GCP TL-I Phase II WORK PLAN

for Objective 4- chickpea

GCP

 ICRISAT, India- Rajeev Varshney, Pooran Gaur, HC Sharma, L Krishnamurthy, Nalini Mallikarjuna, Mahendar Thudi, Siva K. Chamarthi

 ICRISAT, Kenya- NVPR Ganga Rao, Said N. Silim

 Egerton University, Kenya - Paul Kimurto, Richard Mulwa

 Ethiopian Institute of Agricultural Research (EIAR), Ethiopia- Asnake Fikre

 Indian Institute of Pulse Research (IIPR) Kanpur, India- Sushil K Chaturvedi, SD Mahapatra,Aditya Pratap

 University of California-Davis, USA- Doug Cook, Ming Cheng Luo

 DArT Pty Ltd., Yaramulla, Australia- Andrzej Killian

Collaborating Scientists and Institutions

GCP

Genotyping

Introgression

Phenotyping

India, Kenya

& E

thiopia

2007

Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7

SNPs

MA

RS

MA

BC

X

Trait mapping Trait mapping

Reference collection

Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers

Enriched libraries

BAC end sequences

Interspecific population

Intraspecific population Elite lines

25-50 contrast lines

DArTs

SSRs

Genetic maps

Minor effect QTLs

Major effect QTLs

BC3F2

F3

Phase I Har

ness

ing

Diver

sity

Geno

mic

reso

urce

s

Biot

ic s

tres

s re

sist

ance

Abi

otic s

tres

s re

sist

ance

Molec

ular

br

eeding

Capa

city

Building

Dat

a man

agem

net

GCP

Harnessing diversity

Activity 1

Characterization of diversity - extensive phenotyping

MAGIC population Pre-breeding population

GCP

Genotyping

Introgression

Phenotyping

India, Kenya

& E

thiopia

2007

Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7

SNPs

MA

RS

MA

BC

X

Trait mapping Trait mapping

Reference collection

Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers

Enriched libraries

BAC end sequences

Interspecific population

Intraspecific population Elite lines

25-50 contrast lines

DArTs

SSRs

Genetic maps

Minor effect QTLs

Major effect QTLs

BC3F2

F3

Phase I

phenotyping

phenotyping

Pre- breed. populations

MAGIC populations

Subset of MAGIC lines

SUPERIOR LINES

2014

2010

Phase II

Phenotypic data, Markergenotyping data

Dat

a m

anag

emen

t (G

CP

cent

ral r

egis

try &

IC

GG

C)

GCP

Scheme for MAGIC populations

Cavanagh et al. 2008

Parental line Remarks

ICC 4958 Drought-tolerant genotype found to be promising in Ethiopia, Kenya and India; drought-tolerant parent of two mapping populations

ICCV 10 Widely adapted drought-tolerant cultivar found to be promising in India and Kenya

JAKI 9218 Farmer-preferred cultivar in central and southern India

JG 11 Farmer-preferred cultivar in southern India and also performing well in Kenya

JG 130 Farmer-preferred cultivars from central India

JG 16 Farmer-preferred cultivar in northern and central India

ICCV 97105 Farmer-preferred elite line identified in Kenya and Tanzania

ICCV 00108 Farmer-preferred elite line identified in Tanzania

GCP

Timeline for development of MAGIC population

Activity Timeline

Make 28 one-way crosses Oct 2009–Feb 2010

Confirm hybrids by genotyping and make 14 four-way crosses

Mar 2010–Jun 2010

Confirm hybrids by genotyping and make 7 eight-way crosses

Jun 2010–Sep 2010

Grow F1s Oct 2011–Feb 2011

Grow F2 (n=500 minimum) Mar 2011– Jun 2011

Grow F4 (SSD) Jun 2011–Sep 2011

Grow F5 (SSD) Oct 2011– Feb 2012

Grow F6 (SSD) Mar 2012–Jun 2012

Grow F7 (SSD) Jun 2012– Sep 2012

Grow F8 progenies for seed bulking Oct 2012– Feb 2013

Genotyping of selected MAGIC populations Jan 2013–June 2013

Selection of subset of MAGIC lines based on SNP genotyping/haplotype data

June 2013- Sept 2013

•  MAGIC lines with enhanced drought tolerance •  Fine resolution mapping population

GCP

LG 1

Total marker loci - 1821 Inter-marker distance- 2.48cM

LG 4 LG 3 LG 5 LG 2

LG 6 LG 7

LG 8

Activity 2 in TLI Large scale markers and high-density genetic map

GCP

High-throughput & cost-effective marker genotyping

Integrated with Molecular Breeding Platform for facilitating molecular breeding in high-throughput and cost-effective manner e.g. - genotyping of MAGIC population - genotyping of AB- population - genotyping of MABC population - genotyping of MARS population

