New evidence for the synteny of rice chromosome 1 and barley chromosome 3H from rice expressed sequence tags

To provide improved access to the wealth of resources and genomic information that is presently being developed for rice a set of 88 rice expressed sequence tags (ESTs) previously mapped on rice chromosome 1 in the cross 'Nipponbare' × 'Kasalath' was used for comparative mapping in a cross of the barley cultivars 'Igri' and 'Franka'. As expected, most (89%) of the clones gave distinct banding patterns in barley of which about one-third was polymorphic between 'Igri' and 'Franka'. These polymorphisms were mapped, and most of these (56%) confirmed that rice chromosome 1 and barley chromosome 3H are syntenous. All single-copy markers identified conserved collinear positions, while markers with multiple copies did so in a few cases only. The markers that were not fitting in the collinear order were distributed randomly across the barley genome. The comparative maps of barley chromosome 3H and rice chromosome 1 comprise in total 26 common markers covering more than 95% of the genetic length of both chromosomes. A 30-fold reduction of recombination is seen around the barley centromere, and synteny may be interrupted in this region. However, the good overall synteny on a mesoscale (110 cM) justifies the use of rice as a platform for map-based cloning in barley.Key words: Oryza sativa, Hordeum vulgare, RFLP, synteny, comparative mapping.

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Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley

Genome ◽

10.1139/g98-024 ◽

1998 ◽

Vol 41 (3) ◽

pp. 328-336 ◽

Cited By ~ 29

Author(s):

Francesca Gallego ◽

Catherine Feuillet ◽

Monika Messmer ◽

Anja Penger ◽

Andreas Graner ◽

...

Keyword(s):

Leaf Rust ◽

Comparative Mapping ◽

Rust Resistance ◽

Repetitive Sequences ◽

Rice Chromosome ◽

Leaf Rust Resistance ◽

Chromosome 1 ◽

Wheat Leaf Rust ◽

Wheat Leaf ◽

Genomic Regions

The wheat genome is large, hexaploid, and contains a high amount of repetitive sequences. In order to isolate agronomically important genes from wheat by map-based cloning, a simpler model of the genome must be used for identifying candidate genes. The objective of this study was to comparatively map the genomic regions of two wheat leaf rust disease resistance loci, Lr1 and Lr10, in the putative model genomes of rice and barley. Two probes cosegregating with the Lr1 gene on chromosome 5DL of wheat were studied. The rice sequences corresponding to the two probes were isolated and mapped. The two probes mapped to two different rice chromosomes, indicating that the organization of the region orthologous to Lr1 is different in rice and wheat. In contrast, synteny was conserved between wheat and barley in this chromosomal region. The Lrk10 gene cosegregated with Lr10 on chromosome 1AS in wheat. The rice gene corresponding to Lrk10 was mapped on rice chromosome 1, where it occurred in many copies. This region on rice chromosome 1 corresponds to the distal part of the group 3S chromosomes in Triticeae. The synteny is conserved between rice chromosome 1 and the Triticeae group 3S chromosomes up to the telomere of the chromosomes. On group 3S chromosomes, we found a gene that is partially homologous to Lrk10. We conclude that in the genomic regions studied, there is limited and only partially useful synteny between wheat and rice. Therefore, barley should also be considered as a model genome for isolating the Lr1 and Lr10 genes from wheat.Key words: barley, comparative mapping, leaf rust, resistance genes, rice, synteny, wheat.

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Comparative mapping in the pig: localization of 214 expressed sequence tags

Mammalian Genome ◽

10.1007/s00335-002-2242-z ◽

2003 ◽

Vol 14 (6) ◽

pp. 405-426 ◽

Cited By ~ 12

Author(s):

Susanna Cirera ◽

Claus B. Jørgensen ◽

Milena Sawera ◽

Terje Raudsepp ◽

Bhanu P. Chowdhary ◽

...

