Somaclonal Variation

Variation among plants derived from callus culture observed since long
Sugarcane: Heniz (1973), Krishnamurthy et al. (1974), Rice: Oono (1978) Maize: Green (1977)

Larkin & Scowcroft (1981) coined the term Extent of variation: <5% to nearly 100%

Causes of somaclonal variation

Pre-existing: chimera, endoreduplication, natural mutation, mitotic crossing-over Tissue culture induced: media and other factors Age related degeneration Genotype-influenced:

Detection and manifestation

Morphological changes Chromosomal changes: numerical and structural Point mutations Retrotransposon activation : Tos10, Tos17 and Tos19 in rice Changed methylation status : pea, rice, maize through RFLP changes Epigenetic changes

Rice Retrotranposon
(Hirochika et al. PNAS 1996)

Copy number increase of Tos17 during tissue culture. lane 1 & 5: leaves of Nippon bare and C5924; 2-4: callus cultures (3, 12 & 24 month-old) of Nipponbare ; 6: cell line of C5924

A: Tos17 in seed propagated progenies B: Tos17 in plants regenerated from calli of different ages

Tto1 (tobacco): active in tissue culture and more so in protoplasts Tnt1 (tobacco): protoplast culture (enzymes used in protoplasts seems to elicit this response rather than protoplasts per se) Tos17: Tissue culture

Tissue culture-induced novel epialleles of Pericarp color 1 locus of maize

(Rhee et al. Genetics 2010, 186: 843855)
The hypermethylation of P1 locus leads to silencing which gives rise to colourless or pink coloured glumes instead of brick red glumes. This could be reversed by an unlinked modifier called Unstable factor for orange1 (Ufo1).

SSRs were stable in hybrids but inbreds were prone to changes

SSR patterns in callus (C) and regenerants (R1-5) in parental lines (S) and reciprocal hybrids (AD and DA)

Trait
Pl ht Grain yield

SE7 (% parent)
10 short 40 high

Tiller No.
Grain no/plant Grain size Wild type

17 high
40 high unchanged

Mutant

MicroRNA mis-regulation & somaclonal variation

(J. Rodriguez-Enriquez et al. 2011 Trends Plant Sci, 16:242-248)

Mode of regeneration and variation

Axillary bud regeneration Adventitious regeneration
Organogenesis Somatic embryogenesis Maize : High frequency RFLP changes in callus but less variation in embryo-derived plants (Brown 1991) Sugarcane: RAPD pattern highly variable in callus but less variation among regenerated plants (Taylor, 1995)

Nature of variation
Not unique Usually negative More than one variation per regenerant Not always stable/heritable Cannot be directed nor predictable

Relevance of somaclonal variation to practical plant improvement

Sexually propagated crops Apomictically reproducing plants Vegetatively propagated plants

Somaclonal variation and transgenics

Wang et al. (1996): 17 Poplar transgenics for Bt
2-3 yr trial, tested for RAPD/AFLP & SSR changes

All plants show some variation for one of the three tests Phenotypic & mol. Changes not related Highest resistance in a non-transgenic callus-derived plant

Wilson et al. (1994): Bt-cotton, 9 lines

All showed better fiber quality

Prestig et al. (1995): Potato transgenics for PLRV

Many control lines carrying only nptII gene were superior to coat protein transgenics with respect to viral infection

Species Geranium Sweet potato

Origin Callus Meristem tip

Feature Restored fertility, thick dented leaf, upright habit Dark red skin colour

Ref Skirvin & Janick (1976) Moyer + Collins (1983)

Celery

Suspension culture
Protoplast Advt. shoot

Fusarium resistance

Heath-Paglinso et al. (1989) Lacy et al (1996)

Arihara et al. (1995) Hall et al. (1986)

Potato Loganberry

Non-browning, oval tuber, shallow eyes Non-chimeric thornless

Blackberry
Daylily Torenia Rice Brassica juncea

Advt. shoot
Cell suspension Callus ? Callus

Non-chimeric thornless
Male sterility, dwrf White flower, compact Rhizoctonia resistace High yield, earliness Freezing tolerance

Skirvin et al. (1989)

Griesbach (1989) Brand and Bridgen (1989) Xie et al. (1992) Katiyar +Chopra (1995) Li et al. (2010)

St.Augustine grass Callus (Stenostaphrum secundatum) Eleusine coracana callus

High tillering and yield

Radchuk et al. 2012