GCP

TAA170

GA24

STMS11

ICCM0249

CaM0856

Linkage group 5 harboring hot spot for drought related QTLs in TL-I (Act 4) - 4 markers

Diagnostic markers for accelerating molecular breeding

Genetic map

Physical map

BACs

Candidate QTLs

Additional markers

Marker needs to be Polymorphic in D x R - 30 genotypes tested -  50% success

GCP

Genotyping

Introgression

Phenotyping

India, Kenya

& E

thiopia

2007

Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7

SNPs

MA

RS

MA

BC

X

Trait mapping Trait mapping

Reference collection

Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers

Enriched libraries

BAC end sequences

Interspecific population

Intraspecific population Elite lines

25-50 contrast lines

DArTs

SSRs

Genetic maps

Minor effect QTLs

Major effect QTLs

BC3F2

F3

Phase I

phenotyping

SUPERIOR LINES 2014

2010

Phase II

Phenotypic data, Marker/ BAC end sequences

Dat

a m

anag

emen

t (G

CP

cent

ral r

egis

try &

IC

GG

C)

phenotyping

Pre- breed. populations

MAGIC populations

Subset of MAGIC lines

NG

S

sequencing

SSR markers

SNP resources & genotyping platform

High density genetic maps

BAC contigs

GCP

Phase I- Activity: Marker discovery for insect resistance Natural field conditions Detached leaf assay

- No natural variation in cultivated germplasm - QTL discovery based on interspecific mapping population didn’t yield appropriate QTLs

GCP

JG11 × PI 489777 Nov 2010 - Mar 2011 (Cultivated) (Wild)

F1 Jun 2011 - Oct 2011

BC1F1 Nov 2011 - Mar 2012

BC2F1 Jun 2012 – Oct 2012

BC2F2 (Genotyping) Nov 2012 - Mar 2013

BC2F2:3 (Phenotyping) Jun 2013 – Oct 2013

Identification and charecterisation of ABCLs Nov 2013 - Mar 2013

JG 11 ×

JG 11 ×

×

× QTL Analysis

Scheme for AB-QTL approach

GCP

Genotyping

Introgression

Phenotyping

India, Kenya

& E

thiopia

2007

Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7

SNPs

MA

RS

MA

BC

X

Trait mapping Trait mapping

Reference collection

Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers

Enriched libraries

BAC end sequences

Interspecific population

Intraspecific population Elite lines

25-50 contrast lines

DArTs

SSRs

Genetic maps

Minor effect QTLs

Major effect QTLs

BC3F2

F3

Phase I

JG 11 × PI 489777

AB

-QTL app

AB-QTLs

ABCLs Validation of Q

TLs

SUPERIOR LINES 2014

2010

Phase II

Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers

Dat

a m

anag

emen

t (G

CP

cent

ral r

egis

try &

IC

GG

C)

phenotyping

phenotyping

Pre- breed. populations

MAGIC populations

Subset of MAGIC lines

NG

S

sequencing

SSR markers

SNP resources & genotyping platform

High density genetic maps

BAC contigs

Expectations - Candidate markers and QTLs - ABCLs with enhanced resistance to insect resistance - Validation of insect resistance QTL

GCP

-  Root traits -  Yield -  Harvest index -  CID -  OID

- 2000 cylinder (1.2 m long, 20 cm dm)

Phase I- Activity 4: Large scale drought phenotyping

WUE/ TE phenotyping needs to be undertaken

GCP

Genotyping

Introgression

Phenotyping

India, Kenya

& E

thiopia

2007

Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7

SNPs

MA

RS

MA

BC

X

Trait mapping Trait mapping

Reference collection

Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers

Enriched libraries

BAC end sequences

Interspecific population

Intraspecific population Elite lines

25-50 contrast lines

DArTs

SSRs

Genetic maps

Minor effect QTLs

Major effect QTLs

BC3F2

F3

Phase I

Phenotyping

WU

E, TE

Identification of superior lines for drought tolerance

SUPERIOR LINES 2014

2010

Phase II

Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers

Dat

a m

anag

emen

t (G

CP

cent

ral r

egis

try &

IC

GG

C)

phenotyping

phenotyping

Pre- breed. populations

MAGIC populations

Subset of MAGIC lines

JG 11 × PI 489777

AB

-QTL app

AB-QTLs

ABCLs Validation of Q

TLs

NG

S

sequencing

SSR markers

SNP resources & genotyping platform

High density genetic maps

BAC contigs

GCP Expected outputs

1. TE phenotyping reference collection and ICC 4958 × ICC 1882 mapping population

2. Metadata analysis on all set of phenotyping data- best phenotyping methodology

3. Superior lines with enhanced drought tolerance

4. Validation of drought QTL in elite chickpea lines

GCP Crosses: 3 Cultivars x 2 Donors for root traits

BC1: Cultivar x F1 ↓

BC1F1

BC 2: Cultivar x BC1F1 ↓

BC2F1 Subjected to foreground and background selection

BC3: Cultivar x BC2F1 As in BC 2

↓ BC3F1

Selected heterozygous plants for QTL-linked markers and over 90% genome of the recurrent parent

