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A 9.5-kb deletion in the 1st intron of OsMADS51 enhances temperature sensitivity in rice

The Crop Journal 2024年第4期12卷 1031-1040页

作者： Lei Zhao Haifei Hu Junyu Chen Chongrong Wang Yibo Chen Hong Li Daoqiang Huang Zhidong Wang Degui Zhou Rong Gong Yangyang Pan Junliang Zhao Liangyong Ma Shaochuan Zhou Rice Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina State key laboratory of Rice biology and Chinese National Center for Rice Improvement China National Rice Research InstituteHangzhou 310006ZhejiangChina Guangdong laboratory for Lingnan Modern Agriculture Guangzhou 510640GuangdongChina 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 Rice Engineering laboratory Guangzhou 510640GuangdongChina Guangdong key laboratory of New Technology in Rice breeding Guangzhou 510640GuangdongChina

Temperature is an important environmental factor affecting heading date of *** its importance,genes responsible for temperature-sensitive heading in rice have remained *** previous study identified a quantitative trait locus qHd1 which advances heading date under high temperatures.A 9.5-kb insertion was found in the first intron of OsMADS51 in indica variety Zhenshan 97(ZS97).However,the function of this natural variant in controlling temperature sensitivity has not been *** this study,we used CRISPR/Cas9 to knock out the 9.5-kb insertion in *** conducted under cotrolled conditions in phytotrons confirmed that deletion increased temperature sensitivity and advanced heading by downregulating the expression level of ***-hybrid assays in yeast,ChIP-quantitative polymerase chain reaction,electrophoretic mobility shift,and luciferase-based transient transactivation assays collectively confirmed that OsMADS51 affects heading date by regulation of heading date gene *** further determined that the long non-coding RNA HEATINR is generated from the first intron of OsMADS51,offering an explanation for how the 9.5-kb insertion affects temperature *** also found that OsMADS51 was strongly selected in early/late-season rice varieties in South China,possibly accounting for their strong temperature *** insights not only advance our understanding of the molecular mechanisms underlying the temperature-responsive regulation of heading date in rice but also provide a valuable genetic target for molecular breeding.

关键词： OsMADS51 Insertion Long non-coding RNA Oryza sativa

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Genes controlling grain chalkiness in rice

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The Crop Journal 2024年第4期12卷 979-991页

作者： Luo Chen Xiumei Li Minhua Zheng Rui Hu Jingfang Dong Lingyan Zhou Wuge Liu Dilin Liu Wu Yang Rice Research Institute Guangdong Academy of Agricultural SciencesGuangdong Key Laboratory of New Technology in Rice BreedingGuangdong Rice Engineering LaboratoryKey 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 College of Agriculture and biology Zhongkai University of Agriculture and EngineeringGuangzhou 510225GuangdongChina Guangdong Provincial key laboratory for Crop Germplasm Resources Preservation and Utilization Agro-biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

With rising living standards,there is an increasing demand for high-quality *** quality is mainly defined by milling quality,appearance quality,cooking and eating quality,and nutrition *** them,chalkiness is a key trait for appearance quality,which adversely affects cooking and eating quality,head rice yield,and commercial ***,chalkiness is undesirable,and reducing chalkiness is a major goal in rice quality ***,chalkiness is a complex trait jointly influenced by genetic and environmental factors,making its genetic study and precision improvement a huge *** the rapid development of molecular techniques,much knowledge has been gained about the genes and molecular networks involved in chalkiness *** present review describes the major environmental factors affecting chalkiness and summarizes the quantitative trait loci(QTL)associated with *** than 150 genes related to chalkiness formation have been *** functions of the genes regulating chalkiness,primarily those involved in starch synthesis,storage protein synthesis,transcription regulation,organelle development,grain shape regulation,and hightemperature response,are ***,we identify the challenges associated with genetic improvement of chalkiness and suggest potential ***,the review offers insight into the molecular dynamics of chalkiness and provides a strong basis for the future breeding of high-quality rice varieties.

