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An efficient approach for obtaining plant organelle genomes

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oil Crop Science 2020年第3期5卷 129-135页

作者： Shifei Sang Desheng Mei Qamar U.Zaman Jia Liu Hongtao Cheng Li Fu Wenxiang Wang Hui Wang Qiong Hu Key Laboratory for Biology and Genetic Improvement of oil crops Ministry of Agriculture and Rural AffairsOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina

Plant organelle(plastid and mitochondrial)genomes contain substantial information for plant evolution and ***,it’s important to reveal plant whole-genome sequences including plastid and mitochondrial *** decode these sequences,it is required to efficiently separate organelle genomic DNA from nucleus genome,which is difficult and *** this study,an efficient procedure was established to obtain plant organelle genomes without extraction of plastid and *** DNA was extracted from three materials including Sinapis arvensis var.‘Yeyou 18’,a cytoplasmic male sterile line(Nsa CMS)and its corresponding maintainer line‘Zhongshuang 4’.DNA was sequenced by Roche 454 FLXt and Illumina Miseq *** genomes were assembled using the generated reads and public organelle genome *** research presented a procedure that efficiently assembled organelle genomes and subsequent fill gaps by extending the consensus contig *** method enabled us to assemble plant plastid and mitochondrial genomes *** obtained organelle genomes could accelerate understanding of mitochondrial rearrangements and laid a foundation for further study of Sinapis arvensis evolution and sterility gene of Nsa CMS.

关键词： Plastid Mitochondrial Genome sequence Nsa CMS organelle genome

Marker gene excision in transgenic Brassica napus via Agrobacterium-mediated Cre/lox transient expression system

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oil Crop Science 2020年第2期5卷 96-103页

作者： Pandi Wang Xiaojuan Xiong Ping Fu Gang Wu Fang Liu Key Laboratory of Biology and Geneics Improvement of oil crops Ministry of Agriculture and Rural AffairsOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina

oilseed rape(Brassica napus L.)is one of the most important oil crops in the ***,study on marker-free transgene of *** for bio-safety purpose is limited in this allotetraploid *** order to advance marker gene excision research,a newly designed Cre/lox system combining crossing and auto-excision strategy was introduced into *** system consists of 2 sets of independent vectors including pC35 Spro::T7 RP carrying T7 RNA polymerase and pCT7 pro::Cre carrying T7 promoter *** hybridization of 2 according types of transgenic ***,marker gene would be removed as T7 RNA polymerase facilitate T7 promoter to promote Cre gene *** 52 and 46 positive To transgenic lines of these 2 vectors were obtained after identification by PCR and test trip.T1 plants from 3 T0 positive pC35 Spro::T7 RP lines and 2 T0 positive pC35 Spro::T7 RP lines were identified as single copy according to segregation ratio and were chosen for ***,expression of CP4 EPSPS(glyphosate resistance gene)and OXY(bromoxynil resistance gene)were not found in F1 progeny,which proved that the excision was not *** possible reasons for our limited success were investigated and detailed analyses were *** this system is not applicable for generating transgenic *** free from selectable marker gene,it provided valuable experience and clue for further improvement of this *** other advantages and further improvement will be progressed in future work.

关键词： Brassica napus Marker-free Cre/lox Cross Auto-excision Herbicide resistance

Screening and Insert Size Analysis of Candidate C-Genome BAC Clones from Brassica napus

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Wuhan University Journal of Natural Sciences 2012年第4期17卷 351-356页

作者： YAN Xiaohong YUAN Yabin ZHAO Xueya ZHA Minmin DAI Shuang LIU Feng WANG Yuantao WEI Wenhui oil crops Research institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of oil crops Ministry of AgricultureWuhan 430062HubeiChina

Thirty-two C-genome specific candidate bacterial artificial chromosome （BAC） clones were successfully screened from the BAC library by four-dimensional PCR method with the primer pairs of 75 simple sequence repeat （SSR） markers located in the nine C-genome linkage groups of Brassica napus. The screened 32 BAC clones have an average insert size of 114.2 kb with a range of 30–190 kb. They are the first set of C-genome BAC clones screened from B. napus genomic BAC library. The average insert size of this set of BAC clones presented that the constructed BAC library had a high quality. This set of BAC clones can be used as markers to identify individual chromosomes of B. napus C-genome.

关键词： Brassica napus C-genome simple sequence repeat (SSR) marker four-dimensional PCR bacterial artificial chromo- some (BAC) clone

Unraveling waterlogging tolerance-related traits with QTL analysis in reciprocal intervarietal introgression lines using genotyping by sequencing in rapeseed(Brassica napus L.)

