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..
23
Figure6. The most likely pedigree construction from COLONY. Identified parent IDs on the top bar and offspring IDs at the bottom. Red lines emanate
downwards from male parents and yellow lines from females
3.3.2 Mean Allelic Patterns and PIC Values
Out of the 16 simple sequence repeat SSR marker loci evaluated, 100 are polymorphic in the B01, B02, A140, or A127 populations. For the B57 and
A125 populations, the percentages of polymorphic loci are 88 and 94, respectively. The average percentage of polymorphic loci for All populations is
97. In all populations, both the mEgCIR0038 LG 13 and mEgCIR3292 LG 15 SSR marker loci showed the highest average polymorphic information content
PIC=0.84. Meanwhile, the mEgCIR3785 LG 10 showed the highest PIC in T x T PIC=0.79 while and the mEgCIR0038 LG 13 in D x D population
PIC=0.79, respectively Table 5. The mEgCIR0353 LG 16 SSR marker locus Table 5 showed the lowest PIC in the all populations PIC=0.41, in T x T
populations PIC=0.39, and in D self population PIC=0.15. For the All populations, the average PIC over 16loci of SSR markers is 0.74 while that for the
evaluated T x T population is 0.70 and for Dura self is 0.56 Table 6. Meanwhile, the average PIC over loci for each of the evaluated oil palm populations ranged
from 0.39 – 0.55 Table 6.
According to Okoye et al. 2016a,b, the marker loci having PIC value 0.7 is informative while PIC value between 0.4 – 0.7 is moderately informative
and less than 0.4 is not informative. Highvalue of PIC for each locus indicates the locus is informative in distinguishing individuals within populations and among
populations Sajib et al., 2012.In the studied oil palm populations, most of the
B01 B02
B57 Admixture A125,
A127, and A140 T1
T3 T5
T2 T4
T6 D1 D3
D5 D2
D4
24 loci either belong to informative or moderately informative. The 11 loci evaluated
are identified as informative loci having PIC larger 0.7 and four loci are moderately informative having PIC between 0.4 and 0.7 Table 6.
Table6. The polymorphic information content PIC for each SSR marker locus among evaluated oil palm populations
Locus LG
Polymorphic Information Content PIC for each Locus among Populations : A125
A127 A140
B01 B02
B57 Dura
Self TxT
All mEgCIR0802
1 0.45
0.5 0.69
0.43 0.33
0.48 0.58
0.69 0.77
mEgCIR3282 2
0.53 0.53
0.43 0.47
0.56 0.47
0.5 0.76
0.8 mEgCIR0173
3 0.33
0.22 0.11
0.53 0.08
- 0.26
0.52 0.49
mEgCIR3533 4
0.64 0.49
0.46 0.45
0.61 0.25
0.54 0.7
0.76 mEgCIR2813
5 0.5
0.45 0.3
0.44 0.4
0.37 0.42
0.65 0.66
mEgCIR3543 6
0.58 0.58
0.61 0.71
0.37 0.57
0.61 0.63
0.69 mEgCIR0894
7 0.68
0.58 0.67
0.54 0.55
0.46 0.66
0.76 0.79
mEgCIR0886 8
0.59 0.69
0.48 0.05
0.38 0.48
0.71 0.7
0.8 mEgCIR3886
9 0.34
0.57 0.47
0.21 0.59
0.35 0.54
0.74 0.79
mEgCIR3785 10
0.62 0.55
0.65 0.62
0.54 0.48
0.62 0.79
0.82 mEgCIR3362
11 0.65
0.7 0.64
0.54 0.55
0.52 0.7
0.76 0.83
mEgCIR2414 12
0.51 0.59
0.54 0.67
0.58 0.54
0.55 0.77
0.78 mCnCIR0038
13 0.73
0.76 0.6
0.5 0.68
0.37 0.79
0.78 0.84
mEgCIR3546 14
0.59 0.61
0.66 0.65
0.61 0.37
0.63 0.75
0.77 mEgCIR3292
15 0.69
0.76 0.71
0.59 0.56
0.47 0.73
0.76 0.84
mEgCIR0353 16
- 0.24
0.19 0.05
0.15 -
0.15 0.39
0.41
Note: The SSR marker loci and linkage group LG were based on Billotte et al. 2001. Dura Self, combined of the three Dura Self populations B01, B02, and B57; T x T, combined of the
three T x T populations A125, A127, and A140; All, combined all of Dura Self and T x T populations All six populations.
The ranges of PIC in the D Self populations for all studied loci tend to be lower than that of the T x T populations. Moreover, the PIC for all populations is
even higher than either the D Self or T x T populations Table 6. The average alleles per locus in all populations are 8.38 alleles. For the T x T population, the
average alleles per locus are 7.06 alleles while for the Dura Self are 5.63 alleles. Meanwhile, the average alleles per locus over loci for each of the evaluated oil
palm populations ranged from 2.50 – 4.63 Table 6. There are only slight differences found in the average number of effective alleles Ne, private alleles
and locally common alleles 50 over loci for each oil palm population Table 6. The number of effective alleles per locus is associated with the presence of
rare alleles in the studied populations Laurentin, 2009. The private alleles indicate one that occurs at any frequency, but in only one local or subpopulation
and it should have a distinct gene pool relative to the rest of the populations Szpiech Rosenberg, 2011. The locally common allele 50 indicates
number of locally common alleles Freq. 5 and found in 50 or fewer populations Peakall and Smouse, 2012. The highest mean value of PIC over loci
for each of oil palm population is found in A127 population PIC=0.55 and the
25 lowest is in B57 population PIC=0.39. The mean value of PIC over loci for D
Self population is 0.56, for T x T population is 0.70, and for All populations is 0.74, respectively Table 6.
