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OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State key laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species.However,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 populations.To this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations.OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population.Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy.In addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and rice.We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study.The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower color.Taken together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species.For ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

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Targeted mutations of BnPAP2 lead to a yellow seed coat in Brassica napus L.

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Journal of Integrative Agriculture 2024年第2期23卷 724-730页

作者： Wei Huang Ruyu Jiao Hongtao Cheng Shengli Cai Jia Liu Qiong Hu Lili Liu Bao Li Tonghua Wang Mei Li Dawei Zhang Mingli Yan Hunan Research Center of Heterosis Utilization in Rapeseed/Crop Research Institute Hunan Academy of Agricultural SciencesChangsha 410125China Hunan key laboratory of Economic crops genetic improvement and Integrated Utilization/School of Life and Health Science Hunan University of Science and TechnologyXiangtan 411201China key laboratory of biology and genetic improvement of oil crops Ministry of Agriculture and Rural Affairs/Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhan 430062China

The yellow seed trait is preferred by breeders for its potential to improve the seed quality and commercial value of Brassica napus.In the present study,we produced yellow seed mutants using a CRISPR/Cas9 system when the two BnPAP2 homologs were knocked out.Histochemical staining of the seed coat demonstrated that proanthocyanidin accumulation was significantly reduced in the pap2 double mutants and decreased specifically in the endothelial and palisade layer cells of the seed coat.Transcriptomic and metabolite profiling analysis suggested that disruption of the BnPAP2 genes could reduce the expression of structural and regulated genes in the phenylpropanoid and flavonoid biosynthetic pathways.The broad suppression of these genes might hinder proanthocyanidin accumulation during seed development,and thereby causing the yellow seed trait in B.napus.These results indicate that BnPAP2 might play a vital role in the regulatory network controlling proanthocyanidin accumulation.

关键词： yellow seed BnPAP2 proanthocyanidins CRISPR/Cas9

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IbNIEL-mediated degradation of IbNAC087 regulates jasmonic acid-dependent salt and drought tolerance in sweet potato

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Journal of Integrative Plant biology 2024年第2期66卷 176-195页

作者： Xu Li Zhen Wang Sifan Sun Zhuoru Dai Jun Zhang Wenbin Wang Kui Peng Wenhao Geng Shuanghong Xia Qingchang Liu Hong Zhai Shaopei Gao Ning Zhao Feng Tian Huan Zhang Shaozhen He key laboratory of Sweet Potato biology and Biotechnology Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis&Utilization and Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy&BiotechnologyChina Agricultural UniversityBeijing 100193China Sanya Institute of China Agricultural University Sanya 572025China State key laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterKey Laboratory of Biology and Genetic Improvement of MaizeBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Sweet potato(Ipomoea batatas[L.]Lam.)is a crucial staple and bioenergy crop.Its abiotic stress tolerance holds significant importance in fully utilizing marginal lands.Transcriptional processes regulate abiotic stress responses,yet the molecular regulatory mechanisms in sweet potato remain unclear.In this study,a NAC(NAM,ATAF1/2,and CUC2)transcription factor,IbNAC087,was identified,which is commonly upregulated in salt-and drought-tolerant germplasms.Overexpression of IbNAC087 increased salt and drought tolerance by increasing jasmonic acid(JA)accumulation and activating reactive oxygen species(ROS)scavenging,whereas silencing this gene resulted in opposite phenotypes.JA-rich IbNAC087-OE(overexpression)plants exhibited more stomatal closure than wild-type(WT)and IbNAC087-Ri plants under NaCl,polyethylene glycol,and methyl jasmonate treatments.IbNAC087 functions as a nuclear transcriptional activator and directly activates the expression of the key JA biosynthesisrelated genes lipoxygenase(IbLOX)and allene oxide synthase(IbAOS).Moreover,IbNAC087 physically interacted with a RING-type E3 ubiquitin ligase NAC087-INTERACTING E3 LIGASE(IbNIEL),negatively regulating salt and drought tolerance in sweet potato.IbNIEL ubiquitinated IbNAC087 to promote 26S proteasome degradation,which weakened its activation on IbLOX and IbAOS.The findings provide insights into the mechanism underlying the IbNIEL-IbNAC087 module regulation of JA-dependent salt and drought response in sweet potato and provide candidate genes for improving abiotic stress tolerance in crops.

关键词： abiotic tolerance IbNAC087 IbNIEL JA sweet potato

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Genome-wide association study of seedling nitrogen-use efficiency-associated traits in common wheat(Triticum aestivum L.)

