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..