↓ BC3F2

2009-2010 Select homozygous plants for QTL-linked markers ↓

BC3F3 Seed multiplication

↓ Multilocation evaluation BC3F4 lines

TL-I Activity 6 MABC for drought tolerance

Donors

Cultivars

JG 11

Chefe KAK 2

GCP

ICCV 97105: Farmer-preferred desi chickpea elite line identified in Kenya and Tanzania through farmer-participatory varietal selection (FPVS) trials conducted in phase I of TLII. This is being proposed for release in Kenya and Tanzania.

Ejere: Farmer-preferred kabuli chickpea cultivar identified in Ethiopia through FPVS trials conducted in phase I of TLII.

DCP-92-3: Most-popular desi chickpea cultivar in north-eastern India

ICC 4958: Well known drought-tolerant genotype with deep and vigorous root system. It is a drought tolerant parent of two mapping populations for root traits. It has also performed well in Ethiopia, Kenya and India

MABC for drought tolerance by NARS partners Selection of cultivars

GCP Egerton University, Njoro, Kenya

DZARC–Debre Ziet, Ethiopia

IIPR, Kanpur, India

ICCV 97105 × ICC 4958

Ejere × ICC 4958 DCP 92-3 × ICC 4958

Make cross Oct 2009–Mar 2010

Oct 2009–Mar 2010

Nov 2009 – Mar 2010

Grow F1 and make BC1 Apr 2010–Aug 10 Apr 2010–Aug

2010 Jun 2010–Oct 2010

Grow BC1F1, foreground and background selection, make BC2

Oct 2010–Mar 2011

Oct 2010–Mar 2011

Nov 2010–Mar 2011

Grow BC2F1, foreground and background selection, make BC3

Apr 2011–Aug 11 Apr 2011–Aug 2011

Jun 2011–Oct 2011

Grow BC3F1, foreground and background selection, self selected plants

Oct 2011–Mar 12 Oct 2011–Mar 2012

Nov 2011–Mar 2012

Grow BC3F2, select homozygous plants for QTL-linked markers, self selected plants

Apr 2012–Aug 2012

Apr 2012– Aug 2012

Jun 2012–Oct 2012

Grow BC3F3 progenies for seed multiplication

Oct 2012–Mar 2013

Oct 2012–Mar 2013

Nov 2012–Mar 2013

Multilocation evaluation of BC3F4 progenies

Apr 2013 –Aug 2013

Apr 2013–Aug 2013

Nov 2013–Mar 2014

MABC by NARS partners

GCP

Set 1 (2 crosses) Set-2 (3 crosses)

2008/09 Genotyping of F3 plants F2 grown

F4 (Seed mutiplication) Genotyping of F3 plants Multilocation evaluation F4 (Seed mutiplication) of F5 progenies and QTL analysis

Selection and inter-crossing Multilocation evaluation of F3s of F5 progenies and 2009/10 QTL analysis

Five good-by-good crosses involving cultivars from Africa and Asia

TL-I Activity 6 MARS for drought tolerance

GCP

Popu

lation

dev

elop

men

t Re

combi

nation

Popu

lation

de

velopm

ent

1st Recombination cycle 2nd Recombination cycle 3rd Recombination cycle

Multilocation phenotyping

Genotyping

Parent 1 × Parent 2 F1 F2 F3 F3:4 F3:5

Single seed descent 282 F3 progenies 282 progenies

Multilocation phenotyping A B C D E F G H

F1 F1 F1 F1 F1 F1

F1 F2 F3 F3:4

10 plants/family (A-H), 6 sets of 8 families/cross QTL detection

Development of MARS populations continued

GCP

Genotyping

Introgression

Phenotyping

India, Kenya

& E

thiopia

2007

Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7

SNPs

MA

RS

MA

BC

X

Trait mapping Trait mapping

Reference collection

Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers

Enriched libraries

BAC end sequences

Interspecific population

Intraspecific population Elite lines

25-50 contrast lines

DArTs

SSRs

Genetic maps

Minor effect QTLs

Major effect QTLs

BC3F2

F3

Phase I

phenotyping

SUPERIOR LINES 2014

2010

Phase II

Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers, Next generation breeders trained

