Apples and Genetic Bottlenecks

This is the eleventh 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.

Genetic Diversity in Malus x domestica (Rosaceae) through Time in Response to Domestication by Briana L. Gross, Adam D. Henk, Christopher M. Richards, Gannara Fazio, and Gayle M. Volk

Domestication is a selection process. Plants with desirable traits are selected (consciously or unconsciously) and removed from the larger population to be grown out and selected from again. Over time, this series of selections results in a cultivated variety that differs substantially from the larger, origin population. This process, while yielding crop varieties that feed a growing population of humans, also results in a series of genetic bottlenecks, meaning they experience a reduction in genetic variation compared to their wild relatives.

There are two points were bottlenecks occur in the domestication process. The first takes place “during the initial domestication event as a subset of the wild population is brought into a cultivated setting.” This is called a “domestication bottleneck.” The second, known as an “improvement bottleneck,” happens when “modern, elite cultivars are selected from the broad variety of landraces [locally adapted varieties]” that were developed during the original domestication event. This stepwise reduction in genetic diversity “limits the options of plant breeders, even as they face the need to increase crop productivity and sustainability” in today’s changing climate.

Most of what we know about genetic bottlenecks during domestication is derived from studies of annual fruit and grain crops. However, “non-grain crops, and perennials in particular, respond to domestication or are domesticated in ways that are fundamentally different.” For this reason, the authors investigated genetic bottlenecks in apple (Malus x domestica), “one of the most widely distributed perennial fruit crops.” They then compared what they learned to other published studies of annual and perennial fruit crops in order to gain more insight into how genetic diversity is affected in these types of crops during domestication.

The common apple was domesticated in central Asia around 4,000 years ago and is a hybrid of at least three species: Malus sieversii, Malus orientalis, and Malus sylvestris. Today, apples are grown throughout the world, and there are more than 7,500 known cultivars with new cultivars being released regularly. Despite this impressive diversity, just fifteen cultivars make up 90% of apple production in the U.S. The authors of this study analyzed DNA from 11 of the 15 major cultivars as well as DNA from the three main wild progenitor species.

Malus x domestica 'Gala' - One of the top 15 apple varieties produced in the U.S. (photo credit: wikimedia commons)

Malus x domestica ‘Gala’ – One of the top 15 apple varieties produced in the U.S. (photo credit: wikimedia commons)

Perennial fruit crops typically experience “mild genetic bottlenecks” compared to annual fruit crops, and the authors confirmed this to be the case with domesticated apples, finding “no significant reduction in genetic diversity through time across the last eight centuries.” Because apple cultivars are maintained by clonal propagation, they can often be traced back to when they were originally developed, making bottlenecks easier to observe. The authors found that “the most recently developed or described cultivars of apples show little to no reduction in genetic diversity compared with the most ancient cultivars.” Cultivars developed since the 1950’s show increased diversity, which may partly be the result of plant breeders introducing genes from another wild species, Malus floribunda.

After a review of the literature, the authors found that apples have retained the highest amount of genetic diversity through the domestication process compared to other fruits, both annual and perennial. More studies are needed in order to confirm the accuracy and extent of these findings; however, the unique story of apple domestication may help explain why it has been “particularly prone to retaining diversity through time.” First, it was widely distributed across Eurasia during its early days of domestication. Second, it experienced “admixture with cultivars” as it expanded its range. For example, after being introduced to North America, it became naturalized, resulting in gene flow occurring between naturalized individuals and cultivated varieties. Offspring of these populations (“chance seedlings”), were then selected, cloned, and became named cultivars.

Despite the mild genetic bottleneck observed in apples, the authors warned that a “dependence on a small number of cultivars” for the majority of U.S. apple production may be resulting in some loss of genetic variation. Relying on so few cultivars may leave apple production vulnerable to pests, diseases, and climate change. “Careful management” is advised as “the continued genetic resilience of the crop is dependent on the genetic diversity of cultivars that are present in living and cryopreserved collections around the world.”

Malus sylvestris (common crabapple) - One of the three main players involved in the apple domestication story (photo credit: www.eol.org)

Blossoms of Malus sylvestris (common crabapple) – One of three main species involved in the history of apple domestication (photo credit: www.eol.org)

The Nonshattering Trait in Cereal Crops

This is the tenth 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.

Morphological Diversity and Genetic Regulation of Inflorescence Abscission Zones in Grasses by Andrew N. Doust, Margarita Mauro-Herrera, Amie D. Francis, and Laura C. Shand

Seed dispersal is a key aspect of reproduction in plants. Producing seeds requires large amounts of energy and resources, and if the seeds don’t find their way to a suitable environment where they can germinate and grow, then it may be all for naught. There are several modes of seed dispersal (wind, gravity, water, animals, ballistics), and each plant species has its own story to tell in this regard. However, one commonality that most all seed dispersal stories share is “disarticulation [separation] of the seed or fruit from the body of the plant via means of the formation of an abscission zone.”

Seeds are typically dispersed inside fruits, and attached to the fruits may be other plant structures (such as parts of the inflorescence or, in the case of tumbleweeds, the whole plant). The entire dispersal unit (seed, fruit, etc.) is known as a diaspore. In the grass family, a fruit is called a caryopsis. It is a unique fruit because the fruit wall is fused to the seed, making it difficult to distinguish between the two. Methods of disarticulation in grasses are diverse, with diaspores varying greatly in their sizes and the plant parts they contain. Below is a figure from this article showing this diversity. Abscission zones are depicted using red dotted lines.

