Phosphorus in Agriculture: Problems and Opportunities

Sigrid Heuer IRRI, August 27 2012

Molecular breeding of phosphorus-efficient rice: Pup1 training workshop

+ fertilizer

fertilizer
(Indonesia, 2009)

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Outline of presentation:
Sigrid Heuer Pup1 workshop Aug 27-31 2012

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
IRRI 2012; Breeders Garden

IR74-Pup1

IR74

Rice is life
50% of the world population depends on rice 1% more rice needed every year to keep production at a pace with population growth

Million tons milled rice

600

550

Additional rice needed: 116 million tons by 2035

500

450

400

2010 global rice production

350

300

91

93

95

97

99

01

03

05

07

09

11

13

15

17

19

21

23

25

27

29

31

33 20

19

19

19

19

19

20

20

20

20

20

20

20

20

20

20

20

20

20

20

20

20

Asia

Africa

Americas

Rest of World
Sigrid Heuer Pup1 workshop Aug 27-31 2012

20

35

CRP3.3.: GRiSP Global 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

Reform of the CG
CRPs: CGIAR Research Programs
CRP 1.11.3: Dryland Systems, Humid Tropics Systems, Aquatic Agricultural Systems CRP 2: Policies, Institutions and Markets CRP 3.13.7: Wheat, Maize, Rice, Roots/Tubers/Bananas, Grain Legumes, Dryland Cereals, Livestock + Fish CRP 4: Nutrition and Health CRP 5: Water, Land and Ecosystems CRP 6: Forests, Trees and Agro-Forestry CRP 7: Climate Change, Agriculture and Food Security
Sigrid Heuer Pup1 workshop Aug 27-31 2012

Produce more with less : HOW?

Two different major rice production systems: 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
Sigrid Heuer Pup1 workshop Aug 27-31 2012

Rainfed
~40% of total rice area Asia (60 M ha*) *Dawe et al 2010 ~ 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).

Poor soils in poor countries

60% of rainfed-lowland rice in Asia is grown on poor and problem soils
Nepal

NE India Bangladesh

India

Myanmar Thailand Vietnam Cambodia

climate change
Temperature

Sri Lanka

Indonesia

Water level
Adapted from Haefele and Hijmans, 2007

No progress in stress-prone environments without stresstolerant rice varieties

Sigrid Heuer Pup1 workshop Aug 27-31 2012

heat stress floods Snow cover other calamities droughts

Phosphorus in agriculture
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)

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Fertilizer consumption 2007/8 % share of world consumption

40

30

20

P-fixing soils

N fertilizer P fertilizer

10

E. Europe & C. Asia

Africa

3.4 % N 2.5 % P

W. & C. Europe

N. America L. America South Asia

East Asia

others

57.9 % N 56.6 % P

FAO (2008) Current world fertilizer trends and outlook 2011/2012

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)
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 worlds 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

$US metric ton-1

Phosphate Rock Price

http://www.mongabay.com/images/commodities/charts/phosphate_rock.html

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

Phosphate Rock: A limited resource?

Van Kauwenbergh 2010; IFDC report

According to the IFDC study, phosphate rock will be available for the next 300-400 years The bigger problem might be: Morocco: 170,000 mmt (probably 340,000 mmt)
USA: 49,000 mmt
China: 16,800 mmt = 81.3% of global phosphate rock reserves
Sigrid Heuer Pup1 workshop Aug 27-31 2012

FAO Food Price Index

(based on meat, dairy, oil/fat, cereals, sugar )

http://www.fao.org/worldfoodsituation/wfs-home/foodpricesindex/en/

Any increase in food prices will most severely affect poor countries

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Top 20: Population below poverty line

Bangladesh: 40% Philippines: 33% Nepal: 25% India: 25% Germany: 16% South Korea: 15% Indonesia: 13% Vietnam: 11% Thailand: 10% USA: 12%
http://www.indexmundi.com/g/r.aspx?v=69

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Map of global soil phosphorus availability.

