Novel SNP markers and other stress-related genomic regions associated with nitrogen use efficiency in cassava

Joseph Okpani Mbe, Daniel Kwadjo Dzidzienyo, Simon Peter Abah, Damian Ndubuisi Njoku, Joseph Onyeka, Pangirayi Tongoona, Chiedozie Egesi

Front Plant Science; 2024 Apr 4: 15:1376520. doi: 10.3389/fpls.2024.1376520.

Abstract

Cassava productivity is constrained by low soil nitrogen, which is predominant in most cassava-growing regions in the tropics and subtropical agroecology. Improving the low nitrogen tolerance of cassava has become an important breeding objective. The current study aimed to develop cassava varieties with improved nitrogen use efficiency by identifying genomic regions and candidate genes linked to nitrogen use efficiency in cassava. A genome-wide association study (GWAS) was performed using the Genome Association and Prediction Integrated Tool (GAPIT). A panel of 265 diverse cassava genotypes was phenotyped for 10 physiological and agronomic traits under optimum and low-nitrogen regimes. Whole-genome genotyping of these cassava cloneswas performed using the Diversity Arrays Technology (DArTseq) sequencing platform. A total of 68,814 single nucleotide polymorphisms (SNPs) were identified, which were spread across the entire 18 chromosomes of the cassava genome, of which 52 SNPs at various densities were found to be associated with nitrogen use efficiency in cassava and other yield-related traits. The putative genes identified through GWAS, especially those with significant associated SNP markers for NUE and related traits have the potential, if deployed appropriately, to develop cassava varieties with improved nitrogen use efficiency, which would translate to a reduction in the economic and environmental cost of cassava production.

See https://pubmed.ncbi.nlm.nih.gov/38638347/

Figure 8: Manhattan and QQ plots for nitrogen use efficiency, fresh root yield, and other related traits evaluated under the optimal nitrogen regime. The horizontal lines in the Manhattan plots show the threshold p-value at the Bonferroni cutoff point of 0.05.