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《Molecular Plant Breeding》 2015-01
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Characteristics and Distribution of SSR Loci in the Coding Region of Potato Genome and Functional Analysis of Their Encoding Proteins

Sun Tingting;Wang Dawei;Chen Le;Wang Weifeng;Gong Daping;Chen Yaqiong;Sun Yuhe;Key Laboratory of Tobacco Gene Resources, Institute of Tobacco Sciences, Chinese Academy of Agricultural Sciences;  
The amount, type and distribution of simple sequence repeats(SSR) show great differences in different species. This research uses Perl language to develop the program using for exeploring SSR loci in encoding region and software SSR Hunter to verify, that is to analyse the SSR loci distribution in potato genome encoding area. The following result show: 2 920 of all the 56 218 potato coding sequences are found carrying 3 512 SSR loci in total and among of all of the sequences carrying SSR loci, 2 519 sequences carry just one loci(That represent 86% of all the sequences carrying SSR loci); SSR loci contains Tri-nucleotide or Hexa-nucleotide repetitive units have the largest number, the amount of them is 2 358, 1 075 respectively, that means the sum of them represent 98% of all the SSR loci, while the rest type of repetitive unit have less occurrence; The quantity of the different repeats which make up SSR loci is 603; Hexa-nucleotide repetitive unit has at least three repetitions and Tri-nucleotide repetitive unit GAA has the largest number of repetition for 193 times. Under the law of natural selection, in encoding region, the SSR sequence length tends to be integral multiple of codon.Functional classification which piont to encoding region containning SSR loci was done using Pfam database,RPW8 resistant protein function was the most general one. The SSR loci speciality can be used to screen relative coding sequence of different potato spcies.
【Fund】: 国家863高技术研究发展计划项目(2012AA021801)资助
【CateGory Index】: S532
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