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Table 4 Allelic diversity attributes of new SSR markers as revealed across elite genotypes of arabica and robusta, and related coffee taxa

From: Development of new genomic microsatellite markers from robusta coffee (Coffea canephoraPierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies

Primer Id C. arabica (n = 8) C. canephora (n = 8) Coffea spp. (n = 12) Psilanthus spp. (n = 2)
  NA PA$ Allele range Ho He PIC NA PA$ Allele range Ho He PIC NA PA$ Allele range NA PA$ Allele range
CaM02 2 0 252–262 Duplicated loci 2 0 256–268 0.71 0.69 0.67 8 4a,c,k,l 252–278 2 0 262–272
CaM03 6 16 164–184 0.38 0.74* 0.70 6 0 171–194 0.63 0.88 0.83 12 5c,e,f,j,l 165–201 1 1m 187
CaM06 3 0 285–327 Duplicated loci 2 0 275–277 1.00 0.53* 0.56 4 1j 275–289 2 0 275–281
CaM08 1 0 210 Monomorphic 3 116 201–205 0.50 0.43 0.40 4 2b,l 142–201 1 1n 254
CaM09 1 0 135 Monomorphic 3 116 135–139 0.50 0.43 0.40 7 5a,b,g,l 124–211 NA -- --
CaM11 1 0 286 Monomorphic 1 0 286 Monomorphic 4 2c,h 278–295 NA -- --
CaM12 1 0 137 Monomorphic 4 110 122–137 1.00 0.65** 0.61 4 1g 124–137 2 0 131–137
CaM13 2 15 281–286 0.00 0.23 0.23 1 0 286 Monomorphic 7 3j,k 278–336 2 1n 255–283
CaM15 2 0 167–170 Duplicated loci 1 0 167 Monomorphic 2 1l 164–167 2 2m,n 153–156
CaM16 3 0 187–198 0.63 0.51 0.49 4 111 181–198 0.75 0.74 0.72 9 2c,l 177–198 2 0 191–193
CaM17 2 0 175–181 0.88 0.53 0.55 2 0 175–181 0.63 0.46 0.48 3 1l 162–181 2 0 175–181
CaM18 5 0 180–189 Duplicated loci 5 0 178–186 0.38 0.79** 0.75 12 5d,e,j,k 174–189 1 0 175
CaM20 2 0 184–192 0.13 0.46 0.48 3 0 192–200 0.13 0.42* 0.40 3 1d 192–198 NA -- --
CaM21 2 0 158–164 Duplicated loci 4 110 158–162 0.25 0.64** 0.62 9 3a,j,l 154–178 3 3m,n 161–172
CaM22 1 0 103 Monomorphic 6 29,16 99–110 0.43 0.86** 0.80 8 2c,l 82–122 1 0 88
CaM23 1 0 154 Monomorphic 1 0 154 Monomorphic 3 1l 140 154 2 2m,n 152–158
CaM24 2 0 191–197 0.00 0.50** 0.52 4 0 191–198 0.43 0.71 0.67 8 4a,b,g,l 178–204 2 2m,n 177–189
CaM25 4 0 182–185 0.13 0.53** 0.5 3 0 182–184 0.63 0.51 0.48 5 0 182–186 2 0 182–186
CaM26 3 0 252–259 0.00 0.43** 0.42 5 0 247–255 0.25 0.80** 0.76 11 3g,h,k 241–262 1 0 254
CaM27 3 0 150–169 0.13 0.34 0.33 3 0 161–169 0.88 0.68 0.64 8 2a,c 150–169 2 0 161–168
CaM30 2 0 216–229 0.13 0.13 0.12 2 0 216–218 0.63 0.46 0.48 7 2f,j 212–229 4 3m,n 210–225
CaM31 3 0 258–261 Duplicated loci 4 0 258–262 0.38 0.59 0.57 6 2h,k 258–267 1 1m 265
CaM32 4 0 127–145 0.88 0.69 0.68 5 114 145–158 0.75 0.72 0.68 10 2a,e 127–164 3 1m 133–145
