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.
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
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.
Background
Nitrogen (N), phosphorous (P), and potassium (K) are critical nutrient elements necessary for crop plant growth and development. However, excessive inputs will lead to inefficient usage ...and cause excessive nutrient losses in the field environment, and also adversely affect the soil, water and air quality, human health, and biodiversity.
Methods
Field experiments were conducted to study the effects of controlled-release fertilizer (CRF) on seed yield, plant growth, nutrient uptake, and fertilizer usage efficiency for early ripening rapeseed (Xiangzayou 1613) in the red-yellow soil of southern China during 2011–2013. It was grown using a soluble fertilizer (SF) and the same amounts of CRF, such as SF1/CRF1 (3750 kg/hm
2
), SF2/CRF2 (3000 kg/hm
2
), SF3/CRF3 (2250 kg/hm
2
), SF4/CRF4 (1500 kg/hm
2
), SF5/CRF5 (750 kg/hm
2
), and also using no fertilizer (CK).
Results
CRF gave higher seed yields than SF in both seasons by 14.51%. CRF4 and SF3 in each group achieved maximum seed yield (2066.97 and 1844.50 kg/hm
2
, respectively), followed by CRF3 (1929.97 kg/hm
2
) and SF4 (1839.40 kg/hm
2
). There were no significant differences in seed yield among CK, SF1, and CRF1 (
P
>0.05). CRF4 had the highest profit (7126.4 CNY/hm
2
) and showed an increase of 12.37% in seed yield, and it decreased by 11.01% in unit fertilizer rate compared with SF4. The branch number, pod number, and dry matter weight compared with SF increased significantly under the fertilization of CRF (
P
<0.05). The pod number per plant was the major contributor to seed yield. On the other hand, the N, P, and K uptakes increased at first and then decreased with increasing the fertilizer rate at maturity, and the N, P, and K usage efficiency decreased with increasing the fertilizer rate. The N, P, and K uptakes and usage efficiencies of the CRF were significantly higher than those of SF (
P
<0.05). The N accumulation and N usage efficiency of CRF increased by an average of 13.66% and 9.74 percentage points, respectively, compared to SF. In conclusion, CRF significantly promoted the growth of rapeseed with using total N as the base fertilizer, by providing sufficient N in the later growth stages, and last by reducing the residual N in the soil and increasing the N accumulation and N usage efficiency.
A multiomics approach encompassing morphophysiology, ionomic profiling, whole-genome resequencing, transcriptomics, and high-resolution metabolomics reveals that differences in cadmium resistance ...between two rapeseed cultivars is determined by subcellular reallocation.
Abstract
Oilseed rape (Brassica napus) has great potential for phytoremediation of cadmium (Cd)-polluted soils due to its large plant biomass production and strong metal accumulation. Enhanced plant Cd resistance (PCR) is a crucial prerequisite for phytoremediation through hyper-accumulation of excess Cd. However, the complexity of the allotetraploid genome of rapeseed hinders our understanding of PCR. To explore rapeseed Cd-resistance mechanisms, we examined two genotypes, ‘ZS11’ (Cd-resistant) and ‘W10’ (Cd-sensitive), that exhibit contrasting PCR while having similar tissue Cd concentrations, and characterized their different fingerprints in terms of plant morphophysiology (electron microscopy), ion abundance (inductively coupled plasma mass spectrometry), DNA variation (whole-genome resequencing), transcriptomics (high-throughput mRNA sequencing), and metabolomics (ultra-high performance liquid chromatography-mass spectrometry). Fine isolation of cell components combined with ionomics revealed that more Cd accumulated in the shoot vacuoles and root pectins of the resistant genotype than in the sensitive one. Genome and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in pectin modification, ion binding, and compartmentalization. Transcriptomics-assisted gene co-expression networks characterized BnaCn.ABCC3 and BnaA8.PME3 as the central members involved in the determination of rapeseed PCR. High-resolution metabolic profiles revealed greater accumulation of shoot Cd chelates, and stronger biosynthesis and higher demethylation of root pectins in the resistant genotype than in the sensitive one. Our comprehensive examination using a multiomics approach has greatly improved our understanding of the role of subcellular reallocation of Cd in the determination of PCR.