关键词： Rice Grain quality Chalkiness QTL identification Gene

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The ABA synthesis enzyme allele OsNCED2^(T)promotes dryland adaptation in upland rice

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The Crop Journal 2024年第1期12卷 68-78页

作者： Liyu Huang Yachong Bao Shiwen Qin Min Ning Qinyan Li Qingmao Li Shilai Zhang Guangfu Huang Jing Zhang Wensheng Wang Binying Fu Fengyi Hu key laboratory of biology and Germplasm Innovation of Perennial Rice from Ministry of Agriculture and Rural Affairs School of AgricultureYunnan UniversityKunming 650091YunnanChina National key Facility for Crop Gene Resources and genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart,irrigated *** previous study revealed a difference in the frequency of the OsNCED2 gene between upland and irrigated populations.A nonsynonymous mutation(C to T,from irrigated to upland rice)may have led to functional variation fixed by artificial selection,but the exact biological function in dryland adaptation is *** this study,transgenic and association analysis indicated that the domesticated fixed mutation caused functional variation in OsNCED2,increasing ABA levels,root development,and drought tolerance in upland rice under dryland ***2-overexpressing rice showed increased reactive oxygen species-scavenging abilities and transcription levels of many genes functioning in stress response and development that may regulate root development and drought ***2^(T)-NILs showed a denser root system and drought resistance,promoting the yield of rice under dryland ***2^(T)may confer dryland adaptation in upland rice and may find use in breeding dryland-adapted,water-saving rice.

关键词： Upland rice Dryland adaptation ABA Root development Drought tolerance

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Natural variation in MORE GRAINS 1 regulates grain number and grain weight in rice

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Journal of Integrative Plant biology 2024年第7期66卷 1440-1458页

作者： Yingchun Han Qianfeng Hu Nuo Gong Huimin Yan Najeeb Ullah Khan Yanxiu Du Hongzheng Sun Quanzhi Zhao Wanxi Peng Zichao Li Zhanying Zhang Junzhou Li Henan key laboratory of Rice Molecular breeding and High Efﬁciency Production College of AgronomyHenan Agricultural UniversityZhengzhou 450046China Beijing key laboratory of Crop genetic Improvement College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Rice Industrial Technology Research Institute Guizhou UniversityGuiyang 550025China School of Forestry Henan Agricultural UniversityZhengzhou 450046China

Grain yield is determined mainly by grain number and grain *** this study,we identified and characterized MORE GRAINS1(MOG1),a gene associated with grain number and grain weight in rice(Oryza sativa L.),through map-based *** of MOG1 increased grain yield by 18.6%-22.3%under field *** determined that MOG1,a bHLH transcription factor,interacts with OsbHLH107 and directly activates the expression of LONELY GUY(LOG),which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1(EXPLA1),positively regulating grain number per panicle and grain *** variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation,leading to functional *** analysis revealed that Hap-HNW,which results in a greater number and heavier grains,has undergone strong selection but has been poorly utilized in modern lowland rice *** summary,the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway,thereby increasing grain number and grain *** findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.

关键词： grain number grain weight MOG1 natural variation rice

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Isolation and characterization of 16 microsatellite loci from transcriptome-derived sequences of the topmouth culter(Culter alburnus Basilewsky)

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Aquaculture and Fisheries 2024年第5期9卷 739-744页

作者： Shili Liu Yinuo Liu Jianbo Zheng Fei Li Wenping Jiang Meili Chi Shun Cheng Yongyi Jia Jinliang Zhao key laboratory of Freshwater Aquatic genetic Resources Ministry of AgricultureShanghai Ocean UniversityShanghai201306China Shanghai Engineering Research Center of Aquaculture Shanghai Ocean UniversityShanghai201306China National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai201306China key laboratory of Freshwater Aquaculture genetic and breeding of Zhejiang Province Zhejiang Institute of Freshwater FisheriesHuzhou313001China

The topmouth culter(Culter alburnus)is at the top of the food chain and plays an important role in the maintenance of freshwater ecosystem *** is also a commercially important aquaculture fish species in *** establish conservation strategies and breeding programs,a total of 16 polymorphic microsatellite loci were isolated from transcriptome-derived sequences of *** of these loci was assessed against 1 wild and 3 cultured populations in Huzhou,*** number of alleles per locus ranged from 3 to 10 with an average of 5.25.A bottleneck effect was observed in all 4 populations;The ChangXing population showed moderate genetic differentiation when compared with other populations(FST values,0.0695-0.0788).The microsatellite loci would be useful for further studies on population genetic diversity,genetic structure,and assessments of the artificial propagation release effect of ***.