Domesticated crop plants do not exhibit the same levels of disarticulation that their wild relatives do. This is because “nonshattering forms” were selected during early stages of domestication due to their ease of harvest. Today, all domesticated cereal crops are nonshattering, and all began by selecting “a nonshattering phenotype where the grain [did] not fall easily from the inflorescence.”  However, the wild relatives of cereal crops, “as well as grasses as a whole, differ widely in their manner of disarticulation [as indicated in the figure above].” A mutation in the genes that control abscission is what leads to nonshattering phenotypes. Because all domesticated cereal crops began as nonshattering mutants, the authors of this study were interested in investigating whether or not there is a common genetic pathway across all cereal crops and their wild grass relatives that controls the abscission trait.

The “genetic control of loss of shattering” is important to those interested in domestication, thus it “has been studied in all major crops.” Some of these studies suggest that there is a common genetic pathway that controls abscission in cereal crops, while others suggest there may not be. The authors of this study suspect that “there is potential for considerable genetic complexity” in this pathway, and so before we can determine “the extent to which there are elements of a common genetic pathway,” we must first develop “a better understanding of both diversity of disarticulation patterns and genetic evidence for shared pathways across the grasses.”

In an effort to begin to answer this question, the authors used herbaria vouchers to analyze “morphological data on abscission zones for over 10,000 species of grasses.” They also reviewed published scientific studies concerning the genetics of disarticulation in grasses and cereal crops. They determined that “the evidence for a common genetic pathway is tantalizing but incomplete,” and that their results could be used to inform a “research plan that could test the common genetic pathway model more thoroughly.” Further studies can also “provide new targets for control and fine-tuning of the shattering response” in crop plants, which could result in “reducing harvest losses and providing opportunities for selection in emerging domesticated crops.”

Foxtail millet, Setaria italic (photo credit: www.eol.org)

Foxtail millet (Setaria italica), a widely cultivated species of millet, has “shattering genes” similar to those found in sorghum and rice (photo credit: www.eol.org)

 

Cultivated Sunflowers and Their Wild Relatives

This is the ninth 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.

Transistions in Photoperiodic Flowering Are Common And Involve Few Loci in Wild Sunflowers (Helianthus; Asteraceae) by Lucas P. Henry, Ray H. B. Watson, and Benjamin K. Blackman

The seasonal timing of flowering is an important trait to consider in crop plants, because it dictates where geographically a particular crop can be grown and also plays a role in fitness and yield. Flowering time is determined by a combination of genetics and environmental factors. One of the major environmental factors is day length, a phenomenon known as photoperiod response (or photoperiodism).  There are three main types of photoperiod response: short-day (plants flower when “grown in day lengths below a critical maximum threshold”), long-day (plants flower when “grown in day lengths above a critical minimum threshold”) and day-neutral (“plants flower at the same time under all day length conditions”). A plant’s response to day length can be obligate – restricted to a particular response – or facultative – capable but not restricted. Understanding the genetics of photoperiod response is important for breeding efforts, and can help in the development of crop varieties that have improved yields and that can be either grown in broader geographic areas or that are specifically selected for local regions.

Agricultural breeding programs often investigate wild relatives of crop plants for potential traits that could lead to improvements. There is “renewed interest” in these investigations “because genome-enabled methods [of identifying desirable genes] and international investment in germplasm resources have dramatically reduced the associated labor, time, and risk.” The authors of this study, recognizing extensive variation in flowering time in both common sunflower (Helianthus annuus) and its wild relatives, examined the genetic basis for this variation in an effort to support sunflower breeding programs.

Common Sunflower, Helianthus annuus (photo credit: Wikimedia commons)

Common Sunflower, Helianthus annuus (photo credit: wikimedia commons)

Helianthus is a genus consisting of around 70 species, most of which are native to North America (a few occur in South America). Several species in this genus are cultivated as food crops and/or as ornamental plants. H. annuus is the most commonly cultivated species, valued for its edible seeds and the oil they produce as well as for various other things. Wild relatives of H. annuus have “been a frequent source of genetic raw material for agricultural innovation,” aided by the fact that “barriers to interspecies crosses are incomplete or can be overcome through embryo culture or chromosomal doubling.” Helianthus is a diverse genus, including generalist species occurring in “diverse environments over broad geographic regions” and specialist species occurring in “habitats characterized by high temperature, water, or salt stress.” For this reason, “wild sunflowers are prime sources to mine for alleles that confer higher yield in new or marginal” agricultural settings.

A relatively small subset of Helianthus species were involved in this study; however, the subset represented a “phylogenetically dispersed sample.” One interesting finding was that the evolution of an obligate short-day requirement for flowering has occurred in several species, “particularly those with ranges restricted to the southern United States.” The authors suggest that a reason for this finding could be that “long, hot, and humid summers” in this region “may be unfavorable for growth or reproduction.” Thus, while populations of H. annuus “likely escape these conditions by flowering in the long days of late spring,” other Helianthus species put off “flowering until the arrival of cooler, less humid falls.” Flowering during cooler times is beneficial because pollen fertility decreases and seed maturation slows at high temperatures. The risk of fungal pathogens attacking flowers and dispersed seeds is also reduced during periods of lower humidity.

