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Functional genomics of Brassica napus:Progresses,challenges,and perspectives

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Journal of Integrative Plant biology 2024年第3期66卷 484-509页

作者： Zengdong Tan Xu Han Cheng Dai Shaoping Lu Hanzi He Xuan Yao Peng Chen Chao Yang Lun Zhao Qing-Yong Yang Jun Zou Jing Wen Dengfeng Hong Chao Liu Xianhong Ge Chuchuan Fan Bing Yi Chunyu Zhang Chaozhi Ma Kede Liu Jinxiong Shen Jinxing Tu Guangsheng Yang Tingdong Fu Liang Guo Hu Zhao National key laboratory of Crop genetic improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Yazhouwan National laboratory Sanya 572025China

Brassica napus,commonly known as rapeseed or canola,is a major oil crop contributing over 13%to the stable supply of edible vegetable oil worldwide.Identification and understanding the gene functions in the B.napus genome is crucial for genomic breeding.A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B.napus.In this review,we present an overview of the progress made in the functional genomics of B.napus,including the availability of germplasm resources,omics databases and cloned functional genes.Based on the current progress,we also highlight the main challenges and perspectives in this field.The advances in the functional genomics of B.napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B.napus and will expedite the breeding of high quality,high resistance and high yield in B.napus varieties.

关键词： accelerate breeding Brassica napus functional genomics high resistance high yield

OsNAC5 orchestrates OsABI5 to fine-tune cold tolerance in rice

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Journal of Integrative Plant biology 2024年第4期66卷 660-682页

作者： Ruiqing Li Yue Song Xueqiang Wang Chenfan Zheng Bo Liu Huali Zhang Jian Ke Xuejing Wu Liquan Wu Ruifang Yang Meng Jiang College of Agronomy Anhui Agricultural UniversityHefei 230036China Hainan Institute Yazhou Bay Sci-Tech CityZhejiang UniversitySanya 572025China National key laboratory of Rice biology Advanced Seed InstituteZhejiang UniversityHangzhou 311225China State key laboratory of Rice biology and Chinese National Center for Rice improvement China National Rice Research InstituteHangzhou 311401China key laboratory of Germplasm Innovation and genetic improvement of Grain and oil crops(Co-Construction by Ministry and Province) Ministry of Agriculture and Rural AffairsCrop Breeding and Cultivation Research InstituteShanghai Academy of Agricultural SciencesShanghai 201106China

Due to its tropical origins,rice(Oryza sativa)is susceptible to cold stress,which poses severe threats to production.OsNAC5,a NAC-type transcription factor,participates in the cold stress response of rice,but the detailed mechanisms remain poorly understood.Here,we demonstrate that OsNAC5 positively regulates cold tolerance at germination and in seedlings by directly activating the expression of ABSCISIC ACID INSENSITIVE 5(OsABI5).Haplotype analysis indicated that single nucleotide polymorphisms in a NAC-binding site in the OsABI5 promoter are strongly associated with cold tolerance.OsNAC5 also enhanced OsABI5 stability,thus regulating the expression of cold-responsive(COR)genes,enabling fine-tuned control of OsABI5 action for rapid,precise plant responses to cold stress.DNA affinity purification sequencing coupled with transcriptome deep sequencing identified several OsABI5 target genes involved in COR expression,including DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 1A(OsDREB1A),OsMYB20,and PEROXIDASE 70(OsPRX70).In vivo and in vitro analyses suggested that OsABI5 positively regulates COR gene transcription,with marked COR upregulation in OsNAC5-overexpressing lines and downregulation in osnac5 and/or osabi5 knockout mutants.This study extends our understanding of cold tolerance regulation via OsNAC5 through the OsABI5-CORs transcription module,which may be used to ameliorate cold tolerance in rice via advanced breeding.

