Molecular characterization of oil palm germplasm is crucial in utilizing and conserving germplasm with promising traits. This study was conducted to evaluate the genetic diversity structures and relationships among 26 families of MPOB-Senegal oil palm germplasm using thirty-five microsatellite markers. High level of polymorphism (
The African oil palm (Elaeis guineensis) is the most productive among oil-bearing palms. It is endemic largely in West and Central Africa’s tropical lowlands, occurring extensively from 16°N in Senegal to 15°S in Angola [
Over time, the oil palm germplasm collections were screened using various molecular markers to evaluate and investigate the genetic variability between and within the population. Hayati et al. [
Molecular characterization of MPOB-Senegal oil palm germplasm is yet to be evaluated among and within the populations. Also, MPOB-Senegal germplasm populations are adapted to dry weather conditions from their original collection site, which implies that they may possess drought-tolerant characteristics. Therefore, for further exploitation and understanding of valuable genes, genetic diversity and population structures of Senegal germplasm collections should be evaluated using the simple sequence repeat (SSR) marker. Hence, this study was conducted to evaluate the genetic diversity and population structures of MPOB-Senegal oil palm germplasm using microsatellite markers.
Germplasm collection was carried out between July and August 1993 with assistance from the Ministry of Agriculture, Senegal. A total of 104 bunch samples belonging to eight different populations distributed across the southern and northern parts of Senegal were collected (Table
Geographical origins and palm number represent in each family of MPOB-Senegal oil palm germplasm.
No. | Family name | Location | No. of palms | Palm number |
---|---|---|---|---|
1 | SEN02.01 | 45 km from Ziguinchor | 7 | 172, 213, 229, 233, 267, 287, 292 |
2 | SEN02.04 | 6 | 67, 74, 119, 161, 165, 282 | |
3 | SEN02.05 | 6 | 20, 39, 68, 83, 86, 231 | |
4 | SEN02.06 | 10 | 1, 9, 88, 138, 141, 243, 364,383, 386, 410 | |
5 | SEN02.09 | 10 | 73, 105, 118, 124, 289, 343, 365, 368, 379, 408 | |
6 | SEN03.06 | 7 | 17, 192, 225, 250, 253, 277, 301 | |
7 | SEN03.07 | 10 | 29, 35, 37, 72, 254, 286, 353, 357, 359, 366 | |
8 | SEN04.01 | Dar Salam | 10 | 84, 94, 112, 169, 196, 200, 216, 248, 338, 369 |
9 | SEN04.03 | 10 | 22, 55, 77, 79, 109, 184, 206, 215, 294, 348 | |
10 | SEN05.01 | Babadinka 17 km de Ziguinchor | 10 | 120, 132, 227, 251, 262, 271, 335, 342, 351, 363 |
11 | SEN05.02 | 5 | 21, 69, 145, 249, 274 | |
12 | SEN05.03 | 10 | 128, 135, 239, 263, 297, 314, 333, 358, 367, 373 | |
13 | SEN05.04 | 6 | 48, 80, 140, 143, 244, 272 | |
14 | SEN05.05 | 9 | 28, 66, 78, 102, 133, 164, 171, 174, 264, | |
15 | SEN05.08 | 10 | 32, 93, 167, 176, 241, 247, 319, 344, 370, 396 | |
16 | SEN06.01 | Diarone | 7 | 96, 149, 252, 258, 276, 302, 305 |
17 | SEN06.08 | 10 | 45, 91, 163, 187, 207, 214, 228, 283, 336, 382 | |
18 | SEN07.03 | Djiticoumbon | 10 | 10, 89, 114, 130, 194, 376, 392, 398, 400, 402 |
19 | SEN07.04 | 9 | 31, 47, 58, 85, 115, 125, 246, 261, 298 | |
20 | SEN07.05 | 7 | 98, 117, 139, 146, 157, 210, 257 | |
21 | SEN07.08 | 7 | 56, 104, 127, 166, 236, 245, 255 | |
22 | SEN10.03 | Ebaniko | 10 | 23, 87, 110, 134, 173, 189, 278, 310, 323, 407 |
23 | SEN10.05 | 10 | 24, 75, 131, 177, 186, 208, 212, 230, 280, 334 | |
24 | SEN12.01 | Mboro | 9 | 2, 12, 26, 70, 147, 170, 193, 242, 273 |
25 | SEN12.02 | 7 | 4, 30, 54, 95, 183, 201, 222 | |
26 | SEN12.03 | 10 | 3,113, 126, 182, 203, 279, 340, 361, 389, 405 | |
Total | 222 |
The molecular characterization was carried out on a total of twenty-six families from eight populations. Spear leaf (unopened leaves) samples were collected from each palm during the trial; the number of collected samples varied from 5 to 10 palms per family based on the availability of palms with a total sum of 222 palms obtained (Table
A total of 35 highly polymorphic and reproducible markers were selected for this study. The information of the 35 markers was presented in Supplementary Table
Electropherogram profiles from the ABI 3730 DNA Genetic Analyzer showing allele peaks and sizes of some SSR loci (sEg00036, sMg00055, sEg00066, sEg00092).
