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 qSD^s-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 Wx^a allele is associated with dryland indica and Wx^b is found with wetland japonica.

However, a group of Japanese scientists found both existed in the two subspecies and that Wx^b 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.

Notes:
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.



Photographs:
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.

South Carolina 8: Genetics

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 continues looking at the culture’s beliefs about the origins of its plants.

Weather: Some days warmer for a few hours, but cold before noon; last rain 1/28/13; 11:01 hours of daylight today.

The ruthless winds returned yesterday. First they suck up the moisture, then they remove the newly dried dirt and expose more moist ground to be raided. Los Alamos and Santa Fé have been getting snow showers, but we’ve only had clouds.

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 and weeping willow branches.

What’s blooming inside: Zonal geraniums, aptenia.

Animal sightings: Small brown birds.

Weekly update: The facts about Carolina Gold rice and Champneys Pink Cluster rose are sparse. However, because each was important, others have created narratives that fit their beliefs. Not surprisingly those mythic explanations have changed with circumstances to fit our changing expectations for appropriate heroes.

Originally, people gave credit to John Champneys for the hybrid pink rose, but today people prefer Philippe Noisette. That’s not because of Champneys’ Tory leanings, which are largely unknown, but because Noisette married a mulatto in Haiti and lived openly with her and their six children in Charleston.

Earlier, people accepted the view that Hezekiah Maham’s rice, and that of early South Carolina, came from Madagascar. More recently, some scholars, especially Judith Carney, have taken the facts that the early methods for milling and winnowing rice came from Africa and that many of the slaves imported in the years when Henry Laurens was active in the trade came from the rice growing regions of west Africa, to suggest that not only was seed rice imported from Africa, but the entire agricultural tool kit, including irrigation methods, was introduced by Blacks in exchange for adoption of an easier task system of labor.

Few gardeners or farmers care about the origins of their plants, except as amusing trivia. However, the facts and the way they are interpreted can be important social indicators. The differences and similarities in the way two disparate plants are treated may go farther to reveal underlying cultural patterns.

The only facts we tend to accept today come from genetics. Recently, biologists at Florida Southern College have confirmed that all the DNA found in fragment bands in Champneys Pink Cluster is found in Parson’s Pink and existing musk roses. They also confirmed that only half the DNA found in Blush Noisette is shared with Champneys Pink Cluster, and the rest is from some unknown source. They made no attempt to determine which was the pollen and which the seed parent for Champneys’ rose.

Genetic interpretations of the origin of rice are more controversial, because honor is involved. Ya-Long Guo and Song Ge believe the rice genus, Oryza, diverged within the grass family about 15 million years ago during the Miocene and the African varieties separated from the Asian about 7 million years ago.

The closest relative of modern rice, Oryza sativa, is rufipogon, itself dervied from nivara, while the nearest species to domesticated African rice, glaberrima is barthii. Nivara and barthii share a common ancestor. All are considered be part of the same AA genome, distinct from five other groups of modern rice.

The Asian rice divided into two subspecies, wetland japonica and dryland indica, as a result of domestication and the subsequent movement of rice eaters into new habitats. Some, looking at the genetics, argue the one is derived from the other. Others, looking at the archaeological record, believe they resulted from separate events that occurred south of the Himalayas, one in India, Myanmar or Thailand, the other in southern China or Vietnam.

As rice moved from China through Korea to Japan and the Philippines, then southeast to Sulawesi, Borneo, Java, and Sumatra, another, more tropical, subspecies emerged, javanica. This was the one taken to Madagascar. Linguists have determined current Malagasy is closest to the Maanyan language of Borneo, while geneticists have found the DNA of modern residents owes its Asian component to Borneo.

Medieval trade with Arabs on Kilwa island, who had contact through Aden with Gujuart, may have first introduced dryland rice from India. As trade and contacts across the Indian Ocean expanded after Europeans appeared, more ways were opened for rice imports.

In 1986, Koji Tanaka discovered javanica is still grown on the southeast coast of Madagascar where it’s extracted by foot, and milled with a mortar and pestle. In the uplands and west, indica dominates and animals are used to separate the rice. The northeast grows javanica and uses animal labor.