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The Crop Journal 2024年第1期12卷 222-231页

作者： Huawei Shi Weichong Wang Lifeng Gao Jirong Wu Chengmei Hu Huishu Yan Yugang Shi Ning Li Youzhi Ma Yongbin Zhou Zhaoshi Xu Jun Chen Wensi Tang Kai Chen Daizhen Sun Yuxiang Wu Ming Chen College of Agriculture Shanxi Agricultural UniversityJinzhong 030801ShanxiChina National key Facility for Crop Gene Resources and genetic improvement Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Nitrogen(N)fertilizer application is essential for crop-plant growth and development.Identifying genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused by overfertilization.We subjected a panel of 389 wheat accessions to N and chlorate(a nitrate analog)treatments to identify quantitative trait loci(QTL)controlling NUE-associated traits at the wheat seedling stage.Genotyping the panel with a 660K single-nucleotide polymorphism(SNP)array,we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition rate.These SNPs were merged into 49 QTL,of which eight were multi-environment stable QTL and 27 were located near previously reported QTL.A set of 135 candidate genes near the 49 QTL included TaBOX(F-box family protein)and TaERF(ethylene-responsive transcription factor).A Tabox mutant was more sensitive to low-N stress than the wild-type plant.We developed two functional markers for Hap 1,the favorable allele of TaBOX.

关键词： Wheat NUE Genome-wide association study Nitrogen sensitive index Chlorate inhibition rate

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Functional prediction of tomato PLATZ family members and functional verification of Sl PLATZ17

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Journal of Integrative Agriculture 2024年第1期23卷 141-154页

作者： Min Xu Zhao Gao Dalong Li Chen Zhang Yuqi Zhang Qian He Yingbin Qi He Zhang Jingbin Jiang Xiangyang Xu Tingting Zhao College of Horticulture and Landscape Architecture Northeast Agricultural UniversityHarbin 150030China key laboratory of biology and genetic improvement of Horticultural crops(Northeast Region) Ministry of Agriculture and Rural AffairsHarbin 150030China

PLATZ is a novel zinc finger DNA-binding protein that plays an important role in regulating plant growth and development and resisting abiotic stress.However,there has been very little research on the function of this family gene in tomatoes,which limits its application in germplasm resource improvement.Therefore,the PLATZ gene family was identified and analyzed in tomato,and its roles were predicted and verified to provide a basis for in-depth research on SlPLATZ gene function.In this study,the PLATZ family members of tomato were identified in the whole genome,and 19 SlPLATZ genes were obtained.Functional prediction was conducted based on gene and promoter structure analysis and RNA-seq-based expression pattern analysis.SlPLATZ genes that responded significantly under different abiotic stresses or were significantly differentially expressed among multiple tissues were screened as functional gene resources.SlPLATZ17 was selected for functional verification by experiment-based analysis.The results showed that the downregulation of SlPLATZ17 gene expression reduced the drought and salt tolerance of tomato plants.Tomato plants overexpressing SlPLATZ17 had larger flower sizes and long,thin petals,adjacent petals were not connected at the base,and the stamen circumference was smaller.This study contributes to understanding the functions of the SlPLATZ family in tomato and provides a reference for functional gene screening.

关键词： tomato PLATZ family abiotic stresses plant development

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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

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The transcriptional control of LcIDL1–LcHSL2 complex by LcARF5 integrates auxin and ethylene signaling for litchi fruitlet abscission

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Journal of Integrative Plant biology 2024年第6期66卷 1206-1226页

作者： Xingshuai Ma Zidi He Ye Yuan Zhijian Liang Hang Zhang Vilde Olsson Lalun Zhuoyi Liu Yanqing Zhang Zhiqiang Huang Yulian Huang Jianguo Li Minglei Zhao State key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Laboratory for Lingnan Modern Agriculture Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China) Ministry of Agriculture and Rural Affairs Guangdong Litchi Engineering Research Center College of Horticulture South China Agricultural University Dongguan Botanical Garden Section for genetics and Evolutionary biology Department of Biosciences University of Oslo College of Agriculture Guangxi University

At the physiological level, the interplay between auxin and ethylene has long been recognized as crucial for the regulation of organ abscission in plants. However, the underlying molecular mechanisms remain unknown. Here, we identified transcription factors involved in indoleacetic acid(IAA) and ethylene(ET)signaling that directly regulate the expression of INFLORESCENCE DEFICIENT IN ABSCISSION(IDA)and its receptor HAESA(HAE), which are key components initiating abscission. Specifically, litchi IDAlike 1(LcIDL1) interacts with the receptor HAESA-like2(LcHSL2). Through in vitro and in vivo experiments,we determined that the auxin response factor LcARF5 directly binds and activates both LcIDL1 and LcHSL2. Furthermore, we found that the ETHYLENE INSENSITIVE 3-like transcription factor LcEIL3 directly binds and activates LcIDL1. The expression of IDA and HSL2 homologs was enhanced in Lc ARF5and Lc EIL3 transgenic Arabidopsis plants, but reduced in ein3 eil1 mutants. Consistently, the expressions of LcIDL1 and LcHSL2 were significantly decreased in Lc ARF5-and LcEIL3-silenced fruitlet abscission zones(FAZ), which correlated with a lower rate of fruitlet abscission. Depletion of auxin led to an increase in 1-aminocyclopropane-1-carboxylic acid(the precursor of ethylene) levels in the litchi FAZ, followed by abscission activation. Throughout this process, LcRF5 and LcEIL3 were induced in the FAZ. Collectively, our findings suggest that the molecular interactions between litchi AUXIN RESPONSE FACTOR 5(LcARF5)–LcIDL1/LcHSL2 and LcEIL3–LcIDL1 signaling modules play a role in regulating fruitlet abscission in litchi and provide a long-sought mechanistic explanation for how the interplay between auxin and ethylene is translated into the molecular events that initiate abscission.