SSR data were analyzed using Genemapper 4.1 software to identify the allele sizes of each marker. Electropherogram profiles (sample plots) were generated, and allele sizes for the markers were exported as data table for genotyping. Genetic diversity parameters such as allelic frequency, number of alleles per locus (
A total of 384 alleles were regenerated, the number of alleles per locus ranging from 4 to 21, with an average value of 10.971. Markers sMo00053 and sMg00133 detected the highest number of alleles (21), indicating that these markers are the most informative marker while sMg00027, sEg00189, and sEg00092 identified the least number of alleles, with each marker identifying 4, 5, and 6 alleles, respectively (Table
Allelic diversity indices of evaluated markers in Senegal oil palm germplasm.
Marker | |||||||
---|---|---|---|---|---|---|---|
sMg00093 | 13 | 3.346 | 2.147 | 0.871 | 0.542 | 0.485 | 0.612 |
sEg00035 | 7 | 2.154 | 1.393 | 0.417 | 0.155 | 0.242 | 0.281 |
sEg00151 | 8 | 3.192 | 2.007 | 0.752 | 0.465 | 0.407 | 0.536 |
sMg00050 | 13 | 3.885 | 2.614 | 1.034 | 0.492 | 0.555 | 0.783 |
sMo00023 | 10 | 3.962 | 2.783 | 1.113 | 0.659 | 0.607 | 0.784 |
sEg00126 | 11 | 3.115 | 1.859 | 0.731 | 0.277 | 0.409 | 0.642 |
sEg00041 | 9 | 4.885 | 3.311 | 1.322 | 0.677 | 0.675 | 0.819 |
sEg00025 | 7 | 2.654 | 2.177 | 0.808 | 0.594 | 0.498 | 0.613 |
sMg00055 | 9 | 2.923 | 1.964 | 0.776 | 0.634 | 0.457 | 0.536 |
sEg00066 | 8 | 3.269 | 2.141 | 0.878 | 0.549 | 0.511 | 0.663 |
sEg00036 | 10 | 4.423 | 2.759 | 1.153 | 0.632 | 0.601 | 0.715 |
sEg00092 | 6 | 2.577 | 1.415 | 0.476 | 0.283 | 0.257 | 0.283 |
sEg00189 | 5 | 2.038 | 1.423 | 0.401 | 0.234 | 0.236 | 0.289 |
sMg00234 | 11 | 3.654 | 2.748 | 1.072 | 0.296 | 0.604 | 0.775 |
sMo00077 | 9 | 2.769 | 1.659 | 0.561 | 0.247 | 0.303 | 0.370 |
sMg00192 | 13 | 4.885 | 3.207 | 1.308 | 0.644 | 0.666 | 0.825 |
sMg00077 | 10 | 3.846 | 2.494 | 1.037 | 0.549 | 0.565 | 0.736 |
sEg00009 | 10 | 4.577 | 3.496 | 1.331 | 0.909 | 0.702 | 0.792 |
sEg00061 | 7 | 3.385 | 2.673 | 1.063 | 0.892 | 0.620 | 0.673 |
sMo00081 | 10 | 4.115 | 2.880 | 1.144 | 0.584 | 0.610 | 0.727 |
mEgCIR0882 | 12 | 4.962 | 3.490 | 1.336 | 0.763 | 0.678 | 0.791 |
sMg00136 | 9 | 4.038 | 3.084 | 1.185 | 0.787 | 0.650 | 0.739 |
sMo00131 | 16 | 6.231 | 4.662 | 1.597 | 0.869 | 0.755 | 0.859 |
mEgCIR3546 | 13 | 4.077 | 2.843 | 1.121 | 0.717 | 0.609 | 0.727 |
sMg00025 | 9 | 3.192 | 2.498 | 0.978 | 0.791 | 0.577 | 0.649 |
sMo00053 | 21 | 4.192 | 2.820 | 1.085 | 0.524 | 0.567 | 0.771 |
mEgCIR3878 | 15 | 5.231 | 3.487 | 1.339 | 0.680 | 0.667 | 0.763 |
sMg00133 | 21 | 5.231 | 3.637 | 1.385 | 0.647 | 0.692 | 0.822 |
