F Rosa Rubicondior: Black Rice and Creationist Not-So-White Lies

Wednesday 30 September 2015

Black Rice and Creationist Not-So-White Lies

The Birth of a Black Rice Gene and Its Local Spread by Introgression | The Plant Cell

Here's a nice example of how a change in a species' environment can change the meaning of the information in its genome and so change the direction of the species evolution. Of course, it gives the lie to another basic piece of disinformation traditionally foisted on their willing dupes by creationist frauds.

A team of plant geneticists from Japan led by Dr. Takeshi Izawa have worked out the genetic basis of the black colour in black rice and have traced its origins to a mutation in a gene known to science as Kala4, which controls the amount of anthocyanin pigments the plant produces. The wild rice, Oryza rufipogon, has red grains but, due to a mutation in a gene controlling pro-anthocyanidin biosynthesis, domestic rice, Oryza sativa, fails to produce these pigments so remains white.

The precise mechanism of the evolution of the cultivated cultivars of Oryza sativa are unknown but it is probable that ancient humans selected for white grains during the domestication process.

Black rice, by contrast, appears to have been selected for because of its rarity and acquired cultural mystique as "Emperor's Rice" or "Forbidden Rice", so this mutant too has been actively selected for by humans.

The origin and spread of novel agronomic traits during crop domestication are complex events in plant evolution. Wild rice (Oryza rufipogon) has red grains due to the accumulation of proanthocyanidins, whereas most cultivated rice (Oryza sativa) varieties have white grains induced by a defective allele in the Rc basic helix-loop-helix (bHLH) gene. Although the events surrounding the origin and spread of black rice traits remain unknown, varieties with black grains due to anthocyanin accumulation are distributed in various locations throughout Asia. Here, we show that the black grain trait originated from ectopic expression of the Kala4 bHLH gene due to rearrangement in the promoter region. Both the Rc and Kala4 genes activate upstream flavonol biosynthesis genes, such as chalcone synthase and dihydroflavonol-4-reductase, and downstream genes, such as leucoanthocyanidin reductase and leucoanthocyanidin dioxygenase, to produce the respective specific pigments. Genome analysis of 21 black rice varieties as well as red- and white-grained landraces demonstrated that black rice arose in tropical japonica and its subsequent spread to the indica subspecies can be attributed to the causal alleles of Kala4. The relatively small size of genomic fragments of tropical japonica origin in some indica varieties indicates that refined introgression must have occurred by natural crossbreeding in the course of evolution of the black trait in rice.*

Tetsuo Oikawa, Hiroaki Maeda, Taichi Oguchi, Takuya Yamaguchi, Noriko Tanabe, Kaworu Ebana, Masahiro Yano, Takeshi Ebitani, and Takeshi Izawa
The Birth of a Black Rice Gene and Its Local Spread by Introgression
Plant Cell tpc.15.00310; Advance Publication September 11, 2015; doi:10.1105/tpc.15.00310

*© 2015 American Society of Plant Biologists. All rights reserved.

What this team have worked out is the most likely source of this 'black' mutation; probably in the tropical japonica subspecies and that it entered the indica subspecies almost certainly by crossbreeding between the two subspecies, either by chance or by human intervention. However it arrived in the indica subspecies, it has been actively selected for during cultivation by humans.

So, the gene controlling the red pigmentation in the wild ancestor of domestic rice, which presumably evolved because it conveyed a benefit, possibly in an earlier ancestor, has given rise to two different mutations; one which stopped the pigments being produced which gave rise to the white rice generally favoured by most human populations, and one which causes over-production resulting in black rice which gained a cultural cachet and so has been cultivated as a 'special' rice and so preserved in the overall genepool.

Additionally, the intense cultivation of rice, where rice is grown in effective monocultures rather than as scattered plants as it would grow naturally, has hugely increased the probability of crossbreeding and has brought subspecies into closer proximity than would occur without human interventions.

Biologically, what's changed, from the perspective of rice genes, is that humans changed the environment in which they found themselves and the test for fitness became whether humans favoured some mutations over others, so the meaning of the information in those genes was changed by the changed environment and the evolution of rice took on a new direction.

Despite the abundance of these examples of change in the meaning of information, rather than in the quantity of information, creationist frauds continue to tell their willing dupes that evolution is impossible because information can't change by mutation. As ever, this deception depends on the cooperation of these dupes and especially on their carefully maintained ignorance and refusal to understand the fundamentals of a subject they insist they know more about than biologists do.

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