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stress resilience Archives - The Global Plant Council

May 16
0

When lipids meet hormones: plants’ answer to complex stresses

By | Blog, Research

This blog has been reposted with permission from the MSU-DOE Plant Research Laboratory.

Unlike animals, plants can’t run away when things get bad. That can be the weather changing or a caterpillar starting to slowly munch on a leaf. Instead, they change themselves inside, using a complex system of  hormones, to adapt to challenges.

Now, MSU-DOE Plant Research Laboratory scientists are connecting two plant defense systems to how these plants do photosynthesis. The study, conducted in the labs of Christoph Benning and Gregg Howe, is in the journal, The Plant Cell.

At the heart of this connection is the chloroplast, the engine of photosynthesis. It specializes in producing compounds that plants survive with. But plants have evolved ways to use it for other, completely unrelated purposes.

Their trick is to harvest their own chloroplasts’ protective membranes, made of  lipids, the molecules found in fats and oils. Lipids have many uses, from making up cell boundaries, to being part of plant hormones, to storing energy.

If plants need lipids for some purpose other than serving as membranes, special proteins break down chloroplast membrane lipids. Then, the resulting products go to where they need to be for further processing.

For example, one such protein, breaks down lipids that end up in plant seed oil. Plant seed oil is both a basic food component and a precursor for biodiesel production.

Now, Kun (Kenny) Wang, a former Benning lab grad student, reports two more such chloroplast proteins with different purposes. Their lipid breakdown products help plants turn on their defense system against living pests and other herbivores. In turn, the proteins, PLIP2 and PLIP3, are themselves activated by another defense system against non-living threats.

Playing the telephone game inside plants

In a nutshell, the plant plays a version of the popular children’s game, Telephone, with itself. In the real game, players form a line. The first person whispers a message into the ear of the next person in the line, and so on, until the last player announces the message to the entire group.

In plants, defense systems and chloroplasts also pass along chemical messages down a line. Breaking it down:

  1. The plant senses non-living threats, like cold or drought, and indicates it through one hormone (ABA)
  2. This alarm triggers the two identified proteins to breakdown lipids from the chloroplast membrane
  3. The lipid products turn into another hormone (JA) which takes part in the insect defense system. Plant growth slows to a crawl. Energy goes to producing defensive chemicals.

“The cross-talk between defense systems has a purpose. For example, there is mounting evidence that plants facing drought are more vulnerable to caterpillar attacks,” Kenny says. “One can imagine plants evolving precautionary strategies for varied conditions. And the cross-talk helps plants form a comprehensive defense strategy.”

Kenny adds, “The chloroplast is amazing. We suspect its membrane lipids spur functions other than defense or oil production. That implies more Telephone games leading to different ends we don’t know yet. We have yet to properly examine that area.”

“Those functions could help us better understand plants and engineer them to be more resistant to complex stresses.”

Moving on to Harvard Medical School

Kenny recently got his PhD from the MSU Department of Biochemistry and Molecular Biology. He has just started a post-doc position in the Farese-Walther lab at Harvard Medical School.

“They look at lipid metabolism in mammals and have started a project connecting it with brain disease in humans,” Kenny says. “There is increasing evidence that problems with lipid metabolism in the brain might lead to dementia, Alzheimer’s, etc.”

“I benefited a lot from my time at MSU. The community is very successful here: the people are nice, and you have support from colleagues and facilities. Although we scientists should sometimes be independent in our work, we also need to interact with our communities. No matter how good you are, there is a limit to your impact as an individual. That is one of the lessons I applied when looking for my post-doc.”

Photo of the author, Kun (Kenny) Wang. By Kenny Wang

Read the original article here.

Jan 24
0

Reflections from the “Feed the Future” conference in Burkina Faso

By | Blog, Research

By Atsuko Kanazawa, Igor Houwat, Cynthia Donovan

This article is reposted with permission from the Michigan State University team. You can find the original post here: MSU-DOE Plant Research Laboratory

By Atsuko Kanazawa

Atsuko Kanazawa is a plant scientist in the lab of David Kramer. Her main focus is on understanding the basics of photosynthesis, the process by which plants capture solar energy to generate our planet’s food supply.

This type of research has implications beyond academia, however, and the Kramer lab is using their knowledge, in addition to new technologies developed in their labs, to help farmers improve land management practices.

One component of the lab’s outreach efforts is its participation in the Legume Innovation Lab (LIL) at Michigan State University, a program which contributes to food security and economic growth in developing countries in Sub-Saharan Africa and Latin America.

Atsuko recently joined a contingent that attended a LIL conference in Burkina Faso to discuss legume management with scientists from West Africa, Central America, Haiti, and the US. The experience was an eye opener, to say the least.

To understand some of the challenges faced by farmers in Africa, take a look at this picture, Atsuko says.

“When we look at corn fields in the Midwest, the corn stalks grow uniformly and are usually about the same height,” Atsuko says. “As you can see in this photo from Burkina Faso, their growth is not even.”

“Soil scientists tell us that much farmland in Africa suffers from poor nutrient content. In fact, farmers sometimes rely on finding a spot of good growth where animals have happened to fertilize the soil.”

Even if local farmers understand their problems, they often find that the appropriate solutions are beyond their reach. For example, items like fertilizer and pesticides are very expensive to buy.

