A Fine Physical Map of the Rice Chromosome 4

AbstractLarge-scale physical mapping has been a major challenge for plant geneticists due to the lack of techniques that are widely affordable and can be applied to different species. Here we present a physical map of rice chromosome 10 developed by fluorescence in situ hybridization (FISH) mapping of bacterial artificial chromosome (BAC) clones on meiotic pachytene chromosomes. This physical map is fully integrated with a genetic linkage map of rice chromosome 10 because each BAC clone is anchored by a genetically mapped restriction fragment length polymorphism marker. The pachytene chromosome-based FISH mapping shows a superior resolving power compared to the somatic metaphase chromosome-based methods. The telomere-centromere orientation of DNA clones separated by 40 kb can be resolved on early pachytene chromosomes. Genetic recombination is generally evenly distributed along rice chromosome 10. However, the highly heterochromatic short arm shows a lower recombination frequency than the largely euchromatic long arm. Suppression of recombination was found in the centromeric region, but the affected region is far smaller than those reported in wheat and barley. Our FISH mapping effort also revealed the precise genetic position of the centromere on chromosome 10.

Download Full-text

Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4

Genetica ◽

10.1007/s10709-010-9528-y ◽

2010 ◽

Vol 138 (11-12) ◽

pp. 1277-1296 ◽

Cited By ~ 4

Author(s):

Tong Geon Lee ◽

Yong Jin Lee ◽

Dae Yeon Kim ◽

Yong Weon Seo

Keyword(s):

Physical Mapping ◽

Rice Chromosome ◽

Wheat Chromosome ◽

Chromosome 4 ◽

Chromosome Arm

Download Full-text

Physical and Genetic Mapping in the GrassesLolium perenneandFestuca pratensis

Genetics ◽

10.1093/genetics/161.1.315 ◽

2002 ◽

Vol 161 (1) ◽

pp. 315-324 ◽

Cited By ~ 5

Author(s):

J King ◽

I P Armstead ◽

I S Donnison ◽

H M Thomas ◽

R N Jones ◽

...

Keyword(s):

Large Scale ◽

Physical Map ◽

Rice Chromosome ◽

Nucleolar Organizer ◽

Physical Distance ◽

Chromosome 1 ◽

Grass Species ◽

Nucleolar Organizer Regions ◽

Single Chromosome ◽

Large Scale Analysis

AbstractA single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line (2n = 2x = 14). In this line recombination occurs throughout the length of the F. pratensis/L. perenne bivalent. The F. pratensis chromosome and recombinants between it and its L. perenne homeologue can be visualized using genomic in situ hybridization (GISH). GISH junctions represent the physical locations of sites of recombination, enabling a range of recombinant chromosomes to be used for physical mapping of the introgressed F. pratensis chromosome. The physical map, in conjunction with a genetic map composed of 104 F. pratensis-specific amplified fragment length polymorphisms (AFLPs), demonstrated: (1) the first large-scale analysis of the physical distribution of AFLPs; (2) variation in the relationship between genetic and physical distance from one part of the F. pratensis chromosome to another (e.g., variation was observed between and within chromosome arms); (3) that nucleolar organizer regions (NORs) and centromeres greatly reduce recombination; (4) that coding sequences are present close to the centromere and NORs in areas of low recombination in plant species with large genomes; and (5) apparent complete synteny between the F. pratensis chromosome and rice chromosome 1.

Download Full-text

A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription

The Plant Cell ◽

10.1105/tpc.105.031575 ◽

2005 ◽

Vol 17 (6) ◽

pp. 1641-1657 ◽

Cited By ~ 37

Author(s):

Yuling Jiao ◽

Peixin Jia ◽

Xiangfeng Wang ◽

Ning Su ◽

Shuliang Yu ◽

...

Keyword(s):

Expression Analysis ◽

Rice Chromosome ◽

Regulation Of Transcription ◽

Chromosome 4 ◽

Microarray Expression Analysis ◽

Tiling Microarray ◽

Microarray Expression ◽

Chromosome Level

Download Full-text

Method to obtain homozygous introgressing segments in Drosophila to identify the presence of hybrid sterility genes of the reproductive isolation

10.21203/rs.3.rs-110613/v1 ◽

2020 ◽

Author(s):

Francisco García-Franco ◽

Lilian Barandica-Cañon ◽

Ezel Galindo-Pérez ◽

Martha Martínez García ◽

Blanca Chávez-Sandoval

Keyword(s):

