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Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines

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Journal of Integrative Agriculture 2019年第7期18卷 1541-1546页

作者： HUO Dong-ao ZHU Bin TIAN Gui-fu DU Xu-ye GUO Juan CAI Meng-xian School of Life Sciences Buckwheat Research CenterGuizhou Normal University

The economically valuable oil crop Brassica napus(AACC,2 n=38),which arose from interspecific hybridization between the diploid ancestors Brassica rapa(AA,2 n=20) and Brassica oleracea(CC,2 n=18),has a complex *** than 10% of the assembled sequences,most of which belong to the C subgenome,have not been anchored to the corresponding ***,a complete set of monosomic alien addition lines(MAALs,C1–C9) with each of the nine C-subgenome chromosomes added to the extracted A subgenome was obtained from the allotetraploid *** donor Oro,after the ancestral ***(RBR Oro) genome was *** MAALs effectively reduced the complexity of the *** ***,we determined the expression values of genes on unanchored scaffolds in the MAALs and RBR ***,multiple comparisons of these gene expression values were used to determine the affiliations of the nonanchored scaffolds on which the genes were *** total,54.68%(44.11 Mb) of the 80.67 Mb of non-anchored scaffolds belonging to the C subgenome were assigned to corresponding C *** work highlights the potential value of these MAALs in improving the genome quality of ***.

关键词： Brassica napus genome sequence RNA-seq monosomic alien addition lines scaffolds

Physiological responses of Brassica napus to fulvic acid under water stress: Chlorophyll a fluorescence and antioxidant enzyme activity

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The Crop Journal 2015年第5期3卷 434-439页

作者： Ramin Lotfi Mohammad Pessarakli Puriya Gharavi-Kouchebagh Hossein Khoshvaghti Department of Plant Eco-physiology Faculty of Agriculture University of Tabriz School of Plant Science The University of Arizona Department of Agriculture Payame Noor University (PNU)

The ameliorative effect of fulvic acid(0, 300, and 600 mg L-1) on photosystem II and antioxidant enzyme activity of the rapeseed(Brassica napus L.) plant under water stress(60, 100, and 140 mm evaporation from class A pan) was studied using split plots in a randomized complete block design with three replications. Results indicated that application of fulvic acid(FA) improved the maximum quantum efficiency of PSII(Fv/Fm)and performance index(PI) of plants under both well-watered and limited-water conditions. The time span from Foto Fmand the energy necessary for the closure of all reaction centers was significantly increased, but the size of the plastoquinone pool was reduced with increasing water stress levels. Plants treated with FA had higher peroxidase and catalase activities under all irrigation conditions. Activities of ascorbate peroxidase and superoxide dismutase in plants increased with increasing water stress. Malondialdehyde increased under severe water stress, but application of FA significantly decreased lipid peroxidation. Production of reactive oxygen species(ROS) is a common phenomenon in plants under stress. Under this condition, the balance between the production of ROS and the quenching activity of antioxidants is upset, often resulting in oxidative damage. In this study, application of FA significantly increased fluorescence of chlorophyll a, inhibiting ROS production and enhancing antioxidant enzymes activity that destroyed ROS. Thus, ROS in plant cells was reduced under water stress by application of FA and consequently lipid peroxidation was reduced.

关键词： Brassica napus Fluorescence Antioxidant enzyme Wat

Increased BnaMFT-transcript level is associated with secondary dormancy in oilseed rape (Brassica napus L.)

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Journal of Integrative Agriculture 2020年第6期19卷 1565-1576页

作者： LIU Lei FAN Wen-qi LIU Fu-xia YI Xin TANG Tang ZHOU Ying TANG Zi-wei CHEN Guimin ZHAO Xiang-xiang Jiangsu Key Laboratory for Eco-agriculture Biotechnology Around Hongze Lake/Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection/College of Life Science Huaiyin Normal UniversityHuai'an 223300P.R.China School of Food Science and Engineering Yangzhou UniversityYangzhou 225127P.R.China