关键词： ABA signaling ABI5 cold tolerance DREB NAC5 rice

Sugarcane transcription factor ScWRKY4 negatively regulates resistance to pathogen infection through the JA signaling pathway

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The Crop Journal 2024年第1期12卷 164-176页

作者： Dongjiao Wang Wei Wang Shoujian Zang Liqian Qin Yanlan Liang Peixia Lin Yachun Su Youxiong Que key laboratory of Sugarcane biology and genetic Breeding Ministry of Agriculture and Rural AffairsKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina National key laboratory for Tropical Crop Breeding Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesSanya 572024HainanChina

WRKY transcription factors,transcriptional regulators unique to plants,play an important role in defense response to pathogen infection.However,the resistance mechanisms of WRKY genes in sugarcane remain unclear.In the present study,gene ontology(GO)enrichment analysis revealed that WRKY gene family in sugarcane was extensively involved in the response to biotic stress and in defense response.We identified gene ScWRKY4,a classⅡc member of the WRKY gene family,in sugarcane cultivar ROC22.This gene was induced by salicylic acid(SA)and methyl jasmonate(MeJA)stress.Interestingly,expression of ScWRKY4 was down-regulated in smut-resistant sugarcane cultivars but up-regulated in smutsusceptible sugarcane cultivars infected with Sporisorium scitamineum.Moreover,stable overexpression of the ScWRKY4 gene in Nicotiana benthamiana enhanced susceptibility to Fusarium solani var.coeruleum and caused down-regulated expression of immune marker-related genes.Transcriptome analysis indicated suppressed expression of most JAZ genes in the signal transduction pathway.ScWRKY4 interacted with ScJAZ13 to repress its expression.We thus hypothesized that the ScWRKY4 gene was involved in the regulatory network of plant disease resistance,most likely through the JA signaling pathway.The present study depicting the molecular involvement of ScWRKY4 in sugarcane disease resistance lays a foundation for future investigation.

关键词： Disease resistance Expression profile Transcriptome analysis WRKY transcription factors

Heterogeneous expression of stearoyl-acyl carrier protein desaturase genes SAD1 and SAD2 from Linum usitatissimum enhances seed oleic acid accumulation and seedling cold and drought tolerance in Brassica napus

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Journal of Integrative Agriculture 2024年第6期23卷 1864-1878页

作者： Jianjun Wang Yanan Shao Xin Yang Chi Zhang Yuan Guo Zijin Liu Mingxun Chen State key laboratory of Crop Stress biology for Arid Areas/National Yangling Agricultural Biotechnology&Breeding Center/Shaanxi key laboratory of Crop Heterosis/College of Agronomy Northwest A&F UniversityYangling 712100China

Flax(Linum usitatissimum L.)is a versatile crop and its seeds are a major source of unsaturated fatty acids.Stearoyl-acyl carrier protein desaturase(SAD)is a dehydrogenase enzyme that plays a key role in oleic acid biosynthesis as well as responses to biotic and abiotic stresses.However,the function of SAD orthologs from L.usitatissimum has not been assessed.Here,we found that two LuSAD genes,LuSAD1 and LuSAD2,are present in the genome of L.usitatissimum cultivar‘Longya 10’.Heterogeneous expression of either LuSAD1 or LuSAD2 in Arabidopsis thaliana resulted in higher contents of total fatty acids and oleic acid in the seeds.Interestingly,ectopic expression of LuSAD2 in A.thaliana caused altered plant architecture.Similarly,the overexpression of either LuSAD1 or LuSAD2 in Brassica napus also resulted in increased contents of total fatty acids and oleic acid in the seeds.Furthermore,we demonstrated that either LuSAD1 or LuSAD2 enhances seedling resistance to cold and drought stresses by improving antioxidant enzyme activity and nonenzymatic antioxidant levels,as well as reducing membrane damage.These findings not only broaden our knowledge of the LuSAD functions in plants,but also offer promising targets for improving the quantity and quality of oil,and the abiotic stress tolerance of oil-producing crops,through molecular manipulation.

关键词： LuSAD oleic acid cold tolerance drought tolerance Linum usitatissimum Brassica napus

Stable major QTL on chromosomes A07 and A08 increase shelling percentage in peanut(Arachis hypogaea L.)