That is where USAID’s Feed the Future and LIL step in, bringing economists, educators, nutritionists, and scientists to work with local universities, institutions, and private organizations towards designing best practices that improve farming and nutrition.

Atsuko says, “LIL works with local populations to select the most suitable crops for local conditions, improve soil quality, and manage pests and diseases in financially and environmentally sustainable ways.”

Unearthing sources of protein

At the Burkina Faso conference, the Kramer lab reported how a team of US and Zambian researchers are mapping bean genes and identifying varieties that can sustainably grow in hot and drought conditions.

The team is relying on a new technology platform, called PhotosynQ, which has been designed and developed in the Kramer labs in Michigan.

PhotosynQ includes a hand-held instrument that can measure plant, soil, water, and environmental parameters. The device is relatively inexpensive and easy to use, which solves accessibility issues for communities with weak purchasing power.

The heart of PhotosynQ, however, is its open-source online platform, where users upload collected data so that it can be collaboratively analyzed among a community of 2400+ researchers, educators, and farmers from over 18 countries. The idea is to solve local problems through global collaboration.

Atsuko notes that the Zambia project’s focus on beans is part of the larger context under which USAID and LIL are functioning.

“From what I was told by other scientists, protein availability in diets tends to be a problem in developing countries, and that particularly affects children’s development,” Atsuko says. “Beans are cheaper than meat, and they are a good source of protein. Introducing high quality beans aims to improve nutrition quality.”

Science alone is sometimes not enough

But, as LIL has found, good science and relationships don’t necessarily translate into new crops being embraced by local communities.

Farmers might be reluctant to try a new variety, because they don’t know how well it will perform or if it will cook well or taste good. They also worry that if a new crop is popular, they won’t have ready access to seed quantities that meet demand.

Sometimes, as Atsuko learned at the conference, the issue goes beyond farming or nutrition considerations. In one instance, local West African communities were reluctant to try out a bean variety suggested by LIL and its partners.

The issue was its color.

“One scientist reported that during a recent famine, West African countries imported cowpeas from their neighbors, and those beans had a similar color to the variety LIL was suggesting. So the reluctance was related to a memory from a bad time.”

This particular story does have a happy ending. LIL and the Burkina Faso governmental research agency, INERA, eventually suggested two varieties of cowpeas that were embraced by farmers. Their given names best translate as, “Hope,” and “Money,” perhaps as anticipation of the good life to come.

Another fruitful, perhaps more direct, approach of working with local communities has been supporting women-run cowpea seed and grain farms. These ventures are partnerships between LIL, the national research institute, private institutions, and Burkina Faso’s state and local governments.

Atsuko and other conference attendees visited two of these farms in person. The Women’s Association Yiye in Lago is a particularly impressive success story. Operating since 2009, it now includes 360 associated producing and processing groups, involving 5642 women and 40 men.

“They have been very active,” Atsuko remarks. “You name it: soil management, bean quality management, pest and disease control, and overall economic management, all these have been implemented by this consortium in a methodical fashion.”

“One of the local farm managers told our visiting group that their crop is wonderful, with high yield and good nutrition quality. Children are growing well, and their families can send them to good schools.”

As the numbers indicate, women are the main force behind the success. The reason is that, usually, men don’t do the fieldwork on cowpeas. “But that local farm manager said that now the farm is very successful, men were going to have to work harder and pitch in!”

Back in Michigan, Atsuko is back to the lab bench to continue her photosynthesis research. She still thinks about her Burkina Faso trip, especially how her participation in LIL’s collaborative framework facilitates the work she and her colleagues pursue in West Africa and other parts of the continent.

“We are very lucky to have technologies and knowledge that can be adapted by working with local populations. We ask them to tell us what they need, because they know what the real problems are, and then we jointly try to come up with tailored solutions.”

“It is a successful model, and I feel we are very privileged to be a part of our collaborators’ lives.”

This article is reposted with permission from the Michigan State University team. You can find the original post here: MSU-DOE Plant Research Laboratory

Jul 31
0

Chinese plant science and Journal of Experimental Botany

By | Blog, Scientific Meetings, SEB

This week’s post was written by Jonathan Ingram, Senior Commissioning Editor / Science Writer for the Journal of Experimental Botany. Jonathan moved from lab research into publishing and communications with the launch of Trends in Plant Science in 1995, then going on to New Phytologist and, in the third sector, Age UK and Mind.

 In this week of the XIXth International Botanical Congress (IBC) in Shenzhen, it seems appropriate to highlight outstanding research from labs in China. More than a third of the current issue of Journal of Experimental Botany is devoted to papers from labs across this powerhouse of early 21st century plant science.

Collaborations are key, and this was a theme that came up time again at the congress. The work by Yongzhe Gu et al. is a fine example, involving scientists at four institutions studying a WRKY gene in wild and cultivated soybean: in Beijing, the State Key Laboratory of Systematic and Evolutionary Botany at the Institute of Botany in the Chinese Academy of Sciences, and the University of the Chinese Academy of Sciences; and in Harbin (Heilongjiang), the Crop Tillage and Cultivation Institute at Heilongjiang Academy of Agricultural Sciences, and the College of Agriculture at Northeast Agricultural University. Interest here centers on the changes which led to the increased seed size in cultivated soybean with possible practical application in cultivation and genetic improvement of such a vital crop.

