Breeding and genetics for improved productivity and resilience - Claire Domoney, John Innes Center, UK
1. A 10-YEAR RESEARCH STRATEGY
FOR PULSE CROPS
CHAPTER 1: BREEDING & GENETICS FOR
IMPROVED PRODUCTIVITY & RESILIENCE
FAO, Rome
22-23 November, 2016claire.domoney@jic.ac.uk
2. 1. Defining research objectives
2. Tools & Approaches
3. Current capacities & competencies
3. Genetics to underpin breeding
• Yield, resilience & other agricultural production
objectives
• End uses
………… exploiting synergies
Franke et al (2016)
4. Genetics to underpin breeding
• End uses
- Nutrition
- Processing & cooking preferences
- On-farm use
Nature Rev Neurosci 14: 551-564
Normal
villi
Villi in coeliac
disease
Yield vs quality: increasing delivery of high quality
nutrition per hectare
Beta-oxalylamino-L-alanine
5. Genetics to underpin breeding
• End uses
- Nutrition
- Processing & cooking preferences
- On-farm use
Weed suppression
Standing ability
Mihailović et al. (2016) Legume Perspectives 13
Intercropping
6. Genetics to underpin breeding
………… exploiting synergies
CoolseasonWarmseason
Adapted from Lavin et al (2005) Syst Biol 54: 575–594
by Foyer et al (2016) Nature Plants
7. 1. Defining research objectives
2. Tools & Approaches
3. Current capacities & competencies
8. • Conserving & using genetic resources
• Using sequence data in breeding programmes
• Crop modelling & foresight
1.1 1.2 1.3 1.4 1.5 1.6 1U 2.1 2.2 U 3
Understanding germplasm & mutant resources
- Novel mutant alleles of genes: fundamental & breeding
TTCGCCGCAAA--------------GTTTTGA
9. Sampson & Weiss (2013) Bioessays 36:34-38
Lawrenson et al. (2015) Genome Biol. 16:258
- MAS/ SNP platforms/ KASPar assays
- CRISPR/Cas9 genome editing (speed breed)
• Targeted mutagenesis
• Gene insertion or replacement
• Ease of design, flexible, affordable &
efficient
Non-homologous
end joining
Homology-
directed repair
• Conserving & using genetic resources
• Using sequence data in breeding programmes
• Crop modelling & foresight
10. • Conserving & using genetic resources
• Using sequence data in breeding programmes
• Crop modelling & foresight
Yield: integration of many traits
• measure traits affecting yield in many agro-ecological
scenarios
Ghanem et al (2015) Agric
Syst 137: 24–38
Probability of grain yield increase
of simulating different sowing day-
of-year (A) 201, (B) 229, (C) 243,
and (D) 264 as compared to a
sowing day of 152
• Crop modelling & foresight
11. 1. Defining research objectives
2. Tools & Approaches
3. Current capacities & competencies
12. Diamond (2002) Nature 418: 700-707
Centres of pulse domestication
Implementing coherent breeding & genetics
programmes to deliver productivity
Data from FAO (www.faostat.fao.org) & Foyer et al (2016) Nature Plants
GL species/category
13. severe drought risk normal low drought risk
Implementing coherent breeding & genetics
programmes to deliver resilience
Dai (2013) Nature Climate Change 3: 52-58
Credit = CGIAR via Noel; Bernard Vanlauwe (B.Vanlauwe@cgiar.org) for N benefit to cereal following pulse; permission requested
Uses a guide RNA to direct the nuclease. Very efficient in barley and Brassica oleracea: Lawrenson et al. (2015). The paper describes, for the first time, successful genome editing using CRISPR / Cas9 in barley and Brassica oleracea. The mutations generated were inherited by progeny plants in the absence of the T-DNA. Specific opportunities to target members of multigene families in crops.
CRISPR/Cas system (clustered regularly interspaced short palindromic repeats)
These simulations indicated that selection and breeding for lentil accessions in East Africa should consider changes in plant phenology and/or sowing dates.
Ghanem et al: Production potential of Lentil (Lens culinaris Medik.) in East Africa. Yield probability vs planting date shows potential for integration of information on physiology and genetics of This emphasises the geographical component.
Genetics is mostly absent and relies on physiological model. Genetic variation of the model parameters can be assessed (e.g. in RIL populations). That would couple knowledge of allelic variation to location (and predicted climate) through the crop physiology.
1, bambara bean; 2, broad bean and faba bean; 3, chickpea; 4, cowpea; 5, groundnut; 6, lentil; 7, lupin; 8, miscellaneous grain legumes; 9, pea; 10, Phaseolus spp.; 11, pigeonpea; and 12, string bean. Top three grain legumes (excluding soybean) were groundnut (42.8 Mt), chickpea (13.3 Mt) and pea (11.5 Mt). Phaseolus spp. is a significant category of grain legumes by production (23.7 Mt).
Figure 3: World grain legume production in 2013.
a, 121 million tonnes (Mt) of grain legumes (excluding soybean) were produced globally in 2013. Data comprises the grain legumes as cited in Fig. 1 plus string bean. Production of the 12 categories are presented as a stacked column graph by the ten net highest-producing countries (inset). 1, bambara bean; 2, broad bean and faba bean; 3, chickpea; 4, cowpea; 5, groundnut; 6, lentil; 7, lupin; 8, miscellaneous grain legumes; 9, pea; 10, Phaseolus spp.; 11, pigeonpea; and 12, string bean. Of these, the top three grain legumes (excluding soybean) were groundnut (42.8 Mt), chickpea (13.3 Mt) and pea (11.5 Mt). Phaseolus spp. is a significant category of grain legumes by production (23.7 Mt). b, Global soybean production was 278 Mt in 2013, accounting for 70% of global grain legumes produced. The top five soybean-producing countries were the USA (91.4 Mt), Brazil (81.7 Mt), Argentina (49.3 Mt), China (12.0 Mt) and India (11.9 Mt). Data from FAO (www.faostat.fao.org accessed 30/01/2016). The maps were generated using R ver. 3.1.3 (R Core Team 2015) with extension packages, rworldmap80 and RColorBrewer81. Countries indicated in white are where data are unavailable.
The Palmer drought index is based on a supply-and-demand model of soil moisture. Supply is comparatively straightforward to calculate, but demand is more complicated, as it depends on many factors: not just temperature and the amount of moisture in the soil but also hard-to-calibrate factors including evapotranspiration and recharge rates. Palmer tried to overcome such difficulties by developing an algorithm that approximated them based on the most readily available data, precipitation and temperature. The index has been most effective in determining long-term drought, a matter of several months, but it is not as good with conditions over a matter of weeks.