Another important finding was that the diversity in photoperiod response in Helianthus appears to have a “relatively simple genetic architecture.” If this is the case, it could “greatly facilitate rapid crop improvement by marker-assisted selection.” Further studies are necessary, specifically those involving “intra- and interspecific crosses segregating for variation in photoperiod response,” in order to confirm the authors’ findings and justify “broader investment of resources into these applied efforts.”

Nuttall's Sunflower (Helianthus nuttallii), one of Common Sunflower's wild relatives (photo credit: www.eol.org)

Nuttall’s Sunflower (Helianthus nuttallii), one of Common Sunflower’s wild relatives (photo credit: www.eol.org)

While much was learned from this study, the authors acknowledge the need for “future investigations with greater taxonomic and environmental sampling.” Researchers recently produced a “draft genome” for sunflower. This additional resource will greatly aid breeding programs and further inform studies, like this one, that are interested in the “mechanistic factors and ecological agents that have promoted the emergence of the great diversity and lability in photoperiod response observed in wild sunflowers.”

Tales of Weedy Waterhemp and Weedy Rice

This is the eighth 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.

Population Genetics and Origin of the Native North American Agricultural Weed Waterhemp (Amaranthus tuberculatus; Amarantheaceae) by Katherine E. Waselkov and Kenneth M. Olsen

Weeds are “the single greatest threat to agricultural productivity worldwide, costing an estimated $33 billion per year in the United States alone.” Understanding the origins, population structures, and genetic compositions of agricultural weeds will not only help us better mitigate current weed problems but may also help prevent the development of future weed species.

In the introduction, the authors present three modes of weed origination: 1. De-domestication (“domesticated species becoming feral”) 2. Hybridization of domesticated species with related wild species 3. Expansion of wild plants into agricultural ecosystems “through plasticity, adaptation, or exaptation [a shift in function of a particular trait].” In this study, the authors focused on the third mode – the wild-to-weed pathway – claiming that it receives “less attention by evolutionary biologists, even though all weeds without close crop relatives must have followed this pathway to agricultural invasion, and even though this type of weed species is the most common.”  Due to the dearth of research, there are several questions yet to be fully addressed: Does invasion require evolutionary changes in the plant and/or changes in agricultural practices? What is more common, single or multiple wild sources? What are the morphological, physiological, and ecological traits that might “predispose a wild species to expand into agricultural habitats?”

To help answer these questions, the authors turned to waterhemp (Amaranthus tuberculatus), a weed that, since first invading agricultural land in the 1950’s, has “become a major problem for corn and soybean farmers in Missouri, Iowa, and Illinois.” Waterhemp is native to the midwestern United States, where it can be found growing along riverbanks and in floodplains. It is a small seeded, dioecious (“obligately outcrossing”), wind-pollinated, annual plant with fruits that can be either dehiscent or indehiscent. Herbicide resistance has been detected in A. tuberculatus for at least six classes of herbicides, making it a difficult weed to control.

There is evidence that A. tuberculatus was previously in the process of diverging into two species, an eastern one and a western one, geographically separated by the Mississippi River. However, “human disturbance brought the taxa back into contact, and possibly gave rise to the agriculturally invasive strain through admixture.” Using population genetic data, the authors set out to determine if the present-day species would show evidence of a past divergence in progress prior to the 20th century. They also hypothesized that “the agricultural weed originated through hybridization between the two diverged lineages.”

Waterhemp, Amaranthus tuberculatus (photo credit: www.eol.org)

Waterhemp, Amaranthus tuberculatus (photo credit: www.eol.org)

After genotyping 38 populations from across the species range, the authors confirmed that A. tuberculatus was indeed diverging into two species. Today, the western variety (var. rudis) has expanded eastward into the territory of the eastern variety (var. tuberculatus), extending as far as Indiana. Its expansion appears to be facilitated by becoming an agricultural weed. Data did not confirm the hypothesis that the weedy strain was a hybridized version of the two varieties, but instead mainly consists of the western variety, suggesting that “admixture is not a pre-requisite for weediness in A. tuberculatus.”

Further investigation revealed that the western variety may have already been “genetically and phenotypically suited to agricultural environments,” and thus did not require “genetic changes to be successful” as an agricultural weed. “Finer-scale geographic sampling” and deeper genetic analyses may help determine whatever genetic basis there might be for this unfortunate situation.

The Evolution of Flowering Strategies in US Weedy Rice by Carrie S. Thurber, Michael Reagon, Kenneth M. Olsen, Yulin Jia, and Ana L. Caicedo

This paper looks at an agricultural weed that originated from the de-domestication of a crop plant (one of the three modes of weed origination stated above). A weed that belongs to the same species as the crop it invades is referred to as a conspecific weed, and weedy rice is “one of the most devastating conspecific weeds in the United States.”  Oryza sativa is the main species of rice cultivated in the US, and most varieties are from the group tropical japonica. The two main varieties of weedy rice are straw hull (SH) and black-hull awned (BHA), which originated from cultivated varieties in the groups indica and aus respectively. Because weedy rice is so closely related to cultivated rice, it is incredibly difficult to manage, and there is concern that cross-pollination will result in the movement of traits between groups. For this reason, the authors of this study investigated flowering times of each group in order to assess the “extent to which flowering time differed between these groups” and to determine “whether genes affecting flowering time variation in rice could play a role in the evolution of weedy rice in the US.”