Notes: Javanica is now treated as a subspecies of japonica.

Burney, David. “Finding the Connections between Paleoecology, Ethnobotany and Conservation in Madagascar,” Ethnobotany Research and Applications 3:385-389:2005.

Carney, Judith. Black Rice: The African Origins of Rice Cultivation in the Americas, 2001.

Garlake, Peter. The Kingdoms of Africa, 1978.

Guo, Ya-Long and Song Ge. “Molecular Phylogeny of Oryzeae (Poaceae) Based on DNA Sequences from Chloroplast, Mitochondrial, and Nuclear Genomes,” American Journal of Botany 92:1548-1558:2005.

Hurles, Matthew E., Bryan C. Sykes, Mark A. Jobling, and Peter Forster. “The Dual Origin of the Malagasy in Island Southeast Asia and East Africa: Evidence from Maternal and Paternal Lineages,” The American Journal of Human Genetics 76:894-901:2005.

Joshi, S. P., V. S. Gupta, R. K. Aggarwal, P. K. Ranjekar, and D. S. Brar. “Genetic Diversity and Phylogenetic Relationship as Revealed by Inter Simple Sequence Repeat (ISSR) Polymorphism in the Genus Oryza,” Theoretical and Applied Genetics 100:1311-1320:2000.

Tanaka, Koji. “Rice and Rice Culture in Madagascar,” Tonan Ajia Kenkyu 26:367-393:1989.

_____ “Malayan Cultivated Rice and Its Expansion - Part Three,” Agricultural Archaeology 97-107:1997.

Photographs:
1. Tis the season for going through the summer’s pictures to try to identify the unknowns. For years, I thought Green Flower was in the morning glory family, with its five petals joined into a plate. I found nothing. Flower taken 7 September 2008.

2. One day this summer when I was turning every page of Geyata Ajilvsgi’s Wildflowers of Texas, I saw pictures of False Nightshade that had similar flowers, but very dissimilar leaves. This plant has long, narrow, dark green leaves. Leaves taken 2 October 2011.

3. Sometimes they rise a bit and show wavy edges and a backward arch. Leaves taken 26 July 2008.

4. The Solanaceae connection isn’t obvious, despite those occasional leaves. It center doesn’t protrude and the petals are not pinned back like those of tomatoes. Flower taken 6 June 2011.

5. At least one plant has been growing in the gravel of my drive since 1997. Sometimes there were more, but usually only two or three. The leaves would spread into low, round masses, but would not leave the drive and would not accept transplanting.

This year, after I had work done on the drive, and more gravel delivered, the plants in the drive were larger. They also spread down the bank and provided ground cover for some annuals. I don’t know it they are the seed from the same plants, or if new seed was brought in from the north. Plants filling the spaces between larkspur, juniper, Shirley and California poppies, 13 August 2012.

6. The man doing the backhoe work said the plants were common in his area, but he had no name for then. They're just one of those things that grow, that serve no obvious purpose, but aren’t dangerous enough to attack. Plants around blue-gray California poppy, 10 November 2012.

7. I should have known they weren’t a morning glory. They’re cold hearty. After temperatures fell to 15 in mid-November, the leaves disappeared, but the green stems remained. It was only after the snow of mid-December, that everything died. Plant with cottonwood leaves, 21 December 2012.

8. So this week, I followed Ajilvsgi’s lead, and looked up Chamaesaracha in E. O. Wooton and Paul C. Standley’s Flora of New Mexico. It has no pictures and useless descriptions, but did list two species that grow in New Mexico. This is coronopus, even though the USDA doesn’t show it growing in Rio Arriba county. Flower buds, 24 April 2011.

9. The plant has sticky hairs, which is why the pictures often show more dirt than detail. The perennial has some kind of berry which has been used by the Hopi and Navajo, but I’ve never seen one. The common name, Green Leaf Five-eyes, is no more useful than the Green Flower I’ve called it for years, when I protected it. I’ll probably still call it that, at least to myself, and hope it comes back along the bare drive bank. It is one of those plants that may be insignificant, but give pleasure all the same. Plant and flowers, 11 August 2006.

