Genome-Wide Association Study of Nitrogen Use Efficient Traits in Sweetpotato Seeding Stage and Screening and Validation of Candidate Genes

The objective of this paper was to analyze the genetic mechanisms of nitrogen use efficiency (NUE), and to explore the loci and candidate genes associated nitrogen (N) efficient traits, to provide support for the N-efficient molecular breeding and genetic improvement of sweetpotato.

A total of 129 sweetpotato cultivars from all over the world were treated with N deficiency (0 mmol·L^-1) and normal N (14 mmol·L^-1). A hydroponic experiment was conducted to facilitate the genome-wide association study (GWAS) of six phenotypic traits (shoot biomass increment, root biomass increment, shoot N accumulation, root N accumulation, shoot N physiological utilization efficiency, and root N physiological utilization efficiency) of sweetpotato at the seedling stage. The N-efficient candidate genes were identified based on the GWAS and subsequently- verified using RT-qPCR.

There were wide variations among the six traits related to NUE in sweetpotato under the normal N and N deficiency treatment conditions. The coefficient of variation (CV) of the shoot biomass increment under the N deficiency treatment condition was the greatest at 69.5%. The CV of the root N physiological utilization efficiency under N deficiency treatment condition was the smallest at 12.1%. All five traits were significantly correlated except for root N physiological utilization efficiency. The MLM model was used to conduct a GWAS of the six phenotypic trait values. A total of 134 QTL and 888 SNP loci were identified as being significantly associated with four out of the six traits, namely, shoot biomass increment, root biomass increment, root N accumulation, and shoot N physiological utilization efficiency. A total of 93 SNP markers across ten regions were significantly associated with shoot N physiological utilization efficiency with a high reliability. Six N efficiency candidate genes were obtained via gene annotation. RT-qPCR verified that the three candidate genes (itf01g08120.t1, itf01g22030.t1 and itf01g221000.t2) encoded glutamate dehydrogenase, NPH3 protein and TIP41-like protein, respectively, which warrants further research.

A total of 888 SNP loci associated with N utilization traits were detected in 129 sweetpotato cultivars. Among these, 93 SNP loci were significantly associated with shoot N physiological utilization efficiency, and six candidate genes were identified. Preliminary verification indicated that the itf01g08120.t1, itf01G2203.t1 and itf01g22100.t2 genes hold promising value for further research.