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The Crop Journal 2022年第3期10卷 820-829页

作者： Weitao Li Nian Liu Li Huang Yuning Chen Jianbin Guo Bolun Yu Huaiyong Luo Xiaojing Zhou Dongxin Huai Weigang Chen Liying Yan Xin Wang Yong Lei Boshou Liao Huifang Jiang 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

Peanut is a major oilseed and food legume.Shelling percentage(SP),closely associated with seed yield,is a trait whose improvement is a major goal of peanut breeding.In this study,a mapping population(Xuhua 13×Zhonghua 6)was used to map quantitative trait loci(QTL)controlling SP in four environments.Two stable major QTL for SP were mapped on both SSR-and SNP-based genetic maps.q SPA07.1 on chromosome A07 explained up to 31.7%of phenotypic variation,and q SPA08.2 on chromosome A08 explained up to 10.8%.Favorable alleles of q SPA07.1 and q SPA08.2 were derived from the female and male parents,respectively.Eight recombinant inbred lines(RILs)carrying both favorable alleles showed superiority in SP over the two parents in all environmental trials.A combination of the two favorable alleles using the linked markers was verified to increase SP by~5%in the RIL population and by~3%SP in diverse peanut cultivars.q SPA07.1 and q SPA08.2 were delimited to respectively a 0.73-Mb interval harboring 96 genes and a 3.93-Mb interval harboring 238 genes.Respectively five and eight genes with high expression in pods,including enzymes and transcription factors,were assigned as candidate genes for q SPA07.1 and q SPA08.2.These consistent major QTL provide an opportunity for fine mapping of genes controlling SP,and the linked markers may be useful for genetic improvement of SP in peanut.

关键词： Peanut Shelling percentage QTL mapping Genomic region Candidate genes InDel marker

key genes and mechanisms underlying natural variation of silique length in oilseed rape(Brassica napus L.)germplasm

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The Crop Journal 2022年第3期10卷 617-626页

作者： Quaid Hussain Jiepeng Zhan Huabing Liang Xinfa Wang Guihua Liu Jiaqin Shi Hanzhong Wang oil crops Research Institute of the Chinese Academy of Agricultural Sciences Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062HubeiChina

Silique length influences seed yield in oilseed rape.It shows extensive variation in germplasm resources,and identifying the underlying genes and regulatory mechanisms would advance breeding for the trait.In the present study,a genome-wide association study(GWAS)using 331 core accessions planted in 10 environments revealed 13 loci associated with silique length on chromosomes A01,A04,A07,A09,and C03,explaining 6.2%–19.2%of phenotypic variance.Physiological analysis showed that silique length variation was attributable to differences in silique growth rate and/or duration before four weeks after flowering,with levels of endogenous phytohormones(auxin,ethylene,and GA24,GA12,and GA44)playing an important role.Cytological analysis showed that silique length variation was due mainly to differences in cell number followed by cell size.Transcriptomic analysis of two pools of silique walls with opposite length extremes revealed 3248 differentially expressed genes(DEGs).These DEGs were enriched in several pathways(such as cell wall,cell division,and hormone metabolism)associated with cell proliferation and expansion and silique development.Integrating GWAS,RNA-seq,and functional annotation results revealed 15 candidate genes for the major associated locus q SL.A09-3.Of these,Bna A9.ARF18 and Bna A9.CYP78 A9 were validated by haplotype analysis followed by candidate gene association.Sequence variation in the coding region of Bna A9.ARF18 and expression of Bna A9.CYP78 A9 in silique walls were strongly associated with silique length.Our results provide an explanation for the natural variation of silique length in oilseed rape germplasm and offer useful information for its improvement.

关键词： Brassica napus Silique length GWAS RNA-seq Phytohormones Cell number Cell size Bna A9.ARF18 Bna A9.CYP78A9

Computational Tools and Resources for CRISPR/Cas Genome Editing

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 108-126页

作者： Chao Li Wen Chu Rafaqat Ali Gill Shifei Sang Yuqin Shi Xuezhi Hu Yuting Yang Qamar U.Zaman Baohong Zhang oil crops Research Institute Chinese Academy of Agricultural SciencesKey Laboratory for Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062China Graduate School of Chinese Academy of Agricultural Sciences Beijing 100081China Department of biology East Carolina UniversityGreenvilleNC 27858USA

The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)nucleases and their functional variants,as well as in developing precise CRISPR/Cas-derived genome editors.The programmable and robust features of the genome editors provide an effective RNAguided platform for fundamental life science research and subsequent applications in diverse scenarios,including biomedical innovation and targeted crop improvement.One of the most essential principles is to guide alterations in genomic sequences or genes in the intended manner without undesired off-target impacts,which strongly depends on the efficiency and specificity of single guide RNA(sgRNA)-directed recognition of targeted DNA sequences.Recent advances in empirical scoring algorithms and machine learning models have facilitated sgRNA design and off-target prediction.In this review,we first briefly introduce the different features of CRISPR/Cas tools that should be taken into consideration to achieve specific purposes.Secondly,we focus on the computer-assisted tools and resources that are widely used in designing sgRNAs and analyzing CRISPR/Cas-induced on-and off-target mutations.Thirdly,we provide insights into the limitations of available computational tools that would help researchers of this field for further optimization.Lastly,we suggest a simple but effective workflow for choosing and applying web-based resources and tools for CRISPR/Cas genome editing.

