Genome-wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.)

The genetic basis of leaf hair development in upland cotton (Gossypium hirsutum)

Trichomes, which originate from the epidermal cell of aerial organs, provide plants with defense and secretion functions. Although numerous genes have been implicated in trichome development, the molecular mechanisms underlying trichome cell formation in plants remain incompletely understood. Here, we using genome-wide association study (GWAS) across 1037 diverse accessions in upland cotton (Gossypium hirsutum) to identify three loci associated with leaf pubescence (hair) amount, located on chromosome A06 (LPA1), A08 (LPA2) and A11 (LPA3), respectively. GhHD1, a previously characterized candidate gene, was identified on LPA1 and encodes an HD-Zip transcription factor. For LPA2 and LPA3, we identified two candidate genes, GhGIR1 and GhGIR2, both encoding proteins with WD40 and RING domains that act as inhibitors of leaf hair formation. Expression analysis revealed that GhHD1 was predominantly expressed in hairy accessions, whereas GhGIR1 and GhGIR2 were expressed in hairless accessions. Silencing GhHD1 or overexpressing GhGIR1 in hairy accessions induced in a hairless phenotype, whereas silencing GhGIR2 in hairless accessions resulted in a hairy phenotype. We also demonstrated that GhHD1 interact with both GhGIR1 and GhGIR2, and GhGIR1 can interact with GhGIR2. Further investigation indicated that GhHD1 functions as a transcriptional activator, binding to the promoters of the GhGIR1 and GhGIR2 to active their expression, whereas GhGIR1 and GhGIR2 can suppress the transcriptional activation of GhHD1. Our findings shed light on the intricate regulatory network involving GhHD1, GhGIR1 and GhGIR2 in the initiation and development of plant epidermal hairs in cotton.

Natural variation of TBR confers plant zinc toxicity tolerance through root cell wall pectin methylesterification

Zinc (Zn) is an essential micronutrient but can be cytotoxic when present in excess. Plants have evolved mechanisms to tolerate Zn toxicity. To identify genetic loci responsible for natural variation of plant tolerance to Zn toxicity, we conduct genome-wide association studies for root growth responses to high Zn and identify 21 significant associated loci. Among these loci, we identify Trichome Birefringence (TBR) allelic variation determining root growth variation in high Zn conditions. Natural alleles of TBR determine TBR transcript and protein levels which affect pectin methylesterification in root cell walls. Together with previously published data showing that pectin methylesterification increase goes along with decreased Zn binding to cell walls in TBR mutants, our findings lead to a model in which TBR allelic variation enables Zn tolerance through modulating root cell wall pectin methylesterification. The role of TBR in Zn tolerance is conserved across dicot and monocot plant species.

A CRISPR/Cas9-induced male-sterile line facilitating easy hybrid production in polyploid rapeseed (Brassica napus)

Rapeseed is a globally significant oilseed crop cultivated to meet the increasing demand for vegetable oil. In order to enhance yield and sustainability, breeders have adopted the development of rapeseed hybrids as a common strategy. However, current hybrid production systems in rapeseed have various limitations, necessitating the development of a simpler and more efficient approach. In this study, we propose a novel method involving the targeted disruption of Defective in Anther Dehiscence1 of Brassica napus (BnDAD1), an essential gene in the jasmonic acid biosynthesis pathway, using CRISPR/Cas9 technology, to create male-sterile lines. BnDAD1 was found to be dominantly expressed in the stamen of rapeseed flower buds. Disrupting BnDAD1 led to decreased levels of α-linolenic acid and jasmonate in the double mutants, resulting in defects in anther dehiscence and pollen maturation. By crossing the double mutant male-sterile lines with male-fertile lines, a two-line system was demonstrated, enabling the production of F 1 seeds. The male-sterile trait of the bndad1 double mutant lines was maintainable by applying exogenous methyl jasmonate and subsequently self-pollinating the flowers. This breakthrough holds promising potential for harnessing heterosis in rapeseed and offers a simpler and more efficient method for producing hybrid seeds.

Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus)

KEY MESSAGE

Through comprehensive genomic and transcriptomic analyses, we identified a set of 23 genes that act up- or downstream of erucic acid content (EAC) production in rapeseed seeds. We selected example genes to showcase the distribution of single nucleotide polymorphisms, haplotypes associated with EAC phenotypes, and the creation of molecular markers differentiating low EAC and high EAC genotypes. Erucic acid content (EAC) is a crucial trait in rapeseed, with low LEAC oil recognized for its health benefits and high EA oil holding industrial value. Despite its significance, the genomic consequences of intensive LEAC-cultivar selection and the genetic basis underlying EA regulation remain largely unexplored. To address this knowledge gap, we conducted selective signal analyses, genome-wide association studies (GWAS), and transcriptome analyses. Our investigation unveiled the genetic footprints resulting from LEAC selection in germplasm populations, drawing attention to specific loci that contribute to enriching diversity. By integrating GWAS and transcriptome analyses, we identified a set of 23 genes that play a significant role in determining EAC in seeds or are downstream consequences of EA-level alterations. These genes have emerged as promising candidates for elucidating the potential mechanisms governing EAC in rapeseed. To exemplify the findings, we selected specific genes to demonstrate the distribution of single nucleotide polymorphisms and haplotypes associated with different EAC phenotypes. Additionally, we showcased to develop molecular markers distinguishing between LEAC and high EAC genotypes.

Does fungal infection increase the palatability of oilseed rape to insects?

BACKGROUND

Multiple and simultaneous attacks by pathogens and insect pests frequently occur in nature. Plants respond to biotic stresses by activating distinct defense mechanisms, but little is known about how plants cope with multiple stresses. The focus of this study was the combined interaction of fungal infection caused by Leptosphaeria maculans (synonym Plenodomus lingam) and arthropod infestation by the diamondback moth (Plutella xylostella) in oilseed rape (Brassica napus). We hypothesized that infection by the fungal pathogen L. maculans could alter oilseed rape palatability to P. xylostella-chewing caterpillars. Feeding preference tests were complemented with analyses of defense gene transcription, and levels of glucosinolates (GLSs) and volatile organic compounds (VOCs) in L. maculans-inoculated and non-inoculated (control) leaves to determine possible causes of larval choice.

RESULTS

Caterpillars preferred true leaves to cotyledons, hence true leaves were used for further experiments. True leaves inoculated with L. maculans were more palatable to caterpillars over control leaves during the early stage of infection at 3 days post inoculation (dpi), but this preference disappeared in the later stages of infection at 7 dpi. In parallel, genes involved in the salicylic acid and ethylene pathways were up-regulated in L. maculans-inoculated leaves at 3 and 7 dpi; L. maculans increased the level of total aliphatic GLSs, specifically glucobrassicanapin, and decreased the level of glucoiberin at 3 dpi and altered the content of specific VOCs. A group of 55 VOCs with the highest variability between treatments was identified.

CONCLUSION

We suggest that the P. xylostella preference for L. maculans-inoculated leaves in the early stage of disease development could be caused by the underlying mechanisms leading to changes in metabolic composition. Further research should pinpoint the compounds responsible for driving larval preference and evaluate whether the behavior of the adult moths, i.e. the stage that makes the first choice regarding host plant selection in field conditions, correlates with our results on larval host acceptance. © 2024 Society of Chemical Industry.

Genome-wide association study reveals the genetic basis for petal-size formation in rapeseed (Brassica napus) and CRISPR-Cas9-mediated mutagenesis of BnFHY3 for petal-size reduction

Petals in rapeseed (Brassica napus) serve multiple functions, including protection of reproductive organs, nutrient acquisition, and attraction of pollinators. However, they also cluster densely at the top, forming a thick layer that absorbs and reflects a considerable amount of photosynthetically active radiation. Breeding genotypes with large, small, or even petal-less varieties, requires knowledge of primary genes for allelic selection and manipulation. However, our current understanding of petal-size regulation is limited, and the lack of markers and pre-breeding materials hinders targeted petal-size breeding. Here, we conducted a genome-wide association study on petal size using 295 diverse accessions. We identified 20 significant single nucleotide polymorphisms and 236 genes associated with petal-size variation. Through a cross-analysis of genomic and transcriptomic data, we focused on 14 specific genes, from which molecular markers for diverging petal-size features can be developed. Leveraging CRISPR-Cas9 technology, we successfully generated a quadruple mutant of Far-Red Elongated Hypocotyl 3 (q-bnfhy3), which exhibited smaller petals compared to the wild type. Our study provides insights into the genetic basis of petal-size regulation in rapeseed and offers abundant potential molecular markers for breeding. The q-bnfhy3 mutant unveiled a novel role of FHY3 orthologues in regulating petal size in addition to previously reported functions.

