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Genomic Change, Retrotransposon Mobilization and Extensive Cytosine Methylation Alteration in Brassica napus Introgressions from Two Intertribal Hybridizations  [PDF]
Xueli Zhang, Xianhong Ge, Yujiao Shao, Genlou Sun, Zaiyun Li
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0056346
Abstract: Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ~10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4–39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.
Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa
Jinsong Xu, Xiaoju Qian, Xiaofeng Wang, Ruiyuan Li, Xiaomao Cheng, Yuan Yang, Jie Fu, Shunchang Zhang, Graham J King, Jiangsheng Wu, Kede Liu
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-594
Abstract: In this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus.The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.Brassica species are one of the most important crop groups in terms of cultivated acreage, contribution to human and animal diets, and economic value. Of the six cultivated Brassica species, B. napus, B. rapa, B. juncea, and B. carinata provide about 12% of worldwide edible vegetable oil supplies [1]. They also provide many of the vegetables in our daily diet such as cauliflower, broccoli, cabbage, kohlrabi, kale (B. oleracea) and turnip, Pak-choi and Chinese cabbage (B. rapa) [2]. Brassica species are also a valuable source of dietary fiber, vitamin C and other anticancer compounds such as glucosinolates. In addition, rape
Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa
Jun Wang, Derek J Lydiate, Isobel AP Parkin, Cyril Falentin, Régine Delourme, Pierre WC Carion, Graham J King
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-101
Abstract: We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa.Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.Brassica napus is found almost solely in an agricultural setting represented by the oil crops oilseed rape (Canola, rapeseed) and vegetable/fodder crops swede and rutabaga. As one of the most commercially important oil crops, it is grown in most temperate regions of the world including North and South America, Europe, Australia, and East and South Asia, for the production of vegetable oil for human consumption, industrial uses including as a lubricant or biofuel, and a protein meal used as animal feed.Brassica napus is an amphidiploid species (AC genome, n = 1
Genetic load and transgenic mitigating genes in transgenic Brassica rapa (field mustard) × Brassica napus (oilseed rape) hybrid populations
Christy W Rose, Reginald J Millwood, Hong S Moon, Murali R Rao, Matthew D Halfhill, Paul L Raymer, Suzanne I Warwick, Hani Al-Ahmad, Jonathan Gressel, C Neal Stewart
BMC Biotechnology , 2009, DOI: 10.1186/1472-6750-9-93
Abstract: In the absence of interspecific competition, transgenic weed × crop hybrids benefited from having more crop-specific alleles. There was a positive correlation between performance and number of B. napus crop-specific AFLP markers [seed yield vs. marker number (r = 0.54, P = 0.0003) and vegetative dry biomass vs. marker number (r = 0.44, P = 0.005)]. However under interspecific competition with wheat or more weed-like conditions (i.e. representing a situation where hybrid plants emerge as volunteer weeds in subsequent cropping systems), there was a positive correlation between the number of B. rapa weed-specific AFLP markers and seed yield (r = 0.70, P = 0.0001), although no such correlation was detected for vegetative biomass. When genetic load was directly incorporated into the hybrid genome, by inserting a fitness-mitigating dwarfing gene that that is beneficial for crops but deleterious for weeds (a transgene mitigation measure), there was a dramatic decrease in the number of transgenic hybrid progeny persisting in the population.The effects of genetic load of crop and in some situations, weed alleles might be beneficial under certain environmental conditions. However, when genetic load was directly incorporated into transgenic events, e.g., using a TM construct, the number of transgenic hybrids and persistence in weedy genomic backgrounds was significantly decreased.Over the past dozen years, a number of crops, such as soybean, maize, rice, cotton and canola, have been genetically engineered to contain a variety of fitness enhancing transgenes. Some of these transgenes can increase a crop's defenses by conferring resistance to a number of diseases, herbicides, abiotic stresses, and yield reducing herbivores [1]. Consequently, there are environmental and regulatory concerns about the adventitious presence of transgenes, especially with regards to hybridization and introgression into weedy relatives [2]. Specifically, could the introgression of fitness-enhancing tr
