The Chloride Channel (CLC) gene family is reported to be involved in vacuolar nitrate (NO3-) transport. Nitrate distribution to the cytoplasm is beneficial for enhancing NO3- assimilation and plays ...an important role in the regulation of nitrogen (N) use efficiency (NUE). In this study, genomic information, high-throughput transcriptional profiles, and gene co-expression analysis were integrated to identify the CLCs (BnaCLCs) in Brassica napus. The decreased NO3- concentration in the clca-2 mutant up-regulated the activities of nitrate reductase and glutamine synthetase, contributing to increase N assimilation and higher NUE in Arabidopsis thaliana. The genome-wide identification of 22BnaCLC genes experienced strong purifying selection. Segmental duplication was the major driving force in the expansion of the BnaCLC gene family. The most abundant cis-acting regulatory elements in the gene promoters, including DNA-binding One Zinc Finger, W-box, MYB, and GATA-box, might be involved in the transcriptional regulation of BnaCLCs expression. High-throughput transcriptional profiles and quantitative real-time PCR results showed that BnaCLCs responded differentially to distinct NO3- regimes. Transcriptomics-assisted gene co-expression network analysis identified BnaA7.CLCa-3 as the core member of the BnaCLC family, and this gene might play a central role in vacuolar NO3- transport in crops. The BnaCLC members also showed distinct expression patterns under phosphate depletion and cadmium toxicity. Taken together, our results provide comprehensive insights into the vacuolar BnaCLCs and establish baseline information for future studies on BnaCLCs-mediated vacuolar NO3- storage and its effect on NUE.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Core Ideas
Efficiency in genomic selection is not particularly based on detailed genotype profiling facilitated by maximum marker density.
Extensive genome‐wide linkage disequilibrium is a common ...characteristic of breeding pools in many crop species.
Every quantitative trait locus across the genome can be captured by one or a few representative markers.
Fewer representative markers selected in respect of linkage disequilibrium (LD) can capture the association between a genomic region and a phenotypic trait.
Low‐density marker sets enable genomic prediction accuracies in breeding populations with strong LD comparable to those achieved with high‐density genotyping.
Genomic selection (GS) has revolutionized breeding for quantitative traits in plants, offering potential to optimize resource allocation in breeding programs and increase genetic gain per unit of time. Modern high‐density single nucleotide polymorphism (SNP) arrays comprising up to several hundred thousand markers provide a user‐friendly technology to characterize the genetic constitution of whole populations and for implementing GS in breeding programs. However, GS does not build upon detailed genotype profiling facilitated by maximum marker density. With extensive genome‐wide linkage disequilibrium (LD) being a common characteristic of breeding pools, fewer representative markers from available high‐density genotyping platforms could be sufficient to capture the association between a genomic region and a phenotypic trait. To examine the effects of reduced marker density on genomic prediction accuracy, we collected data on three traits across 2 yr in a panel of 203 homozygous Chinese semiwinter rapeseed (Brassica napus L.) inbred lines, broadly encompassing allelic variability in the Asian B. napus genepool. We investigated two approaches to selecting subsets of markers: a trait‐dependent strategy based on genome‐wide association study (GWAS) significance thresholds and a trait‐independent method to detect representative tag SNPs. Prediction accuracies were evaluated using cross‐validation with ridge‐regression best linear unbiased predictions (rrBLUP). With semiwinter rapeseed as a model species, we demonstrate that low‐density marker sets comprising a few hundred to a few thousand markers enable high prediction accuracies in breeding populations with strong LD comparable to those achieved with high‐density arrays. Our results are valuable for facilitating routine application of cost‐efficient GS in breeding programs.
Soil in short-term crop rotation systems (STCR) is still in the initial development stage of farmland soil, whereas after long-term crop rotation treatment (LTCR), soil properties are significantly ...different. This study compares STCR (4 years) and LTCR (30 years) rice-rice-fallow, rice-rice-rape rotation practices under the same soil type background and management system. To reveal ecosystem mechanisms within soils and their effects on rice yield following LTCR, we analyzed the physical, chemical, and microbiological properties of soils with different rotations and rotation times. Relative to STCR, LTCR significantly reduced soil water-stable aggregate (WSA) content in the < 0.053-mm range, while > 2 mm WSA content significantly increased. Soil organic matter increased in fields under LTCR, mainly in > 2 mm, 2–0.25 mm, and < 0.053 mm soil WSA in 0–10 cm soil layer. LTCR was associated with significantly increased total soil organic matter, at the same time being associated with increasing the amount of active organic matter in the 0–20 cm soil layer. The two crop rotation regimes significantly differed in soil aggregate composition as well as in soil N and P, microbial biomass, and community composition. Relative to STCR, LTCR field soils had significantly higher soil organic matter, active organic matter content, soil enzyme activities, and overall microbial biomass, while soil WSA and microbial community composition was significantly different. Our results demonstrate that LTCR could significantly improve soil quality and rice yield and suggest that length of rotation time and rice-rice-rape rotation are critical factors for the development of green agriculture.