sMg00027 | 4 | 2.846 | 2.200 | 0.855 | 0.577 | 0.524 | 0.624 |
sMg00227 | 10 | 4.000 | 2.533 | 1.045 | 0.667 | 0.565 | 0.672 |
sMg00205 | 14 | 3.385 | 2.231 | 0.907 | 0.565 | 0.520 | 0.605 |
sMo00121 | 8 | 2.885 | 1.831 | 0.668 | 0.413 | 0.377 | 0.476 |
mEgCIR3282 | 18 | 5.154 | 3.496 | 1.372 | 0.631 | 0.690 | 0.797 |
mEgCIR0369 | 15 | 5.654 | 3.978 | 1.483 | 0.834 | 0.728 | 0.855 |
sMg00147 | 13 | 4.692 | 2.925 | 1.222 | 0.657 | 0.632 | 0.721 |
Mean | 10.97 | 3.869 | 2.653 | 1.024 | 0.584 | 0.550 | 0.666 |
Allelic diversity indices in families of Senegal oil palm germplasm.
Family | % | Chi2 test | |||||
---|---|---|---|---|---|---|---|
SEN02.01 | 3.486 | 2.425 | 0.923 | 0.558 | 0.503 | 94.29% | 0.81 |
SEN02.04 | 3.029 | 2.251 | 0.832 | 0.567 | 0.474 | 85.71% | 0.94 |
SEN02.05 | 3.371 | 2.540 | 0.950 | 0.542 | 0.523 | 91.43% | 0.93 |
SEN02.06 | 4.057 | 2.673 | 1.036 | 0.552 | 0.545 | 94.29% | 0.49 |
SEN02.09 | 4.343 | 2.772 | 1.079 | 0.591 | 0.560 | 100.00% | 0.33 |
SEN03.06 | 3.943 | 2.956 | 1.100 | 0.536 | 0.583 | 97.14% | 0.42 |
SEN03.07 | 4.257 | 2.681 | 1.078 | 0.563 | 0.568 | 100.00% | 0.36 |
SEN04.01 | 3.571 | 2.385 | 0.912 | 0.484 | 0.494 | 94.29% | 0.84 |
SEN04.03 | 3.914 | 2.598 | 1.018 | 0.619 | 0.551 | 97.14% | 0.31 |
SEN05.01 | 4.400 | 2.873 | 1.143 | 0.620 | 0.598 | 97.14% | 0.13 |
SEN05.02 | 3.686 | 2.886 | 1.084 | 0.697 | 0.594 | 97.14% | 0.57 |
SEN05.03 | 4.286 | 2.971 | 1.149 | 0.631 | 0.609 | 97.14% | 0.33 |
SEN05.04 | 3.429 | 2.565 | 0.995 | 0.600 | 0.558 | 100.00% | 0.16 |
SEN05.05 | 4.314 | 3.036 | 1.181 | 0.610 | 0.621 | 100.00% | 0.56 |
SEN05.08 | 3.971 | 2.592 | 0.992 | 0.614 | 0.530 | 100.00% | 0.28 |
SEN06.01 | 3.886 | 2.825 | 1.068 | 0.626 | 0.571 | 97.14% | 0.29 |
SEN06.08 | 4.429 | 2.864 | 1.147 | 0.709 | 0.600 | 100.00% | 0.04 |
SEN07.03 | 4.686 | 2.947 | 1.162 | 0.670 | 0.593 | 100.00% | 0.08 |
SEN07.04 | 4.029 | 2.852 | 1.035 | 0.583 | 0.538 | 94.29% | 0.38 |
SEN07.05 | 3.686 | 2.587 | 0.982 | 0.583 | 0.531 | 91.43% | 0.47 |
SEN07.08 | 3.571 | 2.610 | 1.003 | 0.584 | 0.554 | 94.29% | 0.88 |
SEN10.03 | 3.571 | 2.380 | 0.918 | 0.490 | 0.500 | 88.57% | 0.78 |
SEN10.05 | 4.171 | 2.818 | 1.102 | 0.586 | 0.586 | 100.00% | 0.59 |
SEN12.01 | 3.743 | 2.395 | 0.947 | 0.525 | 0.510 | 97.14% | 0.59 |
SEN12.02 | 3.200 | 2.301 | 0.893 | 0.564 | 0.508 | 94.29% | 0.77 |
SEN12.03 | 3.571 | 2.203 | 0.887 | 0.476 | 0.490 | 100.00% | 0.43 |
Mean | 3.869 | 2.653 | 1.024 | 0.584 | 0.550 | 96.26% |
SEN: Senegal;
Diversity indices provide important information regarding the rarity and commonness of species in a community. Shannon’s information index (
Among the families, the lowest