Brassica napus cultivars have little or no primary dormancy;however,they are prone to sec on dary dorma ncy in ducti *** dormant seeds can produce volunteer plants,which can result in genetic contamination,reduced quality and biosafety ***,informati on regarding the molecular mecha nism un derlyi ng sec on dary dormancy is *** MOTHER OF FT AND TFL1(MFT)gene,which is evolutionarily conserved in the plant kingdom,acts in a complex gene network in the seed dormancy or germination *** this study,we identified four *** genes that share high homology with AtMFT,named as *** of c/s-acting elements showed that BnaMFT promoters contain multiple seed-specific regulatory elements,and various stress-and hormone-responsive *** experiments validated that BnaMFTs were specifically expressed during seed maturation and in the dry seed,with peaks at 35-42 days after *** were not sufficient for primary dormancy;however,they were significantly enhanced by secondary dormancy induction with PEG6000 ***,BnaMFTtranscripts were elevated by treatment with abscisic acid(ABA),which is known to be accumulated duri ng sec on dary dorma *** results collectively suggest that increased BnaMFT tra nscription levels are associated with sec on dary dorma ncy inducti on in an ABA-depe ndent mariner in ***.

关键词： Brassica napus DELAY OF GERMINATION 1(DOG7) MFT primary dormancy secondary dormancy

Genome-wide association study of heat stresstolerance traits in spring-type Brassica napus *** controlled conditions

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The Crop Journal 2018年第2期6卷 115-125页

作者： Mizanur Rahaman Sujan Mamidi Mukhlesur Rahman Department of Plant Sciences North Dakota State UniversityFargoND 58102USA Hudson Alpha Institute for Biotechnology HuntsvilleAL 35806USA

High temperatures have a detrimental effect on growth, development, and yield of Brassica napus. Even a short period of heat stress can lead to yield losses of 15%–20%. A collection of spring-type accessions available in Germplasm Resources Information Network(GRIN)were used to assess the effect of short periods of high-temperature stress at the early flowering stage of B. napus. Two sets of accessions with three replications per set were grown in a greenhouse at 22/18 °C day/night temperatures. Plants from the second set at the 6-day flowering stage were exposed to heat-stress conditions(maximum temperature up to 35 °C) in a plant growth chamber for five days. The heat-stressed plants were then allowed to recover in a greenhouse. Pollen sterility, sterile/aborted pods, and number of pods on main raceme were recorded for both control(set 1) and heat stressed(set 2) *** susceptibility indices for all three traits were calculated and an association-mapping study was conducted using 37,539 Single Nucleotide Polymorphisms(SNPs) to identify genomic regions controlling the heat stress traits. A total of 5, 8, and 7 quantitative trait loci(QTL) were associated with pollen sterility, sterile/aborted pods, and number of pods on main raceme, respectively. Together they explained respectively 46.3%, 60.5%, and 60.6% of phenotypic variation. Candidate genes in the QTL regions included genes associated with flowering, male sterility, pollen abortion, embryo abortion reducing pollen development,and pod development.

关键词： Brassica napus Heat stress Controlled environment QTL

Physiological and molecular responses to cold stress in rapeseed(Brassica napus L.)

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Journal of Integrative Agriculture 2019年第12期18卷 2742-2752页

作者： YAN Lei Tariq Shah CHENG Yong Lü Yan ZHANG Xue-kun ZOU Xi-ling Oil Crops Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062P.R.China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070P.R.China

Low temperature is one of the most important abiotic factors inhibiting growth, productivity, and distribution of rapeseed(Brassica napus L.). Therefore, it is important to identify and cultivate cold-tolerant germplasm. The objective of this study was to figure out the mechanism of chilling(4 and 2°C) and freezing(–2 and –4°C) stresses along with a control(22°C) in B. napus cultivars(1801 and C20) under controlled environment(growth chamber). The experiment was arranged in a complete randomized design with three replications. Our results exhibited that under chilling and freezing stresses, the increment of proline accumulation, soluble sugar and protein contents, and antioxidant enzyme activity were enhanced more in 1801 cultivar compared with C20 cultivar. At –2 and –4°C, the seedlings of C20 cultivar died completely compared with 1801 cultivar. Hydrogen peroxide(H2 O2) and malondialdehyde contents(MDA) increased in both cultivars, but when the temperature was decreased up to –2 and –4°C, the MDA and H2 O2 contents continuously dropped in 1801 cultivar. Moreover, we found that leaf abscisic acid(ABA) was enhanced in 1801 cultivar under chilling and freezing stresses. Additionally, the transcriptional regulations of cold-tolerant genes(COLD1, CBF4, COR6.6, COR15, and COR25) were also determined using real-time quantitative PCR(RT-q PCR). RT-q PCR showed that higher expression of these genes were found in 1801 as compared to C20 under cold stress(chilling and freezing stresses). Therefore, it is concluded from this experiment that 1801 cultivar has a higher ability to respond to cold stress(chilling and freezing stresses) by maintaining hormonal, antioxidative, and osmotic activity along with gene transcription process than C20. The result of this study will provide a solid foundation for understanding physiological and molecular mechanisms of cold stress signaling in rapeseed(B. napus).