Nitrogen (N) is a macronutrient that is essential for optimal plant growth and seed yield. Allotetraploid rapeseed (A
A
C
C
, 2n = 4x = 38) has a higher requirement for N fertilizers whereas ...exhibiting a lower N use efficiency (NUE) than cereal crops. N limitation adaptation (NLA) is pivotal for enhancing crop NUE and reducing N fertilizer use in yield production. Therefore, revealing the genetic and molecular mechanisms underlying NLA is urgent for the genetic improvement of NUE in rapeseed and other crop species with complex genomes.
In this study, we integrated physiologic, genomic and transcriptomic analyses to comprehensively characterize the adaptive strategies of oilseed rape to N limitation stresses. Under N limitations, we detected accumulated anthocyanin, reduced nitrate (NO
) and total N concentrations, and enhanced glutamine synthetase activity in the N-starved rapeseed plants. High-throughput transcriptomics revealed that the pathways associated with N metabolism and carbon fixation were highly over-represented. The expression of the genes that were involved in efficient N uptake, translocation, remobilization and assimilation was significantly altered. Genome-wide identification and molecular characterization of the microR827-NLA1-NRT1.7 regulatory circuit indicated the crucial role of the ubiquitin-mediated post-translational pathway in the regulation of rapeseed NLA. Transcriptional analysis of the module genes revealed their significant functional divergence in response to N limitations between allotetraploid rapeseed and the model Arabidopsis. Association analysis in a rapeseed panel comprising 102 genotypes revealed that BnaC5.NLA1 expression was closely correlated with the rapeseed low-N tolerance.
We identified the physiologic and genome-wide transcriptional responses of oilseed rape to N limitation stresses, and characterized the global members of the BnamiR827-BnaNLA1s-BnaNRT1.7s regulatory circuit. The transcriptomics-assisted gene co-expression network analysis accelerates the rapid identification of central members within large gene families of plant species with complex genomes. These findings would enhance our comprehensive understanding of the physiologic responses, genomic adaptation and transcriptomic alterations of oilseed rape to N limitations and provide central gene resources for the genetic improvement of crop NLA and NUE.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background and aims The two-component high-affinity nitrate (NO3−) transport system (THATS) proteins (NRT2/NAR2) play key roles in the efficient nitrogen (N) uptake and transport under N limitations. ...We aimed at uncovering the core THATS gene(s) regulating N use efficiency (NUE) in allotetraploid rapeseed (Brassica napus L.). Methods Genomic information, high-throughput transcriptome sequencing and gene co-expression network were integrated to identify and characterize the core THATS genes. Results We identified 17 BnaNRT2 and eight BnaNAR2.1 homologs spanning across the rapeseed genome. Copy number and gene presence/absence variations of BnaNRT2s/BnaNAR2.1 s, undergoing strong purifying selection, occurred. The over-representation of Dof, MYB and WRKY cis-regulatory elements and the enrichment of CpG islands, and protein phosphorylation sites indicated the importance of transcriptional and epigenetic regulation in the BnaNRT2 activities, respectively. qRT-PCR assays and high-throughput RNA-seq revealed that both BnaNRT2s and BnaNAR2.1 s were expressed preferentially in the roots; and they showed significantly differential expression under different N forms or different levels of NO3− supply. A gene co-expression network identified BnaC8.NRT2.1a and BnaC2.NAR2.1 as the core THATS genes. Conclusions The core THATS members can serve as elite gene resources for crop NUE improvement. The transcriptomics-assisted gene co-expression network analysis provides novel insights regarding the rapid identification of central members within large gene families of plant species with complex genomes.