Evaluation of Seed Yield Potential and Traits in Species of Brassica ( B. napus, B. rapa, B. juncea ) under Rain Fed Conditions in Gonbad Area  [cached]
A Faraji,h Hatamzadeh
Journal of Science and Technology of Agriculture and Natural Resources , 2009,
Abstract: Development of oil seed crops is the most important aim in our country to achieve self sufficiency. This study was conducted to assess the suitability of oil brassicas species in rain-fed warm areas of Iran. This research was performed for three years in Agricultural Research stations of Gonbad (Golestan). Twenty varieties and hybrids (B. napus, B. rapa, B. juncea ) were compared in RCBD with three replications under rain fed conditions. Each plot had 4 rows 5-meter long. Combined analysis results indicated that there were significant differences at 1% probability level among years and varieties for No. of days to maturity, No. of pod per plant, oil%, oil and seed yield. The highest seed yield was obtained in the 2nd year (2103.48 kg.ha), followed by the 1th and 3rd year (1771.50 and 1575.13 kg.ha, respectively). Namely, year environment factor had a significant effect on the rape seed product. j-98-102.51-5 (B. juncea), Alexandra and comet (Spring B. napus) showed the highest seed yield (2484, 2326 and 2290 Kg.ha, respectively). Regression analysis via step by step method explained that No. of pod per plant and oil percentage had significant positive effects (508.53 and 96.48 respectively) and No. of days to maturity significant negative effect (-78.63) on the seed yield. Factor analysis extracted four factors. Factor loading of the first three eigen values showed that the first three factors explained 98.794%, sum of variance. Rates of first, second and third factors were 45.575%, 36.816% and 16.403%, respectively. The first factor, second factor and third factor were named productivity factor (seed yield and oil yield), sink factor (No. of pod per plant), fixed capital factor (No. of day to maturity and plant height) respectively. Generally, j-98-102.51-5, Alexandra and comet varieties are advisable for Fall planting under rain fed conditions in Gonbad area because they had the highest seed yield and earliness. Also, we can introduce less No. of days to maturity (earliness) and more No. of pod per plant as select index under rain fed conditions in Gonbad.
The progress of intersubgenomic heterosis studies in Brassica napus
L Maoteng, Q Wei, C Xin, M Jinling
African Journal of Biotechnology , 2010,
Abstract: The new nomenclature of Brassica has been suggested in a previous study by same authours where the symbols of Ar, Aj and An represented the A genome in the Brassica rapa, Brassica juncea and Brassica napus, Bb, Bj and Bc for the B genome of Brassica nigra (black mustard), B. juncea and Brassica carinata, Co, Cn and Cc for the C genome of Brassica oleracea, B. napus and B. carinata. Numerous efforts have focused on exploring novel B. napus (AnAnCnCn) breeding stocks by the hybridization between Brassica species. Thereafter, most interspecific hybrids in Brassicas could be considered as intersubgenomic hybrids. In this review, examples are shown from recent studies on the method for construction of new-typed B. napus with genome composition of ArArCcCc and ArArCnCn, the meiosis and embryo sac development of new-typed B. napus, the appearance of intersubgenomic (AnArCnCc and ArAnCnCn) heterosis and the mechanism for production of intersubgenomic heterosis were described.
Cloning and expression of cinnamoyl-CoA reductase 1(CCR1) gene of Brassica napus L. and Brassica rapa L.