关键词： Genome editing Efficiency and specificity CRISPR/Cas9 sgRNA Computational tool Algorithm

A lignified-layer bridge controlled by a single recessive gene is associated with high pod-shatter resistance in Brassica napus L.

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The Crop Journal 2022年第3期10卷 638-646页

作者： Wen Chu Jia Liu Hongtao Cheng Chao Li Li Fu Wenxiang Wang Hui Wang Mengyu Hao Desheng Mei 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 Graduate School of Chinese Academy of Agricultural Sciences Beijing 100081China

Pod shattering causes severe yield loss in rapeseed(Brassica napus L.)under modern agricultural practice.Identification of highly shatter-resistant germplasm is desirable for the development of rapeseed cultivars for mechanical harvesting.In the present study,an elite line OR88 with strong shatter resistance and a lignified-layer bridge(LLB)structure was identified.The LLB structure was unique to OR88 and co-segregated with high pod-shatter resistance.The LLB structure is differentiated at stage 12 of gynoecium development without any gynoecium defects.genetic analysis showed that LLB is controlled by a single recessive gene.By BSA-Seq and map-based cloning,the resistance gene location was delimited to a0.688 Mb region on chromosome C09.Transcriptome analysis suggested Bn TCP8.C09 as the gene responsible for LLB.The expression of Bn TCP.C09 was strongly downregulated in OR88,suppressing cell proliferation in the pod valve margin.KASP markers linked to the candidate gene were developed.This pod shatter-resistant line could be used in rapeseed breeding programs by direct transfer of the gene with the assistance of the DNA markers.

关键词： Pod shatter Lignified-layer bridge BSA-Seq KASP marker Rapeseed

High efficient broad-spectrum Bradyrhizobium elkanii Y63-1

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oil Crop Science 2023年第4期8卷 228-235页

作者： Piao Leng Fuxiao Jin Song Li Yi Huang Chanjuan Zhang Zhihui Shan Zhonglu Yang Limiao Chen Dong Cao Qingnan Hao Wei Guo Hongli Yang Shuilian Chen Xinan Zhou Songli Yuan Haifeng Chen oil crops Research Institute of Chinese Academy of Agricultural Sciences/key laboratory of biology and genetic improvement of oil crops Ministry of Agriculture and Rural AffairsWuhan430062China

Soybean(Glycine max),the primary source of high-quality plant protein,plays a crucial role as a grain and oil crop in China.Harnessing the full potential of symbiotic nitrogen fixation in soybean production holds immense significance for agriculture and ecology alike.Zhongdou 63,a newly developed early-maturing summer soybean cultivar in 2021,exhibits remarkable traits such as high yield,superior quality,multi-resistance,and wide adaptability.In this study,eight distinct rhizobia strains from diverse regions were meticulously screened to identify highly effective strains specifically suited for Zhongdou 63.The aboveground biomass,plant height,chlorophyll content,root length,nodule number,and nodule dry weight of Zhongdou 63 were measured and the data were subjected to statistical analysis.The results demonstrated that Y63-1 is a predominant strain of Zhongdou 63.Subsequently,we conducted further investigations on the broad-spectrum nodulation characteristics of Y63-1.Ten representative soybean cultivars were individually inoculated with Y63-1 and subsequently analyzed for nodule numbers and nodule dry weight in their symbiotic systems with rhizobia.The findings revealed that Y63-1 effectively formed nodules with all ten soybean varieties tested.In summary,our current study identified highly efficient broad-spectrum Bradyrhizobium elkanii strain Y63-1 as the predominant strain in Zhongdou 63 and provided a theoretical foundation for enhancing yield potential not only in Zhongdou 63 but also in other varieties through inoculation with highly efficient rhizobia in production.

关键词： Soybean Rhizobium Nodule symbiosis Nodulation Broad spectrum