Rice, Oryza sativa (illustration credit: wikimedia commons)

Rice, Oryza sativa (illustration credit: wikimedia commons)

Crop plants have typically been selected for “uniformity in flowering time to facilitate harvesting.” The flowering time of weed species helps determine their effectiveness in competing with crop plants. Flowering earlier than crop plants results in weed seeds dispersing before harvest, “thereby escaping into the seed bank.” Flowering simultaneously with crop plants can “decrease conspicuousness, and seed may be unwittingly collected and replanted” along with crop seeds. Simultaneous flowering of weeds and crops is of special concern when the two are closely related since there is potential for gene transfer, especially when the crop varieties are herbicide resistant as can be the case with rice (“60-65% of cultivated rice in [the southern US] is reported to be herbicide resistant”).

For this study, researchers observed phenotypes and gene regions of a broad collection of Oryza, including cultivated varieties, weed species, and ancestors of weed and cultivated species. They found that “SH weeds tend to flower significantly earlier than the local tropical japonica crop, while BHA weeds tend to flower concurrently or later than the crop.” When the weeds were compared with their cultivated progenitors, it was apparent that both weed varieties had “undergone rapid evolution,” with SH weeds flowering earlier and BHA weeds flowering later than their respective relatives. These findings were consistent with analyses of gene regions which found functional Hd1 alleles in SH weeds (resulting in day length sensitivity and early flowering under short-day conditions) and non-functional Hd1 alleles in BHA weeds (“consistent with loss of day-length sensitivity and later flowering under short-day conditions”). However, the authors determined that there is more to investigate concerning the genetic basis of the evolution of flowering time in weedy rice.

In light of these results, hybridization is of little concern between cultivated rice and SH weeds. BHA weeds, on the other hand, “have a greater probability of hybridization with the crop based on flowering time and Hd1 haplotype.” The authors “predict that hybrids between weedy and cultivated rice are likely to be increasingly seen in US rice fields,” which, considering the current level of herbicide resistant rice in cultivation, is quite disconcerting.

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)

Exploring Pollination Biology in Southwestern China

This is the sixth 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.

Insect Pollination and Self-Incompatibility in Edible and/or Medicinal Crops in Southwestern China, a Global Hotspot of Diversity by Zong-Xin Ren, Hong Wang, Peter Bernhardt, and De-Zhu Li

We rely on pollinators to pollinate at least 75% of our food crops, which is why any talk of pollinator decline tends to make us nervous. It is also why research involving pollinators and pollination is so important. Despite all we know, there is still so much to learn. The authors of this study, recognizing that “there are large gaps in the study of the pollination of economically important and traditionally grown species in China,” set out to help close these gaps. Their research not only has the potential to benefit agricultural communities in China, but also adds to our growing understanding of pollination biology – a science that has become increasingly important in an age of human population growth and shifting climates.

The incredibly diverse Chinese flora includes at least 31,000 plant species. Three hundred of the 1500 species of worldwide cultivated crop plants “originated and/or were domesticated and/or underwent differentiation in China.” Southwestern China has a particularly large amount of botanical diversity and is considered a biodiversity hotspot. In this study concerning agricultural pollination, researchers chose to focus on Yunnan, a province in southwestern China. They chose this region due to its high level of current and historical agriculture and because it is “one of the last refuges of the eastern Asian honeybee, Apis cerana, in China.” They narrowed their research down to 11 species that are important for their culinary and/or medicinal use, some of them having widespread use and others having more local, cultural use. Depending on the species, conclusions were drawn either from available literature, from field studies, or both.

Eastern Asian Honeybee (Apis cerana) on Citrus limonia flowers (photo credit: www.eol.org)

Eastern Asian Honeybee (Apis cerana) on Citrus limonia flowers (photo credit: www.eol.org)

A review of the literature revealed information about each plant’s breeding system, the pollinators involved, ethnobotanical details, and other things. No information was available on the breeding system or pollinators of Panax notoginseng, “one of the most highly valued Chinese medicinal herbs.” Five species were found to be self-compatible (Angelica sinensis, Amomum tsao-ko, Brassica napus, B. campestris, and Gastrodia elata) and four were found to be self-incompatible (Camellia oleifera, Dendrobium catenatum, Fagopyrum esculentum, and Paris plyphylla var. yunnanensis). Codonopsis subglobosa was somewhere in the middle. The authors were intrigued by the persistent self-incompatibility in these domesticated plants (some more recently domesticated than others), noting that “both traditional and modern agricultural practices in China could not always overcome ancestral self-incompatibility mechanisms.” A running theme seemed to be that, if able to produce fruit or seed when hand-pollinated or without the aid of pollinators, the plants consistently performed better when insect pollinated. One of the most interesting findings was that Gastrodia elata, Dendrobium catenatum, and Paris plyphylla var. yunnanensis “persist in cultivation only through hand-pollination.”

