Salinity is a major constraint on crop growth and productivity, limiting sustainable agriculture in arid regions. Understanding the molecular mechanisms of salt-stress adaptation in canola is ...important to improve salt tolerance and promote its cultivation in saline lands. In this study, roots of control (no salt) and 200 mM NaCl-stressed canola seedlings were collected for RNA-Seq analysis and qRT-PCR validation. A total of 5385, 4268, and 7105 DEGs at the three time points of salt treatment compared to the control were identified, respectively. Several DEGs enriched in plant signal transduction pathways were highly expressed under salt stress, and these genes play an important role in signaling and scavenging of ROS in response to salt stress. Transcript expression in canola roots differed at different stages of salt stress, with the early-stages (2 h) of salt stress mainly related to oxidative stress response and sugar metabolism, while the late-stages (72 h) of salt stress mainly related to transmembrane movement, amino acid metabolism, glycerol metabolism and structural components of the cell wall. Several families of TFs that may be associated with salt tolerance were identified, including ERF, MYB, NAC, WRKY, and bHLH. These results provide a basis for further studies on the regulatory mechanisms of salt stress adaptation in canola.
Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously ...investigated.
We developed the software easy-to-annotate Helitron (EAHelitron), a Unix-like command line, and used it to identify Helitrons in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined Helitron density (abundance/Mb) and visualized and examined Helitron distribution patterns. We identified more than 104,653 Helitrons, including many new Helitrons not predicted by other software. Whole genome Helitron density is independent from genome size and shows stability at the species level. Using linear discriminant analysis, de novo genomes (next-generation sequencing) were successfully classified into Arabidopsis thaliana groups. For most Brassicaceae species, Helitron density negatively correlated with gene density, and Helitron distribution patterns were similar to those of A. thaliana. They preferentially inserted into sequence around the centromere and intergenic region. We also associated 13 Helitron polymorphism loci with flowering-time phenotypes in 18 A. thaliana ecotypes.
EAHelitron is a fast and efficient tool to identify new Helitrons. Whole genome Helitron density can be an informative character for plant classification. Helitron insertion polymorphism could be used in association analysis.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Flowering time adaptation is a major breeding goal in the allopolyploid species Brassica napus. To investigate the genetic architecture of flowering time, a genome-wide association study (GWAS) of ...flowering time was conducted with a diversity panel comprising 523 B. napus cultivars and inbred lines grown in eight different environments. Genotyping was performed with a Brassica 60K Illumina Infinium SNP array. A total of 41 single-nucleotide polymorphisms (SNPs) distributed on 14 chromosomes were found to be associated with flowering time, and 12 SNPs located in the confidence intervals of quantitative trait loci (QTL) identified in previous researches based on linkage analyses. Twenty-five candidate genes were orthologous to Arabidopsis thaliana flowering genes. To further our understanding of the genetic factors influencing flowering time in different environments, GWAS was performed on two derived traits, environment sensitivity and temperature sensitivity. The most significant SNPs were found near Bn-scaff_16362_1-p380982, just 13 kb away from BnaC09g41990D, which is orthologous to A. thaliana CONSTANS (CO), an important gene in the photoperiod flowering pathway. These results provide new insights into the genetic control of flowering time in B. napus and indicate that GWAS is an effective method by which to reveal natural variations of complex traits in B. napus.
Brassica napus, an allotetraploid crop, is hypothesized to be a hybrid from unknown varieties of Brassica rapa and Brassica oleracea. Despite the economic importance of B. napus, much is unresolved ...regarding its phylogenomic relationships, genetic structure, and diversification. Here we conduct a comprehensive study among diverse accessions from 183 B. napus (including rapeseed, rutabaga, and Siberian kale), 112 B. rapa, and 62 B. oleracea and its wild relatives. Using RNA-seq of B. napus accessions, we define the genetic diversity and sub-genome variance of six genetic clusters. Nuclear and organellar phylogenies for B. napus and its progenitors reveal varying patterns of inheritance and post-formation introgression. We discern regions with signatures of selective sweeps and detect 8,187 differentially expressed genes with implications for B. napus diversification. This study highlights the complex origin and evolution of B. napus providing insights that can further facilitate B. napus breeding and germplasm preservation.