关键词： Brassica napus L. cold stress morphological features molecular regulation physiological indicators

Co-location of QTL for Sclerotinia stem rot resistance and flowering time in Brassica napus

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The Crop Journal 2019年第2期7卷 227-237页

作者： Jian Wu Peipei Chen Qing Zhao Guangqin Cai Yue Hu Yang Xiang Qingyong Yang Youping Wang Yongming Zhou Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology Yangzhou University National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Agricultural Bioinformatics Key Laboratory of Hubei Province College of Informatics Huazhong Agricultural University Guizhou Rapeseed Institute Guizhou Academy of Agricultural Sciences

Sclerotinia stem rot(SSR) caused by Sclerotinia sclerotiorum(Lib.) de Bary is one of the most devastating diseases of Brassica napus worldwide. Both SSR resistance and flowering time(FT) adaptation are major breeding goals in B. napus. However, early maturing rapeseed varieties, which are important for rice-rapeseed rotation in China, are often highly susceptible to SSR. Here, we found that SSR resistance was significantly negatively correlated with FT in a natural population containing 521 rapeseed inbred lines and a double haploid(DH) population with 150 individual lines, both of which had great variation in FT. Four chromosomal regions on A2, A6, C2, and C8 affecting both SSR resistance and FT were identified using quantitative trait loci(QTL) mapping after constructing a high-density genetic map based on single nucleotide polymorphism markers in the DH ***, we aligned QTL for the two traits identified in the present and previous studies to the B. napus reference genome, and identified four colocalized QTL hotspots of SSR resistance and FT on A2(0–7.7 Mb), A3(0.8–7.5 Mb), C2(0–15.2 Mb), and C6(20.2–36.6 Mb). Our results revealed a genetic link between SSR resistance and FT in ***, which should facilitate the development of effective strategies in both early maturing and SSR resistance breeding and in map-based cloning of SSR resistance QTL.

关键词： Sclerotinia stem rot Brassica napus QTL mapping Flowering time SNP array

Development of a protocol for frost-tolerance evaluation in rapeseed/canola(Brassica napus L.)

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The Crop Journal 2016年第2期4卷 147-152页

作者： Danielle Fiebelkorn Mukhlesur Rahman Department of Plant Sciences North Dakota State University

Spring frost can severely damage or even kill rapeseed/canola(Brassica napus L.) seedlings. A protocol for large scale screening of rapeseed germplasm under frost-simulating conditions has not yet been developed. Accordingly, the present study was conducted to develop a protocol for screening rapeseed germplasm under artificial frost-simulation conditions in a plant growth chamber and in a greenhouse. Nine rapeseed varieties, including three commercial hybrids, three spring types, and three winter types were used. Cold acclimation at 4 °C was applied for 0, 7, or 14 days to two-week old seedlings. The seedlings were treated with four freezing temperatures(- 4 °C,- 8 °C,- 12 °C, and- 16 °C). The length of the freezing period was 16 h, including the ramping of temperature down from 4 °C and up from the respective freezing temperature to 4 °C. Plants were allowed to recover at 4 °C for24 h before they were moved back to the greenhouse. Frost damage was scored on a 0–5scale, where 0 denotes completely dead and 5 denotes no damage. Seedling survival from the freezing treatment increased from the non-acclimation to the cold acclimation treatment. However, no significant differences(P < 0.05) were found between 7 and14 days of acclimation. Frost treatment at- 4 °C resulted in significant differences in seedling damage relative to the other three temperatures, with the- 16 °C treatment resulting in the highest overall seedling damage. Significant differences were found between the spring type and the other two types(hybrid and winter). However, no significant differences were found between the hybrid and winter types. The suggested protocol for the assessment of frost tolerance is acclimation of two-week old seedlings for7 days at 4 °C followed by frost treatment at- 4 °C for 16 h.