The entire 35 amplified SSR markers were polymorphic with the highest level (100%) across the families observed in SEN 02.09, SEN03.07, SEN05.04, SEN05.05, SEN05.08, SEN06.08, SEN07.03, SEN10.05, and SEN12.03. The lowest polymorphism level was recorded in SEN02.04 and SEN10.03 with 85.71% and 88.57% polymorphism. These results showed that most families from the southern part have higher genetic diversity than the northern part of Senegal (Table
The inbreeding coefficient within the families (
Fixation indices and estimates of
Locus | ||||
---|---|---|---|---|
sMg00093 | -0.116 | 0.115 | 0.207 | 0.955 |
sEg00035 | 0.357 | 0.447 | 0.139 | 1.548 |
sEg00151 | -0.142 | 0.133 | 0.241 | 0.788 |
sMg00050 | 0.114 | 0.372 | 0.291 | 0.610 |
sMo00023 | -0.086 | 0.159 | 0.226 | 0.857 |
sEg00126 | 0.323 | 0.569 | 0.363 | 0.438 |
sEg00041 | -0.003 | 0.173 | 0.176 | 1.174 |
sEg00025 | -0.193 | 0.030 | 0.187 | 1.084 |
sMg00055 | -0.389 | -0.182 | 0.149 | 1.429 |
sEg00066 | -0.075 | 0.171 | 0.229 | 0.839 |
sEg00036 | -0.052 | 0.116 | 0.160 | 1.316 |
sEg00092 | -0.100 | 0.001 | 0.091 | 2.483 |
sEg00189 | 0.012 | 0.192 | 0.182 | 1.121 |
sMg00234 | 0.510 | 0.618 | 0.221 | 0.879 |
sMo00077 | 0.184 | 0.332 | 0.181 | 1.132 |
sMg00192 | 0.034 | 0.220 | 0.192 | 1.049 |
sMg00077 | 0.027 | 0.253 | 0.232 | 0.825 |
sEg00009 | -0.295 | -0.147 | 0.114 | 1.949 |
sEg00061 | -0.438 | -0.325 | 0.079 | 2.916 |
sMo00081 | 0.043 | 0.197 | 0.161 | 1.302 |
mEgCIR0882 | -0.126 | 0.036 | 0.144 | 1.489 |
sMg00136 | -0.212 | -0.065 | 0.121 | 1.818 |
sMo00131 | -0.151 | -0.011 | 0.122 | 1.805 |
mEgCIR3546 | -0.177 | 0.013 | 0.161 | 1.298 |
sMg00025 | -0.371 | -0.220 | 0.110 | 2.022 |
sMo00053 | 0.076 | 0.321 | 0.265 | 0.693 |
mEgCIR3878 | -0.020 | 0.108 | 0.126 | 1.738 |
sMg00133 | 0.066 | 0.213 | 0.157 | 1.340 |
sMg00027 | -0.100 | 0.076 | 0.161 | 1.306 |
sMg00227 | -0.181 | 0.007 | 0.159 | 1.324 |
sMg00205 | -0.086 | 0.066 | 0.140 | 1.536 |
sMo00121 | -0.096 | 0.131 | 0.207 | 0.957 |
mEgCIR3282 | 0.086 | 0.209 | 0.135 | 1.608 |
mEgCIR0369 | -0.146 | 0.024 | 0.148 | 1.439 |
sMg00147 | -0.040 | 0.088 | 0.123 | 1.775 |
-0.050 | 0.127 | 0.174 | 1.338 |
In this study, a total of 83 private alleles occurred in most of the families of MPOB-Senegal oil palm germplasm except in SEN05.08 and SEN07.04. The distributions of rare alleles per locus among the families and the frequencies are presented in Supplementary Table
The frequency of private allele varied from 0.050 to 0.667 at each locus of the 35 markers of 26 families (Supplementary Table
The AMOVA results indicated that the highest genetic variation was 83% and occurred within the families, while only 17% genetic variation was observed among the families at
Analysis of molecular variance.
