Genome-wide diversity and structure variation among lablab [Lablab purpureus (L.) Sweet] accessions and their implication in a Forage breeding program
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Date
2021
Journal Title
Journal ISSN
Volume Title
Publisher
Genetic Resources and Crop Evolution
Abstract
Most orphan crops have not been fully
sequenced, hence we rely on genome sequences of
related species to align markers to different chromosomes.
This hinders their utilisation in plant population
improvement programs. Utilising the advances in
the science of sequencing technologies, the population
structure, relatedness, and genetic diversity among
accessions can be assessed quickly for better exploitation
in forage breeding programs. Using DArTseq
technology, we studied the genetic and structural
variation in 65 Lablab purpureus (L.) Sweet conserved
gene-bank accessions using 9320 DArTseqbased
SNPs and 15,719 SilicoDart markers. These
markers had a low discriminating ability with mean
polymorphic information content (P.I.C.) of 0.14 with
DArTseq-based SNPs and 0.13 with SilicoDart markers.
However, the markers had a high mean call rate of
73% with DArTseq-based SNPs and 97% with SilicoDart
markers. Analysis of molecular variance
revealed a high within populations variance (99.4%),
indicating a high gene exchange or low genetic
differentiation (PhiPT = 0.0057) among the populations.
Structure analysis showed three allelic pools in
variable clusters of DK = 3 and 6. Phylogenetic tree of
lablab accessions showed three main groups with
variable membership coefficients. Most pairs of
accessions (40.3%) had genetic distances between
0.10 and 0.15 for SilicoDart markers, while for
DArTseq-based SNPs, (46.5%) had genetic distances
between 0.20 and 0.25. Phylogenetic clustering and
minimum spanning analysis divided the 65 accessions
into three groups, irrespective of their origin. For the
first time, this study produced high-density markers
with good genom coverage. The utilisation of these
accessions in a forage program will base on the
information from molecular-based grouping. The
outcomes uncovered the presence of noteworthy
measure of variety in Uganda, CIAT and ILRI
accessions, thus demonstrating an opportunity for
further marker-trait-association studies.
Description
Keywords
Plant genetic resources, Genetic differentiation, Genetic diversity, SNP, SilicoDart
Citation
Sserumaga, J. P., Kayondo, S. I., Kigozi, A., Kiggundu, M., Namazzi, C., Walusimbi, K., ... & Mugerwa, S. (2021). Genome-wide diversity and structure variation among lablab [Lablab purpureus (L.) Sweet] accessions and their implication in a Forage breeding program. Genetic Resources and Crop Evolution, 68, 2997-3010. https://doi.org/10.1007/s10722-021-01171-