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Genome-wide identification,characterization and functional prediction of the SRS gene family in sesame(Sesamum indicum L.)

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Oil Crop Science 2024年第2期9卷 69-80页

作者： Farjana Afroz Susmi Tasmina Islam Simi Md Nahid Hasan Md Abdur Rahim department of Genetics and Plant breeding Sher-e-Bangla Agricultural UniversityDhaka1207Bangladesh

Sesame(Sesamum indicum L.)is an ancient oilseed crop of the Pedaliaceae family with high oil content and potential health benefits.SHI RELATED SEQUENCE(SRS)proteins are the transcription factors(TFs)specific to plants that contain RING-like zinc finger domain and are associated with the regulation of several physiological and biochemical processes.They also play vital roles in plant growth and development such as root formation,leaf development,floral development,hormone biosynthesis,signal transduction,and biotic and abiotic stress responses.Nevertheless,the SRS gene family was not reported in sesame yet.In this study,identification,molecular characterization,phylogenetic relationship,cis-acting regulatory elements,protein-protein interaction,syntenic relationship,duplication events and expression pattern of SRS genes were analyzed in S.indicum.We identified total six SiSRS genes on seven different linkage groups in the S.indicum genome by comparing with the other species,including the model plant Arabidopsis thaliana.The SiSRS genes showed variation in their structure like2–5 exons and 1–4 introns.Like other species,SiSRS proteins also contained‘RING-like zinc finger'and‘LRP1'domains.Then,the SiSRS genes were clustered into subclasses via phylogenetic analysis with proteins of S.indicum,A.thaliana,and some other plant species.The cis-acting regulatory elements analysis revealed that the promoter region of SiSRS4(SIN_1011561)showed the highest 13 and 16 elements for light-and phytohormone-responses whereas,SiSRS1(SIN_1015187)showed the highest 15 elements for stress-response.The ABREs,or ABA-responsive elements,were found in a maximum of 8 copies in the SiSRS3(SIN 1009100).Moreover,the available RNA-seq based expression of SiSRS genes revealed variation in expression patterns between stress-treated and non-treated samples,especially in drought and salinity conditions in.S.indicum.Two SiSRS genes like SiSRS1(SIN_1015187)and SiSRS5(SIN_1021065),also exhibited variable expression patterns between control vs PEG-tre

关键词： SiSRS gene family SHI Transcription factor Characterization Sesamum indicum

Mucosal immune responses to Ichthyophthirius multifiliis in the ocular mucosa of rainbow trout(Oncorhynchus mykiss,Walbaum),an ancient teleost fish

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Marine Life Science & Technology 2024年第2期6卷 266-279页

作者： Weiguang Kong Guangyi Ding Gaofeng Cheng Peng Yang Zhen Xu Key Laboratory of breeding Biotechnology and Sustainable Aquaculture Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China department of Aquatic Animal Medicine College of FisheriesHuazhong Agricultural UniversityWuhan 430070China

The eye,as a specialized visual organ,is directly exposed to the external environment,and,therefore,it faces constant chal-lenges from external pathogenic organisms and toxins.In the ocular mucosa(OM)of mammals,mucosal-associated lymphoid tissues(MALTs)constitute the primary line of defense.However,the immune defense role of the OM remains unknown in aquatic vertebrates.To gain insights into the immune processes within the OM of teleost fish,we developed an infection model of rainbow trout(Oncorhynchus mykiss)OM using a parasite,Ichthyophthirius multifiliis(Ich).Immunofluorescence,qPCR,and H&E staining revealed that Ich successfully infiltrates the OM of rainbow trout,leading to pathological struc-tural changes,as evidenced by A&B staining.Importantly,the qPCR results indicate an up-regulation of immune-related genes following Ich infection in the OM.Moreover,transcriptome analyses were conducted to detect immune responses and impairments in eye function within the OM of rainbow trout with Ich infection.The results of the transcriptome analysis that Ich infection can cause an extensive immune response in the OM,ultimately affecting ocular function.To the best of our knowledge,our findings represent for the first time that the teleost OM could act as an invasion site for parasites and trigger a strong mucosal immune response to parasitic infection.