Source of variation | df | SS | MS | Est. Var. | % | |
---|---|---|---|---|---|---|
Between families | 25 | 1778.787 | 71.151 | 5.357 | 17% | <0.001 |
Within amilies | 196 | 4994.821 | 25.484 | 25.484 | 83% | <0.001 |
Total | 221 | 6773.608 | 30.841 | 100% |
df: degree of freedom; SS: sum square; MS: mean square; Est. Var.: estimated variance.
The genetic distance among the 26 families based on Nei’s genetic distance is summarized in Table
Pairwise population matrix of Nei genetic distance among the 26 families of MPOB-Senegal oil palm germplasm.
SEN02.01 | SEN02.04 | SEN02.05 | SEN02.06 | SEN02.09 | SEN03.06 | SEN03.07 | SEN04.01 | SEN04.03 | SEN05.01 | SEN05.02 | SEN05.03 | SEN05.04 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SEN02.01 | 0.000 | ||||||||||||
SEN02.04 | 0.252 | 0.000 | |||||||||||
SEN02.05 | 0.212 | 0.281 | 0.000 | ||||||||||
SEN02.06 | 0.163 | 0.100 | 0.197 | 0.000 | |||||||||
SEN02.09 | 0.215 | 0.223 | 0.217 | 0.171 | 0.000 | ||||||||
SEN03.06 | 0.231 | 0.229 | 0.223 | 0.168 | 0.187 | 0.000 | |||||||
SEN03.07 | 0.270 | 0.381 | 0.378 | 0.283 | 0.246 | 0.278 | 0.000 | ||||||
SEN04.01 | 0.277 | 0.302 | 0.272 | 0.228 | 0.290 | 0.190 | 0.391 | 0.000 | |||||
SEN04.03 | 0.296 | 0.267 | 0.337 | 0.258 | 0.295 | 0.275 | 0.428 | 0.226 | 0.000 | ||||
SEN05.01 | 0.247 | 0.262 | 0.323 | 0.224 | 0.310 | 0.278 | 0.403 | 0.258 | 0.233 | 0.000 | |||
SEN05.02 | 0.225 | 0.356 | 0.417 | 0.288 | 0.402 | 0.358 | 0.396 | 0.398 | 0.315 | 0.291 | 0.000 | ||
SEN05.03 | 0.380 | 0.403 | 0.435 | 0.389 | 0.392 | 0.333 | 0.460 | 0.424 | 0.406 | 0.264 | 0.394 | 0.000 | |
SEN05.04 | 0.297 | 0.381 | 0.427 | 0.306 | 0.429 | 0.392 | 0.435 | 0.407 | 0.342 | 0.209 | 0.284 | 0.374 | 0.000 |
SEN05.05 | 0.298 | 0.323 | 0.334 | 0.266 | 0.363 | 0.339 | 0.417 | 0.349 | 0.303 | 0.233 | 0.344 | 0.352 | 0.208 |
SEN05.08 | 0.202 | 0.274 | 0.252 | 0.189 | 0.217 | 0.275 | 0.374 | 0.283 | 0.250 | 0.214 | 0.249 | 0.314 | 0.217 |
SEN06.01 | 0.278 | 0.303 | 0.327 | 0.243 | 0.288 | 0.317 | 0.381 | 0.337 | 0.305 | 0.258 | 0.269 | 0.339 | 0.292 |
SEN06.08 | 0.309 | 0.356 | 0.405 | 0.295 | 0.344 | 0.375 | 0.405 | 0.389 | 0.372 | 0.300 | 0.309 | 0.325 | 0.331 |
SEN07.03 | 0.242 | 0.341 | 0.296 | 0.271 | 0.289 | 0.346 | 0.375 | 0.370 | 0.391 | 0.279 | 0.286 | 0.355 | 0.266 |