关键词： Frost tolerance Controlled environment Brassica napus Seedling

A Novel Chimeric Mitochondrial Gene Confers Cytoplasmic Effects on Seed Oil Content in Polyploid Rapeseed (Brassica napus)

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Molecular Plant 2019年第4期12卷 582-596页

作者： Jun Liu Wanjun Hao Jing Liu Shihang Fan Wei Zhao Linbing Deng Xinfa Wang Zhiyong Hu Wei Hua Hanzhong Wang Key Laboratory of Biology and Genetic Improvement of Oil Crops Ministry of Agriculture and Rural Affairs Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences Wuhan 430062 China Key Laboratory of Tea Biology and Resources Utilization Ministry of Agriculture and Rural Affairs Tea Research Institute of the Chinese Academy of Agricultural Sciences Hangzhou 310008 China

Cytoplasmic effects (CEs) have been discovered to influence a diverse array of agronomic traits in crops, and understanding the underlying mechanisms can help accelerate breeding programs. Seed oil content (SOC) is of great agricultural, nutritional, and economic importance. However, the genetic basis of CEs on SOC (CE-SOC) remains enigmatic. In this study, we use an optimized approach to sequence the cytoplasmic (plastid and mitochondrial) genomes of allotetraploid oilseed rape (Brassica napus) cultivars, 51218 and 56366, that bear contrasting CE-SOC. By combining comparative genomics and genome-wide transcriptome analysis, we identify mitochondria-encoded orf188 as a potential CE-SOC determinant gene. Functional analyses in the model system Arabidopsis thaliana and rapeseed demonstrated that orf188 governs CE-SOC and could significantly increase SOC, strikingly, through promoting the yield of ATP. Consistent with this finding, transcriptional profiling with microarray and RNA sequencing revealed that orf188 affects transcriptional reprogramming of mitochondrial energy metabolism to facilitate ATP production. Intriguingly, orf188 is a previously uncharacterized chimeric gene, and the presence of this genetic novelty endows rapeseed with positive CE-SOC. Our results shed light on the molecular basis of CEs on a key quantitative trait in polyploid crops and enrich the theory of maternal control of oil content, providing new scientific guidance for breeding high-oil rapeseed germplasms.

关键词： cytoplasmic effects seed oil content energy metabolism crop breeding Brassica napus

Mapping loci controlling fatty acid profiles, oil and protein content by genome-wide association study in Brassica napus

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The Crop Journal 2019年第2期7卷 217-226页

作者： Minqiang Tang Yuanyuan Zhang Yueying Liu Chaobo Tong Xiaohui Cheng Wei Zhu Zaiyun Li Junyan Huang Shengyi Liu The Key Laboratory of Biology and Genetic Improvement of Oil Crops The Ministry of Agriculture Oil Crops Research Institute of Chinese Academy of Agricultural Sciences National Key Laboratory of Crop Genetic Improvement National Center of Crop Molecular Breeding Technology National Center of Oil Crop Improvement (Wuhan) Huazhong Agricultural University Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources Faculty of Life Science Hubei University

Optimizing the profile and quantity of fatty acids in rapeseed(Brassica napus L.) is critical for maximizing the value of edible oil and biodiesel. However, selection of these complex seed quality traits is difficult before haplotypes controlling their contents are identified. To efficiently identify genetic loci influencing these traits and underlying candidate genes and networks, we performed a genome-wide association study(GWAS) of eight seed quality traits(oil and protein content, palmitic, stearic, oleic, linoleic, eicosenoic and erucic acids content). The GWAS population comprised 370 diverse accessions, which were phenotyped in five environments and genotyped using 60K SNP arrays. The results indicated that oil and protein contents generally showed negative correlations, while fatty acid contents showed positive or negative correlations,with palmitic and erucic acid contents directly affecting oil content. Seven SNPs on five chromosomes were associated with both seed oil and protein content, and five genes orthologous to genes in Arabidopsis thaliana were predicted as candidates. From resequencing data, besides known haplotypes in Bna ***1.a and Bna ***1.a, three accessions harboring a new haplotype conferring moderate erucic acid content were identified. Interestingly, in a haplotype block, one haplotype was associated with high palmitic acid content and low oil content, while the others showed the reverse effects. This finding was consistent with a negative correlation between palmitic acid and oil contents, suggesting historical selection for high oil content. The identification by this study of genetic variation and complex correlations of eight seed quality traits may be beneficial for crop selection strategies.

关键词： Brassica napus Oil content Fatty acid profiles Association study Haplotypes