Phosphorus in Agriculture:Problems and OpportunitiesMolecular breeding of phosphorus-efficient rice: Pup1 training workshop Sigrid Heuer IRRI, August 27 2012
+ fertilizer
‒ fertilizer (Indonesia, 2009)
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Outline of presentation:
•Introduction – GRISP and Rice production
•Phosphorus Reserves and Consumption: Reason to Panic?
•Breeding for Phosphorus Efficiency – external and internal P-use efficiency
•Pup1: Overview
•Key Messages
•Summary
IR74-Pup1 IR74
IRRI 2012; “Breeders Garden”
Sigrid HeuerPup1 workshop Aug 27-31 2012
Rice is life
300
350
400
450
500
550
600
1991
1993
1995
1997
1999
2001
2003
2005
2007
2009
2011
2013
2015
2017
2019
2021
2023
2025
2027
2029
2031
2033
2035
Asia Africa Americas Rest of World
Million tons milled rice
Additional rice needed:116 million tons by 2035
2010 global rice production
• 50% of the world population depends on rice
• 1% more rice needed every year to keep production at a pace with population growth
Sigrid Heuer Pup1 workshop Aug 27-31 2012
CRP3.3.: GRiSPGlobal Rice Scientific Partnership
IRRI
Theme 1: Harnessing genetic diversity to chart new productivity, quality,
and health horizons
Theme 2: Accelerating the development, delivery, and adoption of improved rice varieties
Theme 3: Ecological and sustainable management of rice-based production systems
Theme 4: Extracting more value from rice harvests through improved quality, processing,
market systems and new products
Theme 5: Technology evaluations, targeting and policy options for enhanced impact
Theme 6: Supporting the growth of the global rice sector
Sigrid Heuer Pup1 workshop Aug 27-31 2012
15 CGIAR centers world-wide
IRRI
Consultative Group of International Agricultural Research
CRP 1.1–1.3: Dryland Systems, Humid Tropics Systems, Aquatic Agricultural SystemsCRP 2: Policies, Institutions and MarketsCRP 3.1–3.7: Wheat, Maize, Rice, Roots/Tubers/Bananas, Grain Legumes, Dryland Cereals, Livestock + FishCRP 4: Nutrition and HealthCRP 5: Water, Land and EcosystemsCRP 6: Forests, Trees and Agro-ForestryCRP 7: Climate Change, Agriculture and Food Security
CRPs: CGIAR Research Programs Reform of the CG
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Irrigated
• ~60% of total rice area Asia (80 M ha*)• ~ 70% of rice production• constant water control • high fertilizer inputs• weed control (by flooding and herbicides)• favorable conditions
Two different major rice production systems:
Produce more with less : HOW?
Rainfed
• ~40% of total rice area Asia (60 M ha*)• ~ 25% of rice production• no or little water control• low to very low fertilizer inputs• weed control difficult and labor intensive • Often unfavorable conditions
Prevalent abiotic stresses:
drought
submergence
salinity
toxicities (Al, Fe)
acidity/alkalinity
nutrient deficiencies (P)….
*Dawe et al 2010
Sigrid HeuerPup1 workshop Aug 27-31 2012
Poor soils in poor countries60% of rainfed-lowland rice in Asia is grown on poor and problem soils
Indonesia
VietnamThailandCambodia
Myanmar
NepalNE India
India
Sri Lanka
Bangladesh
Adapted from Haefele and Hijmans, 2007
No progress in stress-prone environments without stress-tolerant rice varieties
climate change
• heat stress• floods
• other calamities• droughts
Temperature
Water level
Snow cover
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Phosphorus in agriculture
Sigrid Heuer Pup1 workshop Aug 27-31 2012
• Phosphorus is a macro element indispensible for agriculture
• P (and other nutrients) removed with the harvest must be replaced to prevent soil degradation.
• No gene in the world can change that!
