Genetic diversity of the maize germplasm conserved at the national gene bank of Kenya
Date
2018
Authors
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Publisher
University of Delaware
Abstract
Maize (corn) is the third most important crop after wheat and rice globally. In Kenya, its per capita consumption is estimated at 103 kilograms per year and its inadequacy due to biotic and abiotic stresses puts the nation’s food security at risk. Maize breeders in effort to develop newer lines and hybrids combinations with better yield have been consistently inter-crossing a few elite lines. Farmers have increasingly replaced landraces with a few high yielding varieties. The conclusive overview is that the genetic base of the maize breeding pool is constricting, rendering the maize germplasm vulnerable to future threats such as extirpating crop pests and diseases as well as the adverse effects of a deteriorating global crop environment. The raw material for developing newer varieties that are better yielding and climate resilient includes gene bank accessions. Exploration of this collection for utilization in maize improvement however is impeded by failures in accession documentation, agronomic evaluation and characterization of genetic variability. The objectives of this study were to i) characterize the genetic diversity of the gene bank maize collection ii) investigate level of genetic relatedness among accessions. In the current study, 768 samples were genotyped via high-throughput sequencing of restriction fragments (GBS). Results show that for a period of 16 years, the proportion of polymorphic loci remained constant, alleles at minor frequency decreased significantly (p-value<.001) and heterozygosity increased slightly by 0.1%. Proportion of heterozygotes and alleles at minor frequency were found to be highly correlated (r2=-79, P=0.006), indicating that reduction of alleles at minor frequency caused an increase in the proportion of heterozygotes. Pairwise shared allele distance for most gene bank accessions (≥95%) fell between 0.20 and 0.30. Only 130 out of 147,696 comparisons (0.08%) had a shared allele distance <0.1 which indicated low levels of redundancy and high genetic distances among nearly all pairwise comparisons (99.9%). Potential of Heat-diffusion for Affinity-based Transition Embedding was used to capture local connections between SNP markers and reveal two clear genetic sub-divisions from admixed ancestry, which supported the hypothesis of a genetically narrow based maize germplasm due to the founder effect. ☐ Keywords: Maize | Genetic diversity | Single Nucleotide Polymorphisms | Genotyping by Sequencing | Heterozygosity | Minor Allele Frequency | Shared allele distance | PHATE.