A single base change in a DNA sequence that occurs in a significant proportion (more than 1 percent) of a large population (Anand et al, 2003)A difference between the nucleotide at a corresponding locus in one genome as compared to another (Mc Nally et al, 2008).Variation can be
ith A t G C t T t iti
a SNP is a Single Nucleotide Polymorphism
either A to G or C to T transitions or A/G to C/T transversions.
the bulk of genetic variation is due to SNPs
Transitions are interchanges of two-ring purin (A G) or of one-ring pyrimidines (C T): they therefore involve bases of similar shape. Transversions are interchanges of purine for pyrimidine bases, which therefore involve exchange of one-ring and two-ring structures.
Transition are generated at higher frequency than Transversions.
Where Result Effect
In codingregion
May be silent, o.g.,UUG→CUG, leu in both cases sSNP Usually no change inphenotype
In coding region
May change amino acid sequence, e.g., UUC→UUA,phe to leu, Some characterize these as the leastcommon and most valuable SNPs, Many beingpatented
cSNP Phenotype change(may be subtledepending on aminoacid replacement andposition)
SNP effect (Shastry (2009) ; Mammadov, (2012)
In coding region
May create a "Stop"codon, e. g., UCA→UGA,ser to stop
Phenotype change
In coding region
May affect the rate of transcription(up-or down-regulate)
cSNP Possible phenotypeChange
Other regions
No affect on gene products(7).May act as genetic markers for multi-componentdiseases. These are sometimes called anonymous SNPsand are the most common.
rSNP
• Bi-allelic nature results in easier genotyping as opposed to SSRs • Allelic variation might be indicative of function• Association of alleles (2-states) with one another and with phenotypes is easily tested.• Easy to estimate linkage equilibrium/ disequilibrium (gametic phase)
Why use SNPs for mapping and association?
(McNally et al, 2008)
Article : GWAS mapping reveals a rich genetic GWAS mapping reveals a rich genetic
architecture of complex traits in architecture of complex traits in O.sativaO.sativapp
44K (44,100) SNP-Chip
High quality (< 4,5% missing data)~1 SNP per 10kb in 12 chromosomesSummary : Private SNP (spesific); Polymorphic SNP; MAF 0.05
Allele sharing across subpopulations and phenotype variation
Allele sharing clearly tracks subpopulation ~ PCA analysis
Mean IBS (Identical by State) value : TrJ~TempJ : 0,80I~Aus : 0,64
genetic & cultured barries in different subpopulation
TrJ
Indica
Aro
TempJ
IBS between Indv
Aus
Phenotype distribution : morphology, yield component and quality highly domestication
Idv based on phenotype
Naïve vs Mixed model : Phenotype distribution and GWAS for plant height
EMMA Prog : Mixed : adjusment on different level of pop, eliminate low PvalNaïve : no adjusment, high false +
Naïve & Mixed : detected SD1
Naive : detected DGL1 (chr1) and OsBAK1 (chr8)
Naïve : alleles segregate in only 1 subpopulation
Mixed : alleles segregate across subpopulation
Heterogenity in panicle length GWAS for flowering time
GWAS for panicle length :Indica : OsTB1, SLR1 & OsBRI1Aus : FZP, SSD1TrJ: OsLIC & MOC1
Heterogenity in O.sativa
HD1 detected in 3 environment
Research Progress in BB Biogen : GWAS mapping reveals heading and yield GWAS mapping reveals heading and yield
component traits in Indonesian rice (component traits in Indonesian rice (O.sativaO.sativa) ) germplasmgermplasmgermplasmgermplasm
Material genetic :
Wild species, 11
Genotyping : 467 acc, 1535 SNP-
chip, GoldenGateplatform
Released , 29
Introduction, 95
NIL, 34
Local , 136 Double Haploid, 104
Breeding lines, 47
Mutant, 11
Improved lines, 162
Graphical genotyping : Track Introgression
Adv Var
Chr1 Chr2 Chr3 Chr4
Chr5 Chr6 Chr7 Chr8
Chr9 Chr10 Chr11 Chr12
Landraces
Chr1 Chr2 Chr3 Chr4
Chr5
Chr9
Chr6
Chr10
Chr7
Chr11
Chr8
Chr12
0
50
0 10 20 30 40 50
million
Marka SNP Bunga Lapang Bunga Rm KacaGabah Isi Panjang Malai Bunga Lapang MLM
GWAS Heading Date in Indonesian Rice Germplasm
Preliminary Results
-50Chr1
SNP Locus : TBGI068738; Trait : Date to flowering LOC_Os01g72220 (Chr1: 41,837,949‐41,880,601) : WD domain, G‐beta repeat domain Function : progression of the flower over time, from its formation to the mature structure.
Genotipe : FWS22‐2‐2; Silugonggo dan Dodokan