Genetic Dissection Uncovers Genome-Wide Marker-Trait Associations for Plant Growth, Yield, and Yield-Related Traits Under Varying Nitrogen Levels in Nested Synthetic Wheat Introgression Libraries

Abstract

Nitrogen is one of the most important macronutrients for crop growth and metabolism. To identify marker-trait associations for complex nitrogen use efficiency (NUE)-related agronomic traits, field experiments were conducted on nested synthetic wheat introgression libraries at three nitrogen input levels across two seasons. The introgression libraries were genotyped using the 35K Axiom® Wheat Breeder's Array and genetic diversity and population structure were examined. Significant phenotypic variation was observed across genotypes, treatments, and their interactions across seasons for all the 22 traits measured. Significant positive correlations were observed among grain yield and yield-attributing traits and root traits. Across seasons, a total of 233 marker-trait associations (MTAs) associated with fifteen traits of interest at different levels of nitrogen (N0, N60, and N120) were detected using 9,474 genome-wide single nucleotide polymorphism (SNP) markers. Of these, 45 MTAs for 10 traits in the N0 treatment, 100 MTAs for 11 traits in the N60 treatment, and 88 MTAs for 11 traits in the N120 treatment were detected. We identified putative candidate genes underlying the significant MTAs which were associated directly or indirectly with various biological processes, cellular component organization, and molecular functions involving improved plant growth and grain yield. In addition, the top 10 lines based on N response and grain yield across seasons and treatments were identified. The identification and introgression of superior alleles/donors improving the NUE while maintaining grain yield may open new avenues in designing next generation nitrogen-efficient high-yielding wheat varieties.

Meta-QTL Analysis in Rice and Cross-Genome Talk of the Genomic Regions Controlling Nitrogen Use Efficiency in Cereal Crops Revealing Phylogenetic Relationship

“…The root-specific expression of the candidate genes was identified in the MQTL region under the nitrogen-deficit condition, suggesting the role of root traits in improving NUE in plants. The identification of nitrate transporter genes and previously identified marker-trait associations in rice and wheat (Sandhu et al, 2015;Sandhu et al, 2019;Subedi et al, 2019;Kumar et al, 2021;Sandhu et al, 2021) in close proximity to the MQTL/candidate genes/ their orthologues associated with the NUE-related traits in the present study validates the efficacy of the reported MQTL. The 76 MQTLs reported in the present study were used for a further selection of some of the promising MQTL using the criteria; average phenotypic variance >10%, average LOD >4, and the involvement of ≥10 initial QTLs within the MQTL.…”

“…The marker-trait associations associated with grain yield/yield-related traits and plant morphological traits reported in our previous studies were present in the MQTL region reported in the present study. Similarly, the wheat orthologues were present in close proximity to the marker-trait association and nitrate transporter genes identified in our previous study (Kumar et al, 2021;Sandhu et al, 2021) (Figure 6). The identified 20 candidate genes in wheat are nitrogen transporters.…”

“…FIGURE 6 | Schematic representation of the distribution of previously reported single nucleotide polymorphism (SNP) associated with traits of interest, candidate genes reported in the present study, and the nitrate transporter along the 21 chromosomes of wheat. The chromosome map showing the candidate genes reported in the present study in the MQTL gene based on the synteny and their co-location with the previously reported single nucleotide polymorphism (SNP) associated with different nitrogen use efficiency (NUE)-related trait, root traits, yield, and yield-related traits (Sandhu et al, 2021), and the nitrate transporter reported in wheat (Kumar et al, 2021). The numbers below each rice chromosome indicate chromosome numbers.…”

“…The information on the marker trait associated with root traits improving nitrogen use efficiency and grain yield/yield-related traits in rice (Sandhu et al, 2015;Sandhu et al, 2019;Subedi et al, 2019) and wheat (Kumar et al, 2021;Sandhu et al, 2021) was collected from our previous studies. The information on the nitrate transporter gene in wheat and rice was collected from the Ensembl Plants database.…”

“…To check the efficacy of identified MQTL and candidate genes underlying MQTL, a validation panel of the marker-trait association identified in our previous study (Sandhu et al, 2015;Sandhu et al, 2019;Subedi et al, 2019) in rice and wheat (Sandhu et al, 2021) and nitrate transporters reported in rice was made. The identification of previously identified marker-trait associations associated with the nitrogen use efficiency-related traits in rice and nitrate transporter genes in close proximity to the MQTL and candidate genes reported in the present study indicated the robustness of the reported MQTL.…”