What we can do is:
• Make better use of the applied P and reduce P doses
• Access soil P reserves where P is present but unavailable (P-fixing soils)
FAO (2008) Current world fertilizer trends and outlook 2011/2012 56.6 % P
57.9 % N2.5 % P3.4 % N
S+E Asia consume more than 55% of the global fertilizer; Africa less than 3.5%
Higher P application is required on P fixing soils (e.g., Latin America)
P-fixing soils
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Farmers in Sub-Saharan Africa apply only 7 kg nutrients per ha(US >100 kg ha-1; Asia >170 kg ha-1)
Sigrid Heuer Pup1 workshop Aug 27-31 2012
China and India are the world’s biggest consumers of fertilizer
http://www.icis.com/fertilizers/
Sigrid Heuer Pup1 workshop Aug 27-31 2012
… and also the largest producers of rice(followed by Indonesia, Bangladesh and Vietnam)
http://ebookbrowse.com/top-20-production-paddy-rice-2007-mai-2010-pdf-d326696821
Sigrid Heuer Pup1 workshop Aug 27-31 2012
http://www.mongabay.com/images/commodities/charts/phosphate_rock.html
$US metric ton-1
Phosphate Rock Price
Prices spiked in 2008 and are currently still 3 times higher than before
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Likewise:Fertilizer costs (di-ammonium P; ammonia; urea) have almost tripled since 2006
http://www.icis.com/fertilizers/
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Van Kauwenbergh 2010; IFDC report
Morocco: 170,000 mmt (probably 340,000 mmt)
USA: 49,000 mmt
China: 16,800 mmt= 81.3% of global phosphate rock reserves
According to the IFDC study, phosphate rock will be available for the next 300-400 years
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Phosphate Rock: A limited resource?
The bigger problemmight be:
Any increase in food prices will most severely affect poor countries
http://www.fao.org/worldfoodsituation/wfs-home/foodpricesindex/en/
(based on meat, dairy, oil/fat, cereals, sugar )
FAO Food Price Index
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Sigrid Heuer Pup1 workshop Aug 27-31 2012
http://www.indexmundi.com/g/r.aspx?v=69
Bangladesh: 40%
Philippines: 33%
Nepal: 25%
India: 25%
Germany: 16%
South Korea: 15%
Indonesia: 13%
Vietnam: 11%
Thailand: 10%
USA: 12%
Top 20: Population below poverty line
Map of global soil phosphorus availability. Lynch et al 2011; Jaramillo-Velastagui, 2011
Plant available P is too low on about 50% of the world’s agricultural land
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Batjes 2011
Sigrid Heuer Pup1 workshop Aug 27-31 2012
P-fixing soils
MacDonald et al (2010) PNAS
Phosphorus imbalances: too much and too little
Reduce fertilizer application
P-fixing soils
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Over-supply of P fertilizer can be related to high P fixation
Chile
Part of Bolivia,Paraguay, Argentina
Guinea/Bisao, Sierra L, Ivory C
Burma
Nigeria
Florida, Alabama, Georgia
Japan
China, Vietnam
12%18.5%
30%
42-70%
70%
Madagascar50%
16%
3%11%
37%P New Guinea
32.7%
12%
Mozambique 70%
UgandaCongo DR 71%
Angola40.5%
35%
Brazil26%
Batjes 2011
P surplus application
Negative P balance (according to MacDonald et al 2011 )
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Relationship of P fixation and P application (and poverty)
% : Population living below poverty line (http://www.indexmundi.com/map/?v=69)
Deep roots for access to water
Terminal nutrient recycling
Basal fertilizerN+P
External nutrient use efficiency
Nutrient uptake
Early root vigour with large shallow root
system for P uptake
Internal nutrient-use efficiencyTranslocation potentialAlternative pathways
Novel alleles
Weed management Top dress fertilizer (N)
Nutrient transfer from senescing roots
Tolerance to abiotic/ biotic stresses
High-affinity nutrient uptake
Mobilization and foraging of P
Mycorrhizae
High grain NLow grain P Low phytates
Early seedling vigour
Functional stay green
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Vinod and Heuer 2012; AoB, accepted.
