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Breeding by selective introgression: Theory, practices, and lessons learned from rice

The Crop Journal 2021年第3期9卷 646-657页

作者： Fan Zhang Yingyao Shi Jauhar Ali Jianlong Xu zhikang li Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China College of Agronomy Anhui Agricultural UniversityHefei 230036AnhuiChina Rice Breeding Platform International Rice Research Institute(IRRI)Los BañosLaguna 4031Philippines Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Instituteat ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120GuangdongChina

Future demands for increased productivity and resilience to abiotic/biotic stresses of major crops require new technologies of breeding by design(BBD)built on massive information from functional and population genomics research.A novel strategy of breeding by selective introgression(BBSI)has been proposed and practiced for simultaneous improvement,genetic dissection and allele mining of complex traits to realize *** has three phases:a)developing large numbers of trait-specific introgression lines(ILs)using backcross breeding in elite genetic backgrounds as the material platform of BBD;b)efficiently identifying genes or quantitative trait loci(QTL)and mining desirable alleles affecting different target traits from diverse donors as the information platform of BBD;and c)developing superior cultivars by BBD using designed QTL pyramiding or marker-assisted recurrent ***(a)has been implemented massively in rice by many Chinese research institutions and IRRI,resulting in the development of many new green super rice cultivars plus large numbers of ILs in 30+elite genetic ***(b)has been demonstrated in a series of proof-of-concept studies of high-efficiency genetic dissection of rice yield and tolerance to abiotic stresses using ILs and DNA ***(c)has also been implemented by designed QTL pyramiding,resulting in a prototype of BBD in several successful *** BBSI strategy can be easily extended for simultaneous trait improvement,efficient gene and QTL discovery and allele mining of complex traits using advanced breeding lines from crosses between a common"backbone"parent and a set of elite parents in conventional pedigree breeding *** can be relatively easily adopted by breeding programs with small budgets,but the BBSI-based BBD strategy can be fully and more efficiently implemented by large seed companies with sufficient capacity.

关键词： Backcross Trait-specific introgression line Breeding by selective introgression Designed QTL pyramiding

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The landscape of gene-CDS-haplotype diversity in rice:Properties,population organization,footprints of domestication and breeding,and implications for genetic improvement

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Molecular Plant 2021年第5期14卷 787-804页

作者： Fan Zhang Chunchao Wang Min li Yanru Cui Yingyao Shi Zhichao Wu Zhiqiang Hu Wensheng Wang Jianlong Xu zhikang li nstitute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing100081.China College of Agronomy Anhui Agricultural UniversityHefeiAnhui230036China College of Agronomy Hebei Agricultural UniversityBaodingHebei071001China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong518120China Department of Plant and Microbial Biology University of CaliforniaBerkeleyCA94720USA

Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of *** characterized the gene-coding sequence-haplotype(gcHap)diversity of 45963 rice genes in 3010 rice *** an average of 226±390 gcHaps per gene in rice populations,rice genes could be classified into three main categories:12865 conserved genes,10254 subspecific differentiating genes,and 22844 remaining *** found that 39218 rice genes carry>255179 major gcHaps of potential functional ***(87.5%)of the detected gcHaps were specific to subspecies or *** inferred proto-ancestors of local landrace populations reconstructed from conserved predominant(ancient)gcHaps correlated strongly with wild rice accessions from the same geographic regions,supporting a multiorigin(domestication)model of Oryza *** breeding efforts generally increased the gcHap diversity of modern varieties and'caused significant frequency shifts in predominant gcHaps of 14266 genes due to independent selection in the two *** frequencies of“favorable”gcHaps at most known genes related to rice yield in modern varieties suggest huge potential for rice improvement by mining and pyramiding of favorable *** gcHap data were demonstrated to have greater power than SNPs for the detection of causal genes that affect complex *** rice gcHap diversity dataset generated in this study would facilitate rice basic research and improvement in the future.