Lynch et al 2011; Jaramillo-Velastagui, 2011

Plant available P is too low on about 50% of the worlds agricultural land
Sigrid Heuer Pup1 workshop Aug 27-31 2012

P-fixing soils

Batjes 2011

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Phosphorus imbalances: too much and too little

Reduce fertilizer application P-fixing soils

MacDonald et al (2010) PNAS

Over-supply of P fertilizer can be related to high P fixation

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Relationship of P fixation and P application (and poverty)

Florida, 12% Alabama, Georgia 42-70% Guinea/Bisao, Sierra L, Ivory C 32.7% Burma

16% Japan
China, 3% Vietnam 11% P New Guinea 37%

Brazil 26%

Nigeria 70% Angola 40.5%

Uganda Congo DR 71% Mozambique 70%

35%

Chile 12%

Part of Bolivia,30% Paraguay, Argentina 18.5%

Madagascar 50%

Batjes 2011

P surplus application Negative P balance

(according to MacDonald et al 2011 )

% : Population living below poverty line

(http://www.indexmundi.com/map/?v=69) Sigrid Heuer Pup1 workshop Aug 27-31 2012

Approaches towards enhanced nutrient-use efficiency

Pup1
External nutrient use efficiency
Nutrient uptake

Internal nutrientuse efficiency

Translocation potential Alternative pathways Novel alleles

Terminal nutrient recycling

Early seedling vigour Tolerance to abiotic/ biotic stresses

Functional stay green

High grain N Low grain P Low phytates

Basal fertilizer N+P

Weed management

Top dress fertilizer (N) High-affinity nutrient uptake Mobilization and foraging of P Mycorrhizae Nutrient transfer from senescing roots

Early root vigour with large shallow root system for P uptake Deep roots for access to water

Vinod and Heuer 2012; AoB, accepted.

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Pup1 mapping (Matthias Wissuwa; JIRCAS)

Pup1 near isogenic lines
14 12 P uptake (mg plant-1) 10 8 6 4 2

intermediate QTL

Screening Nipponbare of 30 rice accessions NIL C443 Kasalath

Nipponbare

M. Wissuwa, JIRCAS

P-uptake: dry weight: tiller number:

LOD 10.7 (28%) LOD 10.5 (27%) LOD 7.9 (21%) +P -P Nipponbare 13.7 1.8 NIL-C443 Heuer Pup1 workshop 13.9 3.2 Sigrid Kasalath 10.9 3.2

Pup1

P uptake
(mg root weight-1)

Aug 27-31 2012 Wissuwa et al 1998; Theor Appl Genet

Wissuwa and Ae 2001; Plant Breeding

P-responsive genes in rice: No candidate gene in Pup1 region

Chr. 1 Chr. 2 Chr. 3 Chr. 4 Chr. 5 Chr. 6

intermediate QTL

OsPTF1
Yi et al (2005) Plant Physiology

Chr. 7

Chr. 8

Chr. 9

Chr. 10

Chr. 11

Chr. 12

Pup1
major QTL

Heuer et al 2009, J Plant Biotech Sigrid Heuer Pup1 workshop Aug 27-31 2012

ZmPTF1
Overexpression of transcription factor ZmPTF1 improves low phosphate tolerance of maize by regulating carbon metabolism and root growth. Li et al (2011)
Planta 233:11291143 DOI: 10.1007/s00425-011-1368-1

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 the roots.

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

Pup1 markers survey of IRRI breeding lines and diverse varieties

96.2 K1 116.6 K5 170.0 K20-1Mse 170.1 K20-2Bsp 202.8 K29-1 204.5 K29-2 205.2 K29-3 262.2 K41 267.6 K42 269.0 K43 274.2 K45 276.0 K46-1 276.5 K46-2 283.2 K48 301.1 K52 325.0 K59

Ecosystem Subspecies Breeding history

Haplotype I

+Pup1

mainly rainfed-adapted
Your best rainfed varieties might already have Pup1!