CaM33 3 21,6 230–233 0.13 0.34 0.32 7 212,13 226–241 0.71 0.88 0.83 11 5b,d,f,i,k 213–143 1 1m 217
CaM34 2 0 194–199 Duplicated loci 2 0 198–200 0.00 0.23 0.23 5 2e,l 194–209 2 2m,n 166–171
CaM35 3 0 192–211 Duplicated loci 4 0 198–211 0.63 0.69 0.66 7 1g 186–211 1 0 204
CaM36 5 33,7,8 228–253 0.00 0.85** 0.78 7 6except 10,15 230–268 0.17 0.92** 0.86 10 8 a,c,e,f,h,i,h,l 181–262 1 1n 190
CaM38 6 14 214–226 0.38 0.86** 0.81 5 29,10,12,15 227–235 0.17 0.80** 0.74 6 2b,d 220–241 2 0 223–227
CaM39 2 0 174–186 Duplicated loci 3 0 180–194 1.00 0.59* 0.60 9 2b,h 174–205 3 3m,n 208–229
CaM40 5 15 230–240 0.40 0.82 0.75 7 116 226–242 0.50 0.91* 0.86 8 2d,e 232–246 3 0 233–239
CaM41 6 45,6,8 232–243 0.25 0.68** 0.65 5 19 234–242 0.25 0.81** 0.77 4 0 235–242 2 1n 237–244
CaM42 2 0 192–196 0.75 0.50 0.52 2 0 190–192 0.00 0.53* 0.56 7 2e,l 173–199 2 2m,n 191–195
CaM43 3 0 196–211 Duplicated loci 4 211,15 198–203 0.63 0.64 0.64 10 4b,c,e,f 188–224 2 1n 192–196
CaM44 2 16 215–217 0.00 0.23 0.23 2 0 224–226 0.00 0.23 0.23 10 3c,h,l 194–227 3 1n 221–227
CaM45 3 0 151–182 0.50 0.43 0.42 5 210,13 151–235 0.75 0.6 0.57 8 3d,i,k 147–214 3 1m 145–193
CaM46 4 23,6 208–228 0.38 0.69 0.65 6 114 208–223 0.38 0.82** 0.78 7 1e 208–234 2 1n 208–212
CaM49 3 0 191–194 0.38 0.68** 0.66 4 0 190–194 0.71 0.76 0.72 8 3g,j,k 186–194 NA -- --
CaM52 2 0 157–159 0.00 0.23 0.23 3 0 148–158 0.13 0.34 0.33 5 0 148–158 1 0 155
CaM53 1 0 172 Monomorphic 3 22 167–190 0.13 0.24 0.23 5 3i,j,l 125–197 2 2m,n 170–184
CaM54     No amplification 2 0 176–184 0.57 0.44 0.45 1 0 184 1 1n 164
CaM55 2 0 144–151 Duplicated loci 6 215,16 159–178 0.75 0.84 0.79 9 0 144–178 1 0 160
CaM57 3 0 146–188 Duplicated loci 5 0 102–176 0.63 0.77 0.73 9 2a,l 102–174 3 1m 102–156
CaM58 2 0 189–191 Duplicated loci 2 0 183–191 0.75 0.5 0.52 8 2b,l 181–224 2 0 192–193
CaM59 2 0 224–226 0.13 0.13 0.12 3 0 222 –225 0.88 0.69 0.67 4 0 222–228 3 0 222–228
Range 0–6 0–4 -- 0–0.88 0.13–0.86 0.12–0.81 1–7 0–6 -- 0–1.00 0.23–0.88 0.23–0.83 1–13 0–8 -- 0–4 0–3 --
Mean 2.7 0.37 -- 0.29 0.5 0.49 3.78 0.67 -- 0.52 0.63 0.62 7.07 2.42 -- 1.98 0.87 --
SD (±) 1.4 0.87 -- 0.28 0.22 0.21 1.73 1.13 -- 0.29 0.19 0.18 2.87 1.72 -- 0.79 0.95 --
SE (±) 0.3 0.13 -- 0.06 0.05 0.04 0.26 0.17 -- 0.04 0.03 0.03 0.43 0.26 -- 0.12 0.14 --
  1. $: Represents the genotype(s) as per Table 7, wherein the private allele is observed; *: Significant HW dis-equilibrium at P < 0.05; **: Highly significant HW dis-equilibrium at P < 0.01; Markers showing 100% Ho values in arabicas, which are expected to be the result of duplicated loci were not considered for various estimates.