Table7. The mean values of allele per locus, effective allele Ne, private allele, locally common alleles presence in 50 of populations, and
polymorphic information content PIC over loci for each oil palm population
The observed PIC in the studied D Self, T x T, and All populations is also higher than that reported by Solin et al. 2014 for D x P oil palm population. The
results of Okoye et al. 2016a,b revealed the existence of a high percentage of polymorphic loci 83.3 in the entire oil palm materials with the average
PIC=0.73. They also demonstrated that two SSR marker loci sMg00016 and sMg00179 showed PIC=0.80 and PIC=0.85, respectively.
3.3.3 Allelic Frequency across Populations
The calculated allele frequency for the studied oil palm population is grouped into either high P 0.75, intermediate 0.75P0.25, low
0.25P0.01 or rare P0.01 based on propose system of Buchert et al. 1997. It can also be grouped as either common P0.05 or rare P0.05 according to
Marshall and Brown 1975. The groupings of allele frequency over loci for each of the studied oil palm population are presented in Table 7. In all studied oil palm
populations Table 7, only 1-3 .4-7.5 alleles are grouped as high and 0-1 0- 1.7 as rare while the majority of alleles are either intermediate 22-27 or 33.8-
57.5 alleles or low frequency 3-45 or 5.2-61.5 alleles according to criteria proposed by Buchert et al. 1997. The B57 population showed the highest
percentage of intermediate allele frequency group 57.5 while B01 showed the highest percentage of low allele frequency group 61.5, respectively. On the
other hand, B01 population showed the lowest percentage of intermediate 33.8 and B02 population the lowest percentage 5.2 of low allele frequency groups
Table 8. However, the majority of allele frequencies Table 8 belong to the
Populations Total
allele number
Mean values of: Allelelocus
Ne Private
LCommon 50
PIC A125
65 4.38
2.4 0.1
1.2 0.53
A127 58
4.63 2.4
1.0 1.0
0.55 A140
40 3.94
2.0 0.4
1.8 0.51
B01 63
4.13 2.7
0.2 1.3
0.47 B02
69 3.69
2.7 0.1
1.5 0.47
B57 74
2.50 2.9
0.1 1.6
0.39 DSelf
63 5.63
- -
- 0.56
TxT 85
7.06 -
- -
0.70 All
148 8.38
- -
- 0.74
26 common group and the rest belong to the rare group; according to criteria develop
by Marshall and Brown 1975. Table8. Allele classi
fication according to allelic frequencies based on the approach of Buchert et al. 1997 high, intermediate, low and rare and
Marshall and Brown 1975 common and rare
Popu- lations
N High
P 0.75 Intermediate
0.75P0.25 Low
0.25P0.01 Rare
P0.01 Common
P0.05 Rare
P0.05 B01
65 3 4.6
22 33.8 40 61.5
1 1.5 50 76.9
15 23.1 B02
58 2 3.4
23 39.7 3 5.2
1 1.7 47 821.0
11 19.5 B57
40 3 7.5
23 57.5 14 35.0
0 0 39 97.5
1 2.5 A140
63 3 4.8
23 36.5 37 58.7
0 0 52 82.5
11 17.5 A125
69 1 1.4
27 39.1 41 59.4
0 0 56 81.2
13 18.8 A127
74 2 2.7
26 35.1 45 60.8
1 1.4 60 81.1
14 18.9 Note: N, number of total alleles per populations. The X Y, the X indicate number of alleles and
the Y indicate percentages to the total allele in each population.
In the current studied oil palm population, rare alleles P0.05 are observed at the level ranging from 2.5 to 23.1 across loci in each population.
Those numbers are lower than that found among wild oil palm populations, in which rare alleles P0.05 was found in as much as 38 and populations having
similar agro-ecology were also reported to share rare alleles. It was suggested that natural selection had a larger impact on the percentages of rare alleles in the
population than the genetic drift Arias et al., 2013. Rare alleles have also been reported as related to plant adaptation to abiotic and biotic stresses Rajora et al.,
2000. Therefore, it is important to maintain genetic variability in oil palm populations since it increases the possibility of having adaptive responses to biotic
and abiotic stress Maxted et al., 2006; Maxted et al., 2007. The presence of rare alleles may be because there is an enrichment process by having oil palm
germplasm of different origins andor countries Arias et al. 2013. In the current studied oil palm population, enrichment process may have been because of the
presence of illegitimate progenies.
3.3.4 Genetic diversity and differentiation among populations
The parameters of genetic diversity over loci for each studied oil palm population are presented in Table 8. The estimation of genetic diversity within
population is important since it can be used to identify population with relatively high genetic diversity to design and maintain improvement strategies Govindaraj
et al., 2015. In the studied populations, the observed heterozygosity H Obs. values are all higher than the heterozigositas harapan H Exp.. The genetic
diversity observed over loci across the 6 populations studied varied within a range from the lowest H Exp.=0.47 B57 population to the highest H Exp.= 0.62 A127
population while the H Obs. over loci for each population is from the lowest H Obs.= 0.627 B57 population to the highest H Obs=0.84 B02 population. In the
meantime, the H Exp. for the T x T, the D Self, and the All populations are H Exp.=0.74, 0.62, and 0.77, while the H Obs. for the T x T, the D Self, and the All
populations are H Exp.=0.74, 0.68, and 0.72, respectively Table 6. Heterozygosity is an individual or population-level parameter and indicates the
