Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes

Panjabi, Priya; Jagannath, Arun; Bisht, Naveen C.; Padmaja, K Lakshmi; Sharma, Shikha; Gupta, Vibha; Pradhan, Akshay K.; Pental, Deepak

doi:10.1186/1471-2164-9-113

Cited by 201 publications

(232 citation statements)

References 43 publications

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“…However, the number of identified miRNAs is substantially less compared to the, 199 miRNAs belonging to 121 miRNA families identified in Arabidopsis deposited in the miRNA database (http://www.mirbase.org). Many comparative mapping studies of A. thaliana show the presence of an average of 3 copies of an Arabidopsis chromosome segment in the Brassica genome (Panjabi et al, 2008;Parkin et al, 2005;Teutonica and Osborn, 1994;Truco et al, 1996), although this might not hold true for miRNA genes. Therefore, with the availability of complete genome sequences in the near future, the identification of more members of miRNA belonging to previously identified or new miRNA families is expected.…”

Section: Discussionmentioning

confidence: 99%

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA-mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20 th position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.

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Section: Discussionmentioning

confidence: 99%

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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“…Triplication of 24 ancestral GBs theoretically resulted in 72 GBs comprising quasidiploid Brassiceae genomes. Out of the 24 GBs, only 13 (54%) (Parkin et al, 2005;) and 14 (58%) (Panjabi et al, 2008) blocks were found as three or more copies in the rapa (A) genome of B. napus or B. juncea. In the nigra (B) and oleracea (C) genomes, only seven (29%) (Panjabi et al, 2008) and eight (33%) (Kaczmarek et al, 2009) GBs were reported as three or more homoeologous copies in B. juncea and B. oleracea, respectively.…”

Section: Diploidization: Retention Versus Loss Of Genomic Blocksmentioning

confidence: 99%

“…Out of the 24 GBs, only 13 (54%) (Parkin et al, 2005;) and 14 (58%) (Panjabi et al, 2008) blocks were found as three or more copies in the rapa (A) genome of B. napus or B. juncea. In the nigra (B) and oleracea (C) genomes, only seven (29%) (Panjabi et al, 2008) and eight (33%) (Kaczmarek et al, 2009) GBs were reported as three or more homoeologous copies in B. juncea and B. oleracea, respectively. Comparing these data with 83 to 100% of duplicated GBs retained in the Australian species, triplicated Brassiceae genomes show faster diploidization and/or originated earlier (13 to 17 mya suggested by Yang et al, 2006).…”

Section: Diploidization: Retention Versus Loss Of Genomic Blocksmentioning

confidence: 99%

“…The steadily improving knowledge of crucifer genome evolution suggests that the duplication-diploidization process is ongoing and occurred several times across the family. In addition to the three aforemetioned paleopolyploid events, several Brassicaceae groups with diploid-like genomes have experienced additional, more recent WGD events, as exemplified by a whole-genome triplication (;8 to 15 mya) most likely promoting the diversification within the tribe Brassiceae (Lysak et al, 2005(Lysak et al, , 2007Parkin et al, 2005;Panjabi et al, 2008). Such duplications are younger than paleopolyploid events but older than neopolyploid speciation events (e.g., the origin of Arabidopsis suecica, Brassica napus, or Cardamine schulzii) and can be detected by comparative genetic and cytogenetic methods.…”

Section: Introductionmentioning

confidence: 99%

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Fast Diploidization in Close Mesopolyploid Relatives ofArabidopsis

et al. 2010

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Mesopolyploid whole-genome duplication (WGD) was revealed in the ancestry of Australian Brassicaceae species with diploid-like chromosome numbers (n = 4 to 6). Multicolor comparative chromosome painting was used to reconstruct complete cytogenetic maps of the cryptic ancient polyploids. Cytogenetic analysis showed that the karyotype of the Australian Camelineae species descended from the eight ancestral chromosomes (n = 8) through allopolyploid WGD followed by the extensive reduction of chromosome number. Nuclear and maternal gene phylogenies corroborated the hybrid origin of the mesotetraploid ancestor and suggest that the hybridization event occurred ;6 to 9 million years ago.The four, five, and six fusion chromosome pairs of the analyzed close relatives of Arabidopsis thaliana represent complex mosaics of duplicated ancestral genomic blocks reshuffled by numerous chromosome rearrangements. Unequal reciprocal translocations with or without preceeding pericentric inversions and purported end-to-end chromosome fusions accompanied by inactivation and/or loss of centromeres are hypothesized to be the main pathways for the observed chromosome number reduction. Our results underline the significance of multiple rounds of WGD in the angiosperm genome evolution and demonstrate that chromosome number per se is not a reliable indicator of ploidy level.

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“…Currently, a large number of markers are available for the Brassica genomes (A, B, and C) that have been used in recent years to tag simple Mendelian traits and to map quantitative trait loci (Mahmood et al 2007) and can be used to detect interspecific hybrids and genetic introgression. Panjabi et al (2008) used intron polymorphism (IP) markers to identify a high degree of colinearity between the A and B genomes of Brassica juncea with the A genome of B. napus and the B genome of B. nigra, respectively, which suggested low levels of chromosomal change after polyploidization. Cytological observations in digenomic triploids (BBC and CCB) generated from interspecific hybridization between B. carinata and B. nigra and between B. carinata and B. oleracea indicated that the Brassica B genome chromosomes may not form homeologous pairs with chromosomes of the A and C genomes in interspecific crosses (Meng et al 1998).…”

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Analysis of B-Genome Chromosome Introgression in Interspecific Hybrids of Brassica napus × B. carinata

et al. 2011

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Brassica carinata, an allotetraploid with B and C genomes, has a number of traits that would be valuable to introgress into B. napus. Interspecific hybrids were created between B. carinata (BBCC) and B. napus (AACC), using an advanced backcross approach to identify and introgress traits of agronomic interest from the B. carinata genome and to study the genetic changes that occur during the introgression process. We mapped the B and C genomes of B. carinata with SSR markers and observed their introgression into B. napus through a number of backcross generations, focusing on a BC 3 and BC 3 S 1 sibling family. There was close colinearity between the C genomes of B. carinata and B. napus and we provide evidence that B. carinata C chromosomes pair and recombine normally with those of B. napus, suggesting that similar to other Brassica allotetraploids no major chromosomal rearrangements have taken place since the formation of B. carinata. There was no evidence of introgression of the B chromosomes into the A or C chromosomes of B. napus ; instead they were inherited as whole linkage groups with the occasional loss of terminal segments and several of the B-genome chromosomes were retained across generations. Several BC 3 S 1 families were analyzed using SSR markers, genomic in situ hybridization (GISH) assays, and chromosome counts to study the inheritance of the B-genome chromosome(s) and their association with morphological traits. Our work provides an analysis of the behavior of chromosomes in an interspecific cross and reinforces the challenges of introgressing novel traits into crop plants.

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Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes

Cited by 201 publications

References 43 publications

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Fast Diploidization in Close Mesopolyploid Relatives ofArabidopsis

Analysis of B-Genome Chromosome Introgression in Interspecific Hybrids of Brassica napus × B. carinata

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