QTL Mapping by Whole Genome Re-sequencing and Analysis of Candidate Genes for Nitrogen Use Efficiency in Rice

Abstract

Nitrogen is a major nutritional element in rice production. However, excessive application of nitrogen fertilizer has caused severe environmental pollution. Therefore, development of rice varieties with improved nitrogen use efficiency (NUE) is urgent for sustainable agriculture. In this study, bulked segregant analysis (BSA) combined with whole genome re-sequencing (WGS) technology was applied to finely map quantitative trait loci (QTL) for NUE. A key QTL, designated as qNUE6 was identified on chromosome 6 and further validated by Insertion/Deletion (InDel) marker-based substitutional mapping in recombinants from F2 population (NIL-13B4 × GH998). Forty-four genes were identified in this 266.5-kb region. According to detection and annotation analysis of variation sites, 39 genes with large-effect single-nucleotide polymorphisms (SNPs) and large-effect InDels were selected as candidates and their expression levels were analyzed by qRT-PCR. Significant differences in the expression levels of LOC_Os06g15370 (peptide transporter PTR2) and LOC_Os06g15420 (asparagine synthetase) were observed between two parents (Y11 and GH998). Phylogenetic analysis in Arabidopsis thaliana identified two closely related homologs, AT1G68570 (AtNPF3.1) and AT5G65010 (ASN2), which share 72.3 and 87.5% amino acid similarity with LOC_Os06g15370 and LOC_Os06g15420, respectively. Taken together, our results suggested that qNUE6 is a possible candidate gene for NUE in rice. The fine mapping and candidate gene analysis of qNUE6 provide the basis of molecular breeding for genetic improvement of rice varieties with high NUE, and lay the foundation for further cloning and functional analysis.

Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency

“…Previous studies have shown that the differences between NIL15 and NIL19 are on chromosomes 6, 8, 9, and 10 [5] . These regions contain 6 PTR genes, which were LOC_Os06g13200, LOC_Os06g13210, LOC_Os06g15370, LOC_Os06g21900, LOC_Os06g38294, and LOC_Os10g22560.…”

“…The information about the two lines can be found in previous studies [5] . The evenly germinated seeds were selected and cultured in 96-well cultivation instrument with 1.4 mM NH 4 NO 3 (high nitrogen, HN) nutrient solution.…”

“…In the previous study, we identified a NUE-related QTL qNUE6in rice, and LOC_Os06g15370 may be the ideal candidate gene [5] . The annotation for LOC_Os06g15370 is a peptide transporter, and we named this gene as OsPTR10.…”

Fine mapping and gene cloning in the post-NGS era: advances and prospects

“…Similarly, QTL-Seq approach was applied to fine-map bacterial wilt resistance genes and develop diagnostic markers for use in breeding in the case of groundnut (Luo et al 2019a). Adoption of QTL-Seq is increasingly reported for delineating candidate QTLs for both qualitative and quantitative traits (Yang et al 2017;Li et al 2018;Zhang et al 2018;Clevenger et al 2018;Zhang et al 2019;Luo et al 2019b).…”

Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency

“…Recently, researchers have identified several loci that are associated with NUE in rice [3,4] . In the previous study, we identified a major QTL qNUE6 for rice NUE on chromosome 6 in rice, and LOC_Os06g15370 may be the ideal candidate gene [5] . The annotation for…”