title: Physiological, genomic and transcriptional diversity in responses to boron deficiency in rapeseed genotypes.
abstract: Allotetraploid rapeseed (Brassica napus L. AnAnCnCn, 2n=4x=38) is highly susceptible to boron (B) deficiency, a widespread limiting factor that causes severe losses in seed yield. The genetic variation in the sensitivity to B deficiency found in rapeseed genotypes emphasizes the complex response architecture. In this research, a B-inefficient genotype, 'Westar 10' ('W10'), responded to B deficiencies during vegetative and reproductive development with an over-accumulation of reactive oxygen species, severe lipid peroxidation, evident plasmolysis, abnormal floral organogenesis, and widespread sterility compared to a B-efficient genotype, 'Qingyou 10' ('QY10'). Whole-genome re-sequencing (WGS) of 'QY10' and 'W10' revealed a total of 1 605 747 single nucleotide polymorphisms and 218 755 insertions/deletions unevenly distributed across the allotetraploid rapeseed genome (~1130Mb). Digital gene expression (DGE) profiling identified more genes related to B transporters, antioxidant enzymes, and the maintenance of cell walls and membranes with higher transcript levels in the roots of 'QY10' than in 'W10' under B deficiency. Furthermore, based on WGS and bulked segregant analysis of the doubled haploid (DH) line pools derived from 'QY10' and 'W10', two significant quantitative trait loci (QTLs) for B efficiency were characterized on chromosome C2, and DGE-assisted QTL-seq analyses then identified a nodulin 26-like intrinsic protein gene and an ATP-binding cassette (ABC) transporter gene as the corresponding candidates regulating B efficiency. This research facilitates a more comprehensive understanding of the differential physiological and transcriptional responses to B deficiency and abundant genetic diversity in rapeseed genotypes, and the DGE-assisted QTL-seq analyses provide novel insights regarding the rapid dissection of quantitative trait genes in plant species with complex genomes.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yingpeng
authors.initials: Y
authors.lastname: Hua
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Zhou
authors.affiliation: Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Guangda
authors.initials: G
authors.lastname: Ding
authors.affiliation: College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Qingyong
authors.initials: Q
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Shi
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China fangsenxu@mail.hzau.edu.cn.
authors.forename: Fangsen
authors.initials: F
authors.lastname: Xu
mesh_terms: D001895:Boron / Q000172:deficiency* / Q000378:metabolism; D029741:Brassica rapa / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology; D014644:Genetic Variation / Q000235:genetics / Q000502:physiology; D005838:Genotype; D015227:Lipid Peroxidation / Q000502:physiology; D040641:Quantitative Trait Loci / Q000235:genetics; D017382:Reactive Oxygen Species / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D057891:Tetraploidy
chemical_list: D017382:Reactive Oxygen Species; D001895:Boron
keywords: B-deficiency phenotype; Brassica napus; boron (B) efficiency; differentially expressed genes; genomic variations; next-generation sequencing.