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Post-genomics revolution in the design of premiumquality rice in a high-yieldingbackground to meet consumer demands in the 21st century

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Plant Communications 2022年第3期3卷 1-16页

作者： Nese Sreenivasulu changquan zhang Rhowell NTiozon Qiaoquan Liu Consumer Driven Grain Quality and Nutrition Unit Rice Breeding and Innovation PlatformInternational Rice Research InstituteLos Ban˜os 4030Philippines Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular BreedingCollege of AgricultureYangzhou UniversityYangzhou 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhou 225009China Max Planck Institute of Molecular Plant Physiology Am M€uhlenberg 114476 Potsdam-GolmGermany

The eating and cooking quality(ECQ)of rice is critical for determining its economic value in the marketplace and promoting consumer *** has therefore been of paramount importance in rice breeding ***,we highlight advances in genetic studies of ECQ and discuss prospects for further enhancement of ECQ in *** in gene-and genome-editing techniques have enabled improvements in rice *** genes and quantitative trait loci(QTLs)have been shown to regulate starch composition,thereby affecting amylose content and thermal and pasting properties.A limited number of genes/QTLs have been identified for other ECQ properties such as protein content and ***-assisted breeding has identified rare alleles in diverse genetic resources that are associated with superior ECQ *** post-genomics-driven information summarized in this review is relevant for augmenting current breeding strategies to meet consumer preferences and growing population demands.

关键词： amylose amylopectin eating and cooking quality genetics genome editing texture

Starch biosynthesis in cereal endosperms: An updated review over the last decade

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Plant Communications 2021年第5期2卷 1-22页

作者： Lichun Huang Hongyan Tan changquan zhang Qianfeng Li Qiaoquan Liu Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding State Key Laboratory of Hybrid RiceKey Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhou 225009China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province Key Laboratory of Crop Genetics and Physiology of Jiangsu ProvinceYangzhou UniversityYangzhou 225009China

Starch is a vital energy source for living organisms and is a key raw material and additive in the food and non-food *** has received continuous attention in multiple research *** endosperm of cereals(e.g.,rice,corn,wheat,and barley)is the most important site for the synthesis of storage *** 2010,several excellent reviews summarized key progress in various fields of starch research,serving as important references for subsequent *** the past 10 years,many achievements have been made in the study of starch synthesis and regulation in *** present review provides an update on research progress in starch synthesis of cereal endosperms over the past decade,focusing on new enzymes and non-enzymatic proteins involved in starch synthesis,regulatory networks of starch synthesis,and the use of elite alleles of starch synthesis-related genes in cereal breeding *** also provide perspectives on future research directions that will further our understanding of cereal starch biosynthesis and regulation to support the rational design of ideal quality grain.

关键词： cereal starch biosynthesis regulation network endosperm development quality improvement

High-throughput sequencing to evaluate the effects of methamphetamine on the succession of the bacterial community to estimate the postmortem interval

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Forensic Sciences Research 2022年第4期7卷 736-747页

作者： Shujuan Wang Wei Chen Yanjie Shang Lipin Ren Xiangyan zhang Yadong Guo changquan zhang Department of Forensic Science School of Basic Medical SciencesCentral South UniversityChangshaChina

In forensic medical examinations,estimating the postmortem interval(PMI)is an important ***(MA)is a synthetic stimulant that is commonly abused,and estimation of the PMI after MA abuse has become one of the main tasks in forensic *** play a vital role in carrion *** the bacterial succession patterns can be used as a forensic tool to estimate the *** present study aimed to analyse bacterial succession changes during the decomposition of MA to estimate the *** analysed bacterial communities in rabbits treated with three different concentrations of MA(0,22.5,and 90 mg/kg)under the natural conditions of 20°C and 70%humidity by sequencing 16S rRNA gene amplicons using the Illumina MiSeq *** obtained 2374209 high-quality sequences and 2937 operational taxonomic units(OTUs).The relative abundances of the bacterial communities varied markedly in response to different MA ***,in response to the different concentrations of MA,Bacteroidetes became disparate in the rectum in the late *** numbers of bacterial taxa were identified in the rectum and buccal cavity samples,except at the highest concentration of MA in the rectum samples when PMI was 0-h,than were present in live ***,the PMI correlated significantly with bacterial succession at different taxonomic *** results suggested that bacterial community succession could be used as a“microbial clock”to estimate the PMI in cases of MA-related death;however,further study is required to gain a deeper understanding of this concept.