Crops and gardens

Botanic gardens are also part of the picture. In another paper in the same issue, Yang Li et al. from the Key Laboratory of Tropical Plant Resources and Sustainable Use at Xishuangbanna Tropical Botanical Garden in Kunming (Yunnan) and the University of the Chinese Academy of Sciences in Beijing present research on DELLA-interacting proteins in Arabidopsis. Here the authors show that bHLH48 and bHLH60 are transcription factors involved in GA-mediated control of flowering under long-day conditions.

IBC 2017

Naturally, research on rice is important. Wei Jiang et al. from the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University (Wuhan) describe their research on WOX11 and the control of crown root development in the nation’s grain of choice, which will be important for breeders looking to increase crop yields and resilience.

The other work featured is either in Arabidopsis or plants of economic importance: Fangfang Zheng et al. (Qingdao Agricultural University, also with collaborators in Maryland) and Xiuli Han et al. (Beijing); Yun-Song Lai et al. (Beijing/Chengdu – cucumber), Wenkong Yao et al. (Yangling, Shaanxi – Chinese grapevine, Vitis pseudoreticulata), and Xiao-Juan Liu et al. (Tai-an, Shandong – apple).

Development of plant science

Shenzehn has grown rapidly and is now highly significant for life science as home to the China National GeneBank (CNGB) project led by BGI Genomics. The vision as set out by Huan-Ming Yang, chairman of BGI-Shenzhen, is profound – from sequencing what’s already here, often in numbers per species, to innovative synthetic biology.

Shenzehn is also home to another significant institution, the beautiful and scientifically important Fairy Lake Botanic Garden. At the IBC, the importance of biodiversity conservation for effective, economically focused plant science, but also for so many other reasons to do with our intimate relationship with plants and continued co-existence on the planet, was a central theme.

The research highlighted in Journal of Experimental Botany is part of the wider, positive growth of plant science (and, indeed, botany) not just in China, but worldwide. The Shenzehn Declaration on Plant Sciences with its seven priorities for strategic action, launched at the congress, will be a guide for the right development in coming years.

Jun 12
0

Rise in groundwater overuse could hit food prices

By | Blog, Future Directions

By Neena Bhandari

[SYDNEY] The increasing use of groundwater for irrigation poses a major threat to global food security and could lead to unaffordable prices of staple foods. From 2000 to 2010, the amount of non-renewable groundwater used for irrigation increased by a quarter, according to an article published in Nature on March 30. During the same period China had doubled its groundwater use.

The article finds that 11 per cent of groundwater extraction for irrigation is linked to agricultural trade.

“In some regions, for example in Central California or North-West India, there is not enough precipitation or surface water available to grow crops like maize or rice and so farmers also use water from the underground to irrigate,” the article says.

“When a country imports US maize grown with this non-renewable water, it virtually imports non-renewable groundwater.”

Carole Dalin,  Institute for Sustainable Resources at University College, London

The article focused on cases where underground reservoirs or aquifers, are overused. “When a country imports US maize grown with this non-renewable water, it virtually imports non-renewable groundwater,” Carole Dalin, lead author and senior research fellow at the Institute for Sustainable Resources at University College, London, tells SciDev.Net.

Crops such as rice, wheat, cotton, maize, sugar crops and soybeans are most reliant on this unsustainable water use, according to the article. It lists countries in the Middle East and North Africa as well as China, India, Mexico, Pakistan and the US as most at risk.

“Pakistan and India have been locally most affected due to groundwater depletion and exporting agricultural products grown with non-sustainable groundwater. Iran is both exporting and importing and The Philippines is importing from Pakistan, which is non-sustainable. China is importing a lot from India. Japan and Indonesia are importing, mainly from the US,” says Yoshihide Wada, co-author of the report and deputy director of the International Institute for Applied Systems Analysis’s Water Programme, Laxenburg, Austria.

Agriculture is the leading user of groundwater, accounting for more than 80 to 90 per cent of withdrawals in irrigation-intense countries like India, Pakistan and Iran, according to the report.

The researchers say efforts to improve water use efficiency and develop monitoring and regulation need to be prioritised. Governments must invest in better irrigation infrastructure such as sprinkler irrigation and introduce new cultivar or crop rotation to help producers minimise water use.

Wada suggests creating awareness by putting water labels, along the lines of food labels, “showing how much water is used domestically and internationally in produce and whether these water amounts are from sustainable or non-sustainable sources”.

Andrew Western, professor of hydrology and water resources at the University of Melbourne’s School of Engineering, suggests enforceable water entitlement systems and caps on extraction. “In recent decades, water reform in Australia has led to water having a clear economic value made explicit by a water market. This has enabled shifts in water use to cope with short-term climate fluctuations and has also driven a trend of increasing water productivity,” he says.

This piece was produced by SciDev.Net’s Asia & Pacific desk.

 

This article was originally published on SciDev.Net. Read the original article.

May 15
0

Water is key to ending Africa’s chronic hunger cycle

By | Blog, Global Change

By Esther Ngumbi

For Africa to end chronic hunger, governments must invest in sustainable water supplies.

The fields are bare under the scorching sun and temperatures rise with every passing week. Any crops the extreme temperatures haven’t destroyed, the insect pests have, and for many farmers, there is nothing they can do. Now, news about hunger across Africa makes mass media headlines daily.