Haplotype II

0.1

Pup1
Haplotype III

mainly modern, irrigated

Chin et al 2011 Plant Phys (special issue)

Sigrid Heuer Pup1 workshop Aug 27-31 2012

In rainfed rice systems, P deficiency is only one of many problems

Nepal

NE India Bangladesh

India

Myanmar Thailand Vietnam Cambodia

Sri Lanka

P efficiency + tolerance of
Indonesia

Haefele and Hijmans 2007

Drought Submergence Heat Aluminum toxicity Salinity Biotic stresses

Sigrid Heuer Pup1 workshop Aug 27-31 2012

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 (K. McNally; pers com.) Kayan: aus-type, Bangladesh Vandana/Way Rarem: India O. australiensis: Wild rice

japonica

Nepal

NE India Bangladesh

aus

indica

India

Myanmar Thailand Vietnam Cambodia

Sri Lanka

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Adapted from Londo et al 2006

Indonesia

Genetic diversity in rice

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Tolerant varieties often have many adverse agronomic traits:

low yield long duration lodging grain shattering

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Marker-assisted molecular breeding: QTL mapping

tolerant

intolerant

chromosomal region where trait is located

= Quantitative Trait Locus (QTL)

intolerant tolerant

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Marker-assisted backcrossing (MABC)

tolerant donor high yielding variety
Markers:
background (SSR or SNPs) flanking foreground (QTL) F1 and BC to superior variety
242 bp

1 2

123 bp 94 bp

further BC and selfing

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Going beyond MABC: Cloning of tolerance genes

Tolerance genes may not be present in current reference genomes

Pup1
Nipponbare INDEL (~90 kb)
OsPupK4+5 OsPupK20 OsPupK29

Kasalath

OsPSTOL1 PHOSPORUS STARVATION TOLERANCE 1

Sub1A

Sub1
Sub1B Sub1B Sub1C

Sub1C

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Sub1 mega varieties: Submergence screening at IRRI

Recovery of Sub1 varieties after 17 days complete submergence

IR64-Sub1 Samba M-Sub1 IR49830 (Sub1)

Samba-Mahsuri
IR42 IR64 IR64-Sub1

IR64 IR42

Samba Mahsuri
IR49830 (Sub1) IR49830 (Sub1) Samba-Mahsuri IR64 IR64-Sub1 IR42 IR64-Sub1 IR49830 (Sub1) Samba Mahsuri

Samba M-Sub1

IR42
IR49830 (Sub1)

Samba M -Sub1

IR64

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Swarna TDK1 BR11 IR64 Samba Mahsuri

SUB1 in the field (2010)

Pooja

Swarna-SUB1 (yield 4 t ha-1)

Pooja

Pooja (local variety)

Adapted from Mackill et al (2012) Advances Agronomy

Farmers field in Turianbando (Orissa,India): Submerged for 10 days (2.5 m water) Approximately 1000 ha area were totally destroyed

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Pup1 in the field

IRRI, demo plot, DS 2012, P soil

IRRI upland farm, DS 2012, P fertilizer

IRRI, breeders garden, DS 2012 +NPK fertilizer

IR74
IR74-Pup1 IR74 w/o Pup1

IR74-Pup1

IR74 w/o Pup1

IR74-Pup1

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)

Sigrid Heuer Pup1 workshop Aug 27-31 2012

We need more genes soon: Towards holistic, integrated breeding

QTL mapping + validation

Genes with known function

Trait discover y

Forward genetics

Genes in QTLs

Reverse genetics
Genes and markers
Novel alleles

Germplasm screening

Genome sequencin g Mutant Transcript screens profiling

Marker-assisted breeding Conventional breeding

Adapted from Vinod and Heuer 2012

Transgenics

tolerant varieties

Sigrid Heuer Pup1 workshop Aug 27-31 2012

Cheryl Dalid Rico Gamuyao

Nurul Hidayatun Jonghwa Park

JIRCAS JH Chin
Sheryl Catausan

ICABIOGRAD

Juan Pariasca Tanaka

Joko Prasetiyono (M. Bustamam) Sugiono Moeljopawiro

Matthias Wissuwa

Lorie

NIAS: Masahiro Yano

Inez Slamet-Loedin et al (IRRI transformation lab) Paolo Pesaresi University Milano Krystal Donelle Phillip

Rani

Anthony

Thanks to and our other donors for their support!

Thank you for your attention!