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Genomic selection of eight fruit traits in pear

Horticultural Plant Journal 2024年第2期10卷 318-326页

作者： Manyi Sun Mingyue Zhang Satish Kumar Mengfan Qin Yueyuan Liu Runze Wang Kaijie Qi Shaoling Zhang Wenjing Chang Jiaming Li Jun Wu College of Horticulture State Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingJiangsu 210095China State key laboratory of crop biology College of Horticulture Science and EngineeringShandong Agricultural UniversityTai'anShandong 271018China The New Zealand institute for Plant and Food Research Limited Private Bag 1401Havelock North 4157New Zealand Zhongshan Biological Breeding laboratory NanjingJiangsu 210014China

Genomic selection (GS) has the potential to improve selection efficiency and shorten the breeding cycle in fruit tree breeding. In this study,we evaluated the effect of prediction methods, marker density and the training population (TP) size on pear GS for improving its performance and reducing cost. We evaluated GS under two scenarios:(1) five-fold cross-validation in an interspecific pear family;(2) independent validation. Based on the cross-validation scheme, the prediction accuracy (PA) of eight fruit traits varied between 0.33 (fruit core vertical diameter)and 0.65 (stone cell content). Except for single fruit weight, a slightly better prediction accuracy (PA) was observed for the five parametrical methods compared with the two non-parametrical methods. In our TP of 310 individuals, 2 000 single nucleotide polymorphism (SNP) markers were sufficient to make reasonably accurate predictions. PAs for different traits increased by 18.21%-46.98%when the TP size increased from 50to 100, but the increment was smaller (-4.13%-33.91%) when the TP size increased from 200 to 250. For independent validation, the PAs ranged from 0.11 to 0.45 using rrBLUP method. In summary, our results showed that the TP size and SNP numbers had a greater impact on the PA than prediction methods. Furthermore, relatedness among the training and validation sets, and the complexity of traits should be considered when designing a TP to predict the test panel.

关键词： Pear Pyrus Prediction method TP size SNP marker number

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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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Heterogeneous population distribution enhances resistance to wheat lodging by optimizing the light environment

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Journal of Integrative Agriculture 2024年第7期23卷 2211-2226页

作者： Yibo Hu Feng Qin Zhen Wu Xiaoqin Wang Xiaolong Ren Zhikuan Jia Zhenlin Wang Xiaoguang Chen Tie Cai College of Agronomy Northwest A&F UniversityYangling 712100China key laboratory of crop Physi-Ecology and Tillage science in Northwestern Loess Plateau Ministry of Agriculture and Rural AffairsNorthwest A&F UniversityYangling 712100China College of Agronomy Shandong Agricultural University/State Key Laboratory of Crop BiologyTai’an 271018China Xuzhou institute of Agricultural sciences in Jiangsu Xuhuai Area Xuzhou 221131China

Lodging is still the key factor that limits continuous increases in wheat yields today,because the mechanical strength of culms is reduced due to low-light stress in populations under high-yield *** mechanical properties of the culm are mainly determined by lignin,which is affected by the light ***,little is known about whether the light environment can be sufficiently improved by changing the population distribution to inhibit culm ***,in this study,we used the wheat cultivar“Xinong 979”to establish a low-density homogeneous distribution treatment(LD),high-density homogeneous distribution treatment(HD),and high-density heterogeneous distribution treatment(HD-h)to study the regulatory effects and mechanism responsible for differences in the lodging resistance of wheat culms under different population *** with LD,HD significantly reduced the light transmittance in the middle and basal layers of the canopy,the net photosynthetic rate in the middle and lower leaves of plants,the accumulation of lignin in the culm,and the breaking resistance of the culm,and thus the lodging index values increased significantly,with lodging rates of 67.5%in 2020–2021 and 59.3%in 2021–*** HD-h,the light transmittance and other indicators in the middle and basal canopy layers were significantly higher than those under HD,and the lodging index decreased to the point that no lodging *** with LD,the activities of phenylalanine ammonia-Lyase(PAL),4-coumarate:coenzyme A ligase(4CL),catechol-O-methyltransferase(COMT),and cinnamyl-alcohol dehydrogenase(CAD)in the lignin synthesis pathway were significantly reduced in the culms under HD during the critical period for culm formation,and the relative expression levels of TaPAL,Ta4CL,TaCOMT,and TaCAD were significantly ***,the activities of lignin synthesis-related enzymes and their gene expression levels were significantly increased under HD-h compare