Dessoky E, Almowallad S, AlShaqhaa MA, AL-Balawi SM, Darwish DBE, Allohibi A, Omara MY, Althobaiti F. Morphological, Biochemical, and Molecular Characterization of Exotic Brassica Germplasm

Oilseed rape (Brassica napus L.) is an important oilseed crop. We examined the diversity of germplasm expressed at three distinct levels (i.e., morphological, biochemical, and DNA levels). In this study, 150 B. napus L. accessions with three check varieties were provided by Bioresources Conservation Institute. The germplasm was grown in field conditions for data collection of 15 quantitative and nine qualitative agro-morphological traits. The result indicated that for 15 quantitative agro-morphological traits, the highest coefficient of variation was recorded for plant height and days to flowering initiation. For nine qualitative traits, most of the accessions have a spatulate leaf, brown color seeds, yellow flowers, and erect silique attitude. The best adoptable genetically diverse exotic Brassica germplasms were selected, i.e., accessions 24178, 24881, 24199, 24214, 24242, and 24192. Based on biochemical analysis for high oil content and high oleic acid content, chakwal sarsoon and accession 24192 were selected. For high oleic and linoleic acids, accession 24181 performed best, for low erucic acid accessions 24177 and 24195. Based on molecular (SSR) markers, the top 50 selected genotypes were evaluated with 30 SSR markers. The 47 genotypes with three check varieties were clustered in six major groups; the coefficient of similarity ranged between 0.18 and 1.00. Based on SSR data, the germplasms accession 24178 and Abasin were the most diverse genotypes. These genotypes have the capacity and could be used in future breeding programs. High genetic variations were investigated through the SSR among the studied genotypes of Brassica napus L. The present study also concluded that SSR is a better technique for intraspecific genetic diversity. Other modern techniques should be applied such as SNIP for the investigation of a high level of genetic diversity among crop plants in the future.

Genotypic variation of tocopherol content in a representative genetic population and genome-wide association study on tocopherol in rapeseed (Brassica napus)

Tocopherols (Tocs) are a kind of lipid-soluble substance required for the normal physiological function of mammals, particularly their antioxidant capacity. Rapeseed (Brassica napus) oil is an important source of exogenous Tocs. However, the genotypic differences in the total Toc contents, the Toc composition in the seeds, and the molecular markers associated with the seed Toc remain largely unknown. Here, we selected 290 rapeseed accessions based on the resequencing of 991 genomes in a worldwide collection of rapeseed germplasm. The contents of the four Toc isoforms, namely, α-, β-, γ-, and δ-Tocs, were also measured. Results show that the total Toc content and the γ-/α-Toc ratio varied greatly across the accessions from 85.34 to 387.00 mg/mg and 0.65 to 5.03, respectively. Furthermore, we conducted genome-wide association studies on the Tocs, which identified 28 and 73 single nucleotide polymorphisms significantly associated with the variation of total Toc content and γ-/α-Toc ratio, respectively. Bna.C02.VTE4, a putative orthologue of Arabidopsis VITAMIN E DEFICIENT 4, was tightly associated with the γ-/α-Toc ratio. This study recommends specific genetic materials with particularly high total Toc and/or low γ-/α-Toc ratio and the molecular markers and haplotypes associated with these quality traits for rapeseed breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01394-0.