Pup1
Approaches towards enhanced nutrient-use efficiency
Pup1
intermediate QTL
Wissuwa et al 1998; Theor Appl Genet
Wissuwa and Ae 2001; Plant Breeding
Pup1 mapping (Matthias Wissuwa; JIRCAS)
Nipponbare
Kasalath
0
2
4
6
8
10
12
14
P u
pta
ke
(m
g p
lan
t-1
)
Screening of 30 rice accessions
P-uptake: LOD 10.7 (28%)
dry weight: LOD 10.5 (27%)
tiller number: LOD 7.9 (21%)
P uptake(mg root weight-1)
Nipponbare 13.7 1.8 NIL-C443 13.9 3.2 Kasalath 10.9 3.2
+P -P
Nipponbare
NIL C443
Pup1 near isogenic lines
M. Wissuwa, JIRCAS
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Chr. 2 Chr. 4 Chr. 5Chr. 3 Chr. 6
Chr. 12
Pup1
Chr. 11Chr. 10Chr. 8Chr. 7 Chr. 9
Chr. 1
P-responsive genes in rice: No candidate gene in Pup1 region
OsPTF1Yi et al (2005)Plant Physiology
major QTL
intermediate QTL
Heuer et al 2009, J Plant Biotech
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Overexpression of transcription factor ZmPTF1 improves low phosphate tolerance of maize by regulating carbon metabolism and root growth. Li et al (2011)Planta 233:1129–1143DOI: 10.1007/s00425-011-1368-1
ZmPTF1
“ZmPTF1 enhanced the expression of fructose-1,6-bisphosphatase and sucrose phosphate synthase1, participated in sucrose synthesis in the leaves, but decreased them in the root, and reduced the expression of genes involved in sucrose catabolism in theroots.”
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Pup1 gene-based markers
• markers distributed over entire Pup1 region
• dominant and co-dominant
co-dominant
dominant
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Eco
syst
em
Sub
spec
ies
Bre
edin
g hi
stor
y
0.1
K1
K5
K20
-1M
se
K20
-2B
sp
K29
-1K
29-2
K29
-3K
41K
42K
43K
45K
46-1
K46
-2K
48K
52K
59
96.
21
16.6
170
.01
70.1
202
.82
04.5
205
.22
62.2
267
.62
69.0
274
.22
76.0
276
.52
83.2
301
.13
25.0
Haplotype I
Haplotype II
Haplotype III
Pup1 markers survey of IRRI breeding lines and diverse varieties
Chin et al 2011 Plant Phys (special issue)
mainly rainfed-adapted
mainly modern, irrigated
+Pup1
Pup1
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Your best rainfed varieties might already have Pup1!
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Indonesia
VietnamThailandCambodia
Myanmar
NepalNE India
India
Sri Lanka
Bangladesh
In rainfed rice systems, P deficiency is only one of many problems
Haefele and Hijmans 2007
P efficiency + tolerance of Drought
SubmergenceHeat
Aluminum toxicitySalinity
Biotic stresses…
Indonesia
VietnamThailandCambodia
Myanmar
NepalNE India
India
Sri Lanka
Bangladesh
QTL projects at IRRI
• Submergence (Sub1) • Phosphorus deficiency tolerance (Pup1) • Heat• Salinity (SalTol) • Anaerobic germination
• Drought (e.g., DYT12.1)
• Blast resistance (Pi40t)
• ….
• FR13A: aus-type; Orissa • Kasalath and Dular: aus-type, India • N22; aus-type, India• Pokkali: Sri Lanka or Bangladesh: aus introgression• Kayan: aus-type, Bangladesh • Vandana/Way Rarem: India • O. australiensis: Wild rice
japonica
aus indica
Adapted from Londo et al 2006
(K. McNally; pers com.)
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Genetic diversity in rice
Sigrid Heuer Pup1 workshop Aug 27-31 2012
?
Tolerant varieties often have many adverse agronomic traits:
low yieldlong durationlodging grain shattering…
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Marker-assisted molecular breeding: QTL mapping
tolerant intolerant
intolerant tolerant
chromosomal region where trait is located
= Quantitative Trait Locus (QTL)
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Marker-assisted backcrossing (MABC)
tolerant donor high yielding variety
F1 and BC to superior variety
further BC and selfing
1 12 2
242 bp
123 bp94 bp
Markers:
background (SSR or SNPs)flankingforeground (QTL)
?
