Your Food Is a Polyploid

This is the seventh in a series of posts reviewing the 17 articles found in the October 2014 Special Issue of American Journal of Botany, Speaking of Food: Connecting Basic and Applied Science.

Doubling Down on Genomes: Polyploidy and Crop Plants by Simon Renny-Byfield and Jonathan F. Wendel

This is another fascinating but dense article about genetics. The major theme, as the title suggests, is polyploidy and its role in crop domestication and future crop improvements – a sub-theme being that by studying polyploidy in crop plants, we can gain insights into polyploidy generally as it relates to non-crop plants. Polyploidy – or whole genome duplication – is “where an organism possesses more than a diploid complement of chromosomes.” Typically, chromosomes come in sets of two, one set from each parent. Organisms with this type of an arrangement are called diploids. Polyploids are organisms with more than two sets of chromosomes. In general terms, this can occur as a result of two species hybridizing (interspecific hybridization), which is called allopolyploidy, or it can occur as a result of spontaneous genome doubling in a single species, which is called autopolyploidy. This article deals mainly with allopolyploid as polyploidy in crop plants is largely a result of hybridization.

Much of what we know about polyploidy has been discovered relatively recently during what is referred to as the “genomics era.” Traditionally, identifying polyploids was done by examining the number of chromosomes in a cell. Today, technological advances such as next generation sequencing have brought new insights into polyploidy and allowed us to identify evidence of it in organisms that cannot be observed simply by counting chromosomes. Plants that are now considered diploids went through periods of whole genome duplication in the distant past; however, due to genome downsizing and other events, they present themselves as diploids. This historical polyploidy is called paleopolyploidy. Evidence now suggests that all seed plants and flowering plants (angiosperms) are “rightly considered to have a paleopolyploidy ancestry.”

As I did with past articles that were very genetics heavy, I will use the bullet point method to list some of the main things that I learned from the article rather than offering a full review. As with any article that I review, my goal is to present the information in a digestible manner for as wide of an audience as possible without misrepresenting or oversimplifying the science and the research. This seems to be one of the main struggles faced by all who write about science for a general audience – a topic to be explored another time, perhaps.

  • The recent discovery that the genomes of all seed plants and angiosperms have “experienced multiple rounds of whole genome duplication” is “one of the most significant realizations to emerge from the genomics era.” In the past decade, “the ubiquity and scope of whole genome duplication has truly come to light,” and we no longer need to ask, “Is this species a polyploid?,” but rather “how many rounds of whole genome duplication occurred in the ancestral lineage of this taxon, and when was the most recent polyploidy?”
  • Recently formed polyploids are not stable and experience a period of “genomic shock.” They must “overcome an initial fitness cost associated with genomic [deviations].” These “large-scale perturbations [events that alter the function of a biological system] have the potential to add novel genetic material to the genome, potentially useful in the context of domestication and selection.”
  • Plants that appear to be diploids are actually paleopolyploids that have undergone a process called diploidization “in which the genome of a polyploidy is pruned, often by poorly understood mechanisms, such that it returns to a diploid-like condition.” Over time, duplicated genes are removed, DNA is eliminated, chromosome numbers decrease, etc. The organism then presents itself as a diploid, however traces of its polyploidy past remain detectable.
  • It has long been understood that hybrids can exhibit what is known as hybrid vigor (or heterosis) wherein they express traits that are superior to their parents, such as faster growth and higher yields. This is the reason plant breeders make such crosses. Debate continues concerning the “precise causes of heterosis.” Current research is focused on the epigenetic variability that is “induced by hybridization and polyploidy.” Epigenetics, which concerns variation that is not a result of alterations to DNA, is an emerging field that can be advanced through the study of polyploidy. Additionally, “the utilization of epigenetic diversity within crop species will provide a novel avenue for crop improvement in the coming years.”
  • While polyploids have great potential to increase our understanding of genomics and greatly improve “targeted breeding efforts,” they are historically difficult to study mainly due to the large size of their genomes compared to diploids. “Larger genomes are more expensive to sequence and require greater computational finesse.” To date, “only a single example of a ‘complete’ polyploidy genome exists, that of autotetraploid potato.” The authors “anticipate that these methodological challenges will soon be overcome by advances in genome sequencing technologies,” and along with “other powerful approaches,” continued insights into polyploidy will be attained.
Upland cotton (Gossypium hirsutum) is the most widely cultivated species of cotton in the United States. It is an allopolyploid that produces fibers that are "considerably longer, stronger, and whiter than are possible to obtain from any diploid." (photo credit: www.eol.org)