关键词： gene-CDS-haplotype diversity functional alleles genome-wide selection signals evolution

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The Power of Inbreeding： NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication

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Molecular Plant 2016年第7期9卷 975-985页

作者： Hongru Wang Xun Xu Filipe Garrett Vieira Yunhua Xiao zhikang li Jun Wang Rasmus Nielsen Chengcai Chu State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing) Institute of Genetics and Developmental Biology Chinese Academyof Sciences Beijing 100101 China Cotlege of life Sciences University of Chinese Academy of Sciences Beijing 100101 China BGI-Shenzhen Shenzhen 518083 China Centre for GeoGenetics University of Copenhagen 1350 Copenhagen Denmark Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement Chinese Academy of Agricultural Sciences 12 SouthZhong-Guan-Cun Street Beijing 100081 China Department of Integrative Biology University of California Berkeley CA 94720 USA These authors contributed equally to this article.

Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in hu- mans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice （Oryza sativa L.）, which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5~ and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SN Ps in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice,japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.

关键词： inbreeding GWAS rice pericarp color

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Developing green super rice varieties with high nutrient use efficiency by phenotypic selection under varied nutrient conditions

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The Crop Journal 2019年第3期7卷 368-377页

作者： Zilhas Ahmed Jewel Jauhar Ali Yunlong Pang Anumalla Mahender Bart Acero Jose Hernandez Jianlong Xu zhikang li Rice Breeding Platform International Rice Research Institute (IRRI)Los BanosLaguna 4031Philippines Institute of Crop Sciences Chinese Academy of Agricultural ScienceBeijing 100081China Institute of Crop Science College of Agriculture and Food ScienceUniversity of the PhilippinesLos BanosLaguna 4031Philippines

The development of green super rice varieties with improved nutrient use efficiency(NuUE)is a vital target area to increase yield and make it more stable under rainfed *** the present study, we followed an early backcross(BC) breeding approach by using a highyielding and widely adapted Xian variety, Weed Tolerant Rice 1(WTR-1), as a recipient and a Geng variety, Hao-An-Nong(HAN), as a *** from the BC1F2 generation, the BC population went through one generation of selection under irrigated, low-input, and rainfed conditions, followed by four consecutive generations of screening and selection for high grain yield(GY) under six different nutrient conditions(NPK, 75 N,-N,-P,-NP, and-NPK), leading to the development of 230 BC1F6 introgression lines(ILs).These 230 ILs were evaluated under the same six nutrient conditions for 13 agro-morphological and grain yield component traits in comparison to four checks and *** trait variations were observed between the treatments and *** correlations were identified for GY with biomass, panicle length, flag-leaf area, flag-leaf width, filled grain number per panicle,1000-grain weight, and tiller number under-N,-P,-NP, and-NPK *** of 230 ILs,12 were identified as promising under two or more nutrient deficiency *** results demonstrated an efficient inter-subspecific BC breeding procedure with a first round of selection under rainfed-drought conditions, followed by four generations of progeny testing for yield performance under six nutrient *** promising ILs can be useful resources for molecular genetic dissection and understanding the physiological mechanisms of NuUE.

关键词： Nutrient use efficiency Grain yield Nitrogen Phosphorus Green super rice

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Fabrication and characterization of high-sensitivity,wide-range,and flexible MEMS thermal flow velocity sensors

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Microsystems & Nanoengineering 2024年第4期10卷 139-151页

作者： Min li Guangzhao Qin Chen Jia Danyu Zhang zhikang li Xiangguang Han Shusheng Xu libo Zhao Guoxi Luo Cunlang liu Ping Yang Qijing lin State Key Laboratory for Manufacturing Systems Engineering International Joint Laboratory for Micro/Nano Manufacturing and Measurement TechnologiesXi’an Jiaotong University(Yantai)Research Institute for Intelligent Sensing Technology and SystemXi’an Jiaotong UniversityXi’an 710049China School of Instrument Science and Technology Xi’an Jiaotong UniversityXi’an 710049China Shandong Laboratory of Advanced Materials and Green Manufacturing at Yantai Yantai 264000China Brightstone Innovation(Yantai)Research Institute for Micronano Sensing Technology Yantai 264006China Xi’an Jingwei Sensing Technology Co. Ltd.Xi’an 712000China

