5th International Conference on Next Generation Genomics and Integrated Breeding for Crop

Improvement, ICRISAT, Patancheru

Prof M S Swaminathan UNESCO Chair in Ecotechnology, MSSRF, Chennai

Hyderabad, 20 February2015

Next Generation Genomics and the Zero Hunger Challenge

From Mendelian to Integrated Breeding

Gregor Mendel James D Watson Francis Crick 1865 1953

First Genetically Modified Petunia

(1983)

The beginning of Genetic Modification

Source: Robert T Fraley

Impact of genetic alteration of plant architecture on food security

Some Milestones

1943 : Bengal Famine; 3 million children, women and men died of hunger 1963 : Beginning of intensive breeding research on raising the

ceiling to yield 1966 : Increasing PL 480 wheat imports, going upto 10 million tonnes 1968 : Issue of the stamp “Wheat Revolution”, depicting the role of science in agricultural transformation 2013 : Parliament approves the National Food Security Act,

conferring the legal right to food on over 70% of India’s population

Thus, 2013 marks the transition from ‘ship to

mouth’ to ‘right to food’ with home grown food

Comparison of woo-gen (right) and dee-geo-woo-gen strains, the latter containing

the sd1 mutation

The effects of different Rht alleles on plant height in wheat (cv. April

Bearded). The wild-type contains Rht-B1a and Rht-D1a, which are homoeologous (corresponding) genes on the B and D genomes. Rht-

B1c is a more severe allele at the Rht-B1 locus

Source: http://5e.plantphys.net/

The Green Revolution And The Dwarf Phenotype

Genetic Containment of Wheat Rusts

Stem, Leaf and Stripe Rusts

1953 : Composite Varieties – phenotypically similar but

genotypically diverse

1960 : Gene pyramiding

Genetic Shield – gene deployment strategy

March 2009 : Check-mating UG-99, a virulent stem rust

race in wheat

Need for Genetic checkmating of new disease threats Puccinia Path

The Plant Phenomic facility in Phytotron of IARI

o Leaf area o Chlorophyll content o Stem diameter o Plant height / width o Growth rate o Stress pigment concentration o Tip burn o Biomass o Internode length o Color o Leaf rolling

Parameters measured for Plant Phenotyping in Wheat at IARI

Trends in Plant Science December 2011, Vol. 16, No. 12

Control

After 3 days

of salt treatment

Thermal images of durum wheat seedlings

treated with salt – temperature differential of 1ºC

Phenotyping of abiotic stress through thermal imaging

Thermal image of a wheat trial

In this area, we face challenges such as the establishment of robust protocols and screening methods, which integrate non‐invasive, automated high throughput measurement of relevant plant traits both under controlled greenhouse and field scenarios. Plant phenotyping is fast developing as a scientific field that aims to quantify accurately phenotypic traits, and give valuable prognoses for plant environment interaction

Linking Genome to the Phenome

CALORIE DEPRIVATION

PROTEIN DEFICIENCY

MICRONUTRIENT DEFICIENCY

Picture Source: Google images

Three major dimensions of hunger

Pulses Panchayat - Edaiyappatti Village

Overcoming Protein Hunger : Pulses Revolution

2016: International Year of Pulses

Biofortification and Zero Hunger Challenge : 3 Major approaches

1. Naturally occurring biofortified plants like moringa,

sweet potato, nutri-millets and fruits and vegetables, as

well as milk, eggs and other forms of animal protein.

2. Biofortified varieties selected by breeding and

selection, eg, iron rich pearl millet and zinc rich rice

3. Genetically biofortified crops like Golden Rice and iron

rich rice (after appropriate regulatory clearance)

Cultivate and Consume

Evergreen Revolution is the Pathway

o World requires 50% more

rice in 2030 than in 2004

with approximately 30%

less arable land of today

o Mainstreaming ecology in

technology development

and dissemination is the

road to sustainable

agriculture

Green Revolution : Commodity-centred increase in productivity

Change In plant architecture, and harvest index

Change in the physiological rhythm-insensitive to

photoperiodism

Lodging resistance

Evergreen Revolution : increasing productivity in perpetuity without associated ecological harm

Organic agriculture : cultivation without any use of chemical inputs like mineral fertilizers and chemical pesticides

Green Agriculture : conservation farming with the help of integrated pest management, integrated nutrient supply and integrated natural resource management