Dat

a m

anag

emen

t (G

CP

cent

ral r

egis

try &

IC

GG

C)

phenotyping

Pre- breed. populations

MAGIC populations

Subset of MAGIC lines

NG

S

sequencing

SSR markers

SNP resources & genotyping platform

High density genetic maps

BAC contigs

JG 11 × PI 489777

AB

-QTL app

AB-QTLs

ABCLs Validation of Q

TLs

Phenotyping

WU

E, TE

Selection of phenotyping

methodology(ies)

BC3F4

BC3F2

MA

BC

(N

AR

S)

Multilocation

phenotyping

F5

Multilocation

phenotyping

Recom

bination cycles

Multilocation

phenotyping

Molecular Breeding Platform

GCP

Genotyping MBP

MBP Phenotyping

New Activity- trait package

Development of populations

- Act 5.2 of TL II

Markers for FW resistance

CMBN Govt of India

Marker screening for root trait QTL and FW resistance associated markers

(TL I)

GCP

Sub-activities:

Strengthening infrastructure in collaboration with Activity 3 of Objective 5

Organization of a modern breeding workshop for TL-I & TL-II breeders of chickpea

Six MSc and three PhD students trained in chickpea genomics and breeding activities

Activity 6: Capacity-building

GCP

Genotyping

Introgression

Phenotyping

India, Kenya

& E

thiopia

2007

Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7

SNPs

MA

RS

MA

BC

X

Trait mapping Trait mapping

Reference collection

Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers

Enriched libraries

BAC end sequences

Interspecific population

Intraspecific population Elite lines

25-50 contrast lines

DArTs

SSRs

Genetic maps

Minor effect QTLs

Major effect QTLs

BC3F2

F3

Phase I

PhD

studentship

Strengthening

Infrastructure

phenotyping

SUPERIOR LINES 2014

2010

Phase II

Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers, Next generation breeders trained

Dat

a m

anag

emen

t (G

CP

cent

ral r

egis

try &

IC

GG

C)

phenotyping

Pre- breed. populations

MAGIC populations

Subset of MAGIC lines

NG

S

sequencing

SSR markers

SNP resources & genotyping platform

High density genetic maps

BAC contigs

JG 11 × PI 489777

AB

-QTL app

AB-QTLs

ABCLs Validation of Q

TLs

Phenotyping

WU

E, TE

Selection of phenotyping

methodology(ies)

BC3F4

BC3F2

MA

BC

(N

AR

S)

Multilocation

phenotyping

F5

Multilocation

phenotyping

Recom

bination cycles

Multilocation

phenotyping

GCP

  Molecular Breeding Platform

  Databases within ICRISAT (Activity 2/ Obj 5)

  GCP Central Registry

  International Chickpea Genetics & Genomics Consortium (ICGGC)

Data storage & Management

GCP

Genotyping

Introgression

Phenotyping

India, Kenya

& E

thiopia

2007

Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7

SNPs

MA

RS

MA

BC

X

Trait mapping Trait mapping

Reference collection

Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers

Enriched libraries

BAC end sequences

Interspecific population

Intraspecific population Elite lines

25-50 contrast lines

DArTs

SSRs

Genetic maps

Minor effect QTLs

Major effect QTLs

BC3F2

F3

Phase I

phenotyping

SUPERIOR LINES 2014

2010

Phase II

Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers, Next generation breeders trained

Dat

a m

anag

emen

t (G

CP

cent

ral r

egis

try &

IC

GG

C)

phenotyping

Pre- breed. populations

MAGIC populations

Subset of MAGIC lines

NG

S

sequencing

SSR markers

SNP resources & genotyping platform

High density genetic maps

BAC contigs

JG 11 × PI 489777

AB

-QTL app

AB-QTLs

ABCLs Validation of Q

TLs

Phenotyping

WU

E, TE

Selection of phenotyping

methodology(ies)

BC3F4

BC3F2

MA

BC

(N

AR

S)

Multilocation

phenotyping

F5

Multilocation

phenotyping

Recom

bination cycles

Multilocation

phenotyping

PhD

studentship

Strengthening

Infrastructure

GCP In summary…

  Phase II proposal is based on achievements of Phase I of TLI and requirements of TL II and heavily interacted with Mol Breed Platform

  All activities are downstream application oriented

  Flexible- open for more suggestions from TL II

  Diagnostic markers for drought and insect res.

  Superior lines (MAGIC, ABCLs, MABCs, MARS) for drought tolerance and insect resistance

  Mol breeding being undertaken by NARS

GCP