With the rapid development of various fields,including aerospace,industrial measurement and control,and medical monitoring,the need to quantify flow velocity measurements is *** is difficult for traditional flow velocity sensors to fulfill accuracy requirements for velocity measurements due to their small ranges,susceptibility to environmental impacts,and ***,to optimize sensor performance,a flexible microelectromechanical system(MEMS)thermal flow sensor is proposed that combines the working principles of thermal loss and thermal temperature difference and utilizes a flexible cavity substrate made of a low-thermal-conductivity polyimide/SiO_(2)(PI/SiO_(2))composite porous film to broaden the measurement range and improve the *** measurement results show that the maximum measurable flow velocity can reach 30 m/s with a resolution of 5.4mm/*** average sensitivities of the sensor are 59.49 mV/(m s−1)in the medium-to-low wind velocity range of 0–2 m/s and 467.31 mV/(m s^(−1))in the wind velocity range of 2–30 m/*** sensor proposed in this work can enable new applications of flexible flow sensors and wearable devices.

关键词： flow thermal utilize

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The basic helix-loop-helix transcription factor gene,OsbHLH38,plays a key role in controlling rice salt tolerance

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Journal of Integrative Plant Biology 2023年第8期65卷 1859-1873页

作者： Fengping Du Yinxiao Wang Juan Wang Yingbo li Yue Zhang Xiuqin Zhao Jianlong Xu zhikang li Tianyong Zhao Wensheng Wang Binying Fu Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding Chinese Academy of Agricultural SciencesBeijing100081China State Key Laboratory of Crop Stress Biology for Arid Areas College of Life SciencesNorthwest A&F UniversityYangling 712100China Anhui Agricultural University Hefei 230036China Hainan Yazhou Bay Seed Lab/National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China

The plant hormone abscisic acid(ABA)is crucial for plant seed germination and abiotic stress ***,the association between ABA sensitivity and plant abiotic stress tolerance remains largely *** this study,436 rice accessions were assessed for their sensitivity to ABA during seed *** considerable diversity in ABA sensitivity among rice germplasm accessions was primarily reflected by the differentiation between the Xian(indica)and Geng(japonica)subspecies and between the upland-Geng and lowland-Geng *** upland-Geng accessions were most sensitive to ***-wide association analyses identified four major quantitative trait loci containing21 candidate genes associated with ABA sensitivity of which a basic helix-loop-helix transcription factor gene,OsbHLH38,was the most important for ABA *** functional analyses using knockout and overexpression transgenic lines revealed that OsbHLH38 expression was responsive to multiple abiotic *** of OsbHLH38 increased seedling salt tolerance,while knockout of OsbHLH38 increased sensitivity to salt stress.A salt-responsive transcription factor,OsDREB2A,interacted with OsbHLH38 and was directly regulated by ***,OsbHLH38 affected rice abiotic stress tolerance by mediating the expression of a large set of transporter genes of phytohormones,transcription factor genes,and many downstream genes with diverse functions,including photosynthesis,redox homeostasis,and abiotic stress *** results demonstrated that OsbHLH38 is a key regulator in plant abiotic stress tolerance.

关键词： abscisic acid genome-wide association analysis rice salttolerance seedgermination

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Noninvasive fluid bubble detection based on capacitive micromachined ultrasonic transducers

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Microsystems & Nanoengineering 2023年第1期9卷 115-126页