If farm ecology and economics go wrong, nothing else will go right

From Green to an Ever-green Revolution Pathways

o Minor genes based resistance to yellow rust, PBW343 has now become highly susceptible yo yellow rust

o Non-1B-R translocation base

o Area covered during: 2013-14 : 6.0 m ha

o Total production @ 5.5 t/ha : 33 million tons

o Approximate value @ Rs. 13000/t: 42,900 crores

o Additional return to farmers Rs. 6,000 crores

HD2967 PBW343 HD2967

HD 2967: A Miracle Wheat for NWPZ and NEPZ

QTL Pyramided Line with Heat and Drought Tolerance

P159-2 /P 157-8: QTL

pyramided line

(HI1500-Donor) DBW43: High yield

Pusa Basmati 1121 Pusa Basmati 1509

oReduced height

oEarliness

oNon-lodging

oNon-shattering

Pusa Basmati 1509

Pusa Basmati

1121

Milled rice

Cooked rice

There is need

for information

on functional

genomics of

cooked kernel

elongation and

volume

expansion in

Basmati rice

Impact of Public Sector Research : Basmati Revolution

oTotal Export (2013-14): 4.0 million tons

oDomestic consumption : 4.0 million tons

o Annual expenditure on research: Rs. 2 crores

US $ 5.5

billion

(Year)

(Rs.

in

cro

res)

5000

10000

15000

20000

25000

30000

35000

2009-10 2010-11 2011-12 2012-13 2013-14

10889 11354

15449

19391

33000

Integrating conventional breeding techniques with next generation genomics techniques can accelerate progress High through put methodologies: Next Generation Sequencing (NGS) – to understand sequence

variations Transcriptomics – an offshoot of NGS – to study RNA level

differences Proteomics – to understand protein modifications Epigenomics – to investigate DNA modifications Phenomics – Large-scale high throughput phenotyping with very

high time and spatial resolutions

Mendelian to Integrated Breeding : Rapid Progress

Families Common name Scientific name (genotypes sequenced)

Ploidy level Estimated genome size

Poaceae Rice Oryza sativa 2n=2x=24

389 Mb

Bread wheat Triticum aestivum (Chinese Spring/ CS42)

2n=6x=42 (AABBDD)

17 Gb

Einkorn wheat Triticum urartu (G1812/PI428198)

2n=2x=14 (AA)

4.94 Gb

Tusch’s goatgrass Aegilops tauschii (AL8/78)

2n=2x=14 (DD)

4.36 Gb

Maize Zea mays (B73) 2n-=2x=20 2.3 Gb

Sorghum Sorghum bicolor (Moench)

2n=2x=2- 730 Mb

Barley Hordeum vulgare (Morex)

2n=2x=14 5.1 Gb

Genome Information on Crops

Genome information deluge!

Since 1998 many genomes have

been sequenced with due to

Improvements in technologies

Connecting ‘omics’ data with

field level experiments through

a ‘Systems approach’ is the key

to realize the dream of

Evergreen Revolution

o Clustered, regularly interspaced, short palindromic repeat (CRISPR)/ CRISPR-associated protein 9 (Cas9) system is a novel molecular tool for site-specific genome modification

o Targeted editing of functional genes which was not possible until recently is possible with CRISPR.

o Possibility of just modifying existing genes and not introducing new genes

o Possibility to generate marker-free plants that can be rigorously selected using conventional breeding techniques for the desired functions and released as improved varieties

CRISPR – a new technology with great potential for integrated crop breeding

Jennifer A Doudna & Emmanuelle Charpentier Science, 26 Nov 2014, vol 346 Issue 6213

The high throughput and low sequencing costs

resulted in an emerging breeding methodology

designed to identify high density DNA marker

information to accurately predict the genetic value of

breeding candidates for complex traits (Genotyping

By Sequencing – GBS)

Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS)

tool to accelerate plant breeding

Marker Assisted Breeding IR 38 x Jeerige sanna

BI 33 x Jeerige sanna

Azucena x Moromutant

Five mapping populations have been developed and purified. Molecular markers for genes associated with iron uptake, transport and accumulation have been designed. Marker Assisted Selection is eligible for organic certification