Globally, hunger levels are at their highest. In fact, according to the Famine Early Warning Systems Network, over 70 million people across 45 countries will require food emergency assistance in 2017, with Africa being home to three of the four countries deemed to face a critical risk of famine: Nigeria, South Sudan, Sudan and Yemen. African governments, non-governmental organisations (NGOs) and humanitarian relief agencies, including the United Nations World Food Programme, continue to launch short-term solutions such as food relief supplies to avert the situation. Kenya, for example, is handing cash transfers and food relief to its affected citizens. The UN World Food Programme is also distributing food to drought-stricken Somalia. And in Zambia, the government is employing every tool including its military to combat insect pest infestation.

But why are we here? What happened? Why is there such a large drought?

Reasons for chronic hunger

Many African smallholder farmers depend on rain-fed agriculture, and because last year’s rains were inadequate, many farmers never harvested any crops.

Indeed, failed rains across parts of the Horn of Africa have led to the current drought that is affecting Somalia, south-eastern Ethiopia and northern and eastern Kenya.

Then, even in the countries where adequate rains fell, many of the farmers had to farm on depleted soils, and consequently, the yields were lower. Degraded soils and dependence on rain-fed agriculture coupled with planting the wrong crop varieties are some of the fundamental problems that lead to poor harvests and then to hunger. Worsening the situation is the unpredictable climate. Given these fundamental and basic issues that fuel the hunger cycle in Africa, it naturally makes sense to tackle them.

It is not rocket science. Farming goes hand-in-hand with water. There can be no farming without it. While this seems easy to reason, there are few organisations working to make sure that African farmers and citizens have access to permanent water sources. Access to water sources all year round would ensure that farmers can farm year in and year out.

What African governments must do

African governments must, therefore, invest in ensuring that their citizens have access to water. Measures that can be implemented include drilling and rehabilitating boreholes, creating reservoirs and irrigation systems, constructing hand-pumps and implementing water harvesting schemes. Such measures would go a long way and ensure that countries continue to face the same problem both in the short and long term periods.

“If Africa wants to end the recurring droughts, hard decisions must be made.”

Esther Ngumbi, Auburn University in Alabama. United States

Of course it is understandable that it can be hard to choose long-term solutions such as ensuring that citizens have access to permanent water sources year round over investing in short-term solutions when there are people who need help now.

Acknowledging this dilemma, Mitiku Kassa, the Ethiopia’s commissioner for disaster risk management, is reported to have described how hard it was to direct even a fifth of his budget towards well drilling. But such decisions must be made. The Ethiopian government still made that tough decision and sunk hundreds of bore wells throughout the country.

There is a great need to ramp up water harvesting and conservation efforts across the African continent. African governments and other stakeholders need to increase investment in multiple water-storing techniques. Such techniques include rain and flood water harvesting and the construction of water storage ponds and dams. But there should be no need to reinvent the wheel.

Time to learn from others

African countries can learn from other countries. Countries in the developed world have sustained their agriculture efforts by either drilling water wells to ensure they have access to the water they need for farming or by investing in rain and flood water harvesting. In California, for example, there have been a rise in the number of wells being drilled by farmers who use well water for farming. In 2016 alone, farmers in the San Joaquin Valley dug about 2,500 wells, a number that was five times the annual average reported in the last 30 years.

Countries such as Bangladesh, China, India, Myanmar, Sri Lanka and Thailand have made progress and are working on pilot projects that capture, harvest and store flood water. Stored water is then available for use by communities when they need it the most. Harvesting and storing water and making it available for agriculture, especially during the dry seasons, will allow citizens and smallholder farmers to farm throughout the year. These would further improve the resilience of farmers to the unpredictability of climate change.

If Africa wants to end the recurring droughts, hard decisions must be made. By addressing the fundamental and basic issues of long-term availability of water for agriculture, African countries can once and for all end this never-ending cycle of hunger.

Esther Ngumbi is a postdoctoral researcher at the Department of Entomology and Plant Pathology at Auburn University in Alabama, United States. She serves as a 2015 Clinton Global University (CGI U) Mentor for Agriculture and is a 2015 New Voices Fellow at the Aspen Institute. 

This piece was produced by SciDev.Net’s Sub-Saharan Africa English desk.

 

References

Humphrey Nkonde Dramatic threat to maize harvest (Development and Cooperation, 6 March 2017)
Mohammed Yusuf UN: 17 Million People Face Hunger East Africa (Voice of America, 8 March 2017)
Karen McVeigh Somalia famine fears prompt UN call for ‘immediate and massive’ reaction (the Guardian, 3 February 2017)
Emergency food assistance needs unprecedented as Famine threatens four countries (Famine Early Warning Systems Network, 25 January 2017)
Kazungu Samuel Kenya: Red Cross Comes to the Aid of Drought-Hit Kilifi Residents (allAfrica, 2017)
Army worms invades Zambia’s farms (Azania Post, 6 February 2017)
Lesson learned? An urgent call for action in response to the drought crisis in the horn of Africa (Inter Agency Working Group on Disaster Preparedness for East and Central Africa, 2017)
Amanda Little The Ethiopian Guide to Famine Prevention (Bloomberg Business Week, 22 December 2016)
Central Valley farmers drill more, deeper wells as drought limits loom (CBS SF Bay Area, 15 September 2016)
Underground taming floods for irrigation(International Water Management Institute, 2017)

 

This article was originally published on SciDev.Net. Read the original article.

May 01
0

Just add water: Could resurrection plants help feed the world?

