Analysis of Mating System and Gene Flow Patterns of Melia volkensii within Clonal Seed Orchard in Kibwezi Using Microsatellites
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Date
2025-09
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Kenyatta University
Abstract
Melia volkensii (M. volkensii) is an indigenous tree species that grows and develops well
in Kenyan Arid and semi-arid lands (ASALs). There has been a drastic decline in the M.
volkensii population because of the overexploitation and uncontrolled harvesting of the
natural stands where large and best trees are utilized for charcoal and timber, creating a
huge demand for quality planting materials. Melia volkensii improvement programme
began in 2012 to address the sharp decline in their genetic diversity, provide farmers with
improved seeds for commercial plantations in dry lands and produce drought-tolerant and
fast-growing trees adaptable to ASALs. Scions from the best M. volkensii, also known as
candidate plus trees (CPTs), were collected to establish the first generation of clonal seed
orchard to increase the breeding population and genetic resources of M. volkensii. The
distributed materials from a tree seed orchard should always be of the recommended
genetic quality with no or minimal contamination from unimproved wild stands
surrounding the orchard. Therefore there is a need to determine the level and patterns of
gene flow among the elite trees grown in a seed orchard to maintain random outcrossing
in order to minimize loss of diversity. The study was carried out using the M. volkensii
trees grown at the Kenya Forestry Research Institute seed orchard in Kibwezi in Makueni
County. In total, 15 populations which comprised of 618 M. volkensii trees consisting of
four hundred and twenty three open pollinated progenies from ten clones, ninety eight
candidate plus trees and ninety seven individuals from the orchard background
population were studied. Genomic DNA was isolated by CTAB method and amplified by
multiplex PCR reactions using primers previously developed by Hanaoka et al., 2012.
The amplified DNA fragments were screened by capillary electrophoresis on the ABI
3500 genetic analyzer. Parameters of genetic diversity were determined using GenAlEx
6.503; MLTR program was used to determine the mating system in the orchard based on
the mixed mating model. The population had a mean heterozygosity of 0.712, inbreeding
coefficient of -0.035, fixation index of 0.068, a high number of migrants (Nm = 3.952),
with high single (1.014) and multi-locus (1.2) estimates of the outcrossing rates. This
indicates an exclusive out-crossing mating system and existence of gene flow in M.
volkensii, possibly promoting inter-breeding and genetic diversity among the trees in
Kibwezi seed orchard, which is vital for their future survival. Paternity analysis implicitly
assigned 334 out of 423 progenies (78.96%) to 77 out of 98 potential (78.57%) seed
orchard clones, with the unassigned 89 progenies (21.04 %) not matching any of the 98
seed orchard clones thought to be derived from the background population. The
panmictic design of the seed orchard and flowering synchrony with the background
population could have contributed to the pollen introgression in the orchard therefore
regular studies should be done across the other blocks of the orchard to find out the extent
of contamination and then come up with suitable mitigation which might include thinning
and a review of the current isolation distance of 200 metres between the orchard and the
background population to ensure the integrity of the seed source
Description
A Thesis Submitted in Partial Fulfillment of the Requirements for the Award of the Degree of Master of Science (Biotechnology) in the School of Pure and Applied Sciences of Kenyatta University, September, 2025
Supervisors;
1.George Ochieng Asudi
2.Stephen Omondi