GenomicStrategies.pptx

porcupineideaΒιοτεχνολογία

16 Δεκ 2012 (πριν από 4 χρόνια και 8 μήνες)

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. .RajeshP N
. ’ HenryT Nguyens Laboratory
Divisionof PlantSciences and
National Center for SoybeanBiotechnology
Genomic Strategies For
Soybean
Oil ImprovementAnd
Biodiesel Production



Team Members
Breeders
Grover Shannon
J eongLee
DavidSleper
Molecular Biologists
RajeshKumar
BabuValliyodan
Bioinformaticists
Trupti J oshi
DongXu
/Geneticists Genomicists
HenryNguyen
Xiaolei Wu
Non renewable energy
NR
E
RE
Ø

Fossil fuels in use since
5000 years
Ø
Ø

Egyptians used for medicine
and light
Ø
Ø

~ % 80 of the world's
commercial

energy
Ø
Ø

No potential renewable
energy

systems to generate
more than a

fraction of the power by
fossil fuels
US Renewable Energy Consumption
(2008)
v
% Only 7 from renewable
sources
v
v
- , RE Solar energy
, hydroelectric

, wind biomass and
others
v
v
% Biomass comprises of 53
v
v
Biofuel reduces net CO
2
emission
v
v
Also CO and other
pollutants
v
Soybean oil- a promising renewable energy
resource
Ø
Palmitic (11%), Stearic (4%), Oleic (23%), Linoleic
(52%) and Linolenic (8%) fatty acids
Ø
Ø
Yields 93-320% more energy than input
Ø
Ø
73% biodiesel from soybean
Ø
Ø
Releases 100 and 12 times less N
2
and P

Ø
In US, 650 MGY production; 3000MGY capacity
(2008)
(Biodiesel 2020: A Global Market survey)
Ø
Currently contributes 6% diesel use
Ø
Ø
. ; . Hill etal 2006 Fehr etal
2007
Economical importance
v
Seedspecific over expressionof fungal DGAT
from


.% 20to215 byweightoil contentinsoybean
( )Monsanto
v
v
= Incremental increaseinoil Anadditional
./. $179mt


(
://..http wwwcbot com
; , )March10 2008
v
v
, . = In the US 704 million metric tons an
. increased crop value of more than $126
billion

(
://.../.http wwwfas usda gov oilseeds_arc asp
;
/)2007 08
. Lardizabal et al
2008
: NCSB Objectives and strategies
Genomics
Biotechnology
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diversity
Quantitati
ve
Genetics
Bioinformati
cs
Genetic
factors
Soybean oil
improvement
Plant
s
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( )Algae
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engineering
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Ø
( )Plant materials 690

- , Maturity groups III IV and V

- FA and protein extremes
Ø
Ø

Genome wide scanning
using SSRs
Ø
Ø

Phylogenetic analysis
Ø
Ø

Four major clusters
Ø
Ø

. – . Diversity 057 096
( - .)mean 086
Ø
Ø

SNP assay of 192 diverse
germplasm
Ø
Ø

, Phenotyping for fatty acids


protein and
carbohydrates
Ø
Ø

Association mapping
I
I
I
III
IV
Genomics: Quantitative Genetics
Population development
Ø
Ø
Selection of 30 Diverse PI
lines
Ø
Ø
Crossing with Elite this
summer
Ø
Ø
5000 RIL population
Ø
Ø
SNP genotyping
Ø
Ø
High resolution QTL
mapping

. Yu et al
2008
Nested Association
Mapping
Genome
mining
367 lipid
genes
Full length gene
discovery
Promoter
prediction
Comparative
genomics
Phylogenetic
analysis
Conserved domain
prediction
/ SNP discovery Pathway
mapping
: Genomics Bioinformatics
Genetic Engineering for Oil Content
Ø
In Arabidopsis

-
Over expression of yeast SLC1
(Zou et al. 1997)

-
At
DGAT1

(Jako et al. 2001)

Ø
In Major Crops

-
Maize: PH09B (ancestral maize DGAT1 allele)
(Zheng et al. 2008)

-
Soybean: Fungal DGAT2A
(Lardizabal et al. 2008)



Challenge: Impact on starch, protein and
yield
Biotechnology - Strategy

Yeast expression

Gene source
Yarrowia
lipolytica

, ACLs
ACH

, Soybean
Arabidopsis

cb5
High Seed Oil Content
Yeast
Plants
: . Courtesy Dr Rajesh
Kumar
Arabidops
is
Soybea
n
PUFA modulation
Oleic acid
Ø
One double bond - greater oxidative
stability than linoleate and linolenate
Ø
Ø
Reduces cholesterol, transfats
Ø
Ø
Soy diesel, lubricants and cosmetic
products
Ø
Ø
Average about 23% in commercial
genotypes
Ø
Ø
Oleic acid content >50% is desirable
Ø
Ø
Ø
High oleic acid lines
N98-4445A with about 60% oleic acid
(Burton et
al., 2006)


{
Unstable across environments (Oliva et al.,
2006) }
M23 with 45% oleic content
(Takaki and Rahman, 1996)
A transgenic line from DuPont Nemours Co
with 80% oleic acid
{ } Patent Protection
Inheritance of oleic acid
Entry
Combinations
Gen
1
Jake x PI283327
F2:5
386
2
Jake x PI416908
F2:5
285
# of lines sampled for DNA
: .% - .%; : .%Pop 1 183 753 means 361
: .% - .%; : .%Pop 2 204 666 means 410
High oleic PIs is rare in late
maturity groups
: Poster Higher Oleic Acid from Soybean Plant Introductions for
Improved Oil Functionality
- , .. , , , . , Jeong Dong Lee PN Rajesh Kristin Bilyeu David Sleper Henry T Nguyen
. and J Grover Shannon
Golden gate assay
(Illumina)
. I DNA
labeling
. II Bead
assay
. III Bead
express
. IV Bead
studio
High throughput SNP genotyping and
analysis

. V Linkage and QTL
analysis
Significant accomplishments
Ø
Development of genetic materials
Ø
Ø
Capitalizing genetic diversity
Ø
Ø
First genome mining for lipid genes
Ø
Ø
High throughput technology
Ø
Ø
Genetic engineering
Ø
Ø
Metabolomics research
Ø
Challenge

-
To improve oil content and yield

- Systems biology approach


Ø
Ø
Metabolite profiling


- To determine biochemical and genetic networks



regulating seed development and composition
including oil


accumulation

: . Courtesy Dr Babu
Valliyodan
Acknowledgements
Molecular
Biologists
Plant Breeders
Genomicists
Bioinformaticists
Lab members
MSMC andUSB
US biodiesel production and
usage