GWAS identifies genetic loci underlying nitrogen responsiveness in the climate resilient C4 model Setaria italica (L.)

Introduction: N responsiveness is the capacity to perceive and induce morpho-physiological adaptation to external and internal Nitrogen (N). Crop productivity is propelled by N fertilizer and requires the breed-ing/selection of cultivars with intrinsically high N responsiveness. This trait has many advantages in being more meaningful in commercial/environmental context, facilitating in-season N management and not being inversely correlated with N availability over processes regulating NUE. Current lack of its understanding at the physio-genetic basis is an impediment to select for cultivars with a predictably high N response.Objectives: To dissect physio-genetic basis of N responsiveness in 142 diverse population of foxtail millet, Setaria italica (L.) by employing contrasting N fertilizer nutrition regimes. Methods: We phenotyped S. italica accessions for major yield related traits under low (N10, N25) and optimal (N100) growth conditions and genotyped them to subsequently perform a genome-wide associa-tion study to identify genetic loci associated with nitrogen responsiveness trait. Groups of accessions showing contrasting trait performance and allelic forms of specific linked genetic loci (showing haplo-types) were further accessed for N dependent transcript abundances of their proximal genes.Results: Our study show that N dependent yield rise in S. italica is driven by grain number whose respon-siveness to N availability is genetically underlined. We identify 22 unique SNP loci strongly associated with this trait out of which six exhibit haplotypes and consistent allelic variation between lines with con-trasting N dependent grain number response and panicle architectures. Furthermore, differential tran-script abundances of specific genes proximally linked to these SNPs in same lines is indicative of their N dependence in a genotype specific manner.Conclusion: The study demonstrates the value/ potential of N responsiveness as a selection trait and iden-tifies key genetic components underlying the trait in S. italica. This has major implications for improving crop N sustainability and food security.(c) 2022 The Authors. Published by Elsevier B.V. on behalf of Cairo University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).