Camellia oleifera, tea-oil plant, is pollinated by two native solitary bee species. It is avoided by native and introduced honeybees because its nectar contains substances that are toxic to worker bees, including caffeine, raffinose, stachyose, and galactose. Fagopyrum esculentum, common buchwheat, is native to southern China and was likely first domesticated there. It is pollinated by a variety of insects; however, its main pollinator in worldwide cultivation is the European honeybee, Apis mellifera. In China, evidence suggests that when pollinated by native pollinators, buckwheat produces higher yields and larger fruits. Codonopsis subglobosa is an undomesticated but cultivated perennial vine endemic to southwestern China, the roots of which are used as a substitute for ginseng. It can self-pollinate without a vector, but cross-pollination by wasps yields more seeds. Pollination by “hunting wasps” is rare, and C. subglobosa is not the only plant in the area pollinated by them. If the “evolution of hunting wasp pollination systems has evolved repeatedly in unrelated species native to southwestern China,” this region may be a “center for the convergent evolution of hunting wasp pollination.”

Common Buckwheat, Fagopyrum esculentum (photo credit: Wikimedia commons)

Common Buckwheat, Fagopyrum esculentum (photo credit: wikimedia commons)

Beekeeping has been a major part of agriculture in China for centuries. However, the introduction of the European honeybee has caused a significant decline in both wild and managed populations of native honeybees, despite native honeybees being “better adapted to more diffuse nectar resources” than the introduced honeybee. The decline in keeping and managing native honeybees is complicated and involves much more than just the introduction of the European honeybee. Along with the debate about what is best for agriculture in China, is the concern about what introducing non-native pollinators could mean for native flora and fauna. The authors conclude that there is “urgent need for new pollination management policies in China.”

This article ends with suggestions about how to improve and expand pollination biology research in China in order to fill gaps in knowledge, improve agricultural production, and protect and conserve native biodiversity. China is an ideal candidate for such research for several reasons: it has areas like southwestern China that are very species rich, it has a long history of agriculture, and it has numerous unique crops that are specific to Chinese culture. China also has a large and growing population, so improvements that can lead to more sustainable agricultural production will be greatly beneficial in the long run.

Carrots and Strawberries, Genetics and Phylogenetics

This is the fifth 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.

As expected, some of the articles in this issue get into pretty deep discussions about genetics and phylogenetics. Advancements in sequencing and analyzing DNA have not only led to better understanding of genes and their functions but have also given us greater insight into how species are related and their proper place on the phylogenetic tree.  While I have some background in these things and can follow along at a basic level, I certainly don’t feel confident in authoritatively summarizing such findings . I also question whether or not a high level discussion of phylogenetics makes for an interesting and engaging blog post. Plant systematics geeks are aggressively nodding “yes”; other readers’ eyes have glazed over by this point.

I am certainly not arguing that this is not important stuff. When a species we have become familiar with is suddenly given a new scientific name, it is not too annoy those of us who are trying to learn the names of things, rather it is because something novel has been discovered about the way living things are organized, about their life history – the way they came to be.  We should be celebrating advancements that allow us to look back over the millions of years of life on earth and see how various species emerged, evolved, disappeared, were replaced, and ultimately arrived at what we view today. And we should be humbled to know that these present forms are not the climax, that we are simply getting a glimpse in the evolutionary trajectory of the organisms around us. Perhaps it will prompt us to protect them, understanding that every scrap of biodiversity is important and worth conserving. After all, who are we to decide how the story goes?

The sixth and seventh articles in “Speaking of Food” are about carrots and strawberries respectively. Discussion about the genetics and phylogenetics of these plants dominates the articles, with the application being that we can improve these crops by better understanding their genetics, and we can gain insights into plant evolution by better understanding their phylogenetics.  Rather than give you a thorough overview of each of these articles (for reasons stated above), I am offering you bullet points of a few of the things that I learned while reading them.

Phylogenomics of the Carrot Genus (Daucus, Apiaceae) by Carlos Arbizu, Holly Ruess, Douglas Senalik, Philipp W. Simon, and David M. Spooner

  • The domesticated carrot (Daucus carota subsp. sativus) is “the most notable cultivated member of Apiaceae [a family consisting of 455 genera and over 3,500 species] in terms of economic importance and nutrition.”
  • Carrots are our primary source of vitamin A (due to high levels of alpha and beta carotenes), “accounting for about half of dietary intake.”
  • Wild carrot species can be used to improve the domesticated carrot by providing genes that will help with pest and disease resistance, yield increases, better nutrient value, etc.
  • “The taxonomy of D. carota is particularly problematical. It undergoes widespread hybridization experimentally and spontaneously with commercial varieties and other named subspecies.”
  • The researchers, upon examining more than half of the known Daucus species and 9 species that are very closely related, identified several Daucus spp. that “may be easily incorporated in carrot breeding programs.”
  • This study determined “misidentifications in germplasm collections” and highlighted “the difficulty of defining subspecies of D. carota.”
Flowers of Daucus carota (photo credit: www.eol.org)

Flowers of Daucus carota (photo credit: www.eol.org)

Fragaria: A Genus with Deep Historical Roots and Ripe for Evolutionary and Ecological Insights by Aaron Liston, Richard Cronn, and Tia-Lynn Ashman