作者： Jiawei Yuan zhikang li Qi Ma Jie li Zixuan li Yihe Zhao Shaohui Qin Xuan Shi libo Zhao Ping Yang Guoxi Luo Xiaozhang Wang Kwok Siong Teh Zhuangde Jiang State Key Laboratory for Manufacturing Systems Engineering International Joint Laboratory for Micro/Nano Manufacturing and Measurement TechnologiesXi’an Jiaotong University(Yantai)Research Institute for Intelligent Sensing Technology and SystemsXi’an Jiaotong University710049Xi’anChina School of Mechanical Engineering Xi’an Jiaotong University710049Xi’anChina Shandong Laboratory of Yantai Advanced Materials and Green Manufacturing 265503YantaiChina School of Mechanical and Electrical Engineering Shaanxi University of Science and TechnologyXi’an710049Xi’anChina School of Engineering San Francisco State UniversitySan FranciscoCA94132USA

Ultrasonic fluid bubble detection is important in industrial controls,aerospace systems and clinical medicine because it can prevent fatal mechanical failures and threats to ***,current ultrasonic technologies for bubble detection are based on conventional bulk PZT-based transducers,which suffer from large size,high power consumption and poor integration with ICs and thus are unable to implement real-time and long-term monitoring in tight physical spaces,such as in extracorporeal membrane oxygenation(ECMO)systems and dialysis machines or hydraulic systems in *** work highlights the prospect of capacitive micromachined ultrasonic transducers(CMUTs)in the aforementioned application situations based on the mechanism of received voltage variation caused by bubble-induced acoustic energy *** corresponding theories are established and well validated using finite element *** fluid bubbles inside a pipe with a diameter as small as 8 mm are successfully measured using our fabricated CMUT chips with a resonant frequency of 1.1 *** received voltage variation increases significantly with increasing bubble radii in the range of 0.5–2.5 *** studies show that other factors,such as bubble positions,flow velocities,fluid medium types,pipe thicknesses and diameters,have negligible effects on fluid bubble measurement,demonstrating the feasibility and robustness of the CMUT-based ultrasonic bubble detection technique.

关键词： bubble negligible mentioned

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An integrated micromachined flexible ultrasonicinductive sensor for pipe contaminant multiparameter detection

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Microsystems & Nanoengineering 2024年第4期10卷 271-283页

作者： Zheng Yuan Xiaoyu Wu zhikang li Jiawei Yuan Yihe Zhao Zixuan li Shaohui Qin Qi Ma Xuan Shi Zilong Zhao Jiazhu li Shiwang Zhang Weixuan Jing Xiaozhang Wang libo Zhao State Key Laboratory for Manufacturing Systems Engineering International Joint Laboratory for Micro/Nano Manufacturing and Measurement TechnologiesXi’an Jiaotong University(Yantai)Research Institute for Intelligent Sensing Technology and SystemXi’an Jiaotong UniversityXi’an 710049China School of Mechanical Engineering Xi’an Jiaotong UniversityXi’an 710049China School of Instrument Science and Technology Xi’an Jiaotong UniversityXi’an 710049China Shandong Laboratory of Yantai Advanced Materials and Green Manufacturing Yantai 265503China

Pipe contaminant detection holds considerable importance within various industries,such as the aviation,maritime,medicine,and other pertinent *** capability is beneficial for forecasting equipment potential failures,ascertaining operational situations,timely maintenance,and lifespan ***,the majority of existing methods operate offline,and the detectable parameters online are relatively *** constraint hampers real-time on-site detection and comprehensive assessments of equipment *** address these challenges,this paper proposes a sensing method that integrates an ultrasonic unit and an electromagnetic inductive unit for the real-time detection of diverse contaminants and flow rates within a *** ultrasonic unit comprises a flexible transducer patch fabricated through micromachining technology,which can not only make installation easier but also focus the sound ***,the sensing unit incorporates three symmetrical solenoid *** a comprehensive analysis of ultrasonic and induction signals,the proposed method can be used to effectively discriminate magnetic metal particles(e.g.,iron),nonmagnetic metal particles(e.g.,copper),nonmetallic particles(e.g.,ceramics),and *** inclusive categorization encompasses nearly all types of contaminants that may be present in a ***,the fluid velocity can be determined through the ultrasonic Doppler frequency *** efficacy of the proposed detection principle has been validated by mathematical models and finite element *** contaminants with diverse velocities were systematically tested within a 14mm diameter *** experimental results demonstrate that the proposed sensor can effectively detect contaminants within the 0.5−3mm range,accurately distinguish contaminant types,and measure flow velocity.