By | Blog, Research

This week we spoke to Professor Henk Hilhorst (Wageningen University and Research) about his research on desiccation tolerance in seeds and plants.

 

Could you begin by telling us a little about your research?

I am a plant physiologist specializing in seed biology. I have a long research record on various aspects of seeds, including the mechanisms and regulation of germination and dormancy, desiccation tolerance, as well as issues in seed technology. Being six years from retirement now, I decided to extend my desiccation tolerance studies from seeds to resurrection plants, which display vegetative desiccation tolerance. I strongly believe that unveiling of the mechanism of vegetative desiccation tolerance may help us create crops that are truly tolerant to severe drought, rather than (temporarily) resistant.

 

How did you become interested in this field of study, and how has your career progressed?

As with many things in life, it was coincidence. I majored in plant biochemistry and applied for a PhD position in seed biology. After obtaining the degree I was offered a tenure track position in seed physiology by the Laboratory of Plant Physiology at Wageningen University, where I still work as a faculty member. My career has progressed nicely and I am an authority in the field of seed science, editor-in-chief of the journal Seed Science Research, and will become the President of the International Society for Seed Science in September of this year.

I see my current work on vegetative desiccation tolerance as a highlight in my professional life. I have always been more interested in the desiccation tolerance of seeds until about five years ago, when my current collaborator Prof Jill Farrant of the University of Cape Town, South-Africa, made me enthusiastic about these wonderful resurrection plants. We started to work together and published our first study recently in Nature Plants.

Read the paper here ($): A footprint of desiccation tolerance in the genome of Xerophyta viscosa.


 

In your recent paper, you sequenced the genome of the resurrection plant, Xerophyta viscosa, which can survive with less than a 5% relative water content. How is it possible for a plant to lose so much of its water and still survive?

These plants have a lot of characteristics that we’ve seen in seeds. They display protective desiccation tolerance mechanisms in their leaves, including anti-oxidants, protective proteins, and even dismantle their photosynthetic machinery during periods of drought. Even the cell wall structure and composition of resurrection plants resemble those of seeds. We are currently working on a paper describing the striking similarities between seeds and resurrection plants.

 

What was the most interesting discovery you made upon sequencing the genome of the resurrection plant?

First, the similarities between resurrection plants and seeds listed above were also apparent at the molecular level. For example, previous work suggested that the “ABI3 regulon”, consisting of about 100 genes regulated by the transcription factor ABI3, is specific to seeds, but we found that it is almost completely present (and active) in the leaves of Xerophyta viscosa too!

Secondly, we found “islands” or clusters of genes specific for desiccation tolerance that aren’t found in other species. Many of these regulate secondary metabolite pathways.

 

How challenging was it to sequence the genome of this plant? How did you overcome any difficulties?

It was very challenging. First, the species is an octoploid, meaning it has eight copies of each chromosome. This meant that we had to sequence its genome at very high coverage and employing the most advanced sequencing facilities, e.g. PacBio. Getting funding for this complex analysis was another challenge. We then took almost a year to assemble the genome and annotate it at the desired quality.

 

Xerophyta viscosa

Xerophyta viscosa before and after the rains. Image credit: Prof. Henk Hilhorst.

 

You identified some of the most important genes involved in desiccation tolerance. Is it possible to translate this work into other species, such as crops that may be threatened by drought as the climate changes?

That will be our ultimate goal. It’s important to remember that desiccation-sensitive plants, including all our major crops, produce seeds that are desiccation tolerant. This implies that the information for desiccation tolerance is present in the genomes of these crops but that it is only turned on in the seeds. We are trying to determine how this is localized, in order to find a method to turn on the desiccation tolerance mechanism in vegetative parts of the (crop) plant too. In parallel we are expressing some of the key transcription factors from Xerophyta viscosa in some important crops to see how this affects them.

 

Are there any other interesting aspects of Xerophyta viscosa biology?

Contrary to plants that wilt and ultimately die because of (severe) drought, leaves of resurrection species do not show such stress-related senescence. This is related to the engagement of active anti-senescence genes during the drying of the leaves of resurrection species. We are currently investigating these senescence-related mechanisms too.

 

Rose of Jericho (Anastatica hierochuntica)

The rose of Jericho (Anastatica hierochuntica) is another resurrection plant. Image credit: FloraTrek. Used under license: CC BY-SA 3.0.

 

Do you expect to find that different types of desiccation-tolerant plants use the same subset of genes to survive drought, or could they have developed other pathways to resilience?

We expect that the core mechanism is very similar among the resurrection species but that each species may have adapted to its specific environment.

Funding permitting, we will sequence the genomes of at least another ten resurrection species to further clarify the various evolutionary pathways to desiccation tolerance and, importantly, to discriminate between species-specific and desiccation tolerance-specific genes.

 

What advice do you have for early career researchers?

Stick to what you believe in, even if you have to (temporarily) be involved in research that you appreciate less, e.g., because of better funding opportunities.

 

Read Henk’s recent paper in Nature Plants here ($): A footprint of desiccation tolerance in the genome of Xerophyta viscosa.

Apr 13
1

Roots of a second green revolution

By | Blog, Research

This week we spoke to Professor Jonathan Lynch, Penn State University, whose research on root traits has deepened our understanding of how plants adapt to drought and low soil fertility.

 

 

Could you begin by giving us a brief introduction to your research?

