DNA Extraction and SSR Marker Amplification
21
Table3. The observed number of alleles for each SSR marker locus among loci in the evaluated oil palm populations
Locus LG
Num ber of Alleles of each locus f or Populat ions : A125
A127 A140
B01 B02
B57 DuraS
elf TxT
All mEgCIR0802
1 3
4 5
4 2
3 6
7 9
mEgCIR3282 2
5 4
3 4
4 3
5 9
10 mEgCIR0173
3 2
2 2
5 3
1 3
6 6
mEgCIR3533 4
5 4
4 5
5 2
5 7
9 mEgCIR2813
5 4
4 2
3 3
2 4
4 5
mEgCIR3543 6
7 7
4 5
2 3
8 5
8 mEgCIR0894
7 5
5 5
6 5
3 6
9 9
mEgCIR0886 8
6 6
3 2
2 3
8 5
9 mEgCIR3886
9 2
3 3
3 6
3 3
6 6
mEgCIR3785 10
4 4
6 5
3 3
6 10
10 mEgCIR3362
11 6
6 5
4 3
3 7
7 9
mEgCIR2414 12
4 4
3 5
4 3
5 9
9 mCnCIR0038
13 8
7 5
3 6
2 9
8 11
mEgCIR3546 14
4 5
5 5
4 2
5 8
8 mEgCIR3292
15 4
6 5
5 4
3 6
10 11
mEgCIR0353 16
1 3
3 2
3 1
4 3
5 Tot al alleles
70 74
63 66
59 40
90 113
134 Average
4 5
4 4
4 3
6 7
8
Note: Dura Self, combined of three Dura Self populations B01, B02, and B57; T x T, combined of three T x T populations A125, A127, and A140; All, combined of all Dura Self and T x
T populations All six populations.
Table4. Expected allele frequencies based on Mendel genetics model crosses of two parents
No Crosses between parents
Expected alleles Model crosses
Ex. of parent genotypes
No. Freq
1 Het. parents with different alleles
AB x CD 4
1:1:1:1 2
Het. parents with one similar allele AB x AC
3 2:1:1
3 Het. parents with two similar alleles
AB x AB 2
1:1 4
Het, Hom, parents with different alleles AB x CC
3 1:1:2
5 Het. Hom parents with one similar allele
AB x AA 2
3:1 6
Hom, Hom, parents with different alleles AA x BB
2 1:1
7 Hom. Hom parents with similar alleles
AA x AA 1
1
22 The evaluated populations are derived from individual palm to palm
crosses Table 1; therefore, the expected number of allele presence for each locus within each population depended on the genotype of the parents. There would be
seven possible models of segregation based on Mendel genetics, as presented in Table 4. The expected number of alleles per population and the expected allele
frequencies in each model cross are also presented Table 4.
The number of alleles per locus for some loci in the evaluated oil palm populations is larger than the expected values of the model crosses. Based on the
hybridization model Table 4, the expected number of alleleslocus ranges from 1 – 4 while in the evaluated populations, they range from 1 – 7 alleleslocus.
Moreover, some loci showing the expected number of alleles per locus do not show the expected allele segregation ratios for each population Table 4. This
finding was similar to those of Okoye et al. 2016a,b who evaluated genetic diversity of NIFOR oil palm main breeding parent genotypes using SSR markers.
Okoye et al. 2016a,b also found alleles of the studied loci in the evaluated oil palm populations were also more than the expected and the allele frequencies did
not fit to the expected segregation ratios.
Table5. Loci having number of alleles per locus and ratio of allele frequencies that are fit or unfit to the expected based on the model crosses for each studied
oil palm population
Population Total
loci Loci having number of allelelocus Loci having ratio of allele frequency
Fit to the expected Larger than
expected Fit to expected
Unfit to expected B01
16 8
8 2
6 B02
16 12
4 6
6 B57
16 16
8 8
A140 16
9 7
5 4
A125 16
9 7
4 5
A127 16
9 7
3 6
Note: Ratios of allele frequency were evaluated only for loci having number of alleles fit to the expected.
To validate the presence of illegitimate individuals among the studied populations, the genotype data were subjected to analysis using COLONY
software to infer the individual parentage and sibship from multilocus genotypes data. Results of the analysis Fig. 1 indicate that no illegitimate progeny are
found among individuals belonging to the T x T crosses B01, B02, or B57. Inference from the multilocus genotype data indicates all individuals belonging to
the T x T crosses are derived from a pair of parents, i.e. T1 and T2 for B01, T3 and T4 for B02, and T5 and T6 for B57 oil palm populations Fig. 6. On the other
hand, not all of Dura Self individuals are legitimate progenies of their respective parents. The individuals belonging to the Dura Self populations were developed
from selfing of three Dura progenitors Table 1. However, results of COLONY analysis identify five progenitor for individuals belonging to the D Self
populations., i.e. A125, A127 and A140 populations. Fig. 6. Such results pointed out further about the possible presence of illegitimate progenies among
the studied oil palm populations, especially for the Dura Self populations..