Genome analysis, identification, and expression analysis of nitrogen and potassium responsive genes in cassava

Cassava is an important staple food for millions, but its growth is often hindered by poor soil quality and limited access to fertilizers. Efficient utilization of nutrients is essential to maximize the yield and nutritional value of cassava while minimizing resource use and environmental adverse impacts. Thus, identification of nutrient-responsive genotypes as well as genes that govern/regulate nutrient use efficiency is highly imperative to breed nutrient-efficient genotypes to enhance the productivity and resilience of cassava. In this study, we studied the performance of thirty genetically diverse cassava genotypes in the field with low availability of nitrogen (N) and insufficient exchangeable potassium (K) and identified two high N responsive genotypes, 17S36 and 15S409; two low N responsive genotypes, Kumkumrose and Export kappa; two high K responsive genotypes, Ambakkadan and Karutha malabar and two low K responsive genotypes, 17S143 and 16-5. Also, genome-wide analysis resulted in the identification of 39 N-responsive and 22 K-responsive candidate genes with diverse functional groups, including transporter, transcription factors, transferase, kinase, and permease in cassava. Meta-analysis of RNA-seq datasets of 11 cassava tissues revealed constitutive and tissue-specific expression of N-responsive and K-responsive genes. Five N responsive genes MeNRT1, MeNRT3, MeNLP1, MeGPT2 and MeTAR2, displayed enhanced expression in the high N efficient genotypes, 17S36 and 15S409 in comparison with the low N responsive genotypes, Kumkumrose and Export kappa, whereas three K responsive genes, viz., MeKUP3, MeKUP4, and MeKUP8, displayed enhanced expression in the high K efficient genotypes, Ambakkadan and Karutha malabar in comparison with the low K responsive genotypes, 17S143 and 16-5 under nutrient-deprived conditions. Allele mining analysis showed the presence of allelic variations in NRT3, whereas no sequence differences at the allelic level were observed for the AMT1 gene among the genotypes 15S409 and Export Kappa. Thus, our comprehensive analysis unravels the genetic complexity of N responsive and K responsive genes in cassava and provides the basis for the selection of genotypes and candidate genes for further functional analysis and breeding for the development of N responsive and K responsive genotypes.