- , 2017,
Abstract: 【目的】分别克隆甘蓝型油菜(Brassica napus L.)和白菜型油菜(Brassica rapa L.)肉桂酰辅酶A还原酶1(cinnamoyl-CoA reductase 1,CCR1)基因,并进行生物信息学和表达模式分析。【方法】基于甘蓝型油菜和白菜型油菜转录组测序信息,分别从contig文库中获得了一个CCR1基因mRNA转录本片段,利用RACE技术分别获得一个CCR1基因的cDNA全长,对其进行生物学分析,并用实时定量PCR方法分析CCR1基因在甘蓝型和白菜型油菜开花期根、茎、叶、花中的表达差异。【结果】所克隆的甘蓝型油菜和白菜型油菜CCR1基因序列经同源序列比对分析后,将其分别命名为BnCCR1(登录号:KX138521)和BrCCR1(登录号:KX138522)。BnCCR1全长1 388 bp,开放阅读框(ORF)长为1 032 bp,编码343个氨基酸,分子质量11.56 ku,等电点4.99;BrCCR1全长1 366 bp,ORF长为1 026 bp,编码341个氨基酸,分子质量为11.36 ku,等电点5.0。2物种CCR1编码蛋白质二级结构无信号肽和跨膜结构域;亚细胞定位显示该蛋白在细胞质中存在的可能性最大。CCR蛋白多重比对分析显示,BnCCR1和BrCCR1均具有CCR蛋白典型的一个NAD(P)结合域和一个底物结合域(NWYCY)。系统进化树分析结果表明,BnCCR1和BrCCR1与同属十字花科的菘蓝、亚麻荠、拟南芥CCR形成了一个独立分支,且亲缘关系较近;其蛋白质三级结构均与矮牵牛CCR1(PDB:4r1t.1A)蛋白质三级结构相似,结构稳定。实时荧光定量PCR分析结果表明,CCR1基因在白菜型油菜和甘蓝型油菜根、茎、叶、花各器官中均有表达,其中在木质化程度较高的根和茎中表达丰度明显高于叶和花。【结论】从白菜型油菜和甘蓝型油菜中分别克隆到CCR1基因cDNA全长,该基因主要在木质化程度较高的根和茎器官中表达。
【Objective】The research was conducted to clone the cinnamoy-CoA reductase (CCR1) gene of Brassica napus L.and Brassica rapa L.for bioinformatics and expression analysis.【Method】Two mRNAs segments encoding cinnamoyl-CoA reductase (CCR) of Brassica napus L.and Brassica rapa L.were retrieved respectively by screening contig library of published transcriptome database,and full-length cDNAs were cloned by rapid amplification of cDNA ends (RACE),followed by bioinformatics analysis.The differences in expression in root,stem,leaf and flower of these two rapes during blooming period were analyzed by real time PCR.【Result】 The two cloned sequences were named BnCCR1 and BrCCR1 after homologous sequence alignment.BnCCR1 is a 1 388 bp full-length cDNA with a 1 032 bp open reading frame (ORF) and was predicted to encode a protein of 343 amino acids.The predicted protein would have the molecular weight of 11.56 ku and the PI of 4.99.BrCCR1 is a 1 366 bp full-length cDNA with a 1 026 bp ORF and encods a 341 amino acid polypeptide with the molecular weight of 11.36 ku and the PI of 5.0.Secondary structures of these two proteins were composed of mutiple α-helixes,β-folds and random coils,without transmembrane regions or signal peptides.The protein most likely exists in chloroplast according to subcellular localization analysis.The multiple comparison revealed that both BnCCR and BrCCR1 contained a NAD(P) binding domain and a substrate binding domain (NWYCY) typical to CCRs.Phylogenetic tree analysis showed that BnCCR1 and BrCCR1 shared a separate clade with AtCCR1,CsCCR1,and ItCCR and had a close relationship.The 3-D alignment of CCR1 of Brassica napus and Brassica rapa showed high similarity to Petunia hybrida Vilm (POB:4r1t.1A) and had a
Integration of Solexa sequences on an ultradense genetic map in Brassica rapa L.
