Month: August 2021

Legumes are valued worldwide as a sustainable and inexpensive food source and are considered second only to cereals for global food security _¹. In addition to their nitrogen-fixing ability, they are nutritionally valuable providing proteins, essential amino acids, complex carbohydrates and dietary fiber, vitamins and minerals _¹, _² . They have also been ascribed cultural and medicinal roles due to their possession of active bio-compounds _¹. For thousands of years this cultural significance has influenced our selective breeding of only the most palatable and fecund legumes _³. It has followed that in modern times the focus of our scientific research has remained limited to this exclusive, select few. Within the field of genomics, this has given rise to a group of ‘model’ legumes from which all of our current genetic understanding is based.

Rapid developments in DNA and RNA sequencing have greatly advanced our genomic knowledge of these model legumes. Their reference genomes have allowed researchers to decipher key genes, pathways, and networks regulating biological mechanisms and important agronomic traits _{^{2, 4}}. This has allowed for more targeted and efficient breeding and cross-breeding of some major economic legumes such as the Peanut _⁵.

While this is undoubtedly crucial knowledge for food security, our genomic maps remain largely limited to sphere of dietary legumes. The rest is uncharted territory. We have little genomic knowledge of forage legumes in comparison, leaving our agricultural systems vulnerable to the effects of climate change. But, thanks to organizations like the International Center for Tropical Agriculture (CIAT), we do now have genomic references for some of the major animal forage and fodder legumes, including Alfalfa, Soybean and Cowpea _⁶.

The Cowpea (Vigna unguiculata) for example is one of the most important forage legumes in tropical and sub-tropical regions with over 14 million hectares of agricultural land planted with it across the globe _⁷. Thanks to CIAT’s Tropical Legumes Projects, we have identified locations within its genomic map that code for important agronomic traits including drought resistance and efficient seed development.

Genetic markers have been used to target these locations and facilitate more efficient and directed breeding depending on what producers need – (I discuss in the previous post how we might better understand ‘what producers need’ through a conceptual approach that incorporates the different ago-ecological dimensions of a farming system).

Despite these major breakthroughs, large gaps remain in the forage legume germplasm collection. It is still a long way from from being representative of the total geographic diversity of tropical legumes _⁸.

Yet, in a round-about way, this is a positive as it can mean only one thing – that there is an unknown quantity of functionally important genes out there in the wilderness, just waiting to be discovered. Within this diversity are almost certainly to be unique sequences not found within our model set that confer novel ways to adapt and survive the growing effects of climate change. Through the continued genomic mapping of these wild and geographically dispersed species, we can begin to chart new territory. We can learn how these genes are linked to others and how they are passed down through generations. From there we can learn how to breed them quickly and efficiently and integrate them into our agricultural systems.

To keep with the vernacular, what Mr. Peanut and his exclusive club of model legumes need are a few wild characters to liven up the party!

_{^{1 -Maphosa, Y., & Jideani, V. A. (2017). The role of legumes in human nutrition. Functional food-improve health through adequate food, 1, 13.}}

_{^{2 – Dai, X., Zhuang, Z., Boschiero, C., Dong, Y., & Zhao, P. X. (2021). LegumeIP V3: from models to crops—an integrative gene discovery platform for translational genomics in legumes. Nucleic Acids Research, 49(D1), D1472-D1479.}}

_{^{3- Liu, J., Yu, X., Qin, Q., Dinkins, R. D., & Zhu, H. (2020). The impacts of domestication and breeding on nitrogen fixation symbiosis in legumes. Frontiers in genetics, 11, 973.}}

_{^{4 – Pandey, M. K., Roorkiwal, M., Singh, V. K., Ramalingam, A., Kudapa, H., Thudi, M., … & Varshney, R. K. (2016). Emerging genomic tools for legume breeding: current status and future prospects. Frontiers in Plant Science, 7, 455.}}

_{^{5 -Vishwakarma, M. K., Nayak, S. N., Guo, B., Wan, L., Liao, B., Varshney, R. K., & Pandey, M. K. (2017). Classical and molecular approaches for mapping of genes and quantitative trait loci in peanut. In The peanut genome (pp. 93-116). Springer, Cham.}}

_{^{6 -Kulkarni, K. P., Tayade, R., Asekova, S., Song, J. T., Shannon, J. G., & Lee, J. D. (2018). Harnessing the potential of forage legumes, alfalfa, soybean, and cowpea for sustainable agriculture and global food security. Frontiers in plant science, 9, 1314.}}

_{^{7-Agbicodo, E. M., Fatokun, C. A., Muranaka, S., & Visser, R. G. (2009). Breeding drought tolerant cowpea: constraints, accomplishments, and future prospects. Euphytica, 167(3), 353-370.}}

_{^{8-Schultze-Kraft, R., Peters, M., & Wenzl, P. (2020). A historical appraisal of the tropical forages collection conserved at CIAT. In Genetic Resources.}}

Mr. Peanut is taking a break this week, after a busy few months (but don’t worry, he’ll be back soon!).