Genome-wide-association study and transcriptome analysis reveal the genetic basis controlling the formation of leaf wax in Brassica napus

Cuticular wax protects plants from various biotic and abiotic stresses. However, the genetic network of wax biosynthesis and the environmental factors influencing leaf wax production in rapeseed (Brassica napus) remains unclear. Here, we demonstrated the role of leaf wax in the resistance to Sclerotinia infection in rapeseed. We found that leaves grown under high light intensity had higher expression of genes involved in wax biosynthesis, and produced more wax on the leaf surface, compared with those grown under low light conditions. Genome-wide association study (GWAS) identified 89 single nucleotide polymorphisms significantly associated with leaf wax coverage. A cross-analysis between GWAS and differentially expressed genes (DEGs) in the leaf epidermis of the accessions with contrasting differences in wax content revealed 17 candidate genes that control this variation in rapeseed. Selective sweep analysis combined with DEG analysis unveiled 510 candidate genes with significant selective signatures. From the candidate genes, we selected BnaA02.LOX4, a putative lipoxygenase, and BnaCnn.CER1, BnaA02.CER3, BnaC02.CER3, and BnaA01.CER4 (ECERIFERUM1-4) that were putatively responsible for wax biosynthesis, to analyse the allelic forms and haplotypes corresponding to high or low leaf wax coverage. These data enrich our knowledge about wax formation, and provide a gene pool for breeding an ideal leaf wax content in rapeseed.

BnIR: A multi-omics database with various tools for Brassica napus research and breeding

In the post-genome-wide association study era, multi-omics techniques have shown great power and potential for candidate gene mining and functional genomics research. However, due to the lack of effective data integration and multi-omics analysis platforms, such techniques have not still been applied widely in rapeseed, an important oil crop worldwide. Here, we report a rapeseed multi-omics database (BnIR; http://yanglab.hzau.edu.cn/BnIR), which provides datasets of six omics including genomics, transcriptomics, variomics, epigenetics, phenomics, and metabolomics, as well as numerous "variation-gene expression-phenotype" associations by using multiple statistical methods. In addition, a series of multi-omics search and analysis tools are integrated to facilitate the browsing and application of these datasets. BnIR is the most comprehensive multi-omics database for rapeseed so far, and two case studies demonstrated its power to mine candidate genes associated with specific traits and analyze their potential regulatory mechanisms.

Structural variation of GL1 gene determines the trichome formation in Brassica juncea

A 448 kb region on chromosome B02 was delimited to be associated with trichome trait in Brassica juncea, in which the BjuVB02G54610 gene with a structural variation of 3 kb structure variation (SV) encoding a MYB transcription factor was predicted as the possible candidate gene. Mustards (Brassica juncea) are allopolyploid crops in the worldwide, and trichomes are essential quality attributes that significantly influence its taste and palpability in vegetable-use cultivars. As important accessory tissues from specialized epidermal cells, trichomes also play an important role in mitigating biotic and abiotic stresses. In this study, we constructed a F₂ segregating population using YJ27 with intensive trichome leaves and 03B0307 with glabrous leaves as parents. By bulked segregant analysis (BSA-seq), we obtained a 2.1 Mb candidate region on B02 chromosome associated with the trichome or glabrous trait formation. Then, we used 13 Kompetitive Allele Specific PCR (KASP) markers for fine mapping and finally narrowed down the candidate region to about 448 kb in length. Interestingly, among the region, there was a 3 kb sequence deletion that located on the BjuVB02G54610 gene in the F₂ individuals with trichome leaves. Genotyping results of F₂ populations confirmed this deletion (R² = 81.44%) as a major QTL. Natural population re-sequencing analysis and genotyping results further validated the key role of the 3 kb structure variation (SV) of insertion/deletion type in trichome development in B. juncea. Our findings provide important information on the formation of trichomes and potential target gene for breeding vegetable mustards.

Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed (Brassica napus)

Spatial distribution and orientation of pods on the main raceme (stem) and branches could affect rapeseed yield. However, genomic regions underlying the pod orientation were not described in Brassica species. Here, we determined the extent of genetic variation in pod orientation, described as the angles of pedicel on raceme (APR) and angles of the pod on pedicel (APP) among 136 rapeseed accessions grown across three environments of the upper, middle and lower Yangtze River in China. The APR ranged from 59° to 109°, while the APP varied from 142° to 178°. Statistical analysis showed that phenotypic variation was due to genotypic (G) and environmental (E) effects. Using the genome-wide association analysis (GWAS) approach, two QTLs for APR (qBnAPR.A02 and qBnAPR.C02) and two for APP (qBnAPP.A05 and qBnAPP.C05), having minor to moderate allelic effects (4.30% to 19.47%) were identified. RNA-seq analysis revealed 606 differentially expressed genes (DEGs) in two rapeseed accessions representing the extreme phenotypes for pod orientation and different alleles at the QTLs of APR. Three DEGs (BnLAZY4.A02, BnSAUR32.A02, and BnSAUR32.C02) were identified as the most likely candidates responsible for variation in pod orientation (APR). This study elucidates the genomic regions and putative candidate genes underlying pod orientation in B. napus.