关键词： canopy light environment lignin lodging population distribution wheat

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Identification of a von Willebrand factor type A protein affecting both grain and flag leaf morphologies in wheat

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science China(Life sciences) 2024年第10期67卷 2283-2286页

作者： Chunyun Zhou Hongchun Xiong Yong Jia Huijun Guo Meiyu Fu Yongdun Xie Linshu Zhao Jiayu Gu Huiyuan Li Yuting Li Peiyong Xin Jinfang Chu Chengdao Li Luxiang Liu State key laboratory of crop Gene Resources and Breeding/national Engineering laboratory of crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Western crop Genetics Alliance College of ScienceHealthEngineering and EducationMurdoch UniversityPerthWA 6150Australia national Centre for Plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of sciences Beijing 100049China

Dear Editor,The world faces unprecedented challenges for crop yield improvement to feed an expanding human population under limited agricultural resources and an increasingly erratic climate(Wheeler and von Braun,2013).Bread wheat is one of the most widely cultivated cereal crops,with both grain and flag leaf morphologies determining final yield potential(Xie et al.,2015;Zanella et al.,2023).Candidate genes affecting these traits are therefore highly desirable targets for breeding programs.

关键词： breeding crops cultivated

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Endomembrane-biased dimerization of ABCG16 and ABCG25 transporters determines their substrate selectivity in ABA-regulated plant growth and stress responses

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Molecular Plant 2024年第3期17卷 478-495页

作者： Yeling Zhou Yuzhu Wang Dong Zhang Jiansheng Liang institute of Plant and Food science Department of BiologySchool of Life SciencesSouthern University of Science and Technology(SUSTech)Shenzhen 518055China key laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education institutes Southern University of Science and Technology(SUSTech)Shenzhen 518055China jiangsu key laboratory of crop Genetics and Physiology/Co-lnnovation Center for Modern Production Technology of Grain crops Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhou 225009China

ATP-binding cassette(ABC)transporters are integral membrane proteins that have evolved diverse func-tions fulfilled via the transport of various *** Arabidopsis,the G subfamily of ABC proteins is particularly abundant and participates in multiple signaling pathways during plant development and stress *** this study,we revealed that two Arabidopsis ABCG transporters,ABCG16 and ABCG25,engage in ABA-mediated stress responses and early plant growth through endomembrane-specific dimerization-coupled transport of ABA and ABA-glucosyl ester(ABA-GE),*** first revealed that ABCG16 contributes to osmotic stress tolerance via ABA *** specifically,ABCG16 induces cellular ABA efflux in both yeast and plant *** FRET analysis,we showed that ABCG16 forms oblig-atory homodimers for ABA export activity and that the plasma membrane-resident ABCG16 homodimers specifically respond to ABA,undergoing notable conformational ***,we demonstrated that ABCG16 heterodimerizes with ABCG25 at the endoplasmic reticulum(ER)membrane and facilitates the ER entry of ABA-GE in both Arabidopsis and tobacco *** specific responsiveness of the ABCG16-ABCG25 heterodimer to ABA-GE and the superior growth of their double mutant support an inhib-itory role of these twoABCGs in early seedling establishment via regulation of ABA-GE translocation across the ER *** endomembrane-specific analysis of the FRET signals derived from the homo-or heterodimerized ABcG complexes allowed us to link endomembrane-biased dimerization to the transloca-tion of distinct substrates by ABcG transporters,providing a prototypic framework for understanding the omnipotence of ABcG transporters in plant development and stress responses.