关键词： inductive holds ultrasonic

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Selection efficiencies for improving drought/salt tolerances and yield using introgression breeding in rice(Oryza sativa L.)

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The Crop Journal 2013年第2期1卷 134-142页

作者： Ying Wang Lubiao Zhang Afif Nafisah linghua Zhu Jianlong Xu zhikang li Institute of Crop Science The National Facility for Crop Gene Resources and Genetic Improvement Chinese Academy of Agricultural Sciences

The backcross(BC) breeding strategy has been increasingly used for developing high yielding varieties with improved abiotic stress tolerances in rice. In this study, 189Huang-Hua-Zhan(HHZ) introgression lines(ILs) developed from three different selection schemes were evaluated for yield related traits under drought stress and non-stress conditions in the target and off-season winter nursery environments to assess the selection efficiency of BC breeding for improving different complex traits, and led us to five important results. The first result indicated that the primary target traits should be selected first in the target environments(TEs) in order to achieve the maximum genetic gain. Secondly, BC breeding for drought tolerance(DT) in rice was almost equally effective by strong phenotypic selection in the main target environments and in the winter-season of ***, exploiting genetic diversity in the subspecific gene pools is of great importance for future genetic improvement of complex traits in rice. Fourthly, considerable genetic gain can be effectively achieved by selection for secondary target traits among the ILs with the primary traits. Finally, the developed ILs provide useful materials for future genetic/genomic dissection and molecular breeding of complex traits.

关键词： Backcross breeding High yield Drought tolerance Salt tolerance Selection efficiency

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Dominant early heading without yield drag in a sister-line BC breeding progeny DEH_229 is controlled by multiple genetic factors with maineffect loci

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The Crop Journal 2021年第2期9卷 400-411页

作者： Muhiuddin Faruquee Qiang Zhang Lubiao Zhang linyun Xu Wensheng Wang Jiansan Chen Jianlong Xu zhikang li Binying Fu Tianqing Zheng Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement Chinese Academy of Agricultural SciencesBeijing 100081China Shenzhen Institute of Breeding&Innovation Chinese Academy of Agricultural SciencesShenzhen 518120GuangdongChina Institute of Rice Research Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

Dominant early heading(DEH)in rice(Oryza sativa L.)is of interest in both breeding and *** genetic mechanisms underlying DEH have remained largely *** have developed a near-isogenic DEH line without yield drag named DEH_229 by sister-line backcross(BC)breeding with MH63,a restorer,as the genetic *** conducted a pilot genetic investigation under both short-day(SD)and long-day(LD)*** DEH line harbored only 1.06%variation in the genome sequence relative to *** variants were distributed throughout the *** QTL mapping by sequencing(QTL-seq)on an F_(2) population derived from a cross of MH63×DEH_229,57 loci were detected under the SD *** mapping employing a genome-wide association study with accessions from the 3000 rice genome sequencing project(3K-RG),reduced the number of QTL by 43.9%.Using Rice Functional Genomics&Breeding(RFGB)database,the number of SNP cluster regions within the QTL regions reduced by 27.3%.Further comparison of the genome variation between DEH_229 and MH63 in addition to gene annotation information revealed a new DEH allele of DTH3 with multiple variable sites as a possible major factor underlying the early-heading phenotype of DEH_*** InDel marker,ZMEH_1,was designed based on the variation between DEH_229 and MH63 within this *** accounted for 86.0%of heading date variation under both SD and LD conditions in 109 randomly chosen progeny derived from extreme lines of the MH63×DEH_229 *** study reveals the genetic complexity of DEH in the near-isogenic line and may provide useful material and marker information for plant molecular breeding.

关键词： Dominant early heading Yield drag Sister-line BC breeding Multiple genetic factors Cryptic genetic variation(CGV) Rice(Oryza sativa L.)

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