Key message
The mutations
BnA1.CER4
and
BnC1.CER4
produce disordered wax crystals types and alter the composition of epidermal wax, causing increased cuticular permeability and sclerotium resistance.
...The aerial surfaces of land plants are coated with a cuticle, comprised of cutin and wax, which is a hydrophobic barrier for preventing uncontrolled water loss and environmental damage. However, the mechanisms by which cuticle components are formed are still unknown in
Brassica napus
L. and were therefore assessed here.
BnA1.CER4
and
BnC1.CER4,
encoding fatty acyl-coenzyme A reductases localizing to the endoplasmic reticulum and highly expressed in leaves, were identified and functionally characterized. Expression of
BnA1.CER4
and
BnC1.CER4
cDNA in yeast (
Saccharomyces cerevisiae
) induced the accumulation of primary alcohols with chain lengths of 26 carbons. The mutant line
Nilla glossy2
exhibited reduced wax crystal types, and wax composition analysis showed that the levels of branched primary alcohols were decreased, whereas those of the other branched components were increased. Further analysis showed that the mutant had reduced water retention but enhanced resistance to
Sclerotinia sclerotiorum
. Collectively, our study reports that
BnA1.CER4
and
BnC1.CER4
are fatty acyl-coenzyme A reductase genes in
B. napus
with a preference for branched substrates that participate in the biosynthesis of
anteiso
-primary alcohols.
Key message
A candidate branching-controlling gene for
qDBA09
was identified after delimiting a
Brassica napus
recessive locus within a 270-kb interval on chromosome A09.
Although branching is an ...important trait associated with the adaptation and yield potential of rapeseed (
Brassica napus
), the genetic mechanisms underlining branching in this crop remain poorly understood. In this study, we characterized a naturally occurring rapeseed mutant,
db1
, which showed an ultrahigh branching density phenotype. By combining bulked segregant analysis (BSA) and the
Brassica
60K SNP BeadChip Array, we identified two major quantitative trait loci (QTLs),
qDBA09
and
qDBC06
, which were subsequently confirmed using the traditional QTL-mapping approach. Analysis of 208 individuals from a BC
1
F
3
population indicated that the
qDBA09
locus is a single Mendelian factor and that the dense branching phenotype is controlled by a single recessive gene. Furthermore, QTL analysis confirmed that
qDBA09
explained between 9.5 and 70.5% of the variation in branching-related traits. Using 7785 individuals from the BC
1
F
3
population, we mapped
qDBA09
to a DNA fragment of approximately 270 kb in length that contained 27 predicted genes, three of which were identified as potentially involved in the control of the dense branching trait. Based on the reported function of these genes, together with sequence comparisons and co-segregation analysis, we identified a potential candidate gene for the
qDBA09
locus. The present findings lay the foundations for further in-depth research on the branching mechanisms of
B. napus
.
Key message
A candidate gene for male fertility restoration in
Brassica juncea
,
BjRf
, was isolated from a 23-kb interval on chromosome A05 using map-based cloning and BSA methods.
The cytoplasmic ...male sterility/fertility restoration (CMS/
Rf
) system has been extensively used for heterosis in plants. It also provides valuable resources for studying mitochondrial–nuclear coevolution and interaction. The
oxa
CMS, which is a new CMS type reported in
Brassica juncea
(
B. juncea
), has been broadly used in the exploitation and application of heterosis in this species. However, the
oxa
CMS fertility restorer gene
BjRf
has not been reported. In this study, a stable restorer line was successfully constructed via continuous testcross and artificial selection. Besides, a new
Rf
gene was mapped in a 23-kb region on chromosome A05 in
B. juncea
with a genetic distance of 0.5 cM by the method incorporating bulk segregant analysis (BSA) and conventional map-based cloning. Finally,
BjuA017917
, a non-PPR
Rf
gene encoding a guanosine nucleotide diphosphate dissociation inhibitor (GDI), is proposed to be the candidate gene for fertility restoration of the
oxa
CMS line in
B. juncea
. Moreover, a functional marker, CRY3, was developed for marker-assisted selection for
Brassica juncea
breeding.
