CRP-GLDC updates on modernizing crop breeding programs&Product Profiles (PPs)

Janila PasupuletiPrincipal Scientist (Groundnut Breeding) International Crops Research Institute for Semi-Arid Tropics (ICRISAT)Hyderabad – 502324

CRP-Grain Legume and Dry Land Cereals (CRP-GLDC)

http://gldc.cgiar.org/

The CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC) is a

global partnership with a Research for Development investment of US$413

million over five years (2018-2022).

The goal: GLDC aims is to increase the productivity, profitability, resilience and

marketability of critical and nutritious grain legumes and cereals within the

semi-arid and sub-humid dryland agroecologies of sub-Saharan Africa and

South Asia. These agroecologies are where poverty, malnutrition, climate

change and soil degradation are among the most acute globally.

9 crops: Chickpea, cowpea, pigeonpea, groundnut, lentil, Sorghum, pearl millet

and finger millet

13 priority countries Sub-Saharan Africa: Burkina Faso, Ethiopia, Malawi, Mali,

Mozambique, Niger, Nigeria, Sudan, Tanzania, Uganda and Zambia South Asia: India and Myanmar.

Four flagships.

CRP-GLDC & ICRISAT committed

to modernize breeding programs

by closely working with EiB.

Why do we need to modernize the crop breeding programs?OrIs ‘modernizing’ another buzz word?

Genom

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Wid

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Transg

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Phenom

ics

During last 12-15 years, research focus on delivery (seed

systems) and discovery (genomics) at CG dried the funds for

breeding pipelines that weekend the breeding programs at

CG. As a consequence disciplinary teams did not fully align

to the breeding pipelines.

Dom

est

ication

Modernization CG’s crop breeding programs is the need of the hour.Donor investment is a good news!

1. Designing Product Profiles – Developing a variety is not a chance event. Developing variety/parents is by design. Use a strategy to develop designed product starting from choice of parent, breeding method, etc.

2. Enhancing genetic gains, monitoring the progress3. Operational efficiency – value for resources and

time

Breeding teamBreeder – focus on

seed system

Disciplinary teamsGenomics, pathology, physiology, others engaged in basic research that may not feed to breeding pipelines

Breeding team aligned to PPBreeder – manage breeding

& testing pipelineGenomics – develop tools to

deliver product profilesPathology, physiology –

identify traits for selection, and phenotype

Biometrician etc.

Stage gate system of product delivery

Product profiles

CG + NARS partneshipfrom product design to

delivery

What will change?

Product and placement manager

Market, socio-

economic, extension, growers,

GIS, modeling

etc.

Low performing breeding pipelines

Product Advancement (Stage Descriptions)

Stage 1 Stage 2 Stage 3 Stage 4 Stage 5 Stage 6

Product Design Breeding Strategy & Optimization

Product Development & Testing #1

Product Testing #2

Product Multiplication Product Introductions

NARESCGIAR

Private Sector

Trait Family Key Economic TraitsTrait Value

Bench Mark Variety Assessment

Yield (Paddy) Yield 2-Must Have Trait

Mziva

Abiotic Stress Tolerance Drought tolerance 2-Must Have Trait

Mziva

Biotic Resistance (Fungal) Blast 2-Must Have Trait

PI2 & PI9

Biotic Resistance (Bacterial) BLB 2-Must Have Trait

Xa 5, Xa21

Yield (Economic)-Head Rice Head rice recovery 2-Must Have Trait

Makassane

Quality (Aroma) Aroma and flavour 1-Nice to Have

Chupa

Consumer Traits Amylose content 2-Must Have Trait

Chupa

Maturity Intermediate range 2-Must Have Trait

Mziva

Trait Value

1

2

3

Trait Value Descriptors

1) M'ziva is a released variety in Central Mozambique for rainfed ecosystem. 2) Aroma and flavour should be a must. 3) The HRR should be at least at the same level as Makassane (~75%). The traits are ranked by priority from the top.

1-“Nice to Have” are traits that are sometimes appreciated a limited segment of the market but in general the traits very little econmic impact across the broader market. Nice to have traits have the least economical value.

3-"Game Changer" or “Value Added” Traits are significant step-change traits that cause a radical shift in the market. Once the basic package is satisfied, these traits drive market acceptance. They are worth the most provided the basic trait need is satisfied.

= Mziva

= Mziva

2-Must Have Trait or “Basic” Traits are required by the market. An variety could not compete in the market place without these traits. The are a trait that need to be incorporated into the variety.

Discussion Notes

<= Chupa

Standard Evaluation Scale =< 3

= Makassane

CGIAR Variety Replacement Strategy

Market Leading Variety (Replacement): CHUPA (aroma and good flavour)

Trait Benchmarking Details

= Mziva

= Chupa; Nene is ultimate goal

IRRI Breeding Product Profiles (20% Breeding Program Focus)Country or Region: Central and North Mozambique

Market Slot: Rainfed Lowland Rice (semi to long grain)

Standard Evaluation Scale =< 3

1 2 3 4 5

Courtesy: George Kotch, EIB

ü Designing PP’s will not be any more a ‘breeder’s burden’. A multi-disciplinary team and multi-stakeholder engagement will desing the PP.

ü How do we engage multi-stakeholder and multi-disciplineary teams?

ü Crop Network Groups as Platform for product design (BPPs), strategy, development, testing, advancements & delivery (introductions)

ü Crop Networks engage multi-disciplinary teams from NARS, CG, ARI, Private Sector, NGOs and others.

