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

Abstract 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 (2,571.38 cM length) was used for QTL analysis. Thirty six main effect QTLs (17 QTLs for NUE, 13 NUpE and 6QTLs for NUtE) distributed on 12 chromosomes (1B, 1D, 2A, 2B, 3A, 4B, 5A, 5B, 5D, 6A, 6D, and 7A) were identified at 2.52 to 9.27 LOD scores. Individual QTLs explained 6.65–22.89% phenotypic variation. Multi-traits QTLs (Mt-QTLs) and 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 genes in roots and 34 CGs 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 were recommended for MAS for improvement of NUE in wheat.