Introduction:

The sequencing of the full nuclear genome of sesame (Sesamum indicum L.) provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or Simple Sequence Repeats (SSR) in crop genotyping, genetics and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to 3 primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78%) were polymorphic between the 3 genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/), which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies and breeding advancement in sesame, especially in developing countries.

 


Data Statistics

SSR Mining

Total

 

Total number of sequence scaffolds examined

4,449

 

Total number of identified SSRs

138,194

 

Number of sequence scaffolds containing SSR

1,279

 

Number of sequence scaffolds containing more than 1 SSR

877

 

Number of compound SSRs

28,666

 

Number of SSRs present in genic regions

20,167

 

Repeat type

Number of SSRs

Percentage

Mono-nucleotide

67,949

49.17

Di-nucleotide

59,886

43.33

Tri-nucleotide

9,116

6.60

Tetra-nucleotide

933

0.68

Penta-nucleotide

148

0.11

Hexa-nucloetide

162

0.12

Total

138,194

100

 


News
  1. 06/20/2017 SisatBase was online now.
  2. 05/05/2017 MISAweb was embedded in SisatBase.
  3. 04/25/2017 Main function of SisatBase was developed.
  4. 03/18/2017 SisatBase was developed.
  5. 02/10/2017 SSRs were identified in updated sesame genome.
  6. 08/15/2016 This project was started.

Collaborators
Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Sénégal.
     Ndiaga Cisse PI
     Komivi Dossa* Data Mining and experiment design
   
Oil Crops Research Institute, CAAS, PRC.
     Xiurong Zhang PI
     Jingyin Yu Database development and data mining
     Komivi Dossa* Data Mining and experiment design
   
ceraas ocri