Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes. Issue 8 (1st August 2018)

• Record Type: Journal Article
• Authors: Hua, Ying-peng; Zhou, Ting; Liao, Qiong; Song, Hai-xing; Guan, Chun-yun; Zhang, Zhen-hua
• Is Part Of: G3. Volume 8:Issue 8(2018)
• Page Start: 2757
• Page End: 2771
• Publication Date: 2018-08-01
• Subjects: Genetic variants -- genotypes -- nitrogen use efficiency -- rapeseed -- whole-genome re-sequencing; Genetics -- Research -- Periodicals; Genomics -- Periodicals; Genetics; Genomics; Genes; Genetics -- Research; Genomics; Electronic journals; Periodical; Periodicals; Fulltext; Internet Resources; Periodicals; 572.8
• DOI: 10.1534/g3.118.200481
• Languages: English
• ISSNs: 2160-1836

Abstract

Abstract: Nitrogen (N) is a non-mineral macronutrient essential for plant growth and development. Oilseed rape (An An Cn Cn, 2 n = 4 x = 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 50× 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 An and Cn 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.