We are trying to understand how plants adapt to drought and low soil fertility. This is important because all plants in terrestrial ecosystems experience suboptimal water and nutrient availability, so in rich nations we maintain crop yields with irrigation and fertilizer, which is not sustainable in the long term. Furthermore, climate change is further degrading soil fertility and increasing plant stress. This topic is therefore both a central question in plant evolution and a key challenge for our civilization. We need to develop better ways to sustain so many people on this planet, and a big part of that will be developing more resilient, efficient crop plants.

 

Drought is devastating for crops

Drought and low soil fertility are devastating for crops. Image credit: CIAT. Used under license: CC BY-SA 2.0.

 

What got you interested in this field, and how has your career developed over time?

When I was 9 years old I became aware of a famine in Africa related to crop failure and resolved to do something about it. I studied soils and plant nutrition as an undergraduate, and in graduate school worked on plant adaptation to low phosphorus and salinity stress, moving to a research position at the CIAT headquarters in Colombia. Later I moved to Penn State, where I have maintained this focus, working to understand the stress tolerance of staple crops, and collaborating with crop breeders in the USA, Europe, Africa, Asia, and Latin America.

 

Your recent publications feature a variety of different crop plants. Could you talk about how you select a species to study?

We work with species that are important for food security, that grow in our field environments, and that I think are cool. We have devoted most of our efforts to the common bean – globally the most important food legume – and maize, which is the most important global crop. These species are often grown together in Africa and Latin America, and part of our work has been geared to understanding how maize/bean and maize/bean/squash polycultures perform under stress. These are fascinating, beautiful plants with huge cultural importance in human history. They are also supported by talented, cooperative research communities. One nice feature of working with food security crops is that their research communities share common goals of achieving impact to improve human welfare.

 

Common bean (Phaseolus vulgaris)

The common bean (Phaseolus vulgaris) is an important staple in many parts of the world. Image credit: Ervins Strauhmanis. Used under license: CC BY 2.0.

 

Many researchers use Arabidopsis thaliana for plant research, but are crops better suited for root research than the delicate roots of Arabidopsis? Are crop plants more or less difficult to work with in your research than Arabidopsis?

The best research system is entirely a function of your goals and questions. We have worked with Arabidopsis for some questions. Since we work with processes at multiple scales, including crop stands, whole organisms, organs, tissues, and cells, it has been useful to work with large plants such as maize, which are large enough to easily measure and to work with in the field. The most interesting stress adaptations for crop breeding are those that differ among genotypes of the same species, and at that level of organization there is a lot of biology that is specific to that species, that cannot readily be generalized from model organisms with very different life strategies. There has been considerable attention to model genomes and much less attention to model phenomes.

 

You have developed methodologies for the high-throughput phenotyping of crop plants. What does this technique involve and what challenges did you have to overcome to succeed?

We have developed multiple phenotyping approaches – too many to summarize readily here. Our overall approach is simply to develop a tool that helps us achieve our goals. For example, we have developed tools to quantify the root architecture of thousands of plants in the field, to measure anatomical phenotypes of thousands of samples from field-grown roots, to help us determine which root phenotypes might affect soil resource capture, etc. Working with geneticists and breeders, we are constantly asked to measure something meaningful on thousands of plants in a field, in many fields, every season. ARPA-E (the US Advanced Research Projects Agency for Energy) has recently funded us to develop phenotyping tools for root depth in the field, but this is the first time we have been funded to develop phenotyping tools – generally we just come up with things to help us do our work, which fortunately have been useful for other researchers as well.

 

Could you talk about some of the computational models you have developed for investigating plant growth and development?

The biological interactions between plants and their environment are so complex, we need computational (in silico) tools to help us evaluate them. Increasingly, in silico tools can integrate information across multiple scales, from gene expression to crop stands. These tools also allow us to evaluate things that are difficult to measure, such as phenotypes that do not yet exist, or future climates. In silico biology will be an essential tool in 21st Century biology, which will have access to huge amounts of data at multiple scales that can be used to try to understand incredibly complex systems, such as the human brain or roots interacting with living soil. Our main in silico tool is SimRoot, developed over the past 25 years to understand how root phenotypes affect soil resource capture.

Check out a SimRoot model below:


 

You have been working on breeding plants that have improved yield in soils with low fertility. What have you achieved in this work?

In collaboration with crop breeders and colleagues in various nations we have developed improved common bean lines with better yield under drought and low soil fertility that are being deployed in Africa and Latin America, improved soybean lines with better yield in soils with low phosphorus being deployed in Africa and Asia, and are now working with maize breeders in Africa to develop lines with better yield under drought and low nitrogen stress. Many crop breeders are using our methods for root phenotyping to target root phenotypes in their selection regimes in multiple crops.

 

What piece of advice do you have for early career researchers?

You are at the forefront of an unprecedented challenge we face as a species – how to sustain 10 billion people in a degrading environment. Plant biologists are an essential part of the effort to reshape how we live on this planet. Do not doubt the importance of your efforts. Do not lose sight of the very real human impact of your scientific choices. Do not be deterred by the gamesmanship and ‘primate politics’ of science. You can make a difference. We need you.

Apr 06
0

Creole maize reveals adaptation secrets

By | Blog, Future Directions

By Lucina Melesio

[MEXICO CITY] An international team of scientists identified a hundred genes that influence adaptation to the latitude, altitude, growing season and flowering time of nearly 4,500 native maize varieties in Mexico and in almost all Latin American and Caribbean countries.

