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Investigation of Candidate
Loci Associated with Maize
Perennialism
Anjun Ma
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Key Words
Perennialism
Single-nucleotide-polymorphism (SNP)
Genotype-by-sequencing (GBS)
TASSEL pipeline
Genotype-phenotype association study
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Workflow
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SNP
Reference
Sequence
A
C
5’
5’
3’
3’
T
G
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SNP
CTTACGGTGACTGGTGAATGGTTATCGTG
CTTACGGTGACTGGTGAATGGTTATCGTG
CTTACGGTGACTGGTGCATGGTTATCGTG
CTTACGGTGACTGGTGCATGGTTATCGTG
CTTACGGTGACTGGTGAATGGTTATCGTG
CTTACGGTGACTGGTGAATGGTTATCGTG
CTTACGGTGACTGGTGAATGGTTATCGTG
CTTACGGTGACTGGTGAATGGTTATCGTG
CTTACGGTGACTGGTGAATGGTTATCGTG
CTTACGGTGACTGGTGCATGGTTATCGTG
CTTACGGTGACTGGTGCATGGTTATCGTG
CTTACGGTGACTGGTGCATGGTTATCGTG
CTTACGGTGACTGGTGCATGGTTATCGTG
CTTACGGTGACTGGTGCATGGTTATCGTG
CTTACGGTGACTGGTGCATGGTTATCGTG
CTTACGGTGACTGGTGCATGGTTATCGTG
AA x AA
AC x AC
Reference
Sample A
Sample C
Sample B
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GBS
Pros:
Highly reduced genome size (methylation-sensitive RE)
Inexpensive (~$1,700 per lane)
Good for SNP detection and GWAS analysis
Cons:
large amount of missing data (~40-80% with ApeKI)
Difficult to call heterozygotes in highly heterozygous
Technical missing is confounded with biological missing
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GBS Library
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TASSEL Pipeline
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SNP Filters and Scoring
The 1st SNP filter
GBSHapMapFiltersPlugin [Remove minimum allele
frequency (MAF) < 0.01]
The 2nd SNP filter
Remove missing data ratio > 20%
The 3rd SNP filter
Keep SNP with χ2 < 9.49
The 4th SNP filter
Remove neighboring SNPs with the same genotype
pattern
714,158
37,925
10,431
946
597
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Candidate Loci &
Verification
90% = 3.84
S7_5,862,253*
2,566 positions: 597 SNP + 1,969 simulation
S2_27,934,73999% = 4.89
95% = 4.17
Gene Position Annotation
GRMZM2G002642 27,769,950 to 27,776,452 Polypeptide: Ankyrin-like protein
Zm00001d002943 27,769,845 to 27,779,192 NA
AC199765.4_FGT008 27,777,537 to 27,779,027 Enzyme: Cellulase
Zm00001d002944 27,779,321 to 27,782,869 NA
• 2-1A primer set targets the 27,773,017
bp on chromosome 2
• χ2 = 9.16 (P=0.057), df = 4
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Next Step
Test for gene-gene interactions
Identify candidate gene function and
annotation
Gene-expression to regulatory pathway
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Current Work
Bicluster review
Background & publication reading
R/QUBIC package exercise
Revise
Regulatory response to acid-stress in Lactococcus lactis
MG1363
An application of biclustering
Revision and reconstruction
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Thank You