关键词： Culter alburnus Microsatellite genetic diversity

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Searching for plant NLR immune receptors conferring resistance to potyviruses

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The Crop Journal 2024年第1期12卷 28-44页

作者： Xin Hong Shufen Li Xiaofei Cheng Haijian Zhi Jinlong Yin Kai Xu Jiangsu key laboratory for Microbes and Functional Genomics Jiangsu Engineering and Technology Research Center for MicrobiologyCollege of Life SciencesNanjing Normal UniversityNanjing 210023JiangsuChina College of Plant Protection Northeast Agricultural UniversityHarbin 150030HeilongjiangChina National Center for Soybean Improvement National Key Laboratory for Crop Genetics and Germplasm EnhancementKey Laboratory of Biology and Genetic Improvement of Soybean-Ministry of AgricultureNanjing Agricultural UniversityNanjing 210095JiangsuChina

To fight against invasion by pathogens,plants have evolved an elaborate innate immune system,of which the nucleotide-binding domain leucine-rich repeat-containing receptor(NLR)acts as the sensor and immune ***,comprising one of the largest genera of plant viruses,cause severe crop yield losses *** crop resistance to potyviruses can be used in breeding and plant transgenesis to control disease *** review summarizes achievements in mapping and cloning NLR genes conferring dominant resistance against potyvirus in the families Fabaceae,Solanaceae,Brassicaceae,and *** compares mechanisms of potyviral protein recognition and downstream signaling employed by NLRs and discusses strategies for exploiting NLRs to better control diseases caused by potyviruses.

关键词： NLR Potyvirus resistance genetic diversity Mapping Engineer

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LociScan,a tool for screening genetic marker combinations for plant variety discrimination

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The Crop Journal 2024年第2期12卷 583-593页

作者： Yang Yang Hongli Tian Hongmei Yi Zi Shi Lu Wang Yaming Fan Fengge Wang Jiuran Zhao Beijing key laboratory of Maize DNA Fingerprinting and Molecular breeding Maize Research InstituteBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China

To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrimination,it is desirable to identify the optimal marker *** describe a marker combination screening model based on the genetic algorithm(GA)and implemented in a software tool,Loci ***-based variety discrimination power provided the largest optimization space among multiple fitness *** GA parameters,an increase in population size and generation number enlarged optimization depth but also calculation *** algorithm afforded the same optimization depth as GA but vastly increased calculation *** comparison with two other software tools,Loci Scan accommodated missing data,reduced calculation time,and offered more fitness *** large datasets,the sample size of training data exerted the strongest influence on calculation time,whereas the marker size of training data showed no effect,and target marker number had limited effect on analysis speed.

关键词： Plant variety discrimination genetic marker combination Variety discrimination power genetic algorithm

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Computational tools for plant genomics and breeding

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Science China(Life Sciences) 2024年第8期67卷 1579-1590页

作者： Hai Wang Mengjiao Chen Xin Wei Rui Xia Dong Pei Xuehui Huang Bin Han State key laboratory of Maize Bio-breeding Frontiers Science Center for Molecular Design BreedingJoint International Research Laboratory of Crop Molecular BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Sanya Institute of China Agricultural University Sanya 572025China Hainan Yazhou Bay Seed laboratory Sanya 572025China State key laboratory of Tree genetics and breeding Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091China Shanghai key laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China College of Horticulture South China Agricultural UniversityGuangzhou 510640China National Center for Gene Research CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200233China

Plant genomics and crop breeding are at the intersection of biotechnology and information *** by a combination of highthroughput sequencing,molecular biology and data science,great advances have been made in omics technologies at every step along the central dogma,especially in genome assembling,genome annotation,epigenomic profiling,and transcriptome *** advances further revolutionized three directions of *** is genetic dissection of complex traits in crops,along with genomic prediction and *** second is comparative genomics and evolution,which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant *** third direction is the development of deep learning approaches for the rational design of biological sequences,especially proteins,for synthetic *** three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.