Sigrid Heuer Pup1 workshop Aug 27-31 2012
OsPupK4+5
INDEL (~90 kb)
Nipponbare
OsPSTOL1PHOSPORUS STARVATION TOLERANCE 1
Tolerance genes may not be present in current reference genomes
Kasalath
OsPupK20 OsPupK29
Su
b1
ASu
b1
C Su
b1
B
Su
b1
C Su
b1
B
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Pup1
Sub1
Going beyond MABC: Cloning of tolerance genes
Samba M -Sub1
Samba-Mahsuri
Samba M-Sub1
IR64-Sub1
IR49830 (Sub1)
IR64
IR42
IR64
IR64-Sub1
Samba M-Sub1
IR49830 (Sub1)
Samba Mahsuri
IR64
IR64-Sub1IR49830 (Sub1)
IR42
IR64-Sub1
IR64
IR49830 (Sub1)
IR49830 (Sub1)
IR42
Samba-Mahsuri
IR42
Samba Mahsuri
Sub1 mega varieties: Submergence screening at IRRI
Recovery of Sub1 varieties after 17 days complete submergence
SwarnaTDK1BR11IR64
Samba Mahsuri…Sigrid Heuer Pup1 workshop Aug 27-31 2012
Farmer’s field in Turianbando (Orissa,India): Submerged for 10 days (2.5 m water) Approximately 1000 ha area were totally destroyed
Pooja (local variety)
Pooja
Pooja
Swarna-SUB1 (yield 4 t ha-1)
Adapted from Mackill et al (2012) Advances Agronomy
SUB1 in the field (2010)
Sigrid Heuer Pup1 workshop Aug 27-31 2012
IR74 IR74-Pup1
IRRI, demo plot, DS 2012, –P soil
IR74-Pup1 IR74 w/o Pup1
IRRI upland farm, DS 2012, –P fertilizer
IR74-Pup1 IR74 w/o Pup1
IRRI, breeder’s garden, DS 2012+NPK fertilizer
Pup1 in the field
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Sigrid Heuer Pup1 workshop Aug 27-31 2012
Pup1 breeding- how to start:
(i) P-deficiency phenotyping system - do NOT use hydroponics unless you know it also works in the field! - identify field site/soil with low plant-available P but not too many other stresses- in pots: treat with Furadan to disinfect (do NOT autoclave)
(ii) Screen local varieties under +/- P conditions to quantify the effect of P deficiency and to identify tolerant/intolerant accessions
(iii) Genotype your local varieties for presence/absence of PSTOL1 and other Pup1 genes. For PSTOL1, marker K46-1 is best, double check with K46-2)
Mutant screensMutant screens
Trait discover
y
Trait discover
y
Germplasm
screening
Germplasm
screening
QTL mapping + validation
QTL mapping + validation
Genes in QTLs Genes
in QTLs
tolerant varieties
Marker-assisted breeding
Marker-assisted breeding
Transgenics
Genes and markers
Genes and markers
Conventional
breeding
Novel allelesNovel alleles
Transcript profilingTranscript profiling
Reverse genetics Genome
sequencing
Genome sequencin
g
Genes with known function
Genes with known function
Forward genetics
Adapted from Vinod and Heuer 2012
Sigrid Heuer Pup1 workshop Aug 27-31 2012
We need more genes soon: Towards holistic, integrated breeding
NIAS:Masahiro Yano
Matthias Wissuwa
Juan Pariasca Tanaka
JH Chin
Rico Gamuyao
Cheryl Dalid
Lorie
Inez Slamet-Loedin et al(IRRI transformation lab)
Paolo PesaresiUniversity Milano
JIRCAS
Jonghwa Park
ICABIOGRAD
Rani Anthony
Joko Prasetiyono(M. Bustamam)
Sugiono Moeljopawiro
Krystal Donelle Phillip
Nurul Hidayatun
Sheryl Catausan
Thanks to
…and our other donors for their support!
Thank you for your attention!