PMID- 27083560
OWN - NLM
STAT- MEDLINE
DCOM- 20161213
LR  - 20181113
IS  - 1471-2229 (Electronic)
IS  - 1471-2229 (Linking)
VI  - 16
DP  - 2016 Apr 16
TI  - B chromosome contains active genes and impacts the transcription of A chromosomes 
      in maize (Zea mays L.).
PG  - 88
LID - 10.1186/s12870-016-0775-7 [doi]
LID - 88
AB  - BACKGROUND: The dispensable maize (Zea mays L.) B chromosome is highly 
      heterochromatic and widely believed to be devoid of functional genes. Although 
      low-copy B chromosome causes no obvious phenotype variation, its existence might 
      influence A genome gene expression. Previous studies suggested that B chromosomes 
      are evolved from standard chromosomes; therefore, they might contain genic 
      regions showing homology with A chromosome sequences. RESULTS: Our data suggested 
      that maize B chromosome influences the A-genome transcription with stronger 
      effect associated with an increase in copy number of B chromosome. In total 130 
      differently expressed genes were detected in comparison between with and without 
      B chromosome lines. These differentially expressed genes are mainly involved in 
      cell metabolism and nucleotide binding. Using Starter + B, we amplified ten B 
      chromosome loci with high sequence similarity to A-genome genes. Fluorescence in 
      situ hybridization (FISH) confirmed that at least four ~5 kb-sized genes are 
      located on the B chromosome. In addition, through de novo assembly of the reads 
      not unmapped to maize B73 reference genome together with PCR validation, we found 
      three B-located LTR; in particular, one of them, the 3.2 kb comp75688, is 
      expressed in a B-dosage dependent manner. CONCLUSION: We found that in the 
      presence of maize B chromosome, the transcription of A genome genes was altered, 
      with more impact by the increase of the B chromosome number. The B-located 
      transcriptionally active genes showed high similarity to their A-genome 
      homologues, and retrotransposons on B chromosome also have partial homologous to 
      A genome sequences. Our data shed more lights on the genome structure and 
      evolution of the maize B chromosome.
FAU - Huang, Wei
AU  - Huang W
AD  - National Maize Improvement Center of China, Beijing Key Laboratory of Crop 
      Genetic Improvement, China Agricultural University, Beijing, 100193, China.
FAU - Du, Yan
AU  - Du Y
AD  - National Maize Improvement Center of China, Beijing Key Laboratory of Crop 
      Genetic Improvement, China Agricultural University, Beijing, 100193, China.
FAU - Zhao, Xin
AU  - Zhao X
AD  - National Maize Improvement Center of China, Beijing Key Laboratory of Crop 
      Genetic Improvement, China Agricultural University, Beijing, 100193, China.
FAU - Jin, Weiwei
AU  - Jin W
AD  - National Maize Improvement Center of China, Beijing Key Laboratory of Crop 
      Genetic Improvement, China Agricultural University, Beijing, 100193, China. 
      weiweijin@cau.edu.cn.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20160416
PL  - England
TA  - BMC Plant Biol
JT  - BMC plant biology
JID - 100967807
RN  - 0 (Heterochromatin)
SB  - IM
MH  - Base Sequence
MH  - Chromosomes, Plant/*genetics
MH  - Gene Expression Profiling/methods
MH  - Gene Expression Regulation, Plant
MH  - Gene Ontology
MH  - Genes, Plant/*genetics
MH  - Genome, Plant/genetics
MH  - Heterochromatin/genetics
MH  - INDEL Mutation
MH  - In Situ Hybridization, Fluorescence
MH  - Polymorphism, Single Nucleotide
MH  - Pseudogenes/genetics
MH  - Reverse Transcriptase Polymerase Chain Reaction
MH  - Sequence Analysis, RNA/methods
MH  - Sequence Homology, Nucleic Acid
MH  - *Transcription, Genetic
MH  - Zea mays/*genetics
PMC - PMC4833949
OTO - NOTNLM
OT  - B chromosome
OT  - Evolution
OT  - Maize
OT  - RNA-seq
OT  - Transcription
EDAT- 2016/04/17 06:00
MHDA- 2016/12/15 06:00
PMCR- 2016/04/16
CRDT- 2016/04/17 06:00
PHST- 2015/12/23 00:00 [received]
PHST- 2016/04/11 00:00 [accepted]
PHST- 2016/04/17 06:00 [entrez]
PHST- 2016/04/17 06:00 [pubmed]
PHST- 2016/12/15 06:00 [medline]
PHST- 2016/04/16 00:00 [pmc-release]
AID - 10.1186/s12870-016-0775-7 [pii]
AID - 775 [pii]
AID - 10.1186/s12870-016-0775-7 [doi]
PST - epublish
SO  - BMC Plant Biol. 2016 Apr 16;16:88. doi: 10.1186/s12870-016-0775-7.