Biology subjects

Chiedozie Egesi

Publications and source records attributed to Chiedozie Egesi.

3 recordsLinked to original sources

bioRxiv2016

Cassava HapMap: Managing genetic load in a clonal crop species

Cassava (Manihot esculenta Crantz) is an important staple food crop in Africa and South America, however, ubiquitous deleterious mutations may severely reduce its fitness. To evaluate these deleterious mutations in the cassava genome, we constructed a cassava haplotype map using deep sequencing from 241 diverse accessions and identified over 28 million segregating variants. We found that, 1) while domestication modified starch and ketone metabolism pathways for human consumption, the concomitant bottleneck and clonal propagation resulted in a large proportion of fixed deleterious amino acid changes, raised the number of deleterious mutations by 26%, and shifted the mutational burden towards common variants; 2) deleterious mutations are ineffectively purged due to limited recombination in cassava genome; 3) recent breeding efforts maintained the yield by masking the most damaging recessive mutations in the heterozygous state, but unable to purge the mutation burden, which should be a key target for future cassava breeding.

Genetics↗

bioRxiv2016

Widespread natural variation of DNA methylation within angiosperms

To understand the variation in genomic patterning of DNA methylation we compared methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time. These results show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

Plant Biology↗

bioRxiv2015

Genome-wide association and prediction reveals the genetic architecture of cassava mosaic disease resistance and prospects for rapid genetic improvement

Cassava (Manihot esculenta) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Bi-parental mapping studies suggest primarily a single major gene mediates resistance. To be certain and to potentially identify new loci we conducted the first genome-wide association mapping study in cassava with 6128 African breeding lines. We also assessed the accuracy of genomic selection to improve CMD resistance. We found a single region on chromosome 8 accounts for most resistance but also identified 13 small effect regions. We found evidence that two epistatic loci and/or alternatively multiple resistance alleles exist at major QTL. We identified two peroxidases and one thioredoxin as candidate genes. Genomic prediction of additive and total genetic merit was accurate for CMD and will be effective both for selecting parents and identifying highly resistant clones as varieties.

Genomics↗