Perspectives for integrated insect pest protection in oilseed rape breeding

In the past, breeding for incorporation of insect pest resistance or tolerance into cultivars for use in integrated pest management schemes in oilseed rape/canola (Brassica napus) production has hardly ever been approached. This has been largely due to the broad availability of insecticides and the complexity of dealing with high-throughput phenotyping of insect performance and plant damage parameters. However, recent changes in the political framework in many countries demand future sustainable crop protection which makes breeding approaches for crop protection as a measure for pest insect control attractive again. At the same time, new camera-based tracking technologies, new knowledge-based genomic technologies and new scientific insights into the ecology of insect-Brassica interactions are becoming available. Here we discuss and prioritise promising breeding strategies and direct and indirect breeding targets, and their time-perspective for future realisation in integrated insect pest protection of oilseed rape. In conclusion, researchers and oilseed rape breeders can nowadays benefit from an array of new technologies which in combination will accelerate the development of improved oilseed rape cultivars with multiple insect pest resistances/tolerances in the near future.

Mapping of Genetic Locus for Leaf Trichome Formation in Chinese Cabbage Based on Bulked Segregant Analysis

Chinese cabbage is a leafy vegetable, and its leaves are the main edible organs. The formation of trichomes on the leaves can significantly affect its taste, so studying this phenomenon is of great significance for improving the quality of Chinese cabbage. In this study, two varieties of Chinese cabbage, W30 with trichome leaves and 082 with glabrous leaves, were crossed to generate F₁ and F₁ plants, which were self-fertilized to develop segregating populations with trichome or glabrous morphotypes. The two bulks of the different segregating populations were used to conduct bulked segregant analysis (BSA). A total of 293.4 M clean reads were generated from the samples, and plants from the trichome leaves (AL) bulk and glabrous leaves (GL) bulk were identified. Between the two DNA pools generated from the trichome and glabrous plants, 55,048 SNPs and 272 indels were generated. In this study, three regions (on chromosomes 6, 10 and scaffold000100) were identified, and the annotation revealed three candidate genes that may participate in the formation of leaf trichomes. These findings suggest that the three genes-Bra025087 encoding a cyclin family protein, Bra035000 encoding an ATP-binding protein/kinase/protein kinase/protein serine/threonine kinase and Bra033370 encoding a WD-40 repeat family protein-influence the formation of trichomes by participating in trichome morphogenesis (GO: 0010090). These results demonstrate that BSA can be used to map genes associated with traits and provide new insights into the molecular mechanism of leafy trichome formation in Chinese cabbage.

Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

BACKGROUND

Rapeseed (Brassica napus L.) is an important oil crop world-widely cultivated, and seed oil content (SOC) is one of the most important traits for rapeseed. To increase SOC, many efforts for promoting the function of genes on lipid biosynthesis pathway have been previously made. However, seed oil formation is a dynamic balance between lipid synthesis and breakdown. It is, therefore, also reasonable to weaken or eliminate the function of genes involved in lipid degradation for a higher final SOC.

RESULTS

We applied a genome-wide association study (GWAS) on SOC in a collection of 290 core germplasm accessions. A total of 2,705,480 high-quality SNPs were used in the GWAS, and we identified BnaC07g30920D, a patatin-like lipase (PTL) gene, that was associated with SOC. In particular, six single-nucleotide-polymorphisms (SNPs) in the promoter region of BnaC07g30920D were associated with the significant reduction of SOC, leading to a 4.7-6.2% reduction of SOCs. We performed in silico analysis to show a total of 40 PTLs, which were divided into four clades, evenly distributed on the A and C subgenomes of Brassica napus. RNA-seq analysis unveiled that BnPTLs were preferentially expressed in reproductive tissues especially maturing seeds.