Keyword(s):

Expressed Sequence Tags ◽

Comparative Mapping ◽

Expressed Sequence

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Cartographie fine de la région du gène PIS de la chèvre

INRA Productions Animales ◽

10.20870/productions-animales.2000.13.hs.3826 ◽

2020 ◽

Vol 13 (HS) ◽

pp. 141-144

Author(s):

E.P. CRIBIU ◽

L. SCHIBLER ◽

D. VAIMAN

Keyword(s):

Nous Avons ◽

Expressed Sequence Tags ◽

Chromosome 1 ◽

Chromosome Y ◽

Différenciation Sexuelle ◽

Expressed Sequence

Chez les Mammifères, la différenciation sexuelle résulte d’une cascade complexe dont le premier acteur est le gène SRY, porté par le chromosome Y, qui masculinise la gonade indifférenciée. Cependant, certains individus, en l’absence de SRY, présentent un développement testiculaire et une réversion du sexe. Chez la chèvre, par exemple, la réversion du sexe d’individus XX en l’absence du gène SRY ou d’autres séquences du chromosome Y est étroitement liée à l’absence de corne (mutation motte) puisqu’aucun recombinant n’a jamais été observé. Ce syndrome, nommé PIS pour Polled Intersex Syndrome, est causé par des mutations dans un ou deux gènes autosomiques que nous avons localisés dans un premier temps à proximité de deux marqueurs microsatellites d’origine bovine sur le chromosome 1 caprin. Les cartes génétique, cytogénétique et physique de la région ont ensuite été construites à l’aide, d’une part, de banques d’ADN issues de chromosome 1 trié, des bandes 1q42, 1q43 et 1q44 microdisséquées et de grands fragments (BAC) et, d’autre part, de la cartographie comparée avec les gènes ou EST (expressed sequence tags) localisés dans la région humaine homologue. Ces différentes approches ont permis de localiser le gène PIS au sein d’un contig de 1,5 Mb, dans une région de 100 kb autour d’un marqueur microsatellite.

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Phylogenomics provides strong evidence for relationships of butterflies and moths

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.0970 ◽

2014 ◽

Vol 281 (1788) ◽

pp. 20140970 ◽

Cited By ~ 111

Author(s):

Akito Y. Kawahara ◽

Jesse W. Breinholt

Keyword(s):

Amino Acids ◽

Expressed Sequence Tags ◽

Single Copy ◽

Model Organisms ◽

Bootstrap Support ◽

Phylogenomic Analysis ◽

Ecological Studies ◽

Insect Order ◽

Molecular Dataset ◽

Expressed Sequence

Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific core-orthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, all-taxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly–moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order.

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Synteny with rice: analysis of barley malting quality QTLs and rpg4 chromosome regions

Genome ◽

10.1139/g98-027 ◽

1998 ◽

Vol 41 (3) ◽

pp. 373-380 ◽

Cited By ~ 23

Author(s):

F Han ◽

A Kleinhofs ◽

S E Ullrich ◽

A Kilian ◽

M Yano ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Resistance Gene ◽

Quantitative Trait ◽

Rice Chromosome ◽

Chromosome 8 ◽

Chromosome 1 ◽

Barley Chromosome ◽

Malting Quality ◽

Centromere Region ◽

Trait Loci

The barley (Hordeum vulgare L.) chromosome 1 centromere region contains two adjacent overlapping quantitative trait loci (QTLs) for malting quality traits, and the chromosome 7L subtelomere region contains the stem rust (causal agent Puccinia graminis f.sp. tritici) resistance gene rpg4. To facilitate the saturation mapping of these two target regions, a synteny-based approach was employed. Syntenic relationships between the barley target regions and the rice (Oryza sativa) genome were established through comparative mapping. The barley chromosome 1 centromere region was found to be syntenic with rice chromosome 8 and parts of rice chromosomes 3 and 10. A 6- to 15-fold difference in genetic distance between barley and rice in the syntenic region was observed, owing to the apparent suppressed recombination in the barley chromosome 1 centromere region. Barley chromosome 7L was found to be syntenic with rice chromosome 3. The establishment of synteny with rice in the two target regions allows well-established and characterized rice resources to be utilized in fine mapping and map-based cloning studies.Key words: genome synteny, quantitative trait loci, QTL, disease resistance gene, Triticeae.

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