Enhancing yield potential and resilience to abiotic stress through genetic improvement of grain legumes

8:30-8:50 Doug Cook “Agriculture Under Stress”

8:50-9:10 Phil Roberts, UC Riverside “Breeding climate-smart cowpeas for West Africa” 9:10-9:30 Rajeev Varshney, ICRISAT “Enhancing genetic gain in chickpea breeding in marginal environments in Africa and South Asia” 9:30-9:50 Phil McClean, North Dakota State “Modern technologies to access common bean responses to environmental stress” 9:50-10:10 Doug Cook, University of California Davis “Harvesting climatic adaptations from the wild progenitors of chickpea and its symbiotic bacteria” 10:10-10:30 David Kramer, Michigan State University “Data mining at field scales for abiotic stress via photosynthesis”

Agriculture under stress

70% of the freshwater used by humans is for agricultural purposes, often exceeding local regeneration rates. Irrigation alone is not sustainable.

“Meeting humanity’s increasing demand for freshwater and protecting ecosystems at the same time will be one of the most difficult and important challenges of this century” Mekonnen and Hoekstra Sci. Adv. 12 Feb 2016

66% of the human population (4.0 billion people) lives under severe water scarcity (WS > 2.0) at least 1 month of the year. Of these, half a billion people face severe water scarcity all year round.

Year-in, year-out, water availability is the major yield-limiting factor

For agriculture, we need a combined approach. Crop Improvement – Agronomic Practices – Irrigation. The situation is complex. Its not all about water. Often coincident environmental factors, esp. heat. Always coincident biological factors, especially biotic stress. Many of the useful traits are the product of numerous, small-effect genes G x G x E x M = need for modeling. Basic science is essential in support of applied outcomes. -Molecular and physiological mechanisms. -Advanced phenotyping -Genome-enabled predictive breeding -Expanded genetic variation

3 take-home messages

Human impact on earth systems

Mekonnen and Hoekstra, Sci Adv 2016.

Causes: • Low natural availability. • Population density; Irrigation • Use and availability out of phase Ganges basin India, Limpopo basin Southern Africa Consequences: • Decreased river flows (Colorado, Yellow) • Declining ground water and lake levels (Aral Sea, Chad Lake) • Increased salinization, decreased land subsistence, biodiversity loss • Reduced agricultural productivity (6% by 2080)

Annual average monthly blue water scarcity Period: 1996–2005.

Climate change impact on small holder farmers in developing countries

• Countries close to the equator will suffer declines in productivity. – heavily depend on agriculture – already warm environment – lack of infrastructure to adapt to changes – lack of capital to invest in innovation adaptation

• Commodity prices will increase due to the reduction in production.

• Higher commodity prices would increase farm revenue, but hurt poor

farmers who consume more than they produce. – Quantity demanded for food and other farm output falls little when

price rises

Dealing with climatic extremes

Mitigation against causes versus Adaptation to changes

….. creating sustainable and climate resilient agricultural systems

The problem of climate is more than just drought

• Drought • Heat • Cold • Pests and Disease • Nitrogen fixation

Abiotic and biotic stress drive cultivation practices

Overuse and uneven availability

• Legumes are important components of natural systems.

• Food legumes provide ~30% of humankind’s nutritional nitrogen.

Legumes, rhizobia, and symbiotic nitrogen fixation

•Nitrogen fertilizers are not an option. •Degraded soils compound plant nutrition and reduce or preclude N-fixation. •Abiotic stress suppresses legumes’ potential for symbiotic N-fixation. •Few science-based investigations.

In the semi-arid tropics, which harbor most of world’s poor

Host

Environment

Pathogens Symbionts Commensals

Developing crops that yield efficiently under conditions of limiting water

Drought resistance: numerous small-effect loci and 100’s of genes

Morphology – leaf shape and size, stomatal number and regulation – Root system architecture and plasticity (to environment and soil nutrition) Physiology – cuticular wax; ABA content, cytokinins , ET; relative water content, water potential, canopy temperature. TE, WUE. Cellular processes – Osmotic adjustment, membrane stability, proline and sugars Regulation – transpiration vs VPD; responsiveness to soil moisture; water use vs plant development.

100’s of QTLs reported, but few are fully validated and fewer yet are in use by breeding programs. Modeling is needed to understand interactions and select

targets.

Vadez et al. Transpirational response of tolerant and susceptible genotypes to increasing VPD.

For crop improvement, the way forward is genetics

Breeding: novel alleles typically come from domesticated germplasm, … landraces and wild relatives are largely ignored. Biotechnology: accesses alleles from a broader set of organisms (transgenics), and to modify endogenous genetic components (cisgenics).

Biotechnology Root system architecture - Water use strategies – Photosynthesis

- Osmoprotectants

Increased biomass and yield under drought stress TF overexpression: • AP2/ERF – increased assimilation, reduced transpiration. • NF-YB1 – maintains PHS under drought conditions. Tolerance and recovery from drought stress • RNA Chaperones CspA (E. coli) and CspB (Bacillus) “cold stress proteins” • Trans-zeatin synthase expression: Delayed drought-induced senescence

Innovate and think outside of the box!

Unweighted Unifrac

Plants do not live alone. They co-occur with thousands of microbial taxa in highly

structured communities.

Microbes impart functional properties (i.e., “health”) to their plant hosts.

… but we lack a solid understanding of these phenomena

Micronutrient uptake

Drought Tolerance

Phosphate solubilization

Disease Tolerance

Nitrogen Fixation

Micronutrient uptake

Drought Tolerance

Phosphate solubilization

Disease Tolerance

Nitrogen Fixation

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