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
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
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 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
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
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)