QTL analysis for nitrogen use efficiency in wheat (Triticum aestivum L.)

The genetic architecture of nitrogen use efficiency (NUE) and its two component traits i.e. NUpE (N uptake efficiency) and NUtE (N utilization efficiency) was studied using a bi-parental RIL mapping population derived from a cross HUW468 (high NUE)/C306 (low NUE). The mapping population, two parental genotypes and three check genotypes were evaluated under four different N levels (0, 60, 120, and 180 kg/ha) over three years. A genetic map containing 456 SNP markers (2571.38 cM length) was used for QTL analysis. Thirty six main effect QTLs (17 QTLs for NUE, 13 NUpE and 6 QTLs for NUtE) distributed on 12 chromosomes (1B, 1D, 2A, 2B, 3A, 4B, 5A, 5B, 5D, 6A, 6D, and 7A) were identified at 2.52-9.27 LOD scores. Individual QTLs explained 6.65-22.89% phenotypic variation. Multi-traits QTLs (Mt-QTLs) and epistatic QTLs involving first-order epistatic (QTL x QTL) interactions were also discovered. Candidate genes (CGs, as many as 737) were mined from QTL regions which were mainly involved in metabolic process, cellular process and catalytic activity, etc.; differential expression was observed for 49 CGs in roots and 34 in shoots. The CGs encoded important transcription factors, transporters, etc. having a role in NUE. QTLs and CGs reported in this study enriched the available knowledge. Seven QTLs (including three Mt-QTLs) and QTLs involved in six epistatic interactions are recommended for MAS for improvement of NUE in wheat.

Automated summary

This study investigated the genetic basis of nitrogen use efficiency (NUE) and its component traits NUpE and NUtE in wheat. A bi-parental RIL mapping population, along with parental and check genotypes, were evaluated under different nitrogen levels for three years. A genetic map with 456 SNP markers was used for QTL analysis and 36 QTLs for NUE, NUpE, and NUtE were identified. Candidate genes involved in metabolic and cellular processes were found in the QTL regions, some of which showed differential expression in roots and shoots. These findings contribute to the understanding of NUE and provide potential targets for molecular-assisted selection (MAS) in wheat improvement.