SEN07.04 | 0.288 | 0.375 | 0.348 | 0.299 | 0.356 | 0.390 | 0.468 | 0.370 | 0.405 | 0.274 | 0.398 | 0.448 | 0.317 |
SEN07.05 | 0.270 | 0.322 | 0.399 | 0.238 | 0.341 | 0.311 | 0.428 | 0.317 | 0.352 | 0.255 | 0.331 | 0.391 | 0.304 |
SEN07.08 | 0.217 | 0.287 | 0.341 | 0.228 | 0.256 | 0.238 | 0.374 | 0.307 | 0.245 | 0.202 | 0.269 | 0.339 | 0.318 |
SEN10.03 | 0.325 | 0.392 | 0.366 | 0.290 | 0.381 | 0.364 | 0.414 | 0.386 | 0.311 | 0.311 | 0.338 | 0.513 | 0.459 |
SEN10.05 | 0.249 | 0.308 | 0.341 | 0.246 | 0.385 | 0.306 | 0.442 | 0.336 | 0.300 | 0.256 | 0.266 | 0.416 | 0.319 |
SEN12.01 | 0.361 | 0.406 | 0.447 | 0.285 | 0.425 | 0.454 | 0.532 | 0.409 | 0.386 | 0.270 | 0.420 | 0.557 | 0.378 |
SEN12.02 | 0.255 | 0.385 | 0.343 | 0.263 | 0.365 | 0.353 | 0.487 | 0.365 | 0.356 | 0.269 | 0.306 | 0.441 | 0.398 |
SEN12.03 | 0.317 | 0.339 | 0.369 | 0.235 | 0.342 | 0.337 | 0.464 | 0.383 | 0.347 | 0.294 | 0.349 | 0.509 | 0.390 |
Family | SEN05.05 | SEN05.08 | SEN06.01 | SEN06.08 | SEN07.03 | SEN07.04 | SEN07.05 | SEN07.08 | SEN10.03 | SEN10.05 | SEN12.01 | SEN12.02 | SEN12.03 |
SEN05.05 | 0.000 | ||||||||||||
SEN05.08 | 0.191 | 0.000 | |||||||||||
SEN06.01 | 0.279 | 0.167 | 0.000 | ||||||||||
SEN06.08 | 0.312 | 0.238 | 0.201 | 0.000 | |||||||||
SEN07.03 | 0.292 | 0.163 | 0.163 | 0.252 | 0.000 | ||||||||
SEN07.04 | 0.194 | 0.204 | 0.319 | 0.330 | 0.231 | 0.000 | |||||||
SEN07.05 | 0.255 | 0.204 | 0.246 | 0.252 | 0.217 | 0.128 | 0.000 | ||||||
SEN07.08 | 0.275 | 0.241 | 0.254 | 0.339 | 0.246 | 0.296 | 0.246 | 0.000 | |||||
SEN10.03 | 0.454 | 0.369 | 0.382 | 0.433 | 0.384 | 0.420 | 0.405 | 0.294 | 0.000 | ||||
SEN10.05 | 0.344 | 0.272 | 0.316 | 0.323 | 0.300 | 0.335 | 0.293 | 0.235 | 0.157 | 0.000 | |||
SEN12.01 | 0.397 | 0.263 | 0.344 | 0.367 | 0.411 | 0.382 | 0.334 | 0.323 | 0.363 | 0.286 | 0.000 | ||
SEN12.02 | 0.364 | 0.221 | 0.292 | 0.302 | 0.309 | 0.324 | 0.248 | 0.209 | 0.333 | 0.246 | 0.189 | 0.000 | |
SEN12.03 | 0.398 | 0.240 | 0.325 | 0.353 | 0.378 | 0.363 | 0.307 | 0.259 | 0.322 | 0.263 | 0.109 | 0.115 | 0.000 |
SEN: Senegal.
Datasets of 35 SSR markers used in the study of 26 families of MPOB-Senegal germplasm were analyzed using Pop tree software, and the dendrogram was constructed for the result obtained (Figure
Neighbour-Joining (NJ) tree constructed for SSR data based on 26 families of MPOB-Senegal germplasm.