CONCLUSIONS

We identified BnaC07g30920D, a BnPTL gene, that was associated with SOC using GWAS and performed in silico analysis of 40 PTLs in Brassica napus. The results enrich our knowledge about the SOC formation in rapeseed and facilitate the future study in functional characterization of BnPTL genes.

BnaGVD: A genomic variation database of rapeseed (Brassica napus)

Rapeseed (Brassica napus L.) is a typical polyploid crop and one of the most important oilseed crops worldwide. With the rapid progress on high-throughput sequencing technologies and the reduction of sequencing cost, large-scale genomic data of a specific crop have become available. However, raw sequence data are mostly deposited in the sequence read archive of the National Center of Biotechnology Information (NCBI) and the European Nucleotide Archive (ENA), which is freely accessible to all researchers. Extensive tools for practical purposes should be developed to efficiently utilize these large raw data. Here, we report a web-based rapeseed genomic variation database (BnaGVD, http://rapeseed.biocloud.net/home) from which genomic variations, such as single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) across a world-wide collection of rapeseed accessions, can be referred. The current release of the BnaGVD contains 34,591,899 high-quality SNPs and 12,281,923 high-quality InDels and provides search tools to retrieve genomic variations and gene annotations across 1,007 accessions of worldwide rapeseed germplasm. We implement a variety of built-in tools (e.g., BnaGWAS, BnaPCA, and BnaStructure) to help users perform in-depth analyses. We recommend this web resource for accelerating studies on the functional genomics and screening of molecular markers for rapeseed breeding.

Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

BACKGROUND

Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed.

RESULTS

In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus.

CONCLUSION

The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.

BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions

The rapid development of high-throughput sequencing technology and the decrease in sequencing costs provide valuable resources and great opportunities for researchers to investigate genomic variations across hundreds or even thousands of accessions in the post-genomic era. The management and exploration of these large-scale genomic variations heavily rely on programming and command-line environments, which are challenging and time-consuming for most experimental biologists and plant breeders. Here, we present BnaSNPDB, an interactive web portal with a user-friendly interface that provides multiple analysis modules for retrieving, analyzing, and visualizing single nucleotide polymorphisms among 1,007 accessions of worldwide rapeseed germplasm. It is compatible, extendable, and portable to be easily set up on different operating systems, and can be accessed at http://121.41.229.126:3838/bnasnpdb and http://rapeseed.zju.edu.cn:3838/bnasnpdb. Its whole dataset and code are available at https://github.com/YTLogos/BnaSNPDB. This database is essential for accelerating studies on the functional genomics and screening of the molecular markers of molecular-assisted breeding in rapeseed.

Genome-wide identification and characterization of SnRK family genes in Brassica napus

BACKGROUND

Sucrose non-fermenting 1 related protein kinases (SnRK) play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information of SnRK genes was available in Brassica napus, one of important oil crops. Recently, the released sequences of the reference genome of B.napus provide a good chance to perform genome-wide identification and characterization of BnSnRK gene family in the rapeseed.

RESULTS

Totally 114 SnRK genes distributed on 19 chromosomes were identified in the genome of B.napus and classified into three subfamilies on the basis of phylogenetic analysis and the domain types. According to gene structure and motif composition analysis, the BnSnRK sequences showed obvious divergence among three subfamilies. Gene duplication and synteny between the genomes of the rapeseed and Arabidopsis were also analyzed to provide insights into the evolutionary characteristics of BnSnRK family genes. Cis-element analysis revealed that BnSnRKs may response to diverse environmental stresses. Moreover, the expression patterns of BnSnRKs in various tissues and under diverse abiotic stresses were distinct difference. Besides, Single Nucleotide Polymorphisms (SNP) distribution analysis suggests the function disparity of BnSnRK family genes in different genotypes of the rapeseed.

CONCLUSION

We examined genomic structures, evolution features, expression patterns and SNP distribution of 114 BnSnRKs. The results provide valuable information for functional characterization of BnSnRK genes in future studies.