关键词： Ocular mucosa Mucosal immunity Transcriptome analysis Oncorhynchus mykiss Ichthyophthirius multifiliis

Callus proliferation-induced hypoxic microenvironment decreases shoot regeneration competence in Arabidopsis

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Molecular Plant 2024年第3期17卷 395-408页

作者： Dohee Koo Hong Gil Lee Soon Hyung Bae Kyounghee Lee Pil Joon Seo department of Chemistry Seoul National UniversitySeoul 08826Korea Plant Genomics and breeding Institute Seoul National UniversitySeoul 08826Korea Research Institute of Basic Sciences Seoul National UniversitySeoul 08826Korea

Plants are aerobic organisms that rely on molecular oxygen for respiratory energy production.Hypoxic conditions,with oxygen levels ranging between 1%and 5%,usually limit aerobic respiration and affect plant growth and development.Here,we demonstrate that the hypoxic microenvironment induced by active cell proliferation during the two-step plant regeneration process intrinsically represses the regener-ation competence of the callus in Arabidopsis thaliana.We showed that hypoxia-repressed plant regener-ation is mediated by the RELATED TO APETALA2.12(RAP2.12)protein,a memberof the Ethylene Response Factor VIl(ERF-Vll)family.We found that the hypoxia-activated RAP2.12 protein promotes salicylic acid(SA)biosynthesis and defense responses,thereby inhibiting pluripotency acquisition and de novo shoot regeneration in calli.Molecular and genetic analyses revealed that RAP2.12 could bind directly to the SALICYLIC ACID INDUCTION DEFICIENT 2(SID2)gene promoter and activate SA biosynthesis,repressing plant regeneration possibly via a PLETHORA(PLT)-dependent pathway.Consistently,the rap2.12 mutant calli exhibits enhanced shoot regeneration,which is impaired by SA treatment.Taken together,these find-ings uncover that the cell proliferation-dependent hypoxic microenvironment reduces cellular pluripotency and plant regeneration through the RAP2.12-SID2 module.

关键词： callus cell proliferation-induced hypoxia SID2 plant regeneration salicylic acid RAP2.12

A 48-bp deletion upstream of LIGULELESS 1 alters rice panicle architecture

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The Crop Journal 2024年第2期12卷 354-363页

作者： Linhua Wu Min Hu Shuwei Lyu Wenfeng Chen Hang Yu Qing Liu Wei He Chen Li Zuofeng Zhu Rice Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina National Center for Evaluation of Agricultural Wild Plants(Rice) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China State Key Laboratory for Rice Biology and breeding China National Rice Research InstituteHangzhou 310006ZhejiangChina Key Laboratory of Genetics and breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina Guangdong Key Laboratory of New Technology in Rice breeding Guangzhou 510640GuangdongChina Guangdong Rice Engineering Laboratory Guangzhou 510640GuangdongChina

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement.To investigate its molecular mechanisms in rice,we performed map-based cloning and characterization of OPEN PANICLE 1(OP1),a gain-of-function allele of LIGULELESS 1(LG1),controlling the spread-panicle phenotype.This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch.Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1(sp1).Knocking out BRASSINOSTEROID UPREGULATED1(BU1)gene in the background of OP1 complementary plants resulted in compact panicles,suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway.We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

关键词： Upstream region Panicle architecture Gene expression BR Rice

How neonatal diet affects the long-term development of rumination behavior, rumen fermentation and feed digestion in dairy calves fed a high milk level?

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Animal Nutrition 2024年第1期16卷 326-337页

作者： Jianxin Xiao Tianyu Chen Rong Peng Gibson M. Alugongo Hui Yang Shuai Liu Yulin Ma Jingjun Wang Shengli Li Zhijun Cao State Key Laboratory of Animal Nutrition and Feeding International Calf and Heifer Organization College of Animal Science and Technology China Agricultural University Key Laboratory of Low Carbon Culture and Safety Production in cattle in Sichuan Animal Nutrition Institute Sichuan Agricultural University

