  
Hydraulic Conductance ◽  
Chromosome Segment ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Segment Substitution

scholarly journals Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Duminda Sampath Bandara Dissanayake ◽  
Clare Ellen Holleley ◽  
Laura Kate Hill ◽  
Denis O’Meally ◽  
Janine Eileen Deakin ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
In Silico ◽  
Sex Chromosome ◽  
Genomic Sequence ◽  
Sequence Divergence ◽  
Single Copy ◽  
Whole Genome ◽  
Specific Sequence ◽  
Bassiana Duperreyi

Abstract Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.

Characterization of Large Chromosome Segment Introgressions from Triticum turgidum subsp. dicoccoides into Bread Wheat with Simple Sequence Repeat Markers

Crop Science ◽  
2013 ◽  
Vol 53 (4) ◽  
pp. 1555-1565 ◽  
Author(s):  
Wei Zhou ◽  
Yurong Jiang ◽  
Wei Zhang ◽  
Guifang Xu ◽  
Junkang Rong
Keyword(s):  
Bread Wheat ◽  
Simple Sequence Repeat ◽  
Triticum Turgidum ◽  
Chromosome Segment ◽  
Large Chromosome ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Simple Sequence

scholarly journals Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 299
Author(s):  
Taraka Ramji Moturu ◽  
Sansrity Sinha ◽  
Hymavathi Salava ◽  
Sravankumar Thula ◽  
Tomasz Nodzyński ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Rna Polymerase Ii ◽  
Functional Divergence ◽  
Functional Characterization ◽  
Sequence Divergence ◽  
Mirna Biogenesis ◽  
Specific Sequence ◽  
Mirna Genes ◽  
Expression Of Genes ◽  
Function Relationship

Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes.

scholarly journals Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in-silico whole genome subtraction.

2020 ◽  
Author(s):  
Duminda S.B. Dissanayake ◽  
Clare Holleley ◽  
Laura Hill ◽  
D. O’Meally ◽  
J. Deakin ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
In Silico ◽  
Sex Chromosome ◽  
Genomic Sequence ◽  
Sequence Divergence ◽  
Single Copy ◽  
Whole Genome ◽  
Specific Sequence ◽  
Bassiana Duperreyi

Abstract Background: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the heterozygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in-silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results: We generated 96.7 x 109 150bp paired-end genomic sequence reads from a XY male and 81.4 x 109 paired-end reads from an XX female for in-silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as XY male-specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions: The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.

scholarly journals Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction.

2020 ◽  
Author(s):  
Duminda Sampath Bandara Dissanayake ◽  
Clare Ellen Holleley ◽  
Laura Kate Hill ◽  
Denis O’Meally ◽  
Janine Eileen Deakin ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
In Silico ◽  
Sex Chromosome ◽  
Genomic Sequence ◽  
Sequence Divergence ◽  
Single Copy ◽  
Whole Genome ◽  
Specific Sequence ◽  
Bassiana Duperreyi

Abstract Background: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results: We generated 96.7 x 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 x 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions: The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.

scholarly journals Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in-silico whole genome subtraction.

2020 ◽  
Author(s):  
Duminda S.B. Dissanayake ◽  
Clare Holleley ◽  
Laura Hill ◽  
D. O’Meally ◽  
J. Deakin ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
In Silico ◽  
Sex Chromosome ◽  
Genomic Sequence ◽  
Sequence Divergence ◽  
Single Copy ◽  
Whole Genome ◽  
Specific Sequence ◽  
Bassiana Duperreyi

Abstract Background: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results: We generated 96.7 x 10 9 150 bp paired-end genomic sequence reads from a XY male and 81.4 x 10 9 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions: The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi . Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.

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