In addition to the standard set of chromosomes (A chromosomes, As), so-called supernumerary B chromosomes (Bs) have been found causing a numerical chromosome variation. Bs have been considered to be genetically inert elements without any functional genes for a long period, because of the limited experimental methods and its dispensable property. More recently, sequencing of dissected Bs from several organisms has revealed the DNA composition, a vast number of protein-coding genes have been found with the effects on the transcripts and protein expression of the host. In this review, we summarize current understanding of B chromosomes carrying plants including rye (Secale cereale L.), maize (Zea mays L.) and Aegilops (Aegilops speltoides Tausch.), with the emphasis on Bs phenotypic effects, the inheritance mechanism of Bs, the molecular composition of Bs, the effects on host transcription regulation and protein expression upon the presence of Bs. Besides, we discuss the current study state and potential application of B chromosomes, aim to provide a new venue for chromosome engineering and breeding research.
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