Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication

Mun, Jeong‐Hwan; Kwon, Soo Jin; Yang, Tae Jin; Seol, Young-Joo; Jin, Mina; Kim, Jin A.; Lim, Myung Ho; Kim, Jung-Sun; Baek, Seung-Hoon; Choi, Beom-Soon; Yu, Hee‐Ju; Kim, Dae-Soo; Kim, Namshin; Lim, Ki-Byung; Lee, Soo In; Hahn, Jang-Ho; Lim, Yong Pyo; Bancroft, Ian; Park, Beom-Seok

doi:10.1186/gb-2009-10-10-r111

Cited by 194 publications

(192 citation statements)

References 65 publications

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“…Robust molecular cytogenetic karyotypes established for B. rapa, B. oleracea, and B. napus: Numerous molecular cytogenetic studies have reported karyotypes in diploid and amphidiploid Brassica species on mitotic metaphase complements and meiotic prophase (pachytene) chromosomes (e.g., Armstrong et al 1998, Fukui et al 1998Snowdon et al 2002;Koo et al 2004;Lim et al 2005Lim et al , 2007Maluszynska and Hasterok 2005;Howell et al 2008;Kim et al 2009;Mun et al 2009). Among the crop species in the Brassicaceae, the B. rapa genetic, physical, and cytogenetic maps have begun to be integrated by BAC-FISH (Koo et al 2004;Lim et al 2005Lim et al , 2007Yang et al 2007;Kim et al 2009;Mun et al 2009;Xiong et al 2010).…”

Section: Discussionmentioning

confidence: 99%

“…Among the crop species in the Brassicaceae, the B. rapa genetic, physical, and cytogenetic maps have begun to be integrated by BAC-FISH (Koo et al 2004;Lim et al 2005Lim et al , 2007Yang et al 2007;Kim et al 2009;Mun et al 2009;Xiong et al 2010). However, to our knowledge, a complete karyotype analysis that reliably distinguishes each chromosome in B. oleracea and B. napus has not been reported.…”

Section: Discussionmentioning

confidence: 99%

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Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

2011

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Investigating recombination of homoeologous chromosomes in allopolyploid species is central to understanding plant breeding and evolution. However, examining chromosome pairing in the allotetraploid Brassica napus has been hampered by the lack of chromosome-specific molecular probes. In this study, we establish the identification of all homoeologous chromosomes of allopolyploid B. napus by using robust molecular cytogenetic karyotypes developed for the progenitor species Brassica rapa (A genome) and Brassica oleracea (C genome). The identification of every chromosome among these three Brassica species utilized genetically mapped bacterial artificial chromosomes (BACs) from B. rapa as probes for fluorescent in situ hybridization (FISH). With this BAC-FISH data, a second karyotype was developed using two BACs that contained repetitive DNA sequences and the ubiquitous ribosomal and pericentromere repeats. Using this diagnostic probe mix and a BAC that contained a C-genome repeat in two successive hybridizations allowed for routine identification of the corresponding homoeologous chromosomes between the A and C genomes of B. napus. When applied to the B. napus cultivar Stellar, we detected one chromosomal rearrangement relative to the parental karyotypes. This robust novel chromosomal painting technique will have biological applications for the understanding of chromosome pairing, homoeologous recombination, and genome evolution in the genus Brassica and will facilitate new applied breeding technologies that rely upon identification of chromosomes.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

2011

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“…It includes 119 CC-NBS-LRR genes, 64 TIR-NBS-LRR genes, 34 BED-finger-NBS-LRR, and both truncated and unusual NBS and NBS-LRR-containing genes. Similarly, Mun et al (2009) …”

Section: Organization Of Nbs-lrr Genes In the Plant Genomementioning

confidence: 98%

Review Functional characterization and signal transduction ability of nucleotide-binding site-leucine-rich repeat resistance genes in plants

Joshi

Nayak²

2011

Genet. Mol. Res.

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ABSTRACT. Pathogen infection in plants is often limited by a multifaceted defense response triggered by resistance genes. The most prevalent class of resistance proteins includes those that contain a nucleotide-binding site-leucine-rich repeat (NBS-LRR) domain. Over the past 15 years, more than 50 novel NBS-LRR class resistance genes have been isolated and characterized; they play a significant role in activating conserved defense-signaling networks. Recent molecular research on NBS-LRR resistance proteins and their signaling networks has the potential to broaden the use of resistance genes for disease control. Various transgenic approaches have been tested to broaden the disease resistance spectrum using NBS-LRR genes. This review highlights the recent progress in understanding the structure, function, signal transduction ability of NBS-LRR resistance genes in different host-pathogen systems and suggests new strategies for engineering pathogen resistance in crop plants.

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“…Wide hybridizations are normally performed by the application of embryo rescue techniques. The most recent advances in genome sequencing technology, bioinformatics and data mining have opened an avenue for comparative analysis of ESTs, BACs, genes (families), whole chromosomes and even entire genomes to determine evolutionary relationship between these species and their ancestors (Gao et al, 2004;Gao et al, 2006;Punjabi et al, 2008;Mun et al, 2009;Qiu et al, 2009;Nagoaka et al, 2010). …”

Section: Genomic Relationships In Brassica Speciesmentioning

confidence: 99%

Molecular Genetics of Glucosinolate Biosynthesis in Brassicas: Genetic Manipulation and Application Aspects

Hirani¹,

Li²,

Zelmer³

et al. 2012

Crop Plant

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Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication

Abstract: Euchromatic regions of the Brassica rapa genome were sequenced and mapped onto the corresponding regions in the Arabidopsis thaliana genome.

Cited by 194 publications

References 65 publications

Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

Review Functional characterization and signal transduction ability of nucleotide-binding site-leucine-rich repeat resistance genes in plants

Molecular Genetics of Glucosinolate Biosynthesis in Brassicas: Genetic Manipulation and Application Aspects

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