Using Wild Relatives to Improve Crop Plants

This is the thirteenth 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.

Back to the Wilds: Tapping Evolutionary Adaptations for Resilient Crops through Systematic Hybridization with Crop Wild Relatives by Emily Warschefsky, Varma Penmetsa, Douglas R. Cook, and Eric J. B. von Wettberg

The nature of domestication involves the narrowing of genetic diversity through a series of crosses and selections that results in organisms well suited for particular environments and/or purposes. In the short term, this arrangement seems to suit our needs, that is until the climate shifts, novel pests and diseases invade, agricultural soils become degraded, or some other calamity ensues. Then we must select a new form to take the place of the old one that is no longer suitable. Additionally, the varieties currently in use may be doing well within their current parameters, but their performance may be found lacking if placed in different environments or grown in alternate systems, such as one that relies on fewer petrochemical inputs.

The wild relatives of crop plants have a long history of being used in breeding programs to provide specific traits for improving domesticated varieties. Interest in this has increased thanks to technological advancements (such as marker-assisted selection and genomic selection) and the greater availability of germplasm. Introgression (the transfer of genes from one species to another through hybridization and repeated backcrossing) using crop wild relatives has mainly been aimed at introducing traits like resistance to specific pests and diseases, tolerance of certain abiotic stresses, and greater yields. In other words, crop wild relatives are typically screened for a few main traits that might be useful in breeding programs, neglecting the possibility that the introgression of a larger suite of traits may be beneficial long-term.

This article discusses the possibility of using “crop wild relative collections that [have been] systematically built to represent the range of adaptations found in natural populations” to improve crop plants. By using these “purpose-built populations that are hybrids between crops and their wild relatives,” crop plants introgressed with “full sets of wild diversity” will be better adapted to a wide variety of environments, soils, climates, and agricultural systems. In order to “illustrate the gains that are possible,” the authors review published studies of hybridization (both naturally occurring and human mediated). They then “propose a multi-step framework for utilizing naturally occurring variation in wild relatives of crops.”

Grapefruit (Citrus x paradisi) - A hybrid between sweet orange (Citrus sinensis) and shaddock (Citrus maxima) that "occurred far beyond the region of domestication and rather recently [the 18th centruy]." (photo credit: wikimedia commons)

Grapefruit (Citrus x paradisi) – A hybrid between sweet orange (C. sinensis) and shaddock (C. maxima) that “occurred far beyond the region of domestication and rather recently [the 18th century].” (photo credit: wikimedia commons)

Hybridization can occur between two individuals of different cultivars, varieties, subspecies, species, genera, etc. The genetics of the resulting offspring is a combination of the two parents, and depending on the circumstances, a hybridization event “can have drastically different consequences.” For this reason, “hybridization is thought of as both a creative and a restrictive force in evolution.” It is, however, “the potential for the production of novelty that makes hybridization such an intriguing – and potentially useful – phenomenon.”

In their discussion of hybridization between crops and their wild relatives, the authors reveal some “obstacles that limit the use of wild relatives in breeding programs.”

  • Poor Agronomic Performance – “Crop wild relatives often lack important domestication traits.” They may have shattering pods, irregular germination timing, or phenologies that inhibit their use in certain regions.
  • Poor Representation in Germplasm Collections – “Only 2-6% of international germplasm collections are of crop wild relatives.” There are some crop wild relatives that are well-represented, but others have been “poorly collected” or “almost ignored,” and some crops still “lack well-identified wild relatives.” One reason for this disparity is that a large number of these plants “occur in geopolitically unstable areas where collection has long been complicated.”
  • Unpredictability of Phenotypes – “Phenotypes of wild individuals are often assessed in agricultural settings, a largely uninformative practice when the overall wild phenotype is specifically adapted for fitness in the wild but not cultivated settings.” This makes for an inaccurate comparison with domesticated varieties, so when “crop-wild hybrids” are formed, phenotypes are hard to predict. Backcrossing is necessary in order to recover the “essential crop phenotype” while capturing the desired traits of the wild relative.

The authors also highlight the need for conservation of crop wild relatives, as “these species are nearly universally threatened.” The catalog of threats to their survival is similar to so many other threatened species: the loss, fragmentation, and degradation of habitats, climate change, invasive species, and over-harvesting (“in the case of medicinally and pharmaceutically useful species”). One threat, perhaps ironically, is agricultural crops crossing with nearby wild relatives, especially where transgenic genes in crops are being transferred to wild populations. In order to better realize the potential that crop wild relatives have in improving domesticated varieties, they must first be protected in their natural habitats.

Desert sunflower (Helianthus deserticola) - One of three hybrid species born of H. annuus and H. petiolaris, "highlighting the expanded potential of hybrid species...through colonization of extreme habitats where neither parental species can survive." (photo credit: www.eol.org)

Desert sunflower (Helianthus deserticola) – One of three hybrid species born of H. annuus and H. petiolaris, “highlighting the expanded potential of hybrid species…through colonization of extreme habitats where neither parental species can survive.” (photo credit: www.eol.org)

The authors propose a 5 step plan for systematic utilization of crop wild relatives in agricultural breeding programs. The steps include building a comprehensive collection of crop wild relatives, sequencing their genomes, creating purpose-driven hybrid populations between wild relatives and crop plants, developing a predictive network of genotype-phenotype associations, and deploying identified phenotypes into crop breeding efforts. This article is one of the open access articles in this issue. If you are interested in this topic, including this 5 step plan, I encourage you to read the article to learn more. 

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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)