Instead, just for today, I am posting about a news article I read this week regarding the recent wave of Guerilla Gardening. The ‘re-wilding’ of urban landscapes through the somewhat haphazard planting of native wildflower seed bombs.

I have always viewed this as a positive thing, for both native pollinators and biodiversity in general and I am well and truly on the bandwagon! This is made evident by the web page I have dedicated to updating anyone who will listen on the progress of my Beebomb garden.

That was until I came across a recent article in The Irish Times; an Expose’ on the so called “Trinity Debate” by Michael Viney. Apparently, some botanists from Dublin’s Naturalists’ Field Club (DNFC) are not wild about Trinity College’s newly planted wildflower meadow….

Their argument raises some valid points including the displacement of native species and the potentially unnatural composition of species that grow from a typical wildflower mix.

The article states-

“To the DNFC ,“simply introducing colourful flowers … at best provides a short-term food supply for some common insects that are not threatened.

The typical mix of plant species contained in “wildflower” seed packets “is never found growing together in the wild”. Natural habitats, formed by local conditions, grow the plants adapted to them and these colonise the ground by natural means. Conserving natural habitats should be the priority. And even mowing old lawns less often can allow native species already in the soil bank to flower and set seed.“

Given I recently wrote about the importance of ecological context in crop breeding and commercial seed production, in an effort to be slightly less hypocritical I thought it important to give some air time to the lesser known, CON side of the current ‘Re-Wilding’ argument.

So please, have a read of the Irish Times article and feel free to tell me your thoughts on the Trinity Debate in the comment section below!

So far, my blog posts have (I hope) given some insight into why Tropical Forage Legumes are a vital tool in helping us lessen the contribution of agriculture to climate change. They can also help us adapt our agricultural systems to cope with its effects. I have touched on the role of ‘Adaptive Traits’ in both of these endeavors. Today, I hope to delve a little deeper into this with an important case study that aided the development of my conceptual approach to successful trait selection towards the main objective of ‘Climate Proof’ forage legumes.

Adaptive Traits are those that confer some sort of advantage in a given context. In a drought prone area this could be deep roots that can access the below ground water table. Or, as a previous post discussed, in areas where fire is a significant risk , it could be ‘fire-proof’ seed-pods that can withstand extreme heat of wildfire and go on to germinate.

In the context of livestock production there are other factors to consider and a specific set of adaptive traits needed. A recent Review of Tropical Forage Legumes in Brazil highlighted the importance of context and management via a failed attempt to introduce legumes into a livestock grazing system.

A few years ago in Brazil, in an attempt to improve soil health, cattle farmers introduced a native Stylosanthes legume species into their predominantly Brachiaria grass pastures _¹. But far from delivering on the promise of improved productivity, these legumes failed to thrive _¹ . After only a few years they had died out and disappeared from the pasture biome altogether – an expensive and worrying problem for the farmers. An investigation found the ‘Crown-Forming’ structure of these Stylosanthes legumes had unforeseen consequences.

If we look at the diagram above, we see that crown-forming legumes like Alfalfa, Sainfoin (and indeed many Stylosanthes species) display a tall, elongated primary axis _^2. When planted in the pasture, these legumes grew taller than their neighboring grasses and were left exposed above the pasture canopy. As a result, they disproportionately suffered defoliation by livestock _¹. In layman’s terms they were more easily and more often eaten by the cattle until they were ‘grazed-out’ all together. This phenomenon was consistently observed in cattle farms across Brazil and for several years caused significant worry for livestock farmers.

Because legumes play a vital role in soil health and fertility, these Stylosanthes/Brachiaria pastures became degraded and less fertile over time as they reverted back to solely Brachiaria. This resulted in lower quality grazing and lower quality cattle _¹ . This had knock on effects for the economic security of the farmers who are paid in weight per carcass _^3. It also lead to lower systematic efficiency across the board – a big problem for global Food Security and Climate Change.

Unlike these tall, crown-wearing legumes, other legume crops such as many of the Clover cultivars (Trifolium spp.) exhibit shorter axes which spread outwards instead of upwards and keep below the pasture canopy _². They are therefore likely to suffer less defoliation stress and may persist in the pasture biome for longer. Had farmers perhaps used a well matched Trifolium spp. instead of a Stylosanthes spp., this costly problem could have been avoided.

