Sunday, February 17, 2013

South Carolina 9: DNA Studies

When South Carolina congressmen became more vociferous about the supposedly false theories of modern science, I began to wonder how Charleston had ever produced the important innovations in botany that underlay its lifestyle: the selection of new types of rice and roses. Periodically, I’ll be publishing the result of my inquiries into the lives of two innovative growers, Hezekiah Maham (rice) and John Champneys (roses). Previous entries can be found under “South Carolina” in the index at the right.

This entry looks at the mechanics of botanical change. Last week’s entry defined the species name. The photographs are of another mystery plant.

Weather: Maybe a quarter inch of snow Monday night, didn’t survive long the next day; 11:19 hours of daylight today.

What’s still green: Few rose stems; juniper, pine, and other evergreens; yucca, Madonna lily, grape hyacinth leaves.

What’s red: Cholla; apple, apricot, sandbar willow branches.

What’s grey or blue: Winterfat, golden hairy aster leaves.

What’s yellow: Globe willow branches; weeping willow branches much more yellow.

What’s blooming inside: Zonal geraniums, aptenia.

Animal sightings: Small brown birds.

Weekly update: Gregor Mendel was doing his pea inheritance experiments at the same time Darwin was developing the theory of natural selection, but the monk’s work was not publicized until 1900.

Breeders already had enough experience with the variability of hybrids to recognize the statistical patterns he described, that people with blue eyes inherit their eye color from both parents because the blue allele is recessive, and that crossing a red and white pea would produce a red or white flower 25% of the time, and a pink the rest.

Rose growers confirmed his work, especially when they took a hybrid and backcrossed it with one of its parents. It’s easy for them to say Champneys Pink Cluster introduced a recessive gene for reblooming because their efforts produced results that confirmed their expectations.

In 1953, Francis Crick and James Watson published their work on the structure of DNA and scientists began using sophisticated instruments to determine exactly where each gene resided, and what each controlled.

Results for rice specialists have not been as satisfying as those for roses. Dormancy, that single domestication event posited by earlier researchers, was no longer simple because dormancy isn’t a physical trait like color, but either results from the structure of the outer layer of the seed or from the embryo. Its appearance isn’t tied to a single gene, but to areas of DNA that exists on several chromosomes.

A Chinese team found five quantitative trait loci have been identified on five chromosomes, and that dormancy increased in only four cases when they introduced an allele from a highly dormant indica cultivar. They learned the more genes they altered, the greater the dormancy.

A group in Korea found similar complexity when they looked at the literature on shattering, another trait hypothesized to have been central to domestication. The ability for the seed to separate easily at maturity without breaking is the consequence of hormonal processes that create a hardened abscission layer on the pedicel stem that holds the seed to the head.

They found reports that four alleles on four of rice’s twelve chromosomes have been linked to shattering, of which two are involved with the creation of the abscission layer. They also found six broader quantitative trait loci had been identified on six chromosomes.

The group created a shattering mutation by treating a non-shattering japonica variety with N-methyl-N-nitrosourea, then crossed it with five cultivars, including its parent. The results suggested the recessive sh-h gene on chromosome 7 was responsible for shattering. They noted that area was closely linked to the Rc location that controls red hull color and the qSDs-7-1 experimentally tied to dormancy.

The level of amylose, a form of starch, is used to differentiate sticky japonica from fluffy indica rices. However, the tropical japonica javanica falls between the two.

In 1983, researchers for the Carnegie Institution discovered the Wx or waxy gene controlled amylose content in maize pollen and kernels. The gene has since been found in wheat, barley, millet and rice. In rice, the Wxa allele is associated with dryland indica and Wxb is found with wetland japonica.

However, a group of Japanese scientists found both existed in the two subspecies and that Wxb predominates. The distinction between the two occurs during the encoding process when a nucleotide that follows the pattern AGGT in nirvana and rufipogon mutates to AGTT.

In other words, the causative agent isn’t the genetic allele, but something working on that allele during reproduction. Further, the change isn’t permanent, but can revert in the next generation. Another Japanese team found the same kind of change in the African glaberrima rice came from deleting and inserting a new unit in the nucleotide sequence, rather than substituting a T for a G.

Scientists now know a great deal more about rice, but without specimens with known provenance, they can’t say where Hezekiah Maham or John Joshua Ward got his seed. Richard Porcher has found the plats to Maham’s plantation and hopes to unearth some grains. Depending on the results, geneticists may be able to guess if Ward’s Carolina Gold was the direct, but mutant, offspring of Ward, or like the Blush Noisette, has another as yet unidentified parent that blew in from another field.

Researchers have, however, done something more extraordinary, unintentionally duplicated the daily experience of planters who were constantly surprised when their gold hulled rice turned white, or their white turned red. The very randomness of such traits forced them to become better observers, and thus more open to an explanation like that provided by Darwin when it became available.

Carolina Gold Rice Foundation. “Searching the Origins of Carolina Gold,” The Rice Paper November 2009.

Ji, Hyeon-So, Sang-Ho Chu, Wenzhu Jiang, Young-Il Cho, Jang-Ho Hahn, Moo-Young Eun, Susan R. McCouch, and Hee-Jong Koh. “Characterization and Mapping of a Shattering Mutant in Rice That Corresponds to a Block of Domestication Genes,” Genetics 173: 995–1005:2006.

Shure, M., SR Wessler, N. Federoff. “Molecular Identification and Isolation of the Waxy Locus in Maize,” Cell 35:225-233, 1983.

Umeda M, H. Ohtsubo, and E. Ohtsubo. “Diversification of the Rice Waxy Gene by Insertion of Mobile DNA Elements into Introns,” The Japanese Journal of Genetics 66:569-86:1991.

Wan, J. M., L. Jiang, J.Y. Tang, C.M. Wang, M.Y. Hou, W. Jing and L.X. Zhang. “Genetic Dissection of the Seed Dormancy Trait in Cultivated Rice (Oryza sativa L.),” Plant Science 170:786-792:2006.

Yamanaka, Shinsuke, Ikuo Nakamura, Kazuo N. Watanabe, and Yo-Ichiro Sato. “Identification of SNPs in the Waxy Gene among Glutinous Rice Cultivars and Their Evolutionary Significance during the Domestication Process,” Theoretical and Applied Genetics 108:1200-124:2004.

1. A new, white-flowered nightshade appeared in my drive this summer. It either came in the gravel from northern Rio Arriba County, or in the tires of the back hoe that recently had been in the Four Corners area and southern Colorado. 25 August 2012. I now believe it is a Carolina Nettle, Solanum Carolinense

2. The leaves differ from the annual that showed in 2006 near my newly installed, cedar wood fence. That was probably Solanum triflorum. 13 August 2006.

3. This is probably some member of the Black Nightshade complex. Complex means botanists aren’t willing to commit themselves. A number of species names have been given, and they may all be variations on the same plant, or may be different. The one thing they agree is the berries are black. The alternative plant has red berries. 3 February 2013.

4. I don’t know if these berries were once black and faded with the snow, or if the weather turned cold before they could fully mature. I don’t look at every weed every day. 14 December 2012.

5. Blooming plant, 1 September 2012,

6. Closer view of flowers, 1 September 2012.

7. Berries forming, 30 September 2012.

8. Plant yesterday, 16 February 2012.

9. Closer vew of plant yesterday, 16 February 2012.

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