Wei Li, Jiefu Zhang, Yanglong Mou, Jianfeng Geng, Peter BE McVetty, Shengwu Hu, Genyi Li
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-249
Abstract: Three sets of SRAP primers and three sets of tagging primers were used in 77,568 SRAP PCR reactions and the same number of tagging PCR reactions respectively to produce a pooled sample for Illumina's Solexa sequencing. After sequencing, 1.28 GB of sequence with over 13 million paired-end sequences was obtained and used to match Solexa sequences with their corresponding SRAP markers and to integrate Solexa sequences on an ultradense genetic map. The ultradense genetic bin map with 465 bins was constructed using a recombinant inbred (RI) line mapping population in B. rapa. For this ultradense genetic bin map, 9,177 SRAP markers, 1,737 integrated unique Solexa paired-end sequences and 46 SSR markers representing 10,960 independent genetic loci were assembled and 141 unique Solexa paired-end sequences were matched with their corresponding SRAP markers. The genetic map in B. rapa was aligned with the previous ultradense genetic map in B. napus through common SRAP markers in these two species. Additionally, SSR markers were used to perform alignment of the current genetic map with other five genetic maps in B. rapa and B. napus.We used SRAP to construct an ultradense genetic map with 10,960 independent genetic loci in B. rapa that is the most saturated genetic map ever constructed in this species. Using next generation sequencing, we integrated 1,878 Solexa sequences on the genetic map. These integrated sequences will be used to assemble the scaffolds in the B. rapa genome. Additionally, this genetic map may be used for gene cloning and marker development in B. rapa and B. napus.There are several PCR-based molecular marker detection methods such as amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), simple sequence repeats (SSR) and sequence related amplified polymorphism (SRAP) that are commonly used in molecular marker development, genetic mapping, genetic diversity analysis and high density genetic map construction [1]. Compared with
Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers
Charlotte J Allender, Graham J King
BMC Plant Biology , 2010, DOI: 10.1186/1471-2229-10-54
Abstract: Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions) was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained.The distribution of chloroplast haplotypes eliminate any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast haplotypes in B. napus and B. rapa accessions was not correlated with nuclear genetic diversity as determined by AFLPs, indicating that such accessions do not represent recent hybrids. Whilst some chloroplast diversity observed within B. napus can be explained by introgression from inter-specific crosses made during crop improvement programmes, there is evidence that the original hybridisation event resulting in to B. napus occurred on more than one occasion, and involved different maternal genotypes.Brassica napus (rapeseed, oilseed rape, Canola) is an oilseed crop of global economic significance. Over 50 million tonnes of rapeseed were produced in 2007 from an area of 30 million hectares [1]. In addition both tuberous (swede or rutabaga) and leafy forms (fodder rape and kale) of the species are grown as vegetables for human consumption and animal fodder. Oilseed B. napus has only achieved economic importance in the past forty years following an intensive breeding programme to decrease nutritionally undesirable components of the oil and meal, and to increase yields. Attention initially focused on reducing levels of erucic acid in the seed oil, and then reducing levels of aliphatic glucosino
Identification of candidate genes of QTLs for seed weight in Brassica napus through comparative mapping among Arabidopsis and Brassica species  [cached]
Cai Guangqin,Yang Qingyong,Yang Qian,Zhao Zhenxing
BMC Genetics , 2012, DOI: 10.1186/1471-2156-13-105
Abstract: Background Map-based cloning of quantitative trait loci (QTLs) in polyploidy crop species remains a challenge due to the complexity of their genome structures. QTLs for seed weight in B. napus have been identified, but information on candidate genes for identified QTLs of this important trait is still rare. Results In this study, a whole genome genetic linkage map for B. napus was constructed using simple sequence repeat (SSR) markers that covered a genetic distance of 2,126.4 cM with an average distance of 5.36 cM between markers. A procedure was developed to establish colinearity of SSR loci on B. napus with its two progenitor diploid species B. rapa and B. oleracea through extensive bioinformatics analysis. With the aid of B. rapa and B. oleracea genome sequences, the 421 homologous colinear loci deduced from the SSR loci of B. napus were shown to correspond to 398 homologous loci in Arabidopsis thaliana. Through comparative mapping of Arabidopsis and the three Brassica species, 227 homologous genes for seed size/weight were mapped on the B. napus genetic map, establishing the genetic bases for the important agronomic trait in this amphidiploid species. Furthermore, 12 candidate genes underlying 8 QTLs for seed weight were identified, and a gene-specific marker for BnAP2 was developed through molecular cloning using the seed weight/size gene distribution map in B. napus. Conclusions Our study showed that it is feasible to identify candidate genes of QTLs using a SSR-based B. napus genetic map through comparative mapping among Arabidopsis and B. napus and its two progenitor species B. rapa and B. oleracea. Identification of candidate genes for seed weight in amphidiploid B. napus will accelerate the process of isolating the mapped QTLs for this important trait, and this approach may be useful for QTL identification of other traits of agronomic significance.
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