Supplementary Table 16 *Identification of simple sequence repeats: their distribution and
primer design for chickpea genetics and breeding applications

Total number of scaffolds examined 7,163
Total size of examined sequences (bp)532,289,632
Total number of identified SSRs81,845
Number of SSR containing scaffolds1,769
Number of scaffolds containing more than 1 SSR1,150
Number of SSRs present in compound formation12,190
Distribution to different repeat type classes
(excluding mono-nucleotide repeats)
Number of di-nucleotide repeats47,127
Number of tri-nucleotide repeats29,442
Number of tetra-nucleotide repeats3,944
Number of penta-nucleotide repeats 781
Number of hexa-nucleotide repeats551
Primer pairs for SSRs
Scaffolds were used to design primer pairs1,108
Total numbers of primer pairs designed48,298

 

 

 

 

 

 

 

 

 

 

 

 

 

 

*Minimum of six unit for di-, and five units for tri-, tetra-, penta- and hexa-nucleotide repeats
were allowed for searching simple SSRs. Primers were designed on identified SSRs using the
Primer3 v2.3.4 (Rozen et al. 2000) with following criteria: (i) primer length ranging from 18 bp
to 24 bp with an optimum of 20 bp (ii) product size ranging from 100 bp to 350 bp;
(iii) annealing temperature (Ta) between 50-65 °C with 60 °C as optimum;(iv) GC % content in the
range of 40-60%.