This study was to investigate growth performance, rumination development, rumen fermentation and feed digestion in young calves provided high volumes(about 20% of calf birth weight) of milk with or without forage inclusion and how these parameters correlate with each other. Immediately after birth,160 newborn Holstein female calves(41.6 ± 4.2 kg of initial BW) were randomly divided into 2 treatments: 1) starter(CON, only starter) and 2) starter and hay(HAY, both starter and hay). The calves were fed their respective experimental diets from d 4 to 84, after which they were all introduced to similar diets until the end of the experiment on d 196. Treatment had no effect on growth and structural measurements throughout the experimental period. However, treatment had an effect on the other parameters, mainly during the post-weaning period. Forage supplementation tended to reduce starter dry matter intake(P = 0.05), while increasing the forage intake(P < 0.01) and the feed-to-gain ratio(P < 0.01). HAY calves had increased neutral detergent fiber(NDF) and physically effective NDF(peNDF)intakes(P < 0.05) and tended to lower(P < 0.01) starch intake compared to CON calves. The HAY calves had a higher rumination time(P < 0.01), ruminal pH(P < 0.01), and acetate-to-propionate ratio(P = 0.05)compared to the CON calves. Spearman correlation analysis showed that rumination time was positively related to the ruminal p H at d 84(P = 0.01) and 196(P = 0.02). The HAY calves had similar apparent total-tract digestibility of dry matter(DM), NDF and ether extract(EE), but lower digestibility of organic matter(OM, P = 0.03), crude protein(CP, P < 0.01) and starch(P < 0.01) compared to those of the CON calves at week 12. Furthermore, there were no positive relationships between rumination time and nutrient digestibility or between rumination time per kilogram DM and nutrient digestibility. In conclusion, feeding hay to calves fed a high milk level improved rumination during the post-weaning period only, without a concomitant effect on

关键词： Neonatal calf Early forage feeding Rumination Rumen fermentation Nutrient digestibility

ChMYB1-ChbHLH42-ChTTG1 module regulates abscisic acidinduced anthocyanin biosynthesis in Cerasus humilis

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Horticultural Plant Journal 2024年第1期10卷 51-65页

作者： Xiaolong Ji Zhe Li Mingyu Zhang Shaoyu Lang Xingshun Song State Key Laboratory of Tree Genetics and breeding Northeast Forestry UniversityHarbinHeilongjiang 150040China department of Genetics College of Life ScienceNortheast Forestry UniversityHarbinHeilongjiang 150040China

Cerasus humilis is a kind of economic fruit tree peculiar to China,which is widely used in the food,landscape,and pharmaceutical industries.Anthocyanins are a phenolic metabolite that plays an essential role in fruit coloration.However,the regulatory network of C.humilis in anthocyanin biosynthesis is still unclear.In this study,the R2R3-MYB transcription factor ChMYB1 was isolated from the full genome of the species.Yeast one-hybrid,dual-luciferase assays,and GUS staining showed that ChMYB1 significantly increased anthocyanin contents in C.humilis fruit by promoting the expression of ChCHS and ChUFGT by binding MBS(MYB-binding elements).ChMYB1 interacted with ChbHLH42and ChTTG1 to form the MBW complex and further enhanced the expression of ChUFGT.In addition,abscisic acid(ABA)treatment promoted the expression of ChMYB1 and anthocyanin accumulation in C.humilis fruit.Interestingly,ABA treatment enhanced the interaction between ChMYB1 and ChbHLH42.Furthermore,ChABI5 inhibited the interaction between ChMYB1 and ChbHLH42.Our data elucidated the primary molecular mechanism of anthocyanin biosynthesis in C.humilis fruit,deepening the understanding of the regulatory network affecting anthocyanin metabolism in edible fruit crops.

关键词： Cerasus humilis Anthocyanin ChMYB1 Fruit ABA

Multi-environment BSA-seq using large F3 populations is able to achieve reliable QTL mapping with high power and resolution: An experimental demonstration in rice

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The Crop Journal 2024年第2期12卷 549-557页

作者： Yan Zheng Ei Ei Khine Khin Mar Thi Ei Ei Nyein Likun Huang Lihui Lin Xiaofang Xie Min Htay Wai Lin Khin Than Oo Myat Myat Moe San San Aye Weiren Wu College of Life Sciences Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Fujian Provincial Key Laboratory of Crop breeding by Design Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Key Laboratory of Genetics Breeding and Multiple Utilization of CropsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina department of Botany Mawlamyine UniversityMon StateMawlamyineMyanmar department of Botany Dagon UniversityNorth DagonYangonMyanmar

Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability.

