| dc.description.abstract | Thenovelty of mtDNA gene loci, COl in DNA barcoding is undisputed. This is attributed
to its standardized sequencing segment of the cytochrome c oxidase-l gene with the
necessary universality and variability making it a generally acceptable .locus. mtDNA is
robust with threshold for species delineation, not subject to drastic length variation,
frequent mononucleotide repeats or microinversions. However, low nucleotide
substitutionrate of mtDNA in plants precludes its use making the search for alternative
barcoderegions necessary. The putative loci of the plastid region conserved in plant target
lineages can achieve rapid, reproducible, and molecular inferencing yet to be explored in
biodiversitystudies in Kenya. Four are portions of coding genes [matK, rbeL, rpoB, and
rpoCl),. and noncoding spacers (atpF-atpfi tmll-psiiA, and psbK-psbL]. Currently, there
existsno universal barcode for plants and while various combinations have been proposed,
there exists no consensus; the lack thereof impedes progress in getting a suitable DNA
barcode for molecular and phylogenetic inferencing of GeneBank repositories. The
genetic pool of these repositories is not adequately characterized, remains scanty and
undocumented.DNA was obtained from 54 accessions from Kenyan GeneBank followed
by DNA extraction, purification and quantification using DNA Nanodrop, PCR and
sequencing. The feasibility and overall utility of each locus was tested singly and in
combination to establish a locus that could have applicability in delineating
phylogeographically diverse genotypes. Statistical analyses were based on genetic
parameters including analyses of intra- and infra- specific genetic divergence based on
K2P distance matrices on a scale of 0.001 distance units; Wilcoxon signed rank tests and
coalescenceanalyses to delineate independent genetic clades. Results indicate that: matK,
trnH-psbA, psbK-psbL, and rbeL are informative in delineating intra and infraspecific
distances.rbeL had the highest identification efficiency [50%]. DNA barcoding gaps were
evaluatedby comparing intra and infraspecific divergences. Median and Wilcoxon Two-
Sample Tests were used to evaluate distributions. Overall, MLA was more informative
than SLA. The trnH ysbA generated five distinct and well differentiated clusters. The
study revealed 38 haplotypes circulating among Kenyan Cowpea. The atpF_atpH
recorded the highest SNPs [2240] and infraspecific frequencies of SNPs 1100 bp. It is
notable that rbcl. recorded the highest heterozygous sites. Results indicate that matK
»trnH-psbA {P<O.OOOl]. The combinations matK+psbK-psbL and matK+ ysbKpsbL+
_atpF-atpH were informative to {matK+trnH-psbA+atpF--atpH+psbK-psbLJ
[p<O.000]. However, the four loci were more parsimonious than the three loci: matK +
trnH-psbA + atpli-atpll, P<O.OOOl. Overall, the current study reveals low genetic
diversity among Kenyan cowpea but high %GC content as reason for adaptability to
diverse phylogeographic settings. It would appear therefore that rbeL is the most
informative. Pairwise FST values for population differentiation were insignificant
indicating low genetic diversity. The study clearly demonstrates the overall utility of
plastid markers in molecular and phylogenetic inferencing of Kenyan GeneBank
repositories and informs the scanty body of knowledge on the novelty of DNA barcoding
as a tool in cataloguing and phylogenetic inferring at molecular level and acknowledges its
use in future research on genomics | en_US |