Source : Indian Biofortification Network

Era of Biofortification : Golden Rice

o Swarna

o MTU1010

o BPT 5204

o ASD 16

o ADT43

o IR64

o IR36

Sw

arn

a

Gold

en S

warn

a

Source : IARI, New Delhi

Beta-Carotene-enriched Hybrids

0

5

10

15

20

25

Vivek QPM-9 Vivek Hybrid-27

HM-4 HM-8

2.03 1.97 1.85 2.54

21.51

17.02

12.49

21.64

Target hybrids: VQPM9

Vivek Hybrid 27 HM 4 HM 8

Low Erucic Acid Mustard Varieties

Average seed yield - 20.25 q/ha, Oil content - 36.55% Maturity : 140 days, NWPZ

Pusa Mustard 24

Pusa Mustard 29

Seed yield : 21.69 q/ha 1000-seed weight : ~4.0 g Oil content : 37.2% Maturity : 143 days

Moderately tolerant to high temp at seedling & maturity

780

bp

Line 4 Homozygous plants NT P

(b)

650bp

Line 12 Homozygous Transgenic

plants

H2O

M

NT P

(a)

Tissue specific expression of ferritin gene from

mangrove in rice for iron fortification

Avicennia marina Transgenic Rice lines

Stable inheritance of transgenics

Am Fer

Am Fer

Am Fer

Genetic map of Am Fer in transgenics

Source : MSSRF

Sea Level Rise o Global mean sea level has risen by 0.19 [0.17 to 0.21]m, estimated

from a linear trend over the period 1901–2010

o Between 1993 and 2010, the rate was very likely higher at 3.2 [2.8 to 3.6] mm yr–1

o Ocean thermal expansion and glacier mass loss are very likely the dominant contributors to global mean sea level rise during the 20th century

o Global mean sea level will continue to rise during the 21st century. Under all RCP scenarios the rate of sea level rise will very likely exceed that observed during 1971–2010 due to increased ocean warming and increased loss of mass from glaciers and ice sheets

o As the ocean warms, and glaciers and ice sheets reduce, global mean sea level will continue to rise, but at a faster rate than that have been experienced over the past 40 years

Source: SPM, IPCC AR-5

Sea Water Farming

(Sea water constitutes 97% of the world’s water resource)

Sylvi - Aquaculture

Innovations in below sea level farming in Kuttanad

COCONUT - ONE RICE - ONE FISH

Punja season November- February

Low chemical input or Organic Yield- 4.2 t/ha

April- October Monoculture – Giant Prawn (Macrobrachium rosenbergii) Polyculture*- Indian major carps or common carps or Silver carps and grass carps and Giant Prawn Yield- Rice: 4.2 t/ha Fish- Prawn: 480 kg; Carp : 300 kg.

* Recommended practice

Globally Important Agricultural Heritage Sites

Genetic Garden of HALOPHYTES at Vedaranyam

Obligatory halophytes Facultative halophytes

Tolerate high concentration of sodium salts > 3 times of seawater salinity Even demand high NaCl for survival and reproduction 1560 species

Most of the species tolerate only moderate level of salinity Reproduction requires low saline condition Mangroves 60 species

Converting Sea Water into Fresh Water through Halophytes

Deepwater (floating) rice has

three special adaptations:

i. ability to elongate with the

rise of water levels;

ii. develop nodal tillers and

roots from the upper

nodes in the water

iii. the upward bending of the

terminal part of the plant

called 'kneeing' that keeps

the reproductive parts

above the water as flood

water subsides

Genes for Climate Resilience

Genetic Shield against Sea Level Rise

Mangrove Forests

10 days 1 month

CTRL Transgenic C T

Salt tolerant Rice Plants with Mangrove Genes

Transgenic DC2 Control (UT)

Characters

White ponni

with 150mM

NaCl

Transgenic

with 150mM

NaCl

Plant height (cm) 95.10 104.95

No. of productive tillers 9.90 14.20

Panicle length (cm) 17.08 22.45

No. of grains per

panicle

134.60 174.80

100 grain weight (g) 1.45 1.63

Yield per plant (g) 20.30 34.75

Rice plants with Mangrove Genes and Promoter

Performance Evaluation

World must produce 60% more food by 2050 to avoid mass unrest - UN

Agriculture in the 21st century faces multiple challenges: it has to produce more food and fibre to feed a growing population with a smaller rural labour force, more feedstocks for a potentially huge bioenergy market, contribute to overall development in the many agriculture-dependent developing countries, adopt more efficient and sustainable production methods and adapt to climate change.

- Global Agriculture towards 2050 (FAO)

“Farming looks mighty easy

when your plough is a pencil,

and you at a thousand miles

from the corn field”

- Dwight D Eisenhower

Source : Google Image

Need for Strengthening Scientist - Farmer Linkages