Improving crop nitrogen (N) limitation adaptation (NLA) is a core approach to enhance N use efficiency (NUE) and reduce N fertilizer application. Rapeseed has a high demand for N nutrients for ...optimal plant growth and seed production, but it exhibits low NUE. Epigenetic modification, such as DNA methylation and modification from small RNAs, is key to plant adaptive responses to various stresses. However, epigenetic regulatory mechanisms underlying NLA and NUE remain elusive in allotetraploid
. In this study, we identified overaccumulated carbohydrate, and improved primary and lateral roots in rapeseed plants under N limitation, which resulted in decreased plant nitrate concentrations, enhanced root-to-shoot N translocation, and increased NUE. Transcriptomics and RT-qPCR assays revealed that N limitation induced the expression of
,
,
,
, and
, and repressed the transcriptional levels of
,
, and
. High-resolution whole genome bisulfite sequencing characterized 5094 differentially methylated genes involving ubiquitin-mediated proteolysis, N recycling, and phytohormone metabolism under N limitation. Hypermethylation/hypomethylation in promoter regions or gene bodies of some key N-metabolism genes might be involved in their transcriptional regulation by N limitation. Genome-wide miRNA sequencing identified 224 N limitation-responsive differentially expressed miRNAs regulating leaf development, amino acid metabolism, and plant hormone signal transduction. Furthermore, degradome sequencing and RT-qPCR assays revealed the miR827-NLA pathway regulating limited N-induced leaf senescence as well as the miR171-
and miR160-
pathways regulating root growth under N deficiency. Our study provides a comprehensive insight into the epigenetic regulatory mechanisms underlying rapeseed NLA, and it will be helpful for genetic engineering of NUE in crop species through epigenetic modification of some N metabolism-associated genes.
Chlorophyll is a kind of green pigment for plant photosynthesis, which has a direct effect on plant growth. In this study,bioinformatics methods were used to identify the members of SGR gene family ...in Brassica napus, Brassica rapa, Brassica oleracea, and Arabidopsis thaliana. Most of the 28 SGR genes contained four exons, encoding basic proteins. Chromosome mapping and syntenic analysis showed that there was no tandem duplication in the SGR gene family members of Brassica napus.SGR gene family members had a linear relationship, highly homologous in evolution, and very conserved in the evolutionary process. Moreover, a genome-wide association study（GWAS）of chlorophyll content was performed using a Brassica 60K Illumina Infinium SNP array in 203 Brassica napus accessions. Two haplotype regions（Chr.A01: 6,193,165–6,317,757 bp and Chr.C01: 9,059,861–9,906,618 bp）carrying two SGR genes（BnaSGR1a-A01 and BnaSGR1-C01）were detected, which were significantly associated with chlorophyll content. Meanwhile, the regional
Rapeseed(Brassica napus L.) is the main source of edible vegetable oil in China, and increasing seed oil content is the most effective way to increase the supply of rapeseed oil. In this study, 43 ...genes related to lipid synthesis were selected by analyzing the seed transcriptome data of 4 rapeseed inbred lines 25, 35, and 45 days after pollination. Among them, 33 genes were continuously up-expressed and 10 genes were continuously down-expressed from 25 to 45 days of seed development. The main genes included BnLEC1, BnABI5, Bn OLEO4, and BnOBAP1a. At the same time, combined with the resequencing data of 50semi-winter Brassica napus, 3 SNPs and 9 SNPs significantly related to oil content were detected to BnOBAP1a-A10 and BnABI5-A05, respectively, and the oil content of BnOBAP1A-A10__Hap1 was significantly higher than Hap2. The oil content of BnABI5-A05__Hap1 was significantly higher than Hap3. In addition, WGCNA was used to construct gene networks, and we found that BnOBAP1a and BnABI5 were indirectly connected
Low temperature is an important environmental stress factor affecting plant growth and development. The ICE1-CBF-COR inducer of CBF expression1-c-repeat（CRT）-binding factors-cold responsive plays an ...important role in the signaling pathway in response to low temperature stress in plants. To explore the evolution of CBF gene in Brassica napus L. and its function in response to low temperature stress, 11, 6, and 6 CBF genes were detected from Brassica napus, Brassica rapa, and Brassica oleracea, respectively. In addition, the molecular characteristics, protein conserved domains, phylogenetic tree, gene structure, and chromosome distribution were systematically investigated. The results showed that 11 BnaCBF genes could be divided into two subgroups including Subgroup Ⅰ（CBF1/2/3） and Subgroup Ⅱ（CBF4）. Transcriptome sequencing revealed that all the CBF genes of Brassica napus were induced by low temperature, among which four genes in subgroup Ib responded rapidly and durably to cold stress, and two genes in Subg
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