title: Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids.
abstract: BACKGROUND
  Genetic and epigenetic alterations can be invoked by plant tissue culture, which may result in heritable changes in phenotypes, a phenomenon collectively termed somaclonal variation. Although extensive studies have been conducted on the molecular nature and spectrum of tissue culture-induced genomic alterations, the issue of whether and to what extent distinct plant genotypes, e.g., pure-lines, hybrids and polyploids, may respond differentially to the tissue culture condition remains poorly understood.
  
  
  RESULTS
  We investigated tissue culture-induced genetic and epigenetic alterations in a set of rice genotypes including two pure-lines (different subspecies), a pair of reciprocal F1 hybrids parented by the two pure-lines, and a pair of reciprocal tetraploids resulted from the hybrids. Using two molecular markers, amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP), both genetic and DNA methylation alterations were detected in calli and regenerants from all six genotypes, but genetic alteration is more prominent than epigenetic alteration. While significant genotypic difference was observed in frequencies of both types of alterations, only genetic alteration showed distinctive features among the three types of genomes, with one hybrid (N/9) being exceptionally labile. Surprisingly, difference in genetic alteration frequencies between the pair of reciprocal F1 hybrids is much greater than that between the two pure-line subspecies. Difference also exists in the pair of reciprocal tetraploids, but is to a less extent than that between the hybrids. The steady-state transcript abundance of genes involved in DNA repair and DNA methylation was significantly altered in both calli and regenerants, and some of which were correlated with the genetic and/or epigenetic alterations.
  
  
  CONCLUSIONS
  Our results, based on molecular marker analysis of ca. 1,000 genomic loci, document that genetic alteration is the major cause of somaclonal variation in rice, which is concomitant with epigenetic alterations. Perturbed expression by tissue culture of a set of 41 genes encoding for enzymes involved in DNA repair and DNA methylation is associated with both genetic and epigenetic alterations. There exist fundamental differences among distinct genotypes, pure-lines, hybrids and tetraploids, in propensities of generating both genetic and epigenetic alterations under the tissue culture condition. Parent-of-origin has a conspicuous effect on the alteration frequencies.
authors: Key Laboratory of Molecular Epigenetics of the Ministry of Education, MOE, Northeast Normal University, Changchun 130024, China.
authors: Xiaoran
authors: X
authors: Wang
authors: Rui
authors: R
authors: Wu
authors: Xiuyun
authors: X
authors: Lin
authors: Yan
authors: Y
authors: Bai
authors: Congdi
authors: C
authors: Song
authors: Xiaoming
authors: X
authors: Yu
authors: Chunming
authors: C
authors: Xu
authors: Na
authors: N
authors: Zhao
authors: Yuzhu
authors: Y
authors: Dong
authors: Bao
authors: B
authors: Liu
mesh_terms: D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics; D044127:Epigenesis, Genetic; D005838:Genotype; D007178:Inbreeding; D012275:Oryza / Q000235:genetics* / Q000502:physiology; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics; D011123:Polyploidy; D046509:Tissue Culture Techniques
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins
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