关键词： bioinformatics plant genomics breeding by design

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genetic dissection and origin of pleiotropic loci underlying multilevel fiber quality traits in upland cotton(Gossypium hirsutum L.)

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Journal of Integrative Agriculture 2024年第10期23卷 3250-3263页

作者： Hongge Li Shurong Tang Zhen Peng Guoyong Fu Yinhua Jia Shoujun Wei Baojun Chen Muhammad Shahid Iqbal Shoupu He Xiongming Du Zhengzhou Research Base State Key Laboratory of Cotton Bio-breeding and Integrated Utilization/School of Agricultural SciencesZhengzhou UniversityZhengzhou 450001China State key laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research Chinese Academy of Agricultural SciencesAnyang 455000China

Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile ***,the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity,fineness,and neps,which in turn has impeded the genetic improvement and industrial utilization of cotton ***,12 single fiber quality traits were measured using Advanced Fiber Information System(AFIS)equipment among 383 accessions of upland cotton(Gossypium hirsutum L.).In addition,eight conventional fiber quality traits were assessed by the High Volume Instrument(HVI)***-wide association study(GWAS),linkage disequilibrium(LD)block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality *** a result,the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this *** importantly,three novel pleiotropic loci(FM_A03,FF_A05,and FN_A07)regulating fiber maturity,fineness and neps,respectively,were detected based on AFIS *** highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses,including the reported GhKRP6 for fiber length,the newly identified GhMAP8 for maturity and GhDFR for *** origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11,FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton *** findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in ***.

关键词： upland cotton single fiber quality pleiotropic loci candidate genes locus origin

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Single‑cell sequencing reveals the reproductive variations between primiparous and multiparous Hu ewes

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Journal of Animal Science and Biotechnology 2024年第2期15卷 614-631页

作者： Ting Ge Yifan Wen Bo Li Xiaoyu Huang Shaohua Jiang Enping Zhang key laboratory of Animal genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China

Background In the modern sheep production systems,the reproductive performance of ewes determines the economic profitability of *** the genetic mechanisms underlying differences in the litter size is important for the selection and breeding of highly prolific *** sheep,a high-quality Chinese sheep breed,is known for its high fecundity and is often used as a model to study prolificacy *** the current study,animals were divided into two groups according to their delivery rates in three consecutive lambing seasons(namely,the high and low reproductive groups with≥3 lambs and one lamb per season,n=3,respectively).The ewes were slaughtered within 12 h of estrus,and unilateral ovarian tissues were collected and analyzed by 10×Genomics single-cell RNA *** A total of 5 types of somatic cells were identified and corresponding expression profiles were mapped in the ovaries of each ***,the differences in the ovary somatic cell expression profiles between the high and low reproductive groups were mainly clustered in the granulosa ***,four granulosa cell subtypes were *** analysis revealed that the abundance of JPH1 expression and the reduction of LOC101112291 expression could lead to different evolutionary directions of the granulosa ***,the expression levels of FTH1 and FTL in mural granulosa cells of the highly reproductive group were significantly *** genes inhibit necroptosis and ferroptosis of mural granulosa cells,which helps prevent follicular *** This study provides insights into the molecular mechanisms underlying the high fecundity of Hu *** differences in gene expression profiles,particularly in the granulosa cells,suggest that these cells play a critical role in female *** findings also highlight the importance of genes such as JPH1,LOC101112291,FTH1,and FTL in regulating granulosa cell function and follicular development.

关键词： Granulosa cells Hu sheep Lambing number Ovarian somatic cells Single-cell RNA sequencing

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