关键词： abscisic acid ABCG transporter dimerization endomembrane substrate selectivity

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Synthesis of betanin by expression of the core betalain biosynthetic pathway in carrot

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Horticultural Plant Journal 2024年第3期10卷 732-742页

作者： Bo Wang Yahui Wang Yuanjie Deng Quanhong Yao Aisheng Xiong State key laboratory of crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjingJiangsu 210095China Shanghai key laboratory of Agricultural Genetics and Breeding Biotechnology Research Institute of Shanghai Academy of Agricultural ScienceShanghai 201106China

Betalain has received increased attention because of its high nutritional value and crucial physiological *** on the elucidation of its core biosynthetic pathway,betalain can be produced in additional plants by metabolic *** of betalain in carrot(Daucus carota L.)can improve its nutritional quality and economic value by extracting betalain from the fleshy root,non-edible part,and processing residue of *** this study,two different constructs,namely,pYB:mCD(AomelOS,BvCYP76AD1S,and BvDODA1S)and p YB:CDD(BvCYP76AD1S,BvDODA1S,and MjcDOPA5GTS),were introduced into carrot for betanin synthesis by Agrobacterium-mediated *** can be synthetized in both transgenic calli,and p YB:m CD-transgenic callus can be used to produce betacyanin by suspension ***,pYB:mCD-transgenic seedlings can synthetize betanin only by tyrosine *** p YB:CDD-transgenic lines can synthetize betanin in whole *** betanin content in fleshy root of pYB:CDD-transgenic carrot was(63.4±9)μg·g^(-1)fresh weight according to quantitative *** betanin-producing carrot plant materials can be used to synthesize betanin for industrial application or consumption as dietary sources.

关键词： Daucus carota L. Betanin Biosynthesis Metabolic engineering Biofortification

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lcQTH:Rapid quantitative trait mapping by tracing parental haplotypes with ultra-low-coverage sequencing

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Plant Communications 2024年第10期5卷 5-7页

作者： Wenxi Wang Zhe Chen Zhengzhao Yang Zihao Wang Jilu Liu Jie Liu Huiru Peng Zhenqi Su Zhongfu Ni Qixin Sun Weilong Guo Frontiers science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Dear Editor,Gene cloning has a fundamental role in crop research but has long been hindered by high costs and labor requirements,which have limited the numbers of genes that have been functionally characterized,especially in wheat(Liang et al.,2021).Quantitative trait locus(QTL)mapping is the first step in gene cloning,enabling the localization of genomic loci that show significant associations with quantitative *** commonly used strategy is based on single-nucleotide polymorphism(SNP)arrays(Sun et al.,2020).

关键词： trait mapping parental

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Genetic variation in a heat shock transcription factor modulates cold tolerance in maize

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Molecular Plant 2024年第9期17卷 1423-1438页

作者： Lei Gao Lingling Pan Yiting Shi Rong Zeng Minze Li Zhuoyang Li Xuan Zhang Xiaoming Zhao Xinru Gong Wei Huang Xiaohong Yang Jinsheng Lai Jianru Zuo Zhizhong Gong Xiqing Wang Weiwei Jin Zhaobin Dong Shuhua Yang State key laboratory of Plant Environmental Resilience Frontiers Science Center for Molecular Design BreedingCollege of Biological SciencesCenter for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijing 100193China State key laboratory of Maize Bio-breeding National Maize Improvement CenterFrontiers Science Center for Molecular Design BreedingDepartment of Plant Geneticsand BreedingChinaAgricultural UniversityBeijingChina State key laboratory of Plant Genomics and national Plant Gene Research Center Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China

Understanding how maize(Zea mays)responds to cold stress is crucial for facilitating breeding programs of cold-tolerant *** extensive utilization of the genome-wide association study(GWAs)approach for exploring favorable natural alleles associated with maize cold tolerance,few studies have successfully identified candidate genes that contribute to maize cold *** this study,we used a diverse panel of inbred maize lines collected from different germplasm sources to perform a GWAS on var-iations in the relative injured area of maize true leaves during cold stress-a trait very closely correlated with maize cold *** identified HsF21,which encodes a B-class heat shock transcription factor(HSF)that positively regulates cold tolerance at both the seedling and germination *** varia-tions in the promoter of the cold-tolerant HSF21Hap1 allele led to increased HSF21 expression under cold stress by inhibiting binding of the basic leucine zipper bziP68 transcription factor,a negative regulator of cold *** integrating transcriptome deep sequencing,DNA affinity purification sequencing,and targeted lipidomic analysis,we revealed the function of HsF21 in regulating lipid metabolism homeo-stasis to modulate cold tolerance in *** addition,we found that HsF21 confers maize cold tolerance without incurring yield ***,this study establishes HsF21 as a key regulator that en-hances cold tolerance in maize,providing valuable genetic resources for breeding of cold-tolerant maize varieties.