Enhancing nitrogen use efficiency (NUE) in crop plants is an important breeding target to reduce excessive use of chemical fertilizers, with substantial benefits to farmers and the environment. In ...Arabidopsis (Arabidopsis thaliana), allocation of more NO₃⁻ to shoots was associated with higher NUE; however, the commonality of this process across plant species have not been sufficiently studied. Two Brassica napus genotypes were identified with high and low NUE. We found that activities of V-ATPase and V-PPase, the two tonoplast proton-pumps, were significantly lower in roots of the high-NUE genotype (Xiangyou15) than in the low-NUE genotype (814); and consequently, less vacuolar NO₃⁻ was retained in roots of Xiangyou15. Moreover, NO₃⁻ concentration in xylem sap, ¹⁵N shoot:root (S:R) and NO₃⁻ S:R ratios were significantly higher in Xiangyou15. BnNRT1.5 expression was higher in roots of Xiangyou15 compared with 814, while BnNRT1.8 expression was lower. In both B. napus treated with proton pump inhibitors or Arabidopsis mutants impaired in proton pump activity, vacuolar sequestration capacity (VSC) of NO⁻⁻ in roots substantially decreased. Expression of NRT1.5 was up-regulated, but NRT1.8 was down-regulated, driving greater NO₃⁻ long-distance transport fromroots to shoots. NUE in Arabidopsis mutants impaired in proton pumps was also significantly higher than in the wild type col-0. Taken together, these data suggest that decrease in VSC of NO₃⁻ in roots will enhance transport to shoot and essentially contribute to higher NUE by promoting NO₃⁻ allocation to aerial parts, likely through coordinated regulation of NRT1.5 and NRT1.8.
•Reduced V-ATPase and V-PPase activity improved nitrogen use efficiency.•Reduced V-ATPase and V-PPase activity decreased Cd2+ tolerance.•Decreased NO3− vacuolar sequestration capacity (VSC) enhanced ...Atclca-2 Cd2+ VSC.•Enhanced Cd2+ VSC decreased NO3− VSC in AtCAX4-OE.•Regulating Cd2+ and NO3− vacuolar accumulation enhances NUE and Cd2+ tolerance.
The transmembrane transport of NO3− and Cd2+ into plant cell vacuoles relies on the energy from their tonoplast proton pumps, V-ATPase and V-PPase. If the activity of these pumps is reduced, it results in less NO3− and Cd2+ being transported into the vacuoles, which contributes to better nitrogen use efficiency (NUE) and lower Cd2+ tolerance in plants. The physiological mechanisms that regulate the balance between NUE and Cd2+ tolerance remain unknown. In our study, two Brassica napus genotypes with differential NUEs, xiangyou 15 and 814, and Atclca-2 mutant and AtCAX4 over-expression line (AtCAX4-OE) of Arabidopsis thaliana, were used to investigate Cd2+ stress responses. We found that the Brassica napus genotype, with higher NUE, was more sensitive to Cd2+ stress. The AtCAX4-OE mutant, with higher Cd2+ vacuolar sequestration capacity (VSC), limited NO3− sequestration into root vacuoles and promoted NUE. Atclca-2 mutants, with decreased NO3− VSC, enhanced Cd2+ sequestration into root vacuoles and conferred greater Cd2+ tolerance than the WT. This may be due to the competition between Cd2+ andNO3− in the vacuoles for the energy provided by V-ATPase and V-PPase. Regulating the balance between Cd2+ and NO3− vacuolar accumulation by inhibiting the activity of CLCa transporter and increasing the activity of CAX4 transporter will simultaneously enhance both the NUE and Cd2+ tolerance of Brassica napus, essential for improving its Cd2+ phytoremediation potential.
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