关键词： Forensic sciences methamphetamine microbes bacterial community succession postmortem interval high-throughput sequencing

Generation of selectable marker-free soft transgenic rice with transparent kernels by downregulation of SSSⅡ-2

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The Crop Journal 2020年第1期8卷 53-61页

作者： Zhihao Xu Meimei Yu Youwei Yin Cenwen Zhu Wen Ji changquan zhang Qianfeng Li Honggen zhang Shuzu Tang Hengxiu Yu Qiaoquan Liu Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingJiangsu Co-Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou University

The amylose content(AC) of rice endosperm starch varies from 0 to 35%,and is associated with rice cooking and eating *** rice has low AC,generally between 6% and 15%,and its eating quality is high whether it is consumed hot or ***,the appearance quality of current soft rice cultivars needs to be improved,especially opaque *** genetic engineering has improved some agronomic traits of soft rice varieties,but not endosperm *** the present study,a RNAi construct of the soluble starch synthase Ⅱ-2(SSSⅡ-2) and the hygromycin phosphotransferase(HPT) gene were introduced into an elite japonica rice variety,Kangtiaowuyunjing(KWY8) by *** selectable marker-free(SMF) transgenic lines were obtained,and SSSⅡ-2 expression was significantly downregulated in selected transgenic lines,resulting in lower AC of the *** physicochemical properties of the transgenic rice kernels,including gel consistency(GC) and rapid visco analyzer(RVA) profile,differed significantly from those of wild-type rice and were similar to those of a soft rice variety,Nanjing 46(NJ46).These findings indicate that the cooking,eating,and processing qualities of transgenic rice are comparable to those of ***,the transgenic rice endosperm retained a transparent appearance under low-moisture ***,SMF SSSⅡ-2 RNAi rice provides a resource for breeding soft rice with transparent endosperm.

关键词： Rice(Oryza sativa L.) SSSⅡ-2 RNAi Starch quality SMF transgenic lines

Exploration and Validation of the Potential Downstream Genes Underlying ipa1-2D Locus for Rice Panicle Branching

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Phyton-International Journal of Experimental Botany 2021年第3期90卷 773-787页

作者： Lin zhang Dong Xie Zhong Bian Yiting Zou Han Zhou Wenlu Cai Hadi Yeilaghi Xiaolei Fan changquan zhang Qiaoquan Liu Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular BreedingYangzhou UniversityYangzhou225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhou225009China

In recent years,some super hybrid rice varieties were bred with strong culms and large panicles,which are mainly contributed by the ipa1-2D locus.A gain-of-function allele of OsSPL14 is the ipa1-2D and it can greatly increase the panicle primary branch ***,the key downstream genes mediating this trait variation are not fully *** this study,we developed high-quality near-isogenic lines(NILs)with a difference of only 30 kb chromosomal segment covering the ipa1-2D *** the NILs,we explored the impact of ipa1-2D on five sequential stages of early inflorescence development,and found that the locus can greatly enhance the initiation of primary branch meristems.A transcriptomic analysis was performed to unveil the downstream molecular network of ipa1-2D,and 87 genes were found differentially expressed,many of which are involved in metabolism and catalysis *** addition,transgenic lines of overexpression and RNA interference were generated to shape different levels of *** were also used to validate the expression variation explored by *** on the gene annotation,twelve potential downstream targets of ipa1-2D were selected,and their expression variation was confirmed by qRT-PCR analysis both in NILs and transgenic *** research expands the molecular network underlying ipa1-2D and provides novel gene information which might be involved in the control of panicle *** discussed the potential function of identified genes and highlighted their values for future function exploration and breeding application.

关键词： Rice ipa1-2D panicle branching inflorescence meristems gene expression

Introgression of lac6/tl1/du13 improves the palatability of japonica rice

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The Crop Journal 2024年第4期12卷 1259-1265页

作者： Yong Yang Tao zhang Yuliang Shi Yan Lu Qianfeng Li Xiaolei Fan Lichun Huang Lu Chen Xuetang Song Qing Liu changquan zhang Qiaoquan Liu Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009JiangsuChina Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology Yangzhou UniversityYangzhou 225009JiangsuChina Jiang Su(Wu Jin)Rice Research Institute Changzhou 213175JiangsuChina

Amylose content(AC)is a crucial determinant of the eating and cooking quality(ECQ)of rice,with low AC varieties exhibiting a softer texture and greater stickiness-attributes that enhance palatability and are desirable in specific culinary *** harness these traits,significant efforts have been made to manipulate AC to improve rice *** research utilized the MutMap+approach to identify LAC6/TL1,a gene that is an allele of Du13,responsible for low ***6 encodes a C2H2 zinc finger protein,which specifically increases the splicing efficiency of the Wxb allele without affecting the Wxa *** studies of LAC6 revealed that its proper integration could rectify the undesirable AC phenotype,whereas mutations within this gene led to reduced AC and were associated with shorter grain length and decreased thousand-grain *** these drawbacks,such mutations positively impact rice palatability,presenting a trade-off between grain size and eating *** address the challenges posed by the reduced grain weight associated with LAC6 mutations,we developed a specific molecular marker for LAC6,which has been effectively used in breeding programs to select lac6/tl1/du13 homozygous individuals with larger grain *** findings demonstrate that the“small grain”trait associated with lac6/tl1/du13 can be effectively mitigated through combined phenotype-based and marker-assisted *** study highlights the potential of lac6/tl1/du13 as a valuable gene for breeding novel,high-quality soft rice varieties through targeted breeding strategies.

