Plant Genetics and The Future of Food
Professor Pamela Ronald
Dept. Plant Pathology and the Genome Center
Institute of Food and Agricultural Literacy
University of California, Davis

BLS
BLS
BLB BLB BLB
BLB
BLB BLBBacterial blight of rice
Xanthomonas oryzae pv. oryzae (Xoo)
What are the gene6c components
controlling rice/Xoo interac6ons?

Oryza longistaminata

BLS
BLS
BLB BLB BLB
BLB
BLB BLBXa21: Broad-spectrum resistance to Xoo identified
in the wild species Oryza longistaminata
Gurdev
Khush
UC Davis
International
Rice Research
Institute

ENGINEERED
WITH
THE XA21 GENE
CONVENTIONAL
Song et al., 1995

Ronald and Beutler, Science, 2010
1995
XA21
KKinase
Rip1
Text
TLR4
1998
TIR
Plant and Animal Immune Receptors
Pelle
1996
TIR
TOLL
?
Aspergillus fumigatus
Homo sapiens
Neisseria meningitidis

Pruitt et al., 2015 Science Advances
Pruitt et al., 2017 New Phytologist
Microbial raxX is required for activation of
XA21-mediated immunity
RaxX
XA21
Xoo
RaxX
RaxX is a small sulfated protein
SS
S

RaxX21 is similar to the plant peptide hormone
PSY1
• PSY1 is a secreted 18 amino acid peptide.
• PSY1 is sulfated by the plant TyrosylProtein
SulfoTransferase (TPST1).
• PSY1 and TPST1 have homologs in many plants
including Arabidopsis and rice.
• PSY1 promotes cellular proliferation and
expansion

Live root imaging of Arabidopsis tpst1
seedlings treated with RaxX21-sY
Wei Feng
Jose Dinneny
Mock RaxX21-sY

Rice
PSY receptor XA21
Immune response
RaxX
PSY
PSY
PSY
RaxX
Xoo
RaxX
Growth
???
Hypothesis: RaxX is a mimic of the growth promoting
PSY (peptide sulfated on tyrosine) peptides.

• Immune receptors in plants
and animals are remarkably
similar
• Bacterial pathogens produce
peptide hormone mimics
hypothesized to give a
selective advantage

Engineering Rice for Tolerance to Submergence

25% of the world’s rice is grown in flood-prone areas
In Bangladesh and India alone, 4 million tons of rice, enough to
feed 30M people, is lost every year to floods
An old rice
variety,
highly
tolerant to
submergence,
was found in
Eastern India
X

Genomic DNA
Cloned DNA
SSR1A
Genetic Markers
A211rf
The Sub1 region contains genes encoding ethylene response
factor (ERF)-genes: Sub1A, Sub1B and Sub1C
Xu et al., Nature. 2006.
Jung, An, Ronald. Nature Reviews Genetics. 2008.
ERFs are known regulators of stress tolerance
Kenong Xu
Sub1A
Sub1B
Sub1C
DNA sequence atgccgatggaaccatgccgatggaaccatgccgatggaaccatgccgatggaaccatgccgatggaaccatgccgatggaaccatgccgatggaaccatgccgatggaacc

Genetic Engineering Validates Sub1A function

M
202(Sub1)
M
202(Sub1)
Photo: Yufan Zhou, Ronald Lab
CONVENTIONAL
ENGINEERED
WITH
THE SUB1A GENE

Marker assisted breeding to engineer submergence tolerant
rice for farmers
David Mackill, Abdel Ismail and colleagues in the Philippines, India and Bangladesh

Conventional breeding
Marker-assisted breeding
Variety with desired trait Farmers favorite Hybrid
Farmers favorite
with desired trait
Slow
Fast
Imprecise
Precise

Sub1 Time-lapse sequence
IR64 + Sub1 vs. IR64
14 June to 16 October 2007
IRRI ES Plot G14

Performance of Swarna-Sub1 in farmers’ fields
2008, Gotha, UP, India
Swarna
Swarna-Sub1
3-5 fold yield increase

Video courtesy of Gene Hettel IRRI
“I was surprised
and happy when
I saw that the
Sub1 rice
survived the
flood”
Harir Danga farmer, Bangladesh

Raut family
Village of Naugaon,
Orissa, India
In flooded fields in India, villagers were
able to harvest more rice for their families
“Because of the Sub1
variety my family had
more to eat this year
and more money to
spend”
Video courtesy of Gene Hettel IRRI