This case study highlights why commercial legume cultivars must be matched not only with the climate, but also with the specific agricultural context. I discuss this in my literature review and have developed a preliminary, conceptual approach to trait selection in legumes for downstream commercial breeding pipelines. I identify three major dimensions that I consider critical for trait selection and breeding of superior cultivars – Climate Change, External Inputs and Natural Endowments. Some of my previous posts have already discussed climate change. Lets now explore the other dimensions…..

External Inputs

The ‘External Inputs’ dimension could be broadly considered as everything farmers can control and manage _^4,5. It includes factors like the irrigation system in place, animal density per hectare and the relative pasture biome. Defoliation stress by over-grazing for example is related to both herd density and pasture biome and falls within this dimension.

In smaller, lower-input farms with fewer animals, the problem of over-grazing and defoliation might not be such a problem. However, in a larger more industrial scale context, where herds are bigger and grazing is more intense, this should be a major concern. For developing countries in the tropical zone undergoing major livestock intensification, this example is particularly relevant.

Irrigation also has a major contextual impact. A farm that has an irrigation system in place will have a less urgent need for drought resistance legumes compared to a ‘rain-fed’ farm wholly dependent on the weather. This farm will be far more vulnerable to the effects of drought and will need legumes selected or designed to withstand periods of high stress.

Natural Endowments

This dimension broadly encompasses everything that cannot be controlled to any major degree. Depending on the context or discipline, it may be considered as ‘Natural Assets’, ‘Natural Capital’ or ‘Ecosystem Services’ _⁶. It can include elements of the natural landscape such as proximity to natural water bodies, elevation and slope and soil type (i.e. predominantly clay or sand) _^4,5.

These dimensions interact with each in a multitude of ways; the number of computations across the many variables is vast. A farm located on a steep hill with sandy soil for example will experience higher rates of erosion and poor soil quality than one located at the bottom of a valley in predominately clay soil (particularly if located in a region experiencing higher rainfall as a result of climate change). Each context will require different legumes and solutions…..

Trade-Offs

There are also trade-offs involved between agricultural yield and environmental considerations. To strike the right balance between food security and climate change outcomes, genomic approaches to crop breeding should aim to match different cultivars with particular farming systems, ecological contexts and local climates.

As the field of legume genomics advances and commercial breeding strategies improve, we may begin to more accurately target commercial cultivars to suit a specific set of needs. In the meantime, by taking these other dimensions into consideration, we are more likely to prevent costly and largely avoidable mistakes as that experienced in Brazil.

Direction over Perfection

However, as the Sixth IPCC report makes strikingly clear, we are running out of time to meet climate targets _⁷. We cannot wait for the ‘perfect crop’ before we take action. In this (and all) sustainable agricultural endeavors, we should aim for ‘Direction over Perfection’.

By using this contextually based directional approach to trait selection in legumes and other important crops, we are more likely to be successful in developing superior and successful cultivars for climate change action without sacrificing food security.

_{^{1 – Boddey, Robert M, Daniel Rume Casagrande, Bruno GC Homem, and Bruno JR Alves. 2020. ‘Forage legumes in grass pastures in tropical Brazil and likely impacts on greenhouse gas emissions: A review’, Grass and Forage Science, 75: 357-71}}

_{^{2 – Faverjon, L., Escobar-Gutiérrez, A. J., Litrico, I., & Louarn, G. (2017). A conserved potential development framework applies to shoots of legume species with contrasting morphogenetic strategies. Frontiers in Plant Science, 8, 405.}}

_{^{3- Ritchie, Hannah, and Max Roser. 2017. ‘Meat and dairy production’, Our World in Data}}

_{^{4 – Mendelsohn, Robert, and Jinxia Wang. 2017. ‘The impact of climate on farm inputs in developing countries agriculture’, Atmósfera, 30: 77-86.}}

_{^{5 -Pandey, CB, RC Srivastava, and RK Singh. 2009. ‘Soil nitrogen mineralization and microbial biomass relation, and nitrogen conservation in humid‐tropics’, Soil Science Society of America Journal, 73: 1142-49}}

_{^{6 -Martinez-Harms, M. J., Gelcich, S., Krug, R. M., Maseyk, F. J., Moersberger, H., Rastogi, A., … & Pascual, U. (2018). Framing natural assets for advancing sustainability research: translating different perspectives into actions. Sustainability science, 13(6), 1519-1531.}}

_{^{7 -IPCC, 2021: Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change [Masson-Delmotte, V., P. Zhai, A. Pirani, S. L. Connors, C. Péan, S. Berger, N. Caud, Y. Chen, L. Goldfarb, M. I. Gomis, M. Huang, K. Leitzell, E. Lonnoy, J. B. R. Matthews, T. K. Maycock, T. Waterfield, O. Yelekçi, R. Yu and B. Zhou (eds.)]. Cambridge University Press. In Press.}}

Ahead of the COP26 in Glasgow, the IPCC this week released their sixth assessment report on climate change. The landmark report “is a code red for humanity”, says the UN chief. The focus of today’s blog post relates directly to the question of ‘Fire Weather’- One of the report’s key Five Future Impacts.

