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The genetic architecture of seed composition in soybean is refined - - PowerPoint PPT Presentation
The genetic architecture of seed composition in soybean is refined - - PowerPoint PPT Presentation
The genetic architecture of seed composition in soybean is 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
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Chicken shall not live on corn alone. . .
Food and Agriculture Organization, United Nations
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Protein and oil content are negatively correlated . . .
Wilson 1978, ed. Boerma and Specht
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Linkage group I (chromosome 20) QTL for high protein . . .
Chung, et al. 2003, Crop Science
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Genome-wide association (GWA) can reveal genetic architecture with high resolution . . .
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Myles et al. 2009
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Protein & oil content and population structure . . .
38.4 56.3 protein 38.1 47.9 protein
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Phenotypic simulations for GWA in MS-2000 population . . .
Modified from Haun et al. 2011. Plant physiol..
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Simple architecture “easy” to predict . . .
(Compressed Mixed-Linear) (Multi-locus)
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Complex architecture requires more critical evaluation . . .
Highest effect 9th highest effect
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Linkage group I (chr 20) in MS-2000; what about IL-1996? . . .
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Linkage group I (chr 20) in MS-2000; what about IL-1996? . . .
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Linkage group I (chr 20) in MS-2000; what about IL-1996? . . .
?
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GWA scan by eye . . .
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GWA scan by eye . . . Allele has a very low frequency in many populations.
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The LG-I protein QTL is easily missed because selection has driven it to low frequencies . . .
30.5-32.2MB “Domestication” Locus Chung et al. 2014 Bandillo N, . . ., Lorenz A
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Heritability is ~85%, but mostly “high-hanging” fruit . . .
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Quantity and quality . . . ~$5 per ton per 10% increase of an amino acids
Food and Agriculture Organization, United Nations
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No overlap between GWA scan and bi-parental mapping results for cysteine and methionine . . .
Met+Cys QTL identified in Panthee et al. 2009, Molecular Breeding
Near conglycinin QTL, Panthee et al. 2004
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Bi-parental cross Nested Association Mapping (NAM) GWA Resolution
X ? √
Missing alleles for a trait
Many Some Few
Background independence of discovered allele
? √ √
Rare alleles
√ ? X?
Why experimental design and genotyping platforms matters . . .
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