Soil salinity is a serious threat to agriculture sustainability worldwide. Salt tolerance at the seedling stage is crucial for plant establishment and high yield in saline soils; however, little ...information is available on rapeseed (
L.) salt tolerance. We evaluated salt tolerance in different rapeseed accessions and conducted a genome-wide association study (GWAS) to identify salt tolerance-related quantitative trait loci (QTL). A natural population comprising 368
.
cultivars and inbred lines was genotyped with a
60K Illumina Infinium SNP array. The results revealed that 75 single-nucleotide polymorphisms (SNPs) distributed across 14 chromosomes were associated with four salt tolerance-related traits. These SNPs integrated into 25 QTLs that explained 4.21-9.23% of the phenotypic variation in the cultivars. Additionally, 38 possible candidate genes were identified in genomic regions associated with salt tolerance indices. These genes fell into several functional groups that are associated with plant salt tolerance, including transcription factors, aquaporins, transporters, and enzymes. Thus, salt tolerance in rapeseed involves complex molecular mechanisms. Our results provide valuable information for studying the genetic control of salt tolerance in
seedlings and may facilitate marker-based breeding for rapeseed salt tolerance.
Key message
A mitochondria-localized pentatricopeptide repeat protein was identified by positional cloning and transferred into the
hau
CMS line, where it successfully restored fertility
Cytoplasmic ...male sterility (CMS) is a maternally inherited trait that can be controlled by restorer-of-fertility (
Rf
) genes present in the nucleus. The
hau
CMS was identified as a new form of CMS associated with the mitochondrial transcript
orf288
; however, a lack of a restorer gene has limited its utilization in
Brassica
crops. Here, the combination of
Brassica
60 K array with bulk segregant analysis and map-based cloning was used to delimit the
Rfh
locus to an 82.2-kb region on chromosome A09. A candidate gene encoding a mitochondria-localized pentatricopeptide repeat (PPR) protein was identified and transferred into the
hau
CMS line, where it successfully restored the fertility of the
hau
CMS plants. Furthermore, the expression analysis showed that
Rfh
was highly expressed in the flower buds, and the sequence analysis results implied that functional divergence between RFH and rfh could be due to 59 amino acid residue differences in the deduced protein sequences. In addition, a co-separated molecular marker was developed based on the divergent sequences between the dominant and recessive alleles. These results will help enable the heterosis of
Brassica
crops in the future.
Increasing rapeseed yield has always been a primary goal of rapeseed research and breeding. However, flowering time is a prerequisite for stable rapeseed yield and determines its adaptability to ...ecological regions. MIKC-type MADS-box (MICK) genes are a class of transcription factors that are involved in various physiological and developmental processes in plants. To understand their role in floral transition-related pathways, a genome-wide screening was conducted with
(
), which revealed 172 members. Using previous data from a genome-wide association analysis of flowering traits,
and
were identified as candidate flowering genes. Therefore, we used the CRISPR/Cas9 system to verify the function of
and
in
. T0 plants were edited efficiently at the
and
target sites to generate homozygous and heterozygous mutants with most mutations stably inherited by the next generation. Notably, the mutant only showed the early flowering phenotype when all homologous copies of
were edited, indicating functional redundancy between homologous copies. However, no changes in flowering were observed in the
mutant. Quantitative analysis of the pathway-related genes in the
mutant revealed the upregulation of
(
) and
(
) genes, which promoted early flowering in the mutant. In summary, our study created early flowering mutants, which provided valuable resources for early maturing breeding, and provided a new method for improving polyploid crops.
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