关键词： auxin ethylene fruit abscission IDA–HAE/HSL2 litchi

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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

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DIA-based proteome profiling with PRM verification reveals the involvement of ER-associated protein processing in pollen abortion in Ogura CMS cabbage

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Horticultural Plant Journal 2024年第3期10卷 755-770页

作者： Peiwen Wang Lin Zhu Ziheng Li Mozhen Cheng Xiuling Chen Aoxue Wang Chao Wang Xiaoxuan Zhang key laboratory of biology and genetic improvement of Horticultural crops(Northeast Region) Ministry of Agriculture and Rural AffairsNortheast Agricultural UniversityHarbinHeilongjiang 150030China College of Horticulture and Landscape Architecture Northeast Agricultural UniversityHarbinHeilongjiang 150030China

Ogura cytoplasmic male sterility(Ogura CMS)is extensively applied in hybrid seed production in cruciferous crops.However,the posttranscriptional molecular basis of Ogura CMS in cruciferous crops remains elusive.Here,a data-independent acquisition-based proteomic approach coupled with a parallel reaction monitoring-based targeted proteomic assay was used to analyze the proteome dynamics of Ogura CMS cabbage line RM and its maintainer line RF during floral bud development to obtain insights into the mechanism underlying Ogura CMS in cruciferous crops.A total of 9162 proteins corresponding to 61464 peptides were identified in RM and RF floral buds.The proteomic fluctuation of RM was weaker than that of RF.Differences in protein expression between RM and RF gradually enlarged with floral bud development.Fifteen continually up-regulated and eight continually down-regulated proteins were found in RM relative to RF throughout floral bud development.Differentially expressed proteins between RM and RF during floral bud development were implicated in the endoplasmic reticulum(ER)-associated protein processing pathway,in which most of them exhibited down-regulated expression in RM.These data suggest that ER-associated protein processing may be involved in pollen abortion in Ogura CMS cabbage by inhibiting the expression of critical factors.Our findings not only deepen the understanding of the molecular mechanisms of Ogura CMS in cruciferous crops but also provide better guidance for applying Ogura CMS in the hybrid breeding of cruciferous crops.

关键词： Ogura cytoplasmic male sterility(Ogura CMS) Cabbage Data-independent acquisition(DIA) Parallel reaction monitoring(PRM) Pollen development

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A bHLH transcription factor,CsSPT,regulates high-temperature resistance in cucumber

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Horticultural Plant Journal 2024年第2期10卷 503-514页

作者： Yonggui Liang Chenyu Yang Fangyan Ming Bingwei Yu Zhihua Cheng Yixi Wang Zhengkun Qiu Xiaolan Zhang Bihao Cao Shuangshuang Yan key laboratory of biology and genetic improvement of Horticultural crops(South China) Ministry of Agriculture and Rural AffairsGuangdong Vegetable Engineering and Technology Research CenterCollege of HorticultureSouth China Agricultural UniversityGuangzhouGuangdong 510642China State key Laboratories of Agrobiotechnology Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable CropsMOE Joint Laboratory for International Cooperation in Crop Molecular BreedingChina Agricultural UniversityBeijing 100193China

High-temperature stress threatens the growth and yield of crops. Basic helix-loop-helix(bHLH) transcription factors(TFs) have been shown to play important roles in regulating high-temperature resistance in plants. However, the bHLH TFs responsible for high-temperature tolerance in cucumbers have not been identified. We used transcriptome profiling to screen the high temperature-responsive candidate bHLH TFs in cucumber. Here, we found that the expression of 75 CsbHLH genes was altered under high-temperature stress. The expression of the CsSPT gene was induced by high temperatures in TT(Thermotolerant) cucumber plants. However, the Csspt mutant plants obtained by the CRISPR-Cas9 system showed severe thermosensitive symptoms, including wilted leaves with brown margins and reduced root density and cell activity.The Csspt mutant plants also exhibited elevated H_(2)O_(2) levels and down-regulated photosystem-related genes under normal conditions.Furthermore, there were high relative electrolytic leakage(REC), malondialdehyde(MDA), glutathione(GSH), and superoxide radical(O_(2)^(·-)) levels in the Csspt mutant plants, with decreased Proline content after the high-temperature treatment. Transcriptome analysis showed that the photosystem and chloroplast activities in Csspt mutant plants were extremely disrupted by the high-temperature stress compared with wildtype(WT) plants. Moreover, the plant hormone signal transduction, as well as MAPK and calcium signaling pathways were activated in Csspt mutant plants under high-temperature stress. The HSF and HSP family genes shared the same upregulated expression patterns in Csspt and WT plants under high-temperature conditions. However, most bHLH, NAC, and bZIP family genes were significantly down-regulated by heat in Csspt mutant plants. Thus, these results demonstrated that CsSPT regulated the high-temperature response by recruiting photosynthesis components, signaling pathway molecules, and transcription factors. Our results provide important insights into the heat response m

关键词： Cucumber bHLH CsSPT Photosynthesis High temperature

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