  •  Fresh strawberries are fifth on the list of fresh fruit consumption in the United States.
  • “Resistance to a Fragaria-specific powdery mildew has been demonstrated in F. x ananassa [domesticated strawberry] transformed with a peach locus, and the cultivation of such transgenic plants could reduce pesticide usage in strawberry.” Commercial production awaits, though, “due to public resistance, a lack of industry support, and concerns over gene flow to the wild species of Fragaria.”
  • “The modern cultivated strawberry, Fragaria x ananassa, originated in the 18th century in Europe from hybridization between two species imported from North and South America. The parental species, F. virginiana and F. chiloensis, also hybridize naturally in northwestern North America, but there is no evidence that they were ever cultivated by the native Americans in this area.”
  • The stolons of strawberry plants can be used as dental floss!? So said Antoine Nicolas Duchesne in his 1766 book about strawberries. I guess I’ll have to read his account to get more insight into this interesting detail.
  • F. x ananassa has flowers that are self-compatible, but it is “derived from the hybridization of two wild species that show gender dimorphism,” which is common in the genus. For this reason, Fragaria, is “proving to be an exceptional model system for understanding the sexual system and sex chromosome evolution.”
  • Fragaria species occur across a broad range of temperate habitats and elevations from sea level sand dunes to moist, productive meadows to high, dry, mountain summits.” They are adapted to a wide variety of environmental conditions. “This variation represents a potential source of genetic variation for climatic tolerance, disease/pest resistance, and yield-associated traits.”
  • The Fragaria genus, like virtually all genera of flowering plants, includes polyploid species. Researchers conclude that Fragaria is an “ideal system for exploring relationships between ploidy formation, ploidy level, and the coordination of transcriptomic control.” They also believe that continued studies of “ecological and evolutionary genomics in Fragaria has the potential to provide further insights into hybridization.”
  • Finally, the researchers advise that the “familiarity of strawberries provides an opportunity to engage and educate the public about botanical research.”
Broadpetal Strawberry, Fragaria virginiana supsp. platypetala (photo credit: wikimedia commons)

Broadpetal Strawberry, Fragaria virginiana supsp. platypetala (photo credit: wikimedia commons)

An Underutilized Crop and the Cousins of a Popular One

This is the fourth 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.

Genetic Diversity in Carthamus tinctorius (Asteraceae; Safflower), An Underutilized Oilseed Crop by Stephanie A. Pearl and John M. Burke

Safflower (Carthamus tinctorius) was first domesticated in the Fertile Crescent about 4,500 years ago. It was originally desired for its flowers which were used in dye making. Commercial production of safflower began in North America in the 1950’s, where it is now mainly grown for its seeds which are used to produce oil for human consumption and are a main ingredient in bird seed mixes. Despite this, it is categorized as an “underutilized crop,” one “whose genetic potential has not been fully realized.” With increased interest in food security and feeding a growing population, researchers are turning to new and underutilized crops in order to increase the “availability of a diverse assemblage of crop species.”

A major step in improving a crop plant is understanding the genetic diversity that is available within its gene pool. With this aim in mind, researchers observed a “broad cross section of the safflower gene pool” by examining the DNA of a “worldwide sampling of diversity from the USDA germplasm collection [134 accessions consisting of 96 from the Old World and 38 from the New World]”, 48 lines from two major commercial safflower breeding programs in North America, and 8 wild collected safflower individuals.

Safflower, Carthamus tinctorius (photo credit: www.eol.org)

Safflower, Carthamus tinctorius (photo credit: www.eol.org)

Researchers found that the cultivated safflower varieties had a significant reduction in genetic diversity compared to the wild safflower plants. They also noted that the 96 Old World accessions could be grouped into “four clusters that corresponded to four different geographic regions that presumably represent somewhat distinct breeding pools.” They found that the wild safflowers “shared the greatest similarity with the Iran-Afghanistan-Turkey cluster” from the Old World group of accessions, a finding that “is consistent with safflower’s presumed Near Eastern center of origin.”

The researchers determined that there may be “agronomically favorable alleles present in wild safflowers,” and that “expanded efforts to access wild genetic diversity would facilitate the continued improvement of safflower.” Safflower is an important but underused oilseed crop that is adapted to dry climates; studies like this one that can lead to further crop improvements may help bring it out of niche production and into more widespread use.

The Wild Side of a Major Crop: Soybean’s Perennial Cousins from Down Under by Sue Sherman-Broyles, Aureliano Bombarely, Adrian F. Powell, Jane L. Doyle, Ashley N. Egan, Jeremy E. Coate, and Jeff J. Doyle

Soybean production is a major money maker in the United States ($43 billion total revenue in 2012); corn is the only crop that tops it. Soybean oil has myriad uses from food to feedstock and from pharmaceuticals to biofuel. As much as 57% of the world’s seed oil comes from soybeans produced in the United States. Hence, soybean (Glycine max and its wild progenitor, G. soja) is a well researched crop. Most research has been focused on the two annual species in the subgenus Soja; “less well known are the perennial wild relatives of soybean native to Australia, a diverse and interesting group that has been the focus of research in several laboratories.”