关键词： BSA-seq QTL mapping Large F3 population Multi-environment experiment Cross-validation

AP-1 and SP1 trans-activate the expression of hepatic CYP1A1 and CYP2A6 in the bioactivation of AFB1 in chicken

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Science China(Life Sciences) 2024年第7期67卷 1468-1478页

作者： Jiang Deng Jia-Cheng Yang Yue Feng Ze-Jing Xu Kamil Kuča Meng Liu Lv-Hui Sun State Key Laboratory of Agricultural Microbiology Hubei Hongshan LaboratoryFrontiers Science Center for Animal Breeding and Sustainable ProductionCollege of Animal Sciences and TechnologyHuazhong Agricultural UniversityWuhan 430070China department of Chemistry Faculty of ScienceUniversity of Hradec KraloveHradec Kralove 50003Czech Republic

Dietary exposure to aflatoxin B1(AFB1)is harmful to the health and performance of domestic animals.The hepatic cytochrome P450s(CYPs),CYP1A1 and CYP2A6,are the primary enzymes responsible for the bioactivation of AFB1to the highly toxic exo-AFB1-8,9-epoxide(AFBO)in chicks.However,the transcriptional regulation mechanism of these CYP genes in the liver of chicks in AFB1metabolism remains unknown.Dual-luciferase reporter assay,bioinformatics and site-directed mutation results indicated that specificity protein 1(SP1)and activator protein-1(AP-1)motifs were located in the core region-1,063/-948,-606/-541 of the CYP1A1 promoter as well as-636/-595,-503/-462,-147/-1 of the CYP2A6 promoter.Furthermore,overexpression and decoy oligodeoxynucleotide technologies demonstrated that SP1 and AP-1 were pivotal transcriptional activators regulating the promoter activity of CYP1A1 and CYP2A6.Moreover,bioactivation of AFB1to AFBO could be increased by upregulation of CYP1A1 and CYP2A6 expression,which was trans-activated owing to the upregulation of AP-1,rather than SP1,stimulated by AFB1-induced reactive oxygen species.Additionally,nano-selenium could reduce ROS,downregulate AP-1 expression and then decrease the expression of CYP1A1 and CYP2A6,thus alleviating the toxicity of AFB1.In conclusion,AP-1 and SP1 played important roles in the transactivation of CYP1A1 and CYP2A6 expression and further bioactivated AFB1to AFBO in chicken liver,which could provide novel targets for the remediation of aflatoxicosis in chicks.

关键词： aflatoxin B1 CYP1A1 CYP2A6 SP1 AP-1 transcriptional activation

Haploids can be induced in knockout mutants of OsPLA1,but not OsDMP3 or OsDMP6,in rice

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The Crop Journal 2024年第1期12卷 213-221页

作者： Zongkai Liu Yu Zhong Xiaolong Qi Tai An Shuwei Guo Dong Wang Yuwen Wang Bin Feng Zuofeng Zhu Shaojiang Chen Chenxu Liu National Maize Improvement Center Engineering Research Center of Ministry of EducationChina Agricultural UniversityBeijing 100193China National Center for Evaluation of Agricultural Wild Plants(Rice) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Doubled haploid(DH)technology is an important tool in crop breeding because it can significantly accelerate the breeding process.ZmPLA1/MATL/NLD and ZmDMP are two key genes controlling haploid induction(HI)in maize,exhibiting a synergistic effect.However,it is unknown whether knock out of ZmDMP orthologs can stimulate HI in rice.In this study,a ZmPLA1 ortholog(OsPLA1)and two ZmDMP orthologs(OsDMP3 and OsDMP6)were identified in rice.All three genes encode plasma membrane-localized proteins and were highly expressed in mature anthers.Knockout of OsPLA1 in both Minghui 63 and Nipponbare resulted in reduced seed setting rate(SSR)and caused HI.The osdmp3,osdmp6 and the double mutant failed to trigger HI independently,nor increased the haploid induction rate(HIR)when combined with ospla1.Repeated pollinations operations of QX654A with the ospla1 mutant significantly improve SSR,while reducing HIR.RNA-seq profiling of mature ospla1 mutant anthers indicated that a large number of differentially expressed genes(DEGs)were enriched in redox homeostasis and lipid metabolic GO terms,plant hormone signal transduction,and MAPK signaling pathways.These findings provide important insights towards construction of an efficient DH breeding technology and study of the molecular mechanism of HI in rice.

关键词： Doubled haploid breeding Haploid induction Mutation anlaysis Rice