关键词： Rice Dull endosperm Amylose content Wx Breeding

OsbZIP09,a Unique OsbZIP Transcription Factor of Rice,Promotes Rather Than Suppresses Seed Germination by Attenuating Abscisic Acid Pathway

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Rice science 2021年第4期28卷 358-367,I0021-I0023页

作者： Wang Chuxin Zhu Chengchao Zhou Yu Xiong Min Wang Jindong Bai Huang Lu Chenya zhang changquan Liu Qiaoquan Li Qianfeng Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province College of AgricultureYangzhou UniversityYangzhou 225009China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education Yangzhou UniversityYangzhou 225009China

We successfully identified a novel and unique OsbZIP transcription factor,OsbZIP09,whose mutants exhibited longer seeds and less severe pre-harvest sprouting than the wild type,but shared similar germination rate as the wild type under normal germination *** expression of OsbZIP09 was induced by abscisic acid(ABA)and declined as the germination *** a nucleus-localized transcription factor,the conserved binding motif of OsbZIP09 was identified via DNA affinity purification sequencing *** evidences indicated that OsbZIP09 directly enhanced the expression of ABA catabolism gene ABA8ox1,thus reducing ABA *** addition,OsbZIP09 also directly bound to the promoter of LEA3 gene to inhibit its expression,thus further alleviating the suppressive effect of ABA on seed *** results demonstrated that OsbZIP09 likely functions as a brake of the ABA pathway to attenuate the inhibitory effect of ABA on rice seed germination via dual strategies.

关键词： OsbZIP09 pre-harvest sprouting abscisic acid seed germination ABA8ox1 gene LEA3 gene rice transcription factor

Genetic analysis and gene cloning of a triangular hull 1 (tri1) mutant in rice (Oryza sativa L.)

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Chinese Science Bulletin 2013年第3期58卷 2984-2991页

作者： FENG GongNeng zhang changquan TANG MingYong zhang GuiYun XU ChenWu GU MingHong LIU QiaoQuan Key Laboratory of Plant Functional Genomics of Ministry of Education/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province Yangzhou University Yancheng Institute of Technology

Grain shape and size are two key factors that determine rice yield and quality. In the present study, a rice triangular hull mutant (tri1) was obtained from the progeny of japonica rice variety Taipei 309 treated with 60Co γ-rays. Compared to the wild type, the tri1 mutant presents a triangular hull, and exhibits an increase in grain thickness and protein content, but with a slight decrease in plant height and grain weight. Genetic analysis indicated that the mutant phenotype was controlled by a recessive nuclear gene which is stably inherited. Using a map-based cloning strategy, we fine-mapped tri1 to a 47-kb region between the molecular markers CHR0122 and CHR0127 on the long arm of chromosome 1, and showed that it co-segregates with the molecular marker CHR0119. According to the rice genome sequence annotation there are six predicated genes within the mapped region. Sequencing analysis of the mutant and the wild type indicated that there was a deletion of an A nucleotide in exon 3 of the OsMADS32 gene, which could result in a downstream frameshift mutation and premature termination of the predicted polypeptide. Both semi-quantitative and real-time RT-PCR analyses showed that this gene expressed highly in young inflorescences, while expressed at very low levels in other tissues. These results implied that the OsMADS32 gene could be a candidate of TRI1. Taken together, the results of this study lay the foundation for further investigation into the molecular mechanisms regulating rice caryopsis development.

关键词：隐性核基因水稻产量遗传分析克隆策略突变体三角形船体 RT-PCR分析

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Wx^lv、the Ancestral Allele of Rice Waxy Gene

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Molecular Plant 2019年第8期12卷 1157-1166页

作者： changquan zhang Jihui Zhu Shengjie Chen Xiaolei Fan Qianfeng Li Yan Lu Min Wang Hengxiu Yu Chuandeng Yi Shuzhu Tang Minghong Gu Qiaoquan Liu Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding College of AgricultureYangzhou UniversityYangzhou 225009China Co-lnnovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province Yangzhou UniversityYangzhou 225009China

In rice grains,the Waxy (Wx) gene is responsible for the synthesis of amylose,the most important determinant for eating and cooking *** effects of several Wx alleles on amylose content and the taste of cooked rice have been ***,the relationship between artificial selection and the evolution of various Wx alleles as well as their distribution remain *** we report the identification of an ancestral allele,Wx^lv,which dramatically affects the mouthfeel of rice grains by modulating the size of amylose *** demonstrated that WF originated directly from wild rice,and the three major Wx alleles in cultivated rice (Wx^b,Wx^a,and Wx^in) differentiated after the substitution of one base pair at the functional *** data indicate that the Wx^lv allele played an important role in artificial selection and *** findings also shed light on the evolution of various Wx alleles,which have greatly contributed to improving the eating and cooking quality of rice.

关键词： Oryza sativa Waxy eating and cooking quality allelic variation artificial selection