South Carolina 5: Rice and Roses

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.

Maham and Champneys were not part of the social elite who are remembered in family histories. The previous entries covered what little is known about their lives. This one provides what is known about their major achievements.

Weather: Snow from New Year’s Eve has been protecting the land since morning temperatures fell to their post-solstice lows; last snow 12/31/12; 9:54 hours of daylight today.

What’s still green: Few rose stems; juniper, pine, and other evergreens; yucca, garlic. Snow covered most beds.

Most seeds have been dispersed, but some are still being released. Many heads survive as ghosts of themselves, some still surprised that death came so quickly. The older ones, of course, knew and had prepared their shrouds. The skeletons reveal family likenesses.

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

What’s grey or blue: Snow-in-summer, winterfat, golden hairy aster leaves.

What’s yellow: Globe willow branches.

What’s blooming inside: Zonal geraniums, aptenia, petunias.

Animal sightings: Small brown birds.

Weekly update: Hezekiah Maham and John Champneys are an unlikely pair to be the ones responsible for Charleston’s antebellum wealth and beauty. It’s even odder, given South Carolina’s current reputation for fundamentalism, that the actions of the two contributed to the growing body of experience that led people to accept Charles Darwin’s 1859 suggestion that natural selection was the operative cause of evolution.

After the war, Maham needed seed rice for his Pineville area plantation. He died four years later. In the years since he had been so deeply in debt, he must have had some success, because the next year, his younger daughter, Mary’s husband, George Haig died and left the slaves he’d acquired from Maham to his wife for her life.

In 1800, Joshua John Ward was born at Brook Green plantation to Maham’s niece, Elizabeth Cook, and John Ward. Thirty-seven years later, his overseer, James C. Thompson, noticed part of a rice head that was larger than any other Ward had seen.

Ward saved the seed, and planted it the next year on the margins of an old field where it was nearly destroyed by standing water and rats. The following year, he and Thompson planted the seed they’d been able to salvage in a large tub in Thompson’s yard, only to have a slave leave the gate open and a hog eat most of the crop. They transplanted the survivors, and most of the rice was sterile.

In 1840, they took what had survived the hog and rot, and planted half an acre. The next year, Ward planted 21 acres at Brook Green, which his factor sold above the market price. In 1842, Ward tried 400 acres, and the following year planted nothing but the new large grain.

In 1844, Ward made Carolina Gold available commercially. From then until the civil war, the Brook Green rice “commanded the highest price of any rice on the world market in Paris and London.”

Ward claimed his 1838 seed was descended from that planted by his great-uncle in 1785.

Sometime in the early 1800's, either 1802 or 1810 or 1811, John Champneys found a new rose growing on his plantation, which appeared to be a cross between a white musk, cultivated in Europe since the Crusades, and Parson’s Pink, which had been introduced to England from China in 1759.

Philippe Noisette, a son of the head gardener to the future Louis XVIII, had moved to Charleston in 1795 with his Haitian wife after the revolution there. He experimented with the rose, now called Champneys’ Pink Cluster, and in 1814 sent either seeds or plants to his brother who had a nursery in Paris. Either Philippe or Louis Claude crossed the plant with another rose. The hybrid was introduced in Europe as Blush Noisette in 1819.

Meantime, plant stock of some kind was sent to William Price, Jr., who had the best known American nursery on Long Island, and traded plants with his English suppliers. Two years before Champneys died, the Loddiges Nursery outside London offered a new rose, Champigny, in 1818.

Noisettes were the first roses to introduce the recessive gene for reblooming isolated by the Chinese into a fragrant European species. A number of new varieties appeared in France in the 1820's and 1830's. By the 1840's, they were crossed with tea roses, which led in 1867 to La France, the first hybrid tea released by Jean-Baptiste André Guillot the younger.

At the time, Louis Claude Noisette and other French growers were becoming aware of the mechanics of plant reproduction. When Rudolph Jacob Camerarius had argued in 1694 that plants had sexual organs, and pollen was the male agent of fertilization, most ignored him.

In 1729 a 22-year-old Carl Linnaeus expanded his ideas to suggest a method of classifying plants in Introduction to the Floral Nuptials. He continued his work to make reproduction the basis for his description of the natural world and external characteristics, the morphology, the criteria naturalists would use to distinguish species.