In Situ Hybridization ◽

Physical Map ◽

Hybrid Sterility ◽

Bioinformatic Analysis ◽

Chromosome 4 ◽

Genomic Map ◽

Hybrid Lines ◽

First Time ◽

Polythene Chromosomes

Abstract Here, we present for the first time, a method to generate homozygous segmental introgressions, by means of crosses between a pair of synmorphic species. The introgressions were monitored by the cytogenetic method of polygenic chromosome asynapses. Later the introgressions were evaluated in their capacity to produce sterility in segmental males. Also, the smallest segment with the capacity to produce sterility in segmental males was mapped by in situ hybridization of polythene chromosomes, using 8 sequences of BACs clones as probes. Finally, a bioinformatic analysis was carried out to identify the presence of particular genes. From 2 parental strains, D. buzzatii and D. koepferae, 6 simple segmental hybrid lines were generated, whose introgressing segments are distributed along chromosome 4 of these species. From the 6 simple segmental lines and by means of a new crossing strategy, the 6 respective homozygous segmental hybrid offspring were obtained, each of them carrying a specific homozygous introgression. None of the 6 heterozygous introgressions was capable of producing sterility in segmental males, while 4 of the same homozygous introgressions produced total sterility in segmental males, including in this group the two smallest introgressive segments, one of 5.03 % and the other 7.87% with respect to the total length of chromosome 4, which are located in the region F2 to F4 of the standard cytological map based on polythene chromosomes of the Drosophila Repleta group. In situ hybridization, using 8 clones from contig 1065 located along the F2 to F4 region of the physical map of D. buzzattii constructed in BACs, confirmed the precise location of the 6 clones in the chromosomal region F2 to F4 of chromosome 4 of the polygenic chromosomes of both D. buzzatii and D. mojavensis. The bioinformatic analysis of the F2 to F4 region, using the complete genetic sequence of the contig 1065 of D. buzzatti shows the presence of two predicted genes in the genomic map of D. buzzatii (g.1313.t1 and g.1314.t1), and the orthologous association of these 2 genes both with the D. moj_GI22766 gene of D. mojavensis and with the Trivet gene of D. melanogaster.

Download Full-text

A major QTL controlling deep rooting on rice chromosome 4

Scientific Reports ◽

10.1038/srep03040 ◽

2013 ◽

Vol 3 (1) ◽

Cited By ~ 39

Author(s):

Yusaku Uga ◽

Eiji Yamamoto ◽

Noriko Kanno ◽

Sawako Kawai ◽

Tatsumi Mizubayashi ◽

...

Keyword(s):

Rice Chromosome ◽

Chromosome 4 ◽

Major Qtl

Download Full-text

Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana

Genome Research ◽

10.1101/gr.161701 ◽

2001 ◽

Vol 11 (7) ◽

pp. 1167-1174

Author(s):

Klaus Mayer ◽

George Murphy ◽

Renato Tarchini ◽

Rolf Wambutt ◽

Guido Volckaert ◽

...

Keyword(s):

Sequence Data ◽

Rice Genome ◽

Rice Chromosome ◽

Gene Content ◽

Chromosome 2 ◽

Chromosome 4 ◽

Orthologous Genes ◽

Protein Coding ◽

Duplication Events ◽

Conserved Gene

The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than was reported for a previously sequenced segment of the rice genome. Sixteen of the putative genes were supported by matches to ESTs. The predicted products of 29 of the putative genes showed similarity to known proteins, and a further 17 genes showed similarity only to predicted or hypothetical proteins identified in genome sequence data. The region contains a few transposable elements: one retrotransposon, and one transposon. The segment of the rice genome studied had previously been identified as representing a part of rice chromosome 2 that may be homologous to a segment of Arabidopsis chromosome 4. We confirmed the conservation of gene content and order between the two genome segments. In addition, we identified a further four segments of the Arabidopsis genome that contain conserved gene content and order. In total, 22 of the 56 genes identified in the rice genome segment were represented in this set of Arabidopsis genome segments, with at least five genes present, in conserved order, in each segment. These data are consistent with the hypothesis that theArabidopsis genome has undergone multiple duplication events. Our results demonstrate that conservation of the genome microstructure can be identified even between monocot and dicot species. However, the frequent occurrence of duplication, and subsequent microstructure divergence, within plant genomes may necessitate the integration of subsets of genes present in multiple redundant segments to deduce evolutionary relationships and identify orthologous genes.

Download Full-text