Feature: Genetics and the origins of modern cotton

This feature appeared in the July/August 2011 issue of Australian Life Scientist. To subscribe to the magazine, go here.

In 1988 molecular geneticist Professor Jonathan Wendel, of Iowa State University in Ames, Iowa, confirmed an extraordinary 77-year old hypothesis about the origins of the world’s most important fibre crop, upland cotton (Gossypium hirsutum – or ‘hairy Gossypium’).

Using restriction fragment length polymorphisms (RFLPs), Wendel performed comparative analyses of the chloroplast genomes of 40 Gossypium species from Meso-America, Africa, Asia and Australia, including two New World tetraploids, and Pima cotton, G. barbadense.

His findings supported Danish cytogeneticist Dr A. Skovsted’s remarkable proposition in 1934 that the two New World tetraploids – which were independently domesticated around 6000 years ago – arose following a transatlantic hybridisation event between diploid species from opposite sides of the Atlantic Ocean least a million years before humans colonised the New World.

At the XVIII International Botanical Congress in Melbourne in July Wendel spoke about this and other highlights of his fruitful research career exploring the genome secrets of upland cotton, a crop which, like the world’s most important food crop, bread wheat, is a genetic monster that arose in improbable circumstances in prehistoric times.

The account takes us back to the Amerindians in the Peru-Ecuador region, who domesticated G. barbadense, or Pima cotton, around 6000 years ago. Valued for its long and silky fibres, it became the basis of early cotton production in the Caribbean and U.S. Confederate states until it was superseded by long-staple varieties of G. hirsutum. Today it accounts for around two per cent of the global cotton crop.

But it is the Mexican allotetraploid, G. Hirsutum, from Mexico that has commanded Wendel’s attention through 30 years of research. Upland cotton, which constitutes 95 per cent of world cotton production, has half a dozen wild varieties grow that grow across Mexico and down into neighbouring Guatemala.

Wendel’s genome studies indicate that the most likely progenitor of Upland cotton was the sprawling perennial G. hirsutum var. yucatanense, which grows in scattered populations around the coast of Mexico’s Yucatan Peninsula.

The maternally-inherited chloroplast genome indicates its seed parent was a relative of two wild diploid species, G. herbaceum and G. arboreum, that were independently domesticated in the Old World perhaps 5000 years ago.

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Four domestications

Wendel says cotton is unique among the world’s major crops, because it was independently domesticated four times, in different regions of the world: twice from allotetraploid (A + D genomes) progenitors in the New World, and twice from diploid (A genome) progenitors in the Old World.

G. herbaceum, a shrubby wild species from sub-Saharan Africa and Arabia, were domesticated in the region of Ethiopia some 5000 years ago. Its Asian relative, G. arboreum, was likely domesticated in the Indus Valley around the same time, with cultivation later spreading to China.

It is a wild relative of these two A genome species that was the female parent in the cross that gave rise to the New World A + D genome species. The probable pollen donor for the D genome of G. hirsutum was a plant closely related to the Peruvian diploid, G. raimondii.

So how did a seed from a wild diploid Gossypium species find its way across the 7000-odd kilometre breadth of the Atlantic Ocean at least a million years ago to hybridise with a meso-American diploid cousin?

The short answer is: no-one knows, and we’re unlikely to ever know the full story. But Wendel’s research indicates that all New World diploid species trace their origins to trans-Atlantic migrants from Africa or Asia. As for the vector, Wendel plumps for the Constipated Duck Hypothesis; it’s just as probable – or improbable, as the case may be – as any other.

A chloroplast molecular clock dates the emergence of the cosmopolitan genus Gossypium, from the hibiscus family Malvaceae, to between 10 and 20 million years ago, either in Africa or Australia. As the genus spread around the world’s tropical and sub-tropical regions, its species diverged under different selection pressures, developing distinctive karyotopes.

Taxonomists today group the 50-odd Gossypium species in eight distinct genome categories: A to G, and K, that differ as much as threefold in chromosome size, as the result of the proliferation of various families of transposons, or mobile elements.

It was the striking contrast in the sizes of the two diploid sets of chromosomes in 52-chromosome G. hirsutum that led Skovsted, a Malvaceae expert, to conclude more than 75 years ago that the Mexican tetraploid ancestor of upland cotton arose in a rare genetic accident that fused the complete genomes of an Old World D-genome species and a MesoAmerican A-genome species.

Australia is one of the centres of diversity for the genus, with 17 native Gossypium species, including the beautiful mauve-flowered Sturt’s Desert Rose, Gossypium sturtianum, which constitutes the floral emblem of the Northern Territory. In 1993, Wendel spent six weeks in Western Australia’s Kimberley region, chopper-hopping around the rugged, inaccessible landscape, and discovering a new Gossypium species in the process.

“The Australian species form the coolest clade on the planet,” he says. “You have these wild, herbaceous perennials with massive, fire-adapted underground rootstocks, and long vegetative runners. They flower in the dry season, when everything else is dying off, and produce their seed capsules at ground level, where they are accessible to ants. The ants harvest the seed, which lacks lint, and carry it underground as soon as it ripens.”

This feature appeared in the July/August 2011 issue of Australian Life Scientist. To subscribe to the magazine, go here.

Read part II: The remarkable cotton genome.