Creole — or native — varieties of maize are derived from improvements made over thousands of years by local farmers, and contain genes that help them adapt to different environments.

“We are now using this analysis to find other genes that are of vital importance to breeders, such as those resistant to extreme heat, frost or drought — environmental conditions associated with climate change and that could affect maize production.”

Sarah Hearne, CIMMYT

“Latin American breeders will be able to use these results to identify native varieties that could contribute to improved adaptation”, Edward Buckler, a Cornell University researcher and co-author of the study published in Nature Genetics (February 6), told SciDev.Net.

The information on the genetic markers described in the study will be available online, said Sarah Hearne, a researcher at the International Maize and Wheat Improvement Center (CIMMYT) and co-author of the study. “Meanwhile, any breeder can contact us to request information”, she said.

“We are now using this analysis to find other genes that are of vital importance to breeders, such as those resistant to extreme heat, frost or drought — environmental conditions associated with climate change and that could affect maize production”, Hearne said.

Maize ears from CIMMYT’s collection, showing a wide variety of colors and shapes. CIMMYT’s germplasm bank contains about 28,000 unique samples of cultivated maize and its wild relatives, teosinte and Tripsacum. These include about 26,000 samples of farmer landraces—traditional, locally-adapted varieties that are rich in diversity. The bank both conserves this diversity and makes it available as a resource for breeding.
Photo credit: Xochiquetzal Fonseca/CIMMYT.

Studying native maize varieties is extremely difficult because of their genetic variation. Although domesticated, they are wilder than commercial varieties.

For this study, the researchers cultivated hybrid creole varieties in various environments in Latin America and identified regions of the genome that control growth rates. They looked into where the varieties came from and what genetic features contributed to their growth in that environment.

 In comments to SciDev.Net, James Holland, a researcher at North Carolina State University, Jeffrey Ross-Ibarra, a researcher at the University of California Davis, and Rodomiro Ortiz, a researcher at the Swedish University of Agricultural Sciences — who did not participate in the study — commended the magnitude of the study and the original method developed by the researchers to access the rich set of genetic information about native maize varieties.

Hearne added that the research team has initiated a “pre-breeding” programme with a small group of breeders in Mexico. As part of that programme, CIMMYT delivers to breeders materials from its germplasm bank of Creole maize; it also provides molecular information the breeders can use to generate new varieties.

This piece was produced by SciDev.Net’s Latin America and Carribean edition.

This article was originally published on SciDev.Net. Read the original article.

Mar 31
0

Global Plant Council stress resilience commentaries published in Food and Energy Security

By | Blog, Scientific Meetings, SEB

In October 2015, researchers from around the world came together in Iguassu Falls, Brazil, for the Stress Resilience Symposium, organized by the Global Plant Council and the Society for Experimental Biology (SEB), to discuss the current research efforts in developing plants resistant to the changing climate. (See our blog by GPC’s Lisa Martin for more on this meeting!)

Building on the success of the meeting, the Global Plant Council team and attendees compiled a set of papers to provide a powerful call to action for stress resilience scientists around the world to come together to tackle some of the biggest challenges we will face in the future. These four papers were published in the Open Access journal Food and Energy Security alongside an editorial about the Global Plant Council.

In the editorial, the Global Plant Council team (Lisa Martin, Sarah Jose, and Ruth Bastow) introduce readers to the Global Plant Council mission, and describe the Stress Resilience initiative, the meeting, and introduce the papers that came from it.

In the first of the commentaries, Matthew Gilliham (University of Adelaide), Scott Chapman (CSIRO), Lisa Martin, Sarah Jose, and Ruth Bastow discuss ‘The case for evidence-based policy to support stress-resilient cropping systems‘, commenting on the important relationships between research and policy and how each must influence the other.

Global Plant Council President Bill Davies (Lancaster University) and CIMMYT‘s Jean-Marcel Ribaut outline the ways in which research can be translated into locally adapted agricultural best practices in their article, ‘Stress resilience in crop plants: strategic thinking to address local food production problems‘.

In the next paper, ‘Harnessing diversity from ecosystems to crops to genes‘, Vicky Buchanan-Wollaston (University of Warwick), Zoe Wilson (University of Nottingham), François Tardieu (INRA), Jim Beynon (University of Warwick), and Katherine Denby (University of York) describe the challenges that must be overcome to promote effective and efficient international research collaboration to develop new solutions and stress resilience plants to enhance food security in the future.

University of Queensland‘s Andrew Borrell and CIMMYT‘s Matthew Reynolds discuss how best to bring together researchers from different disciplines, highlighting great examples of this in their paper, ‘Integrating islands of knowledge for greater synergy and efficiency in crop research‘.

In all of these papers, the authors suggest practical short- and long-term action steps and highlight ways in which the Global Plant Council could help to bring researchers together to coordinate these changes most effectively.

Read the papers in Food and Energy Security here.

Mar 14
0

Lentils under the lens: Improving genetic diversity for sustainable food security

By | Blog, Research

This week’s post comes to us from Crystal Chan, project manager of the Application of Genomic Innovation in the Lentil Economy project led by Dr. Kirstin Bett at the Department of Plant Sciences, University of Saskatchewan.

 

Could you begin with a brief introduction to your research?