Samba
Samba-Sub1
Samba-Sub1
IR64-Sub1
IR49830 (Sub1)
IR64
IR42
IR64
IR64-Sub1
Samba-Sub1
IR49830 (Sub1)
Samba
IR64
IR64-Sub1 IR49830 (Sub1)
IR42
IR64-Sub1
IR64
IR49830 (Sub1)
IR49830 (Sub1)
IR42
Samba
IR42
Samba
Xu et al., Nature 2006; Slide Courtesy of D. Mackill
Sub1 is sufficient to confer tolerance to
nearly all intolerant varieties (3-5 fold yield increase)
New Sub1 lines after 17 days submergence in IRRI field

Chen et al; In prep
Xu et al., Nature. 2006
Fukao et al, 2006. Plant Cell 18: 2021-2034
ethanolic
fermentation
genes
Submergence
GA
Ethylene
Sub1ASub1C
RAmy3D α-expansins
Sus3
Pdc2
Pdc4
Adh1
Adh2
Cell elongation
&
carbohydrate breakdown
}
ethanolic
fermentation
genes
The Sub1 locus activates a “hold your breath” strategy that conserves
the shoot meristem and energy reserves until the flood subsides
SBP

New Tools for Genetic Analysis

Arabidopsis genome sequence:
2000: 7 years, $70 million, 500 people
2017: 4 days, $1K
Whole Genome Sequencing/Gene Discovery
D’Hont et al., 2012

Nipponbare
Kitaake
Fast neutron
irradiation
Sequenced 1504 mutants
M2M1 M3
10,000 seeds 7,000 lines Storage
Li et al., 2017, Plant Cell, In Press and BioRxiv
Li et al., 2016, Molecular Plant
Creation of a sequenced rice mutant population for forward and
reverse genetics

1504 lines sequenced (45 fold coverage)
91,513 mutations affecting 32,307 genes
58% of all rice genes affected
Li et al., 2017, Plant Cell

GENOME-WIDE DISTRIBUTION OF FN-INDUCED
MUTATIONS
FN-induced mutations are distributed evenly across the genome.

MUTATIONS AND AFFECTED GENES
33
SBS: single base substitutions; DEL: deletions; INS: insertions; INV:
inversions; TRA: translocations; and DUP: tandem duplications.
Deletions mutate the greatest number of genes.

http://www.inetbio.org/ricenet/.
Computational biology identifies genes and
networks controlling valuable agronomic traits
Linkage of ~70% of the 41,203 rice genes
50 million data points; 5 species

35
Iden6fica6on of a gene networks predicted to
control the rice stress responses
Lee, Marcoce and Ronald. 2011. PNAS Lee et al., 2015, NAR

WT(ubi-Xa21) Mutant
Identification for a
rice mutant
displaying deep
primary roots
using 3D
phenotypic and
genetic
cosegregation
analysis
Images: Kevin Lehner (Benfey Lab) Topp et al., PNAS 2013

How do you Know Foods with New Genes are Safe to Eat?

Andrew Campbell
Fake News Plagues Ag and Food

Where do farmers get
their seeds?
The UC Davis Institute for Food &
Agricultural Literacy
Gluten probably won’t kill you
and a gluten-free diet probably
won’t either

• Plant crops with enhanced resilience
to the changing climate
• Enhance food security and nutri6on
• Support farmers and rural
communi6es
• Keep food affordable
• Foster soil fer6lity, biodiversity and
ecologically based farming prac6ces
Goals of sustainable agriculture

Collaborators
Dave Macill, Kenong Xu (UC Davis/IRRI)
Jürg Felix, Hubert Kalbacher, Markus Albert
(University of Tübingen, Germany)
Youssef Belkhadir (Gregor Mendel Institute, Austria)
C Petzold, L Chan (JBEI/LBNL Berkeley, USA)
K Lehner, P Benfey (Duke University)
Jose Dinneny and Wei Feng
(The Carnegie Institute of Plant Biology, USA)
E Marcotte, Michelle Robinson and Jenny Brodbelt
(UT Austin, USA)
Insuk Le (Yonsei University)
Xiang Li and Chang Liu (UC Irvine)
Ronald Lab
Anna Joe
Mawsheng Chern
Rory Pruitt
Guotian Li
Ben Schwessinger
Nick Thomas
Furong Liu
DeeDee Luu
Tsung Chi Chen
Rashmi Jain
Tony Wei
Daniel Caddell
Randy Ruan
Weiguo Zhang
Shannon Albers