ü Good news! IAVAO networks in WCA; OFID grant for groundnut network in Asia. Hybrid Parent Researh Consortium (HPRC) for Sorghum in Asia and ESA.

Product Profiles (BPPs)

1.Example of a PP developed for a targetbreeding zone in India

Consultations with multi-disciplinary teams of stakeholder were conducted for Pigeon pea and Finger millet at ICRISAT with support from EiB.

Enhancing genetic gains

1. Speed breeding/rapid generation turnover2. Choice of parents3. Assessing the genetic gain 4. Enhancing selection efficiency 5. Increasing heritability of trials

Speed breeding / rapid generation turn over

4-5 cycles per year through speed breeding facilities (manipulation of growing conditions temperature, light and photoperiod)

Single seed decent method of breeding amenable to RGT

Choice of parents – breeding by desing.

Key considerations

1. Is all variability useful? Large variability vs useful variability for target trait in the desirable range

2. Elite or adapted vs unadapted – Elite or adapted gene pool is first choice, if variability is available. When variability is not avialable in breeding gene pool or when broadening gene base for a trait (like disease resistance) is needed then upon the unadapted gene pool.

3. Recycling of elite lines as parents4. BMS will help in looking at pedigree and performance and/or genotype

simultaneously to make decisions on choice of parents.

• Breeding progress is measured by comparing finished lines, we estimated breeding progress during 1996-2010 for the ICRISAT bred groundnut varieties

• An annual pod yield increase of 6-53 kg/ha, equivalent to 0.22 to 2.4 % (0.75%) was recorded in Spanish Bunch varieties

• Scope to improve hundred seed weight and shelling outturn, in future to further enhance pod yield

Measure progress - For ex. genetic gain in ICRISAT’s Spanish types

Peanut processing

High Throughput Genotyping Platform (HTGP) @ 1.5 USD per sample for genotyping including DNA isolation

Hybridization

F2

:::::::::::

:::::::::::

Select parents and design hybridization nursery

Confirm F1 hybridity

Use markers for resistance to rust, LLS and high oleic in relevant crosses

F1

F3 I I I I I I IGenotype confirmed plant progeny rows

Plant tagging Leaf sample collectionGenotyping

Genotyping dataDecision on advancing, backcrossing

Phenotype selection from F3 onwards till F6-7

SNP ID Intertek SNP ID Trait Category

snpAH0002 GKAMFAD2B High oleic acid content

snpAH0004 GKAMA02GL582Late leaf spot

resistance

snpAH0005 GKAMA02GL975Late leaf spot

resistance

snpAH0010 GKAMA02GL829 Late leaf spot resistance

snpAH0011 GKAMA02GL779 Late leaf spot resistance

snpAH0015 GKAMA03QR786 Rust resistance

snpAH0017 GKAMA03QR517 Rust resistance

snpAH0018 GKAMA03QR796 Rust resistance

snpAH0021 GKAMA03QR661 Rust resistance

snpAH0026 GKAMA03GR173 Rust resistance

High Throughput Genotyping Platform

Peanut

processing

Robust and High Throughput Phenotyping for quality – XRF and NIRS

Constituent N* Mean Range Maths treatment RSQ** 1-VR#

Oil (%) 142 48.69 40.08-57.31 1,4,4,1 0.83 0.80

Protein (%) 114 27.68 19.73-35.64 4,6,6,1 0.87 0.75

Palmitic acid (%) 208 11.42 6.77-16.06 2,4,4,1 0.88 0.80

Oleic acid (%) 208 52.12 23.44-80.79 2,4,4,1 0.97 0.95

Linoleic acid (%) 208 27.12 2.77-51.46 2,4,4,1 0.97 0.95

Calibration equation for estimating different quality traits in whole groundnut kernels using NIRS

Early Generation Testing at target zones to fizsuperior allele combinations

Peanut processing

At Kadiri (FDR)

At KasbeDigraj(FDR)

At Junagadh (High Oleic) At Vijayapura

(drought tolerance)

Enables selection of progenies showing superior performance in target environments

Operational efficiency

1. Breeding Management System (BMS)2. Bar-code labelling and digital data capturing devices3. Mechanization and automation 4. Seed inventory system5. Quality control6. Standard operating procedures (SoP’s)

3.Data management systemsBar Code LabellingØ Use of hand held devices such as tablets with laser

scanners facilitates rapid data recording and transfer

Breeding Management System (BMS)Ø An application that combines data storage with

data analysis and retrieval, maintaining pedigree of entries, and nurseries including trial designing

Seed Inventory Management System

Seed Inventory Management System Ø Global inventory! Transparent! Ø Integrated with electronic weighing balances for

withdrawing seedsØ To adopt SIMS crop wise standardization is on

the way Current season offline inventory

information is requested to breedersInputs of location details of seed storage

is awaitedNomenclature for Stock and Lot ID is

awaitedØ Once information is available information will

be uploaded into SIMS in 4-6 Weeks

Seed processing

Regeneration nursery

Seed inventory management system

Long term store (100

seeds)

Medium term store

(1000 seeds)

Trails/nurseries

Short term store

Finished lines with a new

name

Quality Control and SOPs

Quality Control (QC) Ø QC processes for ICRISAT generated lines. Ø Genetic fingerprinting is the surest way for authenticity.

Standard operating procedures for groundnut breeding and testing.http://oar.icrisat.org/10653/1/Standard%20Operating%20Procedures.pdfStandard operating procedure for collecting leaf discs for SNP analysis through Intertek.

Thank you for your attention