SSR SSR SSR is also known as microsatellite
![SSR SSR](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-1.jpg)
![SSR - SSR is also known as microsatellite or short tandem repeat (STR). - SSR - SSR is also known as microsatellite or short tandem repeat (STR). -](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-2.jpg)
![SSR - it was studied in human (1989), and was found to be common SSR - it was studied in human (1989), and was found to be common](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-3.jpg)
![Types of SSR (A)n, (T)n, (C)n, (G)n – mononucleotide SSRs (AT)n, (CG)n, (GT)n – Types of SSR (A)n, (T)n, (C)n, (G)n – mononucleotide SSRs (AT)n, (CG)n, (GT)n –](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-4.jpg)
![Types of SSR Compound SSRs: ATATATATCACACA - (AT)4(CA)3 CCGCCGATATATAT (CCG)3(AT)4 - Types of SSR Compound SSRs: ATATATATCACACA - (AT)4(CA)3 CCGCCGATATATAT (CCG)3(AT)4 -](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-5.jpg)
![Types of SSR Perfect SSR motifs: AAAAAA - (A)12 ATATATATAT - (AT)9 CCGCCGCCGCCG Imperfect Types of SSR Perfect SSR motifs: AAAAAA - (A)12 ATATATATAT - (AT)9 CCGCCGCCGCCG Imperfect](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-6.jpg)
![How to detect SSR? - these tandemly repeated units are usually franked by unique How to detect SSR? - these tandemly repeated units are usually franked by unique](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-7.jpg)
![- detection of variation in SSR can be done using metaphor agarose gel or - detection of variation in SSR can be done using metaphor agarose gel or](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-8.jpg)
![Characteristics of SSR - each SSR is controlled by one locus. - each locus Characteristics of SSR - each SSR is controlled by one locus. - each locus](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-9.jpg)
![](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-10.jpg)
![Stutter Bands in SSR - very often there are minor bands in addition to Stutter Bands in SSR - very often there are minor bands in addition to](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-11.jpg)
![SSR - PCR amplification protocols used for SSRs are general standard. - several PCR SSR - PCR amplification protocols used for SSRs are general standard. - several PCR](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-12.jpg)
![Multiplexing in SSRs Locus A Locus B Multiplexing in SSRs Locus A Locus B](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-13.jpg)
![](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-14.jpg)
![EST-SSR - EST (Expressed Seqeunce Tag) sequences are generated from c. DNA (may be EST-SSR - EST (Expressed Seqeunce Tag) sequences are generated from c. DNA (may be](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-15.jpg)
![Transferability of SSRs - SSR primers developed for one particular species are normally applicable Transferability of SSRs - SSR primers developed for one particular species are normally applicable](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-16.jpg)
![SSR - Disadvantage: high cost in developing the SSR primers. - Advantage: primers developed SSR - Disadvantage: high cost in developing the SSR primers. - Advantage: primers developed](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-17.jpg)
- Slides: 17
![SSR SSR](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-1.jpg)
SSR
![SSR SSR is also known as microsatellite or short tandem repeat STR SSR - SSR is also known as microsatellite or short tandem repeat (STR). -](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-2.jpg)
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 = TGTGTGTG (AAT)6 (CA)8 = AATAATAAT
![SSR it was studied in human 1989 and was found to be common SSR - it was studied in human (1989), and was found to be common](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-3.jpg)
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.
![Types of SSR An Tn Cn Gn mononucleotide SSRs ATn CGn GTn Types of SSR (A)n, (T)n, (C)n, (G)n – mononucleotide SSRs (AT)n, (CG)n, (GT)n –](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-4.jpg)
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
![Types of SSR Compound SSRs ATATATATCACACA AT4CA3 CCGCCGATATATAT CCG3AT4 Types of SSR Compound SSRs: ATATATATCACACA - (AT)4(CA)3 CCGCCGATATATAT (CCG)3(AT)4 -](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-5.jpg)
Types of SSR Compound SSRs: ATATATATCACACA - (AT)4(CA)3 CCGCCGATATATAT (CCG)3(AT)4 -
![Types of SSR Perfect SSR motifs AAAAAA A12 ATATATATAT AT9 CCGCCGCCGCCG Imperfect Types of SSR Perfect SSR motifs: AAAAAA - (A)12 ATATATATAT - (AT)9 CCGCCGCCGCCG Imperfect](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-6.jpg)
Types of SSR Perfect SSR motifs: AAAAAA - (A)12 ATATATATAT - (AT)9 CCGCCGCCGCCG Imperfect SSR motifs: AAAAATAAAA ATATACATAT - (A)14 - (AT)9 - (CCG)7
![How to detect SSR these tandemly repeated units are usually franked by unique How to detect SSR? - these tandemly repeated units are usually franked by unique](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-7.jpg)
How to detect SSR? - these tandemly repeated units are usually franked by unique conserved sequences. Therefore, primers could be designed to amplify the SSRs.
![detection of variation in SSR can be done using metaphor agarose gel or - detection of variation in SSR can be done using metaphor agarose gel or](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-8.jpg)
- 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.
![Characteristics of SSR each SSR is controlled by one locus each locus Characteristics of SSR - each SSR is controlled by one locus. - each locus](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-9.jpg)
Characteristics of SSR - each SSR is controlled by one locus. - each locus is controlled by many alleles (216 alleles). - mutational rates are high in microsatellite regions. - it is co-dominantly inherited. - the franking regions of SSR are conserved within species.
![](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-10.jpg)
![Stutter Bands in SSR very often there are minor bands in addition to Stutter Bands in SSR - very often there are minor bands in addition to](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-11.jpg)
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.
![SSR PCR amplification protocols used for SSRs are general standard several PCR SSR - PCR amplification protocols used for SSRs are general standard. - several PCR](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-12.jpg)
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.
![Multiplexing in SSRs Locus A Locus B Multiplexing in SSRs Locus A Locus B](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-13.jpg)
Multiplexing in SSRs Locus A Locus B
![](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-14.jpg)
![ESTSSR EST Expressed Seqeunce Tag sequences are generated from c DNA may be EST-SSR - EST (Expressed Seqeunce Tag) sequences are generated from c. DNA (may be](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-15.jpg)
EST-SSR - EST (Expressed Seqeunce Tag) sequences are generated from c. DNA (may be derived from c. DNA 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.
![Transferability of SSRs SSR primers developed for one particular species are normally applicable Transferability of SSRs - SSR primers developed for one particular species are normally applicable](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-16.jpg)
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.
![SSR Disadvantage high cost in developing the SSR primers Advantage primers developed SSR - Disadvantage: high cost in developing the SSR primers. - Advantage: primers developed](https://slidetodoc.com/presentation_image_h2/8b6b15d4b0d25d63c4a3dcf61f80a898/image-17.jpg)
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.
Microsatellite instability
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