Given the agricultural importance of soybean and the increasing demands that will be placed on this crop as population rises, it is imperative that improvements continue to be made. Exploring soybean’s “extended gene pool,” including both its annual “brother” and its perennial “cousins,” will aid in making these improvements.

Soybean's wild annual relative, Glycine soja (photo credit: www.eol.org)

Soybean’s wild annual relative, Glycine soja (photo credit: www.eol.org)

Perennial soybeans in the subgenus Glycine include around 30 species. They are adapted to a wide variety of habitats “including desert, sandy beaches, rocky outcrops, and monsoonal, temperate, and subtropical forests.” They are of particular interest to researchers because several of them are allopolyploids, meaning that they have more than the usual two sets of chromosomes and that the additional sets of chromosomes were derived from different species. The authors state that “the distributional differences between diploids and independently formed polyploids [in the subgenus Glycine] suggests underlying ecological, physiological, and molecular differences related to genome doubling and has led to the development of the group as a model for studying allopolyploidy.” The group is also worth studying because they demonstrate resistance to various soybean pathogens and are adapted to a variety of environmental conditions.

By continuing to work with soybean’s perennial cousins to gain a better understanding of “polyploidy and legume evolution,” the authors hope to apply their research to achieve increases in soybean yields. Past research suggests that the study of polyploidy in the perennial soybeans could lead to crop improvements in areas such as photosynthesis, nitrogen fixation, flowering time, and disease resistance.

Glycine tomentella - one of soybean's perennial cousins (photo credit: www.eol.org)

Glycine tomentella – one of soybean’s perennial cousins (photo credit: www.eol.org)

 

Dethroning Industrial Argiculture: The Rise of Agroecology

This is the third 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.

Think Globally, Research Locally: Paradigms and Place in Agroecological Research by Heather L. Reynolds, Alex A. Smith, and James R. Farmer

Before I get into the review, I have to say that it is too bad this article was not selected as one of the open access articles. For me, it really sums up the reasons why this special issue exists at all, and it reads like a clarion call for more research, promotion, and implementation of science-based sustainable agriculture. If I could reprint the whole thing here I would, because my poor excuse for a review will not suffice. Unfortunately, in order to read this article (and most of the other articles I am reviewing here), you will have to pay, unless you otherwise have access through a personal or institutional subscription.  The open access debate is a can of worms that I won’t open here…just saying I wish more people could read this.

In their introduction, the authors discuss the “basic to applied science continuum.” Scientists who choose to do research that is more on the applied side of the spectrum may find it easier to secure funding (due to “convincing social benefits”), but will also find themselves directly confronted with social issues and values. There can be some discomfort involved in this, and so scientists must carefully determine their level of engagement. However, “neither social nor ecological systems can be understood in isolation,” and instead “must be studied as an integrated social ecological system.” Applied science must be carried out in order to address pressing socio-ecological issues, and so scientists interested in this type of research should know what they’re getting into and must “consider what societal values and paradigms they are supporting with their research.”

Applied science research involving agriculture finds itself intertwined with an economic paradigm that is focused on growth – “increased production and consumption of goods and services as indicated by increasing gross domestic product.” The authors argue that this is not sustainable and that agricultural research should be guided in directions that are more place-based and that keep the finite nature of the planet in mind.

“Since the 1940’s, agriculture has evolved toward an increasingly industrial, corporate, and globalized model, involving large-scale, centralized monoculture production requiring inputs of highly concentrated (fossil) fuel, machinery, water, and synthetic pesticides and fertilizers.” The Green Revolution brought new crop varieties and inputs that helped increase yields significantly, but also had the result of increasing irrigated land by 97%, “the use of nitrogen by 638%, phosphorous fertilizer by 203%, and pesticides by 845% during the latter half of the 20th century.” Industrial agriculture, while highly productive, is a juggernaut that requires incredible amounts of energy, petrochemicals, and water, and despite it’s best efforts, still doesn’t feed the world. Social and political issues are to blame for the food distribution problem; however, in the meantime, industrial agriculture is having profound effects on the environment, “including soil erosion and degradation, biodiversity loss, and water and air pollution on local and global scales.” Coupled with all of the environmnental costs of industrial agriculture are the social costs: “local agroecological knowledge has…been displaced by the  knowledge embodied in industrial inputs and sophisticated farming equipment and techniques,” and widespread industrial agriculture has been linked to increases in cancer, obesity and other human health issues.

photo credit: wikimedia commons

photo credit: wikimedia commons

The expansion of industrial agriculture has largely been driven by the economic paradigm of the United States and other industrialized nations that is focused on growth above all else. This paradigm neglects to acknowledge the “biophysical limits” of planet Earth – “an inescapably finite place, with a constant rate of net solar income and zero inputs of matter beyond the occasional asteroid.” Growth has its limits, and unless those limits are respected, we will find ourselves in dire straits. A warming climate and an increasing level of extinctions are major signs that we have approached the limit. It is time to rethink things.

The question of how to address this dilemma is incredibly complex. The authors of this study offer two broad solutions: reform our economic system and rethink our scientific research efforts. First, the economic problem. A finite planet cannot abide a growth above all else economic approach. The authors propose evolving towards a steady-state economy, in which “the product of population and per capita consumption mildly fluctuates at a scale for which energy and material throughput at current technological capabilities does not strain or exceed the regenerative and assimilative capacity of Earth’s natural capital.” In this economic system, “overdeveloped” countries like the United States will need to find ways to “strategically degrow.”