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Journal of Integrative Agriculture 2020年第8期19卷 1974-1983页

作者： DING Xiao-yu XU Jin-song HUANG He QIAO Xing SHEN Ming-zhen CHENG Yong ZHANG Xue-kun Key Laboratory of oil Crop Biology and Genetic Improvement Ministry of Agriculture and Rural Affairs/Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhan 430070P.R.China

Soil waterlogging is a major environmental stress that suppresses the growth and productivity of rapeseed(Brassica napus L.).Natural genetic variations in waterlogging tolerance(WT)were observed but no QTL mapping has been done for WT related traits in *** this study,QTL associated with three WT related traits including relative root length(RRL),relative hypocotyl length(RHL)and relative fresh weight(RFW)were dissected using a set of reciprocal introgression lines(ILs)derived from the cross GH01×ZS9,which showed significant difference in ***-by-sequencing(GBS)of the populations were performed,totally 1468 and 1450 binned SNPs were identified for GIL(GH01 as the recurrent parent)and ZIL(ZS9 as the recurrent parent)population,respectively.A total of 66 distinct QTLs for WT at the seedling establishment stage including 31 for RRL,17 for RHL and 18 for RFW were *** the 66 QTLs,20(29.4%)QTLs were detected in both genetic backgrounds and then they were integrated into six QTL clusters,which can be targeted in rapeseed breeding for improvement of WT through marker-assisted selection(MAS).Based on the physical positions of SNPs and the functional annotation of the Arabidopsis thaliana genome,56 genes within the six QTL cluster regions were selected as preliminary candidate genes,then the resequencing and transcriptome information about parents were applied to narrow the extent of candidate *** genes were determined as candidates for the six QTL clusters,some of them involved in RNA/protein degradation,most of them involved in oxidation-reduction *** findings provided genetic resources,candidate genes to address the urgent demand of improving WT in rapeseed breeding.

关键词： Brassica napus candidate genes marker-assisted selection quantitative trait loci mapping waterlogging tolerance

Screening Chinese soybean genotypes for Agrobacterium-mediated genetic transformation suitability

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2013年第4期14卷 289-298页

作者： Zhang-yue SONG Jing-luan TIAN Wei-zhe FU Lin LI Ling-hong LU Lian ZHOU Zhi-hui SHAN Gui-xiang TANG Hui-xia SHOU College of Life Sciences Zhejiang University oil crops Research institute Chinese Academy of Agricultural Sciences College of Agriculture and Biotechnology Zhejiang University

The Agrobacterium-mediated transformation system is the most commonly used method in soybean *** of soybean genotypes favorable for Agrobacterium-infection and tissue regeneration is the most important step to establish an efficient genetic transformation *** this study,twenty soybean genotypes that originated from different soybean production regions in China were screened for transient infection,regeneration capacity,and stable transgenic *** genotypes,Yuechun 04-5,Yuechun 03-3,and Tianlong 1,showed comparable stable transgenic efficiencies with that of the previously reported American genotypes Williams 82 and Jack in our experimental *** the Tianlong 1,the average stable transformation efficiency is 4.59%,higher than that of control genotypes(Jack and Williams 82),which is enough for further genomic research and genetic *** polymerase chain reaction(PCR),LibertyLink strips,and β-glucuronidase(GUS) staining assays were used to detect the insertion and expression of the transgene,leaves painted with 135 mg/L Basta could efficiently identify the transformants.

关键词： Soybean Agrobacterium-mediated transformation Genotypes Stable transgenic efficiency

BnaSD.C3 is a novel major quantitative trait locus affecting semi-dwarf architecture in Brassica napus L.

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农业科学学报:英文版 2023年第10期22卷 2981-2992页

作者： WANG Xiao-dong CAI Ying PANG Cheng-ke ZHAO Xiao-zhen SHI Rui LIU Hong-fang CHEN Feng ZHANG Wei FU San-xiong HU Mao-long HUA Wei ZHENG Ming ZHANG Jie-fu Provincial Key Laboratory of Agrobiology/institute of Industrial crops Jiangsu Academy of Agricultural Sciences/Key Laboratory of Cotton and RapeseedMinistry of Agriculture and Rural AffairsNanjing 210014P.R.China 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

Plant height is a key plant architectural trait that affects the seed yield,harvest index and lodging resistance in Brassica napus L.,although the genetic mechanisms affecting plant height remain ***,a semi-dwarf mutant,df34,was obtained by ethyl methanesulphonate-induced *** analysis showed that the semi-dwarf phenotype is controlled by one semi-dominant gene,which was located on chromosome C03 using a bulked segregant analysis coupled with whole-genome sequencing,and this gene was named *** BnaSD.C3 was fine-mapped to a 297.35-kb segment of the“Darmor-bzh”genome,but there was no potential candidate gene for the semi-dwarf trait underlying this ***,the interval was aligned to the Zhongshuang 11 reference ***,combining structural variation analysis,transcriptome sequencing,phytohormone analyses and gene annotation information,BnaC03G0466900ZS and BnaC03G0478900ZS were determined to be the most likely candidate genes affecting the plant height of *** study provides a novel major locus for breeding and new insights into the genetic architecture of plant height in ***.

