Genomic changes associated with somaclonal variation in banana (Musa spp.)

Abstract

The molecular basis of somaclonal variation is not precisely known, but both genetic and epigenetic mechanisms have been proposed. The available evidence points toward the openUP (June 2007) existence of labile portions of the genome that can be modulated when the cells undergo the stress of tissue culture. Therefore, the hypothesis that there are identifiable and predictable DNA markers for the early diagnosis of somaclonal variation has been tested.Representational difference analysis was used to isolate unique fragments of DNA (difference products) between visible culture-induced off-type and normal banana plants.Markers generated from six difference products differentiated between some of the offtype and normal pairs. The genomic region around one of these difference products has been extensively characterized and has a high degree of polymorphism, with variation in up to 10% of the nucleotides sequenced in the region. This same region has been shown to vary in other pairs of off-type and normal banana plants derived from tissue culture as well as in plants propagated commercially in vitro. The data are consistent with the hypothesis that there is at least one particularly labile portion of the genome that is especially susceptible to the stress imposed during tissue culture and that is associated with higher rearrangement and mutation rates than other portions of the genome.Consequently, the regions that are reported here have the potential to be used as early detection tools for identifying somaclonal variants.

The potential of high-resolution BAC-FISH in banana breeding

“…Only recently studies appeared addressing the complexity of the banana genome using molecular and cytogenetic tools (Doležel et al 1994(Doležel et al , 1997Osuji et al 1997;D'Hont et al 2000;Aert et al 2004;Pillay et al 2004;Bartoš et al 2005;Heslop-Harrison and Scharzacher 2007;Ohl et al 2007; Thomas-Hall et al 2007). Such tools may in the long term be helpful in establishing breeding programs if more information on the genetic constitutions of the crossing partners becomes available.…”

Epigenetics in plant tissue culture

“…When plants experience stress, they show a multitude of responses, which may include epigenetic variation (Molinier et al 2006). Oh et al (2007) hypothesised that labile portions of the genome are affected by stress during micropropagation of Musa. Alterations in methylation have been reported in response to water deficiency (Labra et al 2002), osmotic stress (Kovařik et al 1997), heavy metals (Aina et al 2004), and-in tissue culture-heat (Baránek et al 2010).…”

Efficiency of sequence related amplified polymorphism (SRAP) and target region amplified polymorphism (TRAP) markers in detecting banana somaclonal variants

“…The inherent instability of the cultivar being micropropagated was another major factor influencing the production of dwarf off-types. Oh et al (2007) reported that the molecular basis of somaclonal variation is not precisely known, but both genetic and epigenetic mechanisms have been proposed; whereas James et al (2007) stated that the source of this variation may be derived from variation pre-existing in the mother plant or it may be induced in vitro. Sales and Butardo (2014) reported that somaclonal variation is due to prolonged subculture and high 2, 4-D concentration.…”