SSR

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SSR
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SSR

• SSR is also known as microsatellite or short
  tandem repeat (STR).
• segment of DNA consists of tandemly repeated
  unit, each between 1 and 10 base-pairs in length,
  such as (TG)n or (AAT)n.
• (TG)8 TGTGTGTGTGTGTGTG
• (AAT)6 AATAATAATAATAATAAT

(CA)8
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SSR

• it was studied in human (1989), and was found to
  be common in plants and animals.
• they are widely dispersed throughout eukaryotic
  genomes and often highly polymorphic due to
  variation in the number of repeat units.
• it shows high level of intra and interspecific
  variation.
• these high rates of mutation can be explained
  most frequently by slipped strand mispairing
  (slippage) during DNA replication.
• mutation may also occur during recombination
  during meiosis.

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Types of SSR
(A)n, (T)n, (C)n, (G)n mononucleotide
SSRs (AT)n, (CG)n, (GT)n dinucleotide SSRs
(ATT)n, (CCG)n, (GTA)n trinucleotide
SSRs (CCGG)n, (TATC)n tetranucleotide SSRs
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Types of SSR
Compound SSRs ATATATATCACACAATATATATCACACA
- (AT)4(CA)3 CCGCCGATATATATCCGCCGATATATAT -
(CCG)3(AT)4
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Types of SSR
Perfect SSR motifs AAAAAAAAAAAA -
(A)12 ATATATATATATATATAT -
(AT)9 CCGCCGCCGCCGCCGCCGCCG -
(CCG)7 Imperfect SSR motifs AAAAATAAAAAAAA
- (A)14 ATATATATACATATATAT - (AT)9
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How to detect SSR?

• these tandemly repeated units are usually
  franked by unique conserved sequences. Therefore,
  primers could be designed to amplify the SSRs.

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• detection of variation in SSR can be done using
  metaphor agarose gel or polyacrylamide gel.
• variation between individuals is because of
  different alelles due to the number of tandemly
  repeated units.

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Characteristics of SSR

• each SSR is controlled by one locus.
• each locus is controlled by many alleles (2-16
  alleles).
• mutational rates are high in microsatellite
  regions.
• it is co-dominantly inherited.
• the franking regions of SSR are conserved within
  species.

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Stutter Bands in SSR

• very often there are minor bands in addition to
  the major bands. These minor bands are called
  stutter bands (shadow bands) and they usually
  differ (smaller in size) from the major bands by
  a few nucleotides.
• these stutter bands arise from slipped-strand
  mispairing during PCR.

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SSR

• PCR amplification protocols used for SSRs are
  general standard.
• several PCR products (different SSR loci) can be
  pooled (multiplexing) for electrophoresis.
  Multiplexing allows rapid genotyping of large
  sample sizes across several loci.

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Multiplexing in SSRs
Locus A
Locus B
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EST-SSR

• EST (Expressed Seqeunce Tag) sequences are
  generated from cDNA (may be derived from cDNA
  library).
• these ESTs may contain SSR motifs. Tandem Repeat
  Finder (a computer software) is normally used to
  screen SSR motifs from ESTs.
• the SSR derived from EST is called EST-SSR. They
  normally contain trinucleotide repeat units.
• primers to amplify EST-SSR are designed based on
  the EST sequence franking the SSR motif.
• EST-SSR is particularly useful for QTL mapping.

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Transferability of SSRs

• SSR primers developed for one particular species
  are normally applicable across wide range of
  related species.
• Examples
• SSR transferability from lychee to pulasan is 58
• SSR transferability from lychee to logan is 92
• the rate of transferability depends on the
  evolutionary distance and the complexity of the
  genome of the species.
• transferability is normally higher for EST-SSRs
  compared to SSRs.

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SSR

• Disadvantage high cost in developing the SSR
  primers.
• Advantage primers developed for one particular
  species are normally applicable across wide range
  of related species.