The most important work for breeders appeared in 1793, when Christian Konrad Sprengel described his practical experiments with pollination. Still, more than a generation passed before the first controlled rose hybrid was introduced by Beauregard in Angiers in 1839. Safrano, a grandparent of La France, combined a yellow China with a Bourbon, itself a spontaneous hybrid of Parson’s Pink and a damask found on La Réunion in 1823 by Edouard Perichon.

At the time Maham acquired his gold husked seed and Champneys bought his pink shrub rose, observation and selection were the only methods available to farmers to improve their crops. In 1843, Ward’s relative through his mother’s sister, Robert Allston complained that poor rice came from the “commingling of the grain” which happened when different varieties were planted in adjacent fields, and planters were “careless” in selecting their seed stock.

The year before Ward introduced Carolina Gold, Allston described the types of rice then growing in the state. His classification criteria were morphological: seed husk color, size, shape, and awns, also called beards.

The most important variety, which he attributed to Maham, had a gold shell. This coexisted with white rice, which had a creamy hull; guinea rice, which he said looked like guinea corn, a form of African sorghum or millet, and proud rice, a red grain with a white husk and awn like gold seed.

Allston contrasted these with attempts to improve the quality of the crop, either through introducing new seed or careful selection. His example of the first was a bearded variety brought from the East Indies the year before. As an illustration of “improvement” through “a long-continued, careful selection of the seed,” he mentioned the long grain rice about to be introduced by Ward.

At the time Carolina Gold and Safrano were introduced in 1844 and 1839, Darwin was back in England from his five year voyage on the Beagle and working out an explanation for the endemic species he’d seen in the Galapagos islands.

It’s his name we associate with the revolution in plant breeding, even though he drew on the work of men like Sprengel. Similarly, while J. J. Ward and Louis Claude Noisette received the credit and profits for developing new plant varieties, they needed the experience of Hezekiah Maham and John Champneys, and the support of men like Robert Allston and Philipe Nosette.

Innovation can only come from a combination of shared interests and special individuals.

Notes: Mary Charlotte Cook, Ward’s maternal aunt, married Benjamin Allston Sr. Allston’s uncle was William Allston, the father of Robert Francis Withers Allston.

Allston, Robert. A Memoir of the Introduction and Planting of Rice in South Carolina, 1843, reprinted in several other publications, including James Dunwoody, The Industrial Resources, Etc., of the Southern and Western States, volume 2, 1852.

Camerarius, Rudolph Jacob. Epistolae de Sexa Plantarum, 1694.

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

Darwin, Charles. On the Origin of Species, 1859.

Hurst, C. C. “Notes on the Origin and Evolution of Our Garden Roses,” 1941, reprinted in Graham Stuart Thomas, The Old Shrub Roses, 1955.

Linnaeus, Carl. Praeludia sponsaliorum plantarum, 1730.

_____. Systema Naturae, first edition 1735.

Spengle, Christian Konrad. Das entdeckte Geheimnis der Natur im Bau und in der Befruchtung der Blumen, 1793.

Ward, Joshua John. Letter to Robert Allston, 16 November 1843, incorporated in later editions by Allston and reprinted by the Carolina Gold Rice Foundation, The Rice Paper, November 2009.

Photographs:
1. Tahoka daisy, empty seed heads, 1 January 2013, composite family.

2. Zinnia, flower head, 1 January 2013, composite family.

3. Coral bells, flower stalk, 1 January 2013, saxifrage family.

4. Heavenly Blue morning glory, seed capsule, 1 January 2013, convolvus family.

5. Datura, seed head, 1 January 2013, convolvus family.

6. Oriental poppy, seed head, 1 January 2013, poppy family.

7. Sensation cosmos, flower head with some seeds visible, 1 January 2013, composite family.

8. Garlic chives, some seeds have dropped, but not all; 1 January 2013, allium family.

9. Creeping baby’s breath, seed capsules, 1 January 2013, pink family.

10. Mexican hat, seed had disintegrating, 1 January 2013, composite family.