Strategic degrowth will require dismantling the behemoth that is industrial agriculture. Rethinking applied scientific research will assist in this. Rather than a “one-size-fits-all” approach (an approach that has fueled industrial agriculture for decades), research must evolve towards a “custom-fit” approach in order to address the environmental and social conditions of each individual area. Scientists will have to “go local,” collaborating with farmers, land-owners, and other local experts in order to do “place-based” research that will result in “location-specific expertise.”

Urban Farm in Chicago, Illinois (photo credit: wikimedia commons)

 An urban farm in Chicago, Illinois (photo credit: wikimedia commons)

The authors argue for “community-based participatory research,” which relies on scientists and other professionals collaborating to develop research projects, collect data, and arrive at solutions that will address problems particular to local areas. They offer an example of working with farmers in Indiana to research the use of wild bees for agricultural pollination. The data they collected, while helpful for farmers in other areas, was specific to their area of study and “lent credibility to [their] conclusions” when presented to local audiences.

This is a short but dense article that should be read in its entirety if you have access to it. I will end by offering the authors’ description of sustainable agriculture: “the application of ecological and cultural knowledge to local, decentralized, biodiversity-promoting, closed loop food production for a steady-state economy…the farm system is viewed as an agroecological system….wherein traditional and scientific knowledge of ecological interactions are employed to build system fertility, productivity, and resilience from within, thus promoting food sovereignty and autonomy.”

The Legacy of a Leaky Dioecy

This is the second 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.

The Ecological Side of an Ethnobotanical Coin: Legacies in Historically Managed Trees by Nanci J. Ross, M. Henry H. Stevens, Andrew W. Rupiper, Ian Harkreader, and Laura A. Leben

As much as we like to think otherwise, pre-Colombian Native Americans altered the natural landscape in drastic and measurable ways. What we often consider an unaltered, pristine natural area before European colonization, actually has human fingerprints all throughout it. Determining just how deep these fingerprints go, however, is a challenge that requires careful and thorough anthropological and ecological studies.

Many such studies have been done, mostly at the community and ecosystem level. For example, Native Americans used fire extensively as a land management tool. This is how prairies were maintained as prairies. Today, forests in eastern North America that were once dominated by oaks have shifted over to maple dominated forests. This is largely (although not solely) because anthropogenic fires have ceased and wildfires are now suppressed. If fires had never been used as a management tool, would oaks (an important Native American food source) have ever maintained such dominance?

Native Americans participated in the domestication of numerous plant species. Much of this was done by way of – as Charles Darwin termed it – unconscious selection. Rather than selecting specific individuals and breeding them to achieve a desired type, they would simply discard undesirable plants and maintain desirable ones. Much of this selection, especially for woody, perennial species was done through land management techniques – such as fire – as opposed to typical cultivation. The authors of this article, interested in whether or not the “legacy” of this method of selection through land management could be observed today in an individual species, developed a preliminary study to begin to answer this question.

Diospyros – a genus in the ebony family (Ebenaceae) consisting of around 500 species – is mainly pantropical with a few species occurring in temperate regions. One temperate species is Diospyros virginiana – common persimmon – which “has a broad distribution throughout the United States from Connecticut south to Florida and west to the eastern edge of Nebraska.” Persimmons were used and managed extensively by Native Americans; however, they are “now viewed as a rare, weedy, wild fruit tree that is known primarily by hobbyists and wild harvesters.”

Fruits of common persimmon, Diospyros virginiana )photo credit: Wikimedia commons)

Fruits of common persimmon, Diospyros virginiana (photo credit: wikimedia commons)

D. virginiana is a dioecious species, meaning that it produces male flowers and female flower on separate individuals. Despite this, some individuals have been reported bearing both male and female flowers while others have been seen having perfect flowers along with either male or female flowers. Some trees have even been reported to be dioecious one year and then having perfect flowers and/or some combination of male, female, and perfect flowers the next year. This variation from the norm – what the authors call “leaky dioecy” – can either be a result of artificial selection or environmental pressures. The authors hypothesized that “leaky dioecy in D. virginiana is a result of historical selection by Native Americans for trees with copious fruit production.” This preliminary study was designed to see if climate and soil conditions might be the reason for the observed “sex expression.”

Skipping ahead, the authors found “no compelling evidence…to suggest segregation due to environmental factors,” signaling them to “move forward in [their] investigation of potential long-term impacts of historical management on the evolution of reproductive traits in American persimmon without the noise of a strong environmental driver.” The authors go on to discuss challenges in their study, including the length of time since “extensive management” making it hard to “uncover a signal of precontact management” and the limitations of having to rely on herbarium specimens. Either way, it is a worthy study to pursue. Even if it does not reveal the full story of how Native Americans managed persimmons in pre-colonial times, further insight into “adaptive flexibility in reproductive systems of long-lived perennial species” and other interesting things that persimmons might teach us will be well worth the effort.

Characteristic bark of common persimmon, Diospyros virginiana (photo credit: www.eol.org)

Characteristic bark of common persimmon, Diospyros virginiana (photo credit: www.eol.org)