Throughout my research on Tropical Forage Legumes and Agriculture, I have found the theme of fire to be alarmingly sparse in the current literature. This is made even more apparent against the backdrop of wildfires currently burning in Europe, Africa and America. Moreover, the world recently witnessed unprecedented wildfires in Australia that devastated rural and agricultural communities and wiped out many native and endemic species found nowhere else on earth and never to be recovered. The threat of climate change and fire weather is already having a monumental impact on food security and biodiversity.

In relation to food security, my previous posts have explored how legumes can help improve both agricultural efficiency and resilience against climate change. A key question for both is how (and where) to build fire recovery mechanisms into our agricultural systems?

Historical records and soil profiles tell us that wildfire in the tropical zone has previously occurred in intervals of hundreds to thousands of years _¹. Perhaps unsurprisingly then, the consideration of fire is not a priority for farmers and researchers in tropical regions. However, as the planet warms and historical weather systems begin to change, wildfire will increase in frequency and intensity.

Changes to inter-annual variability of climactic phenomena such as the El Niño Southern Oscillation will cause big decreases in rainfall across the tropics _². This will ‘dry out’ biomass fuels, making them more combustible, increasing both the frequency and intensity of wildfire _². Historically humid topical regions in West Africa, southeast Asia and Latin America for example have experienced an increasing frequency and severity of wildfires in recent decades _¹.

One solution to this problem might lie in places like the Mediterranean, Australia, South Africa, and America. Regions where the native flora have evolved to not only survive wildfires but depend on them for their reproduction. The restoration and management of farming systems against wildfire may be improved by increased knowledge of fire-related germination responses for functionally important groups of plant species – Those such as Tropical Forage Legumes _³.

Besides vegetative sprouting, post-fire seed germination maintains fire affected ecosystems and is an adaptive trait of many legumes species ^₄. Some of the Fabaccae family for example produce a hard seed coating that requires the extreme temperature of fire to germinate ^₄. The hard coat also prevents water absorption and decay in the soil during prolonged inter-fire periods ^₅. Integrating such adaptive mechanisms into commercial legume breeding could be a key strategy for fire-proofing agricultural ecosystems.

As I mentioned in my previous post, by exploring the untapped potential of wild, uncultivated legumes, we will likely find many species that produce these hard, fire-loving seeds. However, in another post we see how integrating uncultivated species into an agricultural setting is fraught with difficulties. It is a delicate balancing act to develop commercial cultivars that can compete with other agricultural crops. Legumes that lie dormant in the soil for years, even decades, before they germinate are likely to be both functionally and economically unhelpful for farmers. Particularly small-scale operations for whom the cost of new and improved cultivar seeds is proportionally large. Moreover, other concurrent morphological characteristics found in these ‘fire-loving’ legumes may be incompatible with certain agricultural systems.

We do not yet have all the answers to such problems and the challenge to incorporate more functionally diverse legumes into agricultural systems remains significant. The solution to this particular problem may lie in developing a seed mixture of functionally complementary legume cultivars – some that can germinate and grow quickly and others that can lie dormant for decades until they are needed for fire recovery. Such an endeavor will take time. Time we can ill-afford as the Sixth IPCC report highlights.

Nevertheless, the need to design tropical agricultural systems with some degree of post-fire recovery potential (and the need to adjust crop genomic and breeding research objectives to match) is a key take-away message of my CCAFS research project.

_{1 -Cochrane, M. A. (2003). Fire science for rainforests. Nature, 421(6926), 913-919.}

_{2 –Herawati, H., & Santoso, H. (2011). Tropical forest susceptibility to and risk of fire under changing climate: A review of fire nature, policy and institutions in Indonesia. Forest Policy and Economics, 13(4), 227-233.}

_{3 -Wiggers, M. S. (2011). Some like it hot: fire and legume germination in the longleaf pine ecosystem (Doctoral dissertation).}

_{4 -Doussi, M. A., & Thanos, C. A. (1994, November). Post-fire regeneration of hardseeded plants: ecophysiology of seed germination. In Proceedings of the 2nd International Conference on Forest Fire Research (Vol. 2, pp. 1035-1044). Coimbra.}

_{5-SOUZA, F. H., & MARCOS-FILHO, J. Ú. L. I. O. (2001). The seed coat as a modulator of seed-environment relationships in Fabaceae. Brazilian Journal of Botany, 24, 365-375.}