phosphorus in agriculture: problems and opportunities (molecular breeding of phosphorus-efficient...

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

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2007

2009

2011

2013

2015

2017

2019

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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


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


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


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


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)

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


Farmers in Sub-Saharan Africa apply only 7 kg nutrients per ha(US >100 kg ha-1; Asia >170 kg ha-1)


China and India are the world’s biggest consumers of fertilizer

http://www.icis.com/fertilizers/


… 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


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


Likewise:Fertilizer costs (di-ammonium P; ammonia; urea) have almost tripled since 2006

http://www.icis.com/fertilizers/


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


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



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


Batjes 2011


P-fixing soils

MacDonald et al (2010) PNAS

Phosphorus imbalances: too much and too little

Reduce fertilizer application

P-fixing soils


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 )


Relationship of P fixation and P application (and poverty)

% : Population living below poverty line (http://www.indexmundi.com/map/?v=69)

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


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


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


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.”


Pup1 gene-based markers

• markers distributed over entire Pup1 region

• dominant and co-dominant

co-dominant

dominant


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


Your best rainfed varieties might already have Pup1!


Indonesia


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


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.)


Genetic diversity in rice


?

Tolerant varieties often have many adverse agronomic traits:

low yieldlong durationlodging grain shattering…


Marker-assisted molecular breeding: QTL mapping

tolerant intolerant

intolerant tolerant

chromosomal region where trait is located

= Quantitative Trait Locus (QTL)


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)

?


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


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)


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



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


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!

phosphorus in agriculture: problems and opportunities (molecular breeding of phosphorus-efficient...

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