Mapping of the QTLs governing grain nutrients in wheat (Triticum aestivum L.) under nitrogen treatment using high-density SNP markers

IntroductionMicronutrient deficiencies, particularly zinc (Zn) and iron (Fe), are prevalent global health issues, especially among children, that lead to hidden hunger. Wheat is a primary food source for billions of people, but it contains low essential minerals. According to recent studies, the optimum application of nitrogen (N) fertilizers can significantly enhance the micronutrient uptake and accumulation in wheat grains.MethodsThe aims of this study were to identify superior wheat recombinant inbred lines (RILs) of RAJ3765 × HD2329 with high nutrients in grain using the multi-trait genotype–ideotype distance index (MGIDI) and to identify quantitative trait loci (QTLs)/genes associated with grain nutrient content using a single-nucleotide polymorphism (SNP)-based genetic linkage map. The parents and their RIL population were grown under control and nitrogen-deficient (NT) conditions, and nutrient content was determined using inductively coupled plasma optical emission spectroscopy (ICP-OES).Results and discussionAnalysis of variance and descriptive statistics showed a significant difference among all the nutrients. The highest mean values of grain iron concentration (GFeC) and grain zinc concentration (GZnC) were 52.729 and 35.137 mg/kg, respectively, under the control condition, while the lowest mean values were 41.016 and 33.117 mg/kg, respectively, recorded under NT; a similar trend was observed in all the elements. Genotyping was carried out using the 35K Axiom® Wheat Breeder’s Array. A genetic linkage map was constructed using 2,499 polymorphic markers identified for parents across 21 wheat chromosomes. Genetic linkage mapping identified a total of 26 QTLs on 17 different chromosomes. A total of 18 QTLs under the control condition and eight QTLs under the nitrogen stress condition were identified. QTLs for each nutrient were selected based on the high percentage of phenotypic variation explained (PVE%) and logarithm of odds (LOD) score value of more than 3. The LOD scores for studied nutrients varied from 3.04 to 13.42, explaining approximately 1.1% to 27.83% of PVE. One QTL was mapped for grain calcium concentration (GCaC), whereas two QTLs each for grain potassium concentration (GKC), GFeC, grain copper concentration (GCuC), and grain nickel concentration (GNiC) were mapped on different chromosomes. Four QTLs were mapped each for GZnC, grain manganese concentration (GMnC), and grain molybdenum concentration (GMoC), while the highest five were linked to grain barium concentration (GBaC). In silico analysis of these chromosomal regions identified putative candidate genes that code for 30 different types of proteins, which play roles in many important biochemical or physiological processes. Putative candidate gene magnesium transporter MRS2-G linked to GFeC and probable histone-arginine methyltransferase CARM1 and ABC transporter C family were found to be linked to GZnC. These QTLs can be utilized to generate cultivars adapted to climate change by marker-assisted gene/QTL transfer.