Journal
G3-GENES GENOMES GENETICS
Volume 8, Issue 8, Pages 2757-2771Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/g3.118.200481
Keywords
Genetic variants; genotypes; nitrogen use efficiency; rapeseed; whole-genome re-sequencing
Categories
Funding
- National Key Research & Development Program of China [2017YFD0200100, 2017YFD0200103]
- National Natural Science Foundation of China [31101596, 31372130]
- Hunan Provincial Recruitment Program of Foreign Experts
- National Oilseed Rape Production Technology System of China
- Ministry of Education of China
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Nitrogen (N) is a non-mineral macronutrient essential for plant growth and development. Oilseed rape (A(n)A(n)C(n)C(n), 2n = 4x = 38) has a high requirement for N nutrients whereas showing the lowest N use efficiency (NUE) among crops. The mechanisms underlying NUE regulation in Brassica napus remain unclear because of genome complexity. In this study, we performed high-depth and -coverage whole-genome re-sequencing (WGS) of an N-efficient (higher NUE) genotype XY15 and an N-inefficient (lower NUE) genotype 814 of rapeseed. More than 687 million 150-bp paired-end reads were generated, which provided about 93% coverage and 50x depth of the rapeseed genome. Applying stringent parameters, we identified a total of 1,449,157 single-nucleotide polymorphisms (SNPs), 335,228 InDels, 175,602 structure variations (SVs) and 86,280 copy number variations (CNVs) between the N-efficient and -inefficient genotypes. The largest proportion of various DNA polymorphisms occurred in the inter-genic regions. Unlike CNVs, the SNP/InDel and SV polymorphisms showed variation bias of the A(n) and C-n subgenomes, respectively. Gene ontology analysis showed the genetic variants were mapped onto the genes involving N compound transport and ATPase complex metabolism, but not including N assimilation-related genes. On basis of identification of N-starvation responsive genes through high-throughput expression profiling, we also mapped these variants onto some key NUE-regulating genes, and validated their significantly differential expression between the N-efficient and -inefficient genotypes through qRT-PCR assays. Our data provide genome-wide high resolution DNA variants underlying NUE divergence in allotetraploid rapeseed genotypes, which would expedite the effective identification and functional validation of key NUE-regulating genes through genomics-assisted improvement of crop nutrient efficiency.
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