justin n. vaughn, zenglu li group, uga - soybase.org...the genetic architecture of seed composition...
TRANSCRIPT
The genetic architecture of seed composition in soybeanis refined by genome-wide association scans across
multiple populations
Justin N. Vaughn, Zenglu Li Group, UGA
Song Q, . . ., Cregan P
Wen Z, . . ., Wang D
Bandillo N, . . ., Lorenz A
Sonah H, . . ., Nguyen H
Sonah H, . . ., Belzile F
Chicken shall not live on corn alone. . .
Foo
d an
d A
gric
ultu
re O
rgan
izat
ion,
Uni
ted
Nat
ions
Protein and oil content are negatively correlated . . .
Wilson 1978, ed. Boerma and Specht
Linkage group I (chromosome 20) QTL for high protein . . .
Chu
ng, e
t al.
2003
, Cro
p S
cien
ce
Genome-wide association (GWA) can reveal geneticarchitecture with high resolution . . .
Myl
es e
t al.
2009
Protein & oil content and population structure . . .
38.4 56.3 protein
38.1 47.9 protein
Phenotypic simulations for GWA in MS-2000 population . . .
Modified from Haun et al. 2011. Plant physiol..
Simple architecture “easy” to predict . . .
(Compressed Mixed-Linear)
(Multi-locus)
Complex architecture requires more critical evaluation . . .
Highest effect9th highest effect
Linkage group I (chr 20) in MS-2000; what about IL-1996? . . .
Linkage group I (chr 20) in MS-2000; what about IL-1996? . . .
Linkage group I (chr 20) in MS-2000; what about IL-1996? . . .
?
GWA scan by eye . . .
GWA scan by eye . . .
Allele has a very low frequency in many populations.
The LG-I protein QTL is easily missed because selection hasdriven it to low frequencies . . .
30.5-32.2MB“Domestication”LocusChung et al. 2014
Bandillo N, . . ., Lorenz A
Heritability is ~85%, but mostly “high-hanging” fruit . . .
Quantity and quality . . .
~$5 per ton per 10% increase of an amino acids
Foo
d an
d A
gric
ultu
re O
rgan
izat
ion,
Uni
ted
Nat
ions
No overlap between GWA scan and bi-parental mappingresults for cysteine and methionine . . .
Met+Cys QTL identified in Panthee et al. 2009, Molecular Breeding
Near conglycinin QTL,Panthee et al. 2004
Bi-parental cross Nested AssociationMapping (NAM) GWA
Resolution X ? √Missing alleles for a
trait Many Some Few
Backgroundindependence ofdiscovered allele
? √ √
Rare alleles √ ? X?
Why experimental design and genotyping platforms matters . . .
Thanks to
Zenglu LiLi LabRoger BoermaRandy NelsonQijian SongPerry CreganEster PeregrineJim Orf
Wayne ParrotTom JacobsMaria Ortega
Contact me ([email protected]) or Zenglu ([email protected])