关键词： heat shock factor HSF21 cold tolerance natural variation bZiP68 lipid metabolism maize

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The response of roots and the rhizosphere environment to integrative cultivation practices in paddy rice

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Journal of Integrative Agriculture 2024年第6期23卷 1879-1896页

作者： Hanzhu Gu Xian Wang Minhao Zhang Wenjiang Jing Hao Wu Zhilin Xiao Weiyang Zhang Junfei Gu Lijun Liu Zhiqin Wang Jianhua Zhang Jianchang Yang Hao Zhang Jiangsu key laboratory of crop Genetics and Physiology/Jiangsu key laboratory of crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops/Agricultural College Yangzhou UniversityYangzhou 225009China Taizhou institute of Agricultural science Jiangsu Academy of Agricultural SciencesTaizhou 225300China State key laboratory of Agrobiotechnology School of Life SciencesThe Chinese University of Hong KongShatinHong Kong 999077China Department of biology Faculty of ScienceHong Kong Baptist UniversityKowloonHong Kong 999077China

Integrative cultivation practices(ICPs)are essential for enhancing cereal yield and resource use ***,the effects of ICP on the rhizosphere environment and roots of paddy rice are still poorly *** this study,four rice varieties were produced in the *** variety was treated with six different cultivation techniques,including zero nitrogen application(0 N),local farmers’practice(LFP),nitrogen reduction(NR),and three progressive ICP techniques comprised of enhanced fertilizer N practice and increased plant density(ICP1),a treatment similar to ICP1 but with alternate wetting and moderate drying instead of continuous flooding(ICP2),and the same practices as ICP2 with the application of organic fertilizer(ICP3).The ICPs had greater grain production and nitrogen use efficiency than the other three *** length,dry weight,root diameter,activity of root oxidation,root bleeding rate,zeatin and zeatin riboside compositions,and total organic acids in root exudates were elevated with the introduction of the successive cultivation *** enhanced nitrate nitrogen,the activities of urease and invertase,and the diversity of microbes(bacteria)in rhizosphere and non-rhizosphere soil,while reducing the ammonium nitrogen *** nutrient contents(ammonium nitrogen,total nitrogen,total potassium,total phosphorus,nitrate,and available phosphorus)and urease activity in rhizosphere soil were reduced in all treatments in comparison with the non-rhizosphere soil,but the invertase activity and bacterial diversity were *** main root morphology and physiology,and the ammonium nitrogen contents in rhizosphere soil at the primary stages were closely correlated with grain yield and internal nitrogen use *** findings suggest that the coordinated enhancement of the root system and the environment of the rhizosphere under integrative cultivation approaches may lead to higher rice production.

关键词： rice(Oryza sativa L.) nitrogen use efficiency grain yield integrative cultivation practices roots

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Constructing the metabolic network of wheat kernels based on structure-guided chemical modification and multi-omics data

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Journal of Genetics and Genomics 2024年第7期51卷 714-722页

作者： Zhitao Tian Jingqi Jia Bo Yin Wei Chen national key laboratory of crop Genetic Improvement and national Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhanHubei 430070China Hubei Hongshan laboratory WuhanHubei 430070China

Metabolic network construction plays a pivotal role in unraveling the regulatory mechanism of biological activities,although it often proves to be challenging and labor-intensive,particularly with non-model *** this study,we develop a computational approach that employs reaction models based on the structure-guided chemical modification and related compounds to construct a metabolic network in *** construction results in a comprehensive structure-guided network,including 625 identified metabolites and additional 333 putative reactions compared with the Kyoto Encyclopedia of Genes and Genomes *** a combination of gene annotation,reaction classification,structure similarity,and correlations from transcriptome and metabolome analysis,a total of 229 potential genes related to these reactions are identified within this *** validate the network,the functionality of a hydroxycinnamoyltransferase(TraesCS3D01G314900)for the synthesis of polyphenols and a rhamnosyltransferase(TraesCS2D01G078700)for the modification of flavonoids are verified through in vitro enzymatic studies and wheat mutant tests,*** research thus supports the utility of structure-guided chemical modification as an effective tool in identifying causal candidate genes for constructing metabolic networks and further in metabolomic genetic studies.

关键词： Metabolic network Chemical modification Genetic study Wheat kernel Multi-omics

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