The evaluation of genetic diversity and relatedness among 26 families of MPOB-Senegal oil palm germplasm using 35 polymorphic SSR markers showed 384 alleles with a mean value of 10.97 alleles per locus. The number of alleles per marker ranged from 4 to 21 alleles. This was higher than the total number of alleles reported by Shah et al. [
The mean percentages of polymorphic loci of MPOB-Senegal germplasm using 35 SSR markers were 96.26%. This was higher than the mean values reported by Hayati et al. [
The comparisons of results of the percentage of polymorphic loci have also been recorded among studies where microsatellites were used. A higher result was reported in the current study than Singh et al. [
The observed number of alleles per locus (
Senegal is located in the extreme part of West Africa [
The fixation indices
Moges et al. [
According to Zeng et al. [
The analysis of molecular variance (AMOVA) shows that genetic variations were greater within the families. The total genetic diversity (
The genetic correlation among the families is quite variable, ranging from 0.100 to 0.557. It is not surprising that the lowest genetic distance value (0.100) was recorded between SEN02.04 and SEN02.06; this is because the two families belong to the same population, namely, population 2. Generally, there is a strong relationship between genetic distance and geographical locations [
The UPGMA dendrogram was constructed that showed the genetic similarity and dissimilarity among the families. Among the total 8 populations, populations 2, 3, 4, 5, 6, 7, and 10 were situated in the southern part of Senegal whereas population 12 was located in the northern part, separated by Gambia. The populations in the southern part were within an 80 km radius. Populations 2 and 3 were collected around 45 km from Ziguinchor while population 5 was collected around 17 km from Ziguinchor whereas population 4 was from Dar Salam. Among the three main clusters as revealed by the dendrogram, families from the same population were not assembled in the same cluster; however, a grouping of families from different populations was formed. The families of populations 2 and 3 were grouped in cluster I. Additionally, families SEN04.01 and SEN05.02 were contained in cluster I while the rest of the families from populations 4 and 5 were grouped with families of populations 6 and 7 in cluster II. This is due to the limited geographical distance in the collection sites of populations 2, 3, 4, 5, 6, 7, and 10 (not more than 80 km).
On the other hand, two families of population 10 and family SEN07.08 were grouped with three northern outlying families from population 12 to form cluster III, which may be due to the genetic similarity among the families and the high number of migrants (
The simple sequence repeat markers are useful in detecting the genetic variability and relationship among MPOB-Senegal oil palm germplasm. It shows a high degree of sensitivity for discriminating genetic variability, thereby providing ample opportunity for further genetic improvement. This will assist oil palm breeders in identifying redundancies in the collection and development strategies for field conservation. The presence of relatively high different allele, effective alleles, and heterozygosity indicates that MPOB-Senegal germplasm possesses unique traits which could be used in the future breeding program. Among the SSR markers employed, sMo00053 and sMg00133 were the most informative markers for MPOB-Senegal oil palm germplasm due to their capability to detect both the highest private alleles and the rare alleles. SEN07.05 and SEN12.03 were unique families due to the highest occurrence of rare alleles. Also, SEN05.03 and SEN12.03 families had the highest private alleles. The information obtained from this study could be vital in core collection establishment without any loss of genetic variations.
The datasets used and analyzed during the current study are available within the manuscript.
The authors declare that they have no known competing financial interests or personal relationships that could have influenced the work reported in this paper.
Khin Aye Myint and Zulkifli Yaakub contributed equally to this manuscript.
The authors wish to thank Malaysian Palm Oil Board (MPOB) and Universiti Putra Malaysia (UPM) for providing research materials, facilities, and financial support to carry out this study. The authors express their appreciation to the Organization of Women Scientists for Developing World (OWSD) and Sida (Swedish International Development Cooperation Agency).
Supplementary Table 1: list of selected polymorphic SSR markers for MPOB-Senegal oil palm germplasm. Supplementary Table 2: distribution of private, rare (bold), and unique alleles among the 26 MPOB-Senegal germplasms for 35 microsatellite loci. Supplementary Table 3: allele frequencies of private allele and rare allele (<0.10, bold) in 26 families of MPOB-Senegal using 36 SSR markers.