Our research focuses on the smart use of diverse genetic materials and wild relatives in the lentil (Lens culinaris) breeding program.

Canada has become the world’s largest producer and exporter of lentils in recent years. Lentils are an introduced species to the northern hemisphere and, until recently, our breeding program at the University of Saskatchewan involved just a handful of germplasms adapted to our climatic condition. With dedicated breeding efforts we have achieved noteworthy genetic gains in the past decade, but we are missing out on the vast genetic diversity available within the Lens genus. This is a major dilemma faced by all plant breeders: do we want consistency (sacrificing genetic diversity and reducing genetic gains over time) or diversity (sacrificing some important fixed traits and spending lots of time and resources in “backcrossing/rescue efforts”)?

 

In our current research, we use genomic tools to understand the genetic variability found in different lentil genotypes and the basis of what makes lentils grow well in different global environments (North America vs. Mediterranean countries vs. South Asian countries). We will then develop molecular breeding tools that breeders can use to improve the diversity and productivity of Canadian lentils while maintaining their adaptation to the northern temperate climate.

 

What first led you to this research topic?

Dr. Albert (Bert) Vandenberg, professor and lentil breeder at the University of Saskatchewan, noticed one of the wild lentil species was resistant to several diseases that devastate the cultivated lentil. After years of dedicated breeding effort, he was able to transfer the resistance traits to the cultivated lentil, but it took a lot of time and resources. We began looking into other beneficial traits and became fascinated with the domestication and adaptation aspects of lentil – after all lentil is one of the oldest cultivated crops, domesticated by man around 11,000 BC! With the rapid advance in genomic technology, we can start to better understand the biology and develop tools to harness these valuable genetic resources.

 

You have been involved in the development of tools that assist researchers to build databases of genomics and genetics data. Could you tell us more about projects such as Tripal?

Over the past six years, Lacey Sanderson (bioinformaticist in our group) has developed a database for our pulse research program at the University (Knowpulse, http://knowpulse.usask.ca/portal/). The database is specifically designed to present data that is relevant to breeders, as our group has a strong focus on variety development for the Canadian pulse crop industry. Knowpulse houses genotypic information from past and on-going lentil genomics projects, and includes tools for looking up genotypes as well as comparing the current genome assembly (currently v1.2) and other sequenced legume genomes. The tools are being developed in Tripal, an open-source toolkit that provides an interface between the data and a Drupal web content management system, in collaboration with colleagues at Washington State University.

 

At the moment we are developing new functionalities that will allow us to store and present germplasm information as well as phenotypic data. We are also working with our colleagues at Washington State University (under the “Tripal Gateway Project” funded by the National Science Foundation) to enhance interconnectivity between Knowpulse and other legume databases, such as the Legume Information Service (LIS) and Soybase, to facilitate comparative genomic studies.

How challenging are pulse genomes to assemble? How closely related are the various crops?

We had the fortune to lead the lentil genome sequencing initiative thanks to the support from producer groups and governments across the globe.  The lentil genome is really challenging to assemble! We see nice synteny between lentil and the model legume, medicago, however the lentil genome is much bigger. We see a significant increase in genome size between chickpea and beans versus lentil (and pea for that matter), yet we have evidence to show that genome duplication is not the cause of the size increase. There are a lot of very long repetitive elements sprinkled around the genome, which makes its sequencing and proper assembly very challenging. Not to mention understanding the role of these long repetitive elements in biological functions…

 

What insights into crop domestication have you gained from these genomes?

That’s what we are working on right now under the AGILE (“Application of Genomics to Innovation in the Lentil Economy”) project. Stay tuned!

 

Do you work with breeders to develop new cultivars? What sorts of traits are most important? 

Breeding is at the core of our work – both Kirstin and Bert are breeders (Kirstin has an active dry bean breeding program when she’s not busy with genomic research). All our research aims to feed information to the breeders so that they can make better crossing and selection decisions. Our work in herbicide tolerance has led to the development and implementation of a molecular marker to screen for herbicide resistance. With that marker we save time (skipping a crossing cycle) and forego the herbicide spraying test for all of our early materials.

Disease resistance and drought tolerance are also important for the growers. Visual quality (seed shape, size, color) are very important too as our customers are very picky as to what sort of lentils they like to buy/eat.

What does the future of legume/lentil agriculture hold?

Lentils have been a staple food in many countries for centuries and have been gaining popularity in North America in recent years as people are looking for plant-based protein sources. Lentils are high in fibre, protein, and complex carbohydrates, while low in fat and calories, and have a low glycemic index. They are suitable for vegetarian/vegan, gluten-free, diabetic, and heart-smart diets. Lentils also provide essential micronutrients such as iron, zinc and folates. Lentils are widely recognized as nutrient-dense food that could serve as part of the solution to combat global food and nutritional insecurity.

In modern agriculture, adding lentil or other leguminous crops in the crop rotation helps improve soil structure, soil quality, and biotic diversity, as well as enhancing soil fertility through their ability to fix nitrogen. Because pulse crops require little to no nitrogen fertilizer, they use half of the non-renewable energy inputs of other crops, reducing greenhouse gas emissions.

2016 was marked by the United Nations as the International Year of Pulses, which was great as many people have become more aware of the benefits of pulse crops on the plate and in the field.

 

Follow us on twitter (@Wildlentils) for research updates!

 

All images are credited to Mr Derek Wright.