Upland cotton (Gossypium hirsutum) is the most widely cultivated species of cotton in the United States. It is an allopolyploid, and it produces fibers that are “considerably longer, stronger, and whiter than are possible to obtain from any diploid.” (photo credit: www.eol.org)

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Palm Oil Production and Its Threat to Biodiversity

Improvements in cultivated varieties of oil palms could have devastating ecological effects. This is according to an article published in a recent issue of Science. Doom doesn’t have to be the story though, if – as the authors suggest – governments and conservation organizations take proper action to safeguard vulnerable land.

Palm oil is a versatile vegetable oil derived from the fruits of oil palms. It has myriad culinary uses and is also used in the manufacturing of cosmetics and the production of biofuel. Oil palms have high yields, easily outyielding other major oil crops like soybean, rapeseed, and sunflower. Oil palms are grown in the tropics in developing countries where land and labor are inexpensive. As human population grows, demand for palm oil increases. To meet the demand, tropical forests are converted into agricultural land. The majority of palm oil production occurs in Southeast Asian countries like Indonesia and Malaysia. However, palm oil production is expected to increase in African and Latin American countries as new varieties better suited for these particular environments become available.

oil world graph

Genome sequencing of oil palm may allow plant breeders to develop varieties that are disease resistant, drought tolerant, and able to grow in salinized soils. Already making its debut, though, is a new variety of oil palm that is boasting yields from 4 tons to as much as 10 tons per hectare. Higher yielding varieties could be the solution to preventing more tropical forests from being converted into oil palm plantations. Or could they lead to more growth? Intrigued by the development of improved varieties of oil palms and other tropical crops, the authors of this study developed computer models in order to determine what this might mean for the future.

African Oil Palm (Elaeis guineensis) is the species of oil palm most commonly grown for palm oil production.

African Oil Palm (Elaeis guineensis) is the species of oil palm most commonly grown in palm oil production (photo credit: www.eol.org)

The results of simulations suggested two possible outcomes: one potentially positive and the other largely negative. On the positive side, “an assumed 56% increase in oil palm yield per tree in Malaysia and Indonesia” could result in ” around 400,000 hectares of agricultural land…taken out of production in Brazil, India, and Canada.” This is because less land will be needed to meet the demand, and the increased availability and resulting lower price of palm oil will outcompete other oil crops (like rapeseed, which is one of Canada’s main agricultural crops). However, the author’s seem to assume that agricultural land taken out of production will be restored back into natural lands. I find this argument hard to accept. Anecdotal evidence suggests that if farmers are no longer making a profit from a particular crop, they will choose to either grow something more profitable or sell their land to developers. A concerted effort would have to be made to capture this land and ensure that it remain uncultivated and undeveloped. Also, as the author’s point out, restoring land in Canada is very different from restoring or protecting tropical land. Loss of biodiversity is a much greater risk in areas where the level of biodiversity per hectare is high.

On the negative side, higher yields can encourage increased production. Tropical forest conversion may accelerate if farmers see an opportunity for growth. Additionally, improved varieties may increase palm oil production in African and Latin American countries, resulting again in more land conversion and deforestation. This effect may also become the story, not just for oil palms, but for cacao, eucalyptus, coffee, and other tropical crops as varietal improvements are achieved.

Oil Palm Friuits (photo credit: www.eol.org)

Oil Palm Friuits (photo credit: www.eol.org)

In light of this predicted consequence, the authors of this study recommend that governments, working together with conservation organizations and industry associations, regulate the conversion of agricultural lands and ensure that certain areas are specifically set aside for conservation. This means that “models of the drivers of environmental change” must be developed that “incorporate feedbacks at a range of scales” so that measures can be put into place to address “the unintended negative consequences of technical advances.”

More information on sustainable palm oil production can be found here.