关键词： Brassica napus L. fine mapping phytohormone analysis plant height transcriptome analysis

Two ABCI family transporters,OsABCI15 and OsABCI16,are involved in grain-filling in rice

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Journal of Genetics and Genomics 2024年第5期51卷 492-506页

作者： Bin Ma Xiubiao Cao Xiaoyuan Li Zhong Bian Qi-Qi Zhang Zijun Fang Jiyun Liu Qun Li Qiaoquan Liu Lin Zhang Zuhua He Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology Agricultural College of Yangzhou UniversityYangzhouJiangsu 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsu 225009China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology&EcologyChinese Academy of SciencesShanghai 200032China institute of Biotechnology Hangzhou Academy of Agricultural SciencesHangzhouZhejiang 310024China Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education Yangzhou UniversityYangzhouJiangsu 225009China

Seed development is critical for plant reproduction and crop yield,with panicle seed-setting rate,grain-filling,and grain weight being key seed characteristics for yield ***,few genes are known to regulate grain ***,we identify two adenosine triphosphate(ATP)-binding cassette(ABC)I-type transporter genes,OsABCI15 and OsABCI16,involved in rice *** genes are highly expressed in developing seeds,and their proteins are localized to the plasma membrane and ***,knockout of OsABCI15 and OsABCI16 results in a significant reduction in seed-setting rate,caused predominantly by the severe empty pericarp phenotype,which differs from the previously reported low seed-setting phenotype resulting from failed *** analysis indicates that OsABCI15 and OsABCI16 participate in ion homeostasis and likely export ions between filial tissues and maternal tissues during grain ***,overexpression of OsABCI15 and OsABCI16 enhances the seed-setting rate and grain yield in transgenic plants and decreases ion accumulation in brown ***,the OsABCI15/16 orthologues in maize exhibit a similar role in kernel development,as demonstrated by their disruption in transgenic ***,ourﬁndings reveal the important roles of two ABC transporters in cereal grain filling,highlighting their value in crop yield improvement.

关键词： ABC transporters Rice Grain filling Ion homeostasis Grain yield

Complete organelle genomes of Sinapis arvensis and their evolutionary implications

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The Crop Journal 2020年第4期8卷 505-514页

作者： Shifei Sang Hongtao Cheng Desheng Mei Li Fu Hui Wang Jia Liu Wenxiang Wang Qamar U.Zaman Kede Liu Qiong Hu oil crops Research institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biology and Genetic Improvement of oil crops Ministry of Agriculture and Rural AffairsWuhan 430062HubeiChina National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070HubeiChina

Sinapis arvensis,belonging to the genus Sinapis of the family Brassicaceae,has good agronomic characters that make it a valuable genetic resource for crop improvement and is a cytoplasmic source of heterologous cytoplasmic male sterility(CMS).In addition,*** has played an important role in the evolution of the six major cultivated Brassica species involved in the triangle of *** next-generation sequencing,we assembled and revealed the gene composition of *** cytoplasmic *** chloroplast genome comprises 153,590 bp,with 112 individual genes,including 4 r RNA,29 t RNA,and 79 proteincoding *** mitochondrial genome comprises 240,024 bp,with 54 genes,including 18 t RNA,three r RNA and 33 protein-coding *** structure and evolutionary analysis indicated that the sequences of the *** organellar genomes were more similar to those of Brassica nigra and *** than to those of other Brassicaceae *** mitochondrial open reading frames displaying chimeric structural features and encoding hypothetical proteins with transmembrane domains may account for the infertility of Nsa CMS previously derived from somatic cell hybridization between *** and *** results will not only contribute to utilize the germplasm resource of ***,and comprehend the evolution of organelle genomes within the Brassicaceae family,but also help to identify genes conditioning the alloplasmic male sterility of Nsa CMS in ***.

关键词： species. organelle evolutionary

Repression of microRNA 160 results in retarded seed integument growth and smaller final seed size in cotton

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The Crop Journal 2020年第4期8卷 602-612页

作者： Nian Liu Shuchang Wu Zhonghua Li Anam Qadir Khan Haiyan Hu Xianlong Zhang Lili Tu National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070HubeiChina Key Laboratory of Biology and Genetic Improvement of oil crops Ministry of Agriculture and Rural AffairsOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan 430062HubeiChina

microRNA 160(miR160),targeting auxin response factors(ARFs),plays many roles in plant *** investigated the role of the mi R160/ARF axis in regulation of cotton seed *** mi R160 activity,specifically in the seed coat,led to smaller seeds and less fiber production owing to attenuated growth of the maternal *** electron microscopy and histology showed that expansion of cells in the integument was retarded in mi R160-suppressed *** Gh ARF genes were targeted by mi R160 and were upregulated in mi R160-suppressed lines,indicating that a mi R160/ARF axis is present in *** genes(Ghir_A05 G003740,Scaffold1878 G000010,Ghir_D09 G024980,Ghir_A11 G010730,and Ghir_A05 G041590),associated with reduced seed development were downregulated in mi R160-suppressed *** results suggest that the mi R160/ARF axis controls maternal integument growth to influence seed size by directly or indirectly regulating seed development-associated genes.

关键词： size cotton maternal