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A novel Effective Panicle Number per Plant 4 haplotype enhances grain yield by coordinating panicle number and grain number in rice
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作者 Yun Wang Xiaoqian Wang +6 位作者 Laiyuan Zhai Sundus Zafar Congcong Shen Shuangbing Zhu Kai Chen Yun Wang jianlong xu 《The Crop Journal》 SCIE CSCD 2024年第1期202-212,共11页
Increasing effective panicle number per plant(EPN)is one approach to increase yield potential in rice.However,molecular mechanisms underlying EPN remain unclear.In this study,we integrated mapbased cloning and genome-... Increasing effective panicle number per plant(EPN)is one approach to increase yield potential in rice.However,molecular mechanisms underlying EPN remain unclear.In this study,we integrated mapbased cloning and genome-wide association analysis to identify the EPN4 gene,which is allelic to NARROW LEAF1(NAL1).Overexpression lines containing the Teqing allele(TQ)of EPN4 had significantly increased EPN.NIL-EPN4^(TQ) in japonica(geng)cultivar Lemont(LT)exhibited significantly improved EPN but decreased grain number and flag leaf size relative to LT.Haplotype analysis indicated that accessions with EPN4-1 had medium EPN,medium grain number,and medium grain weight,but had the highest grain yield among seven haplotypes,indicating that EPN4-1 is an elite haplotype of EPN4 for positive coordination of the three components of grain yield.Furthermore,accessions carrying the combination of EPN4-1 and haplotype GNP1-6 of GNP1 for grain number per panicle showed higher grain yield than those with other allele combinations.Therefore,pyramiding of EPN4-1 and GNP1-6 could be a preferred approach to obtain high yield potential in breeding. 展开更多
关键词 RICE Effective panicle number per plant Grain number per panicle HAPLOTYPE Grain yield potential
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A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance 被引量:3
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作者 Yixue Bao Ziyan Zeng +9 位作者 Wei Yao Xiao Chen Mengwei Jiang Akbar Sehrish Bo Wu Charles A.Powell Baoshan Chen jianlong xu Xingtan Zhang Muqing Zhang 《Horticulture Research》 SCIE CSCD 2023年第4期13-22,共10页
The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and ha... The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing,Oxford Nanopore 50-kb ultra-long,and high-throughput chromatin conformation capture technologies.The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps,while a total of 633.0 Mb genomic sequences were generated.The origination analysis identified 338.5Mb genomic sequences originating from citron(53.5%),147.4Mb frommandarin(23.3%),and 147.1Mb frompummelo(23.2%).The genome included 30528 protein-coding genes,and most of the assembled sequences were found to be repetitive sequences.Several significantly expanded gene families were associated with plant-pathogen interactions,plant hormone signal transduction,and the biosynthesis of major active components,such as terpenoids and f lavor compounds.Most HLB-tolerant genes were expanded in the lemon genome,such as 2-oxoglutarate(2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1,cell wall-related genes,and lignin synthesis genes.Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon.Our results provide insight into lemon genome evolution,active component biosynthesis,and genes associated with HLB tolerance. 展开更多
关键词 SYNTHESIS insight RESOLVED
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Rice3K56 is a high-quality SNP array for genome-based genetic studies and breeding in rice(Oryza sativa L.) 被引量:1
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作者 Chaopu Zhang Min Li +14 位作者 Lunping Liang Jun Xiang Fan Zhang Chenyang Zhang Yizhen Li Jing Liang Tianqing Zheng Fanlin Zhang Hua Li Binying Fu Yingyao Shi jianlong xu Bingchuan Tian Zhikang Li Wensheng Wang 《The Crop Journal》 SCIE CSCD 2023年第3期800-807,共8页
Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-d... Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide,which was then tested extensively in 192 representative rice samples.Printed on the Gene Titan chips of Affymetrix Axiom each containing 56,606 SNP markers,the Rice3K56 array has a high genotyping reliability(99.6%),high and uniform genome coverage(an average of 6.7-kb between adjacent SNPs),abundant polymorphic information and easy automation,compared with previously developed rice SNP arrays.When applied in rice varietal differentiation,population diversity analysis,gene mapping of 13 complex traits by a genome-wide association study analysis(GWAS),and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations,these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding. 展开更多
关键词 Rice3K56 SNP array GENOTYPING Genetic analysis Molecular breeding
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Molecular mechanisms of salinity tolerance in rice 被引量:17
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作者 Tianxiao Chen Sergey Shabala +7 位作者 Yanan Niu Zhong-Hua Chen Lana Shabala Holger Meinke Gayatri Venkataraman Ashwani Pareek jianlong xu Meixue Zhou 《The Crop Journal》 SCIE CSCD 2021年第3期506-520,共15页
Salinity is one of the major abiotic stresses which impose constraints to plant growth and production.Rice(Oryza sativa L.)is one of the most important staple food crops and a model monocot plant.Its production is exp... Salinity is one of the major abiotic stresses which impose constraints to plant growth and production.Rice(Oryza sativa L.)is one of the most important staple food crops and a model monocot plant.Its production is expanding into regions that are affected by soil salinity,requiring cultivars more tolerant to saline conditions.Understanding the molecular mechanisms of such tolerance could lay a foundation for varietal improvement of salt tolerance in rice.In spite of extensive studies exploring the mechanism of salt tolerance,there has been limited progress in breeding for increased salinity tolerance.In this review,we summarize the information about the major molecular mechanisms underlying salinity tolerance in rice and further discuss the limitations in breeding for salinity tolerance.We show that numerous gene families and interaction networks are involved in the regulation of rice responses to salinity,prompting a need for a comprehensive functional analysis.We also show that most studies are based on whole-plant level analyses with only a few reports focused on tissue-and/or cell-specific gene expression.More details of salt-responsive channel and transporter activities at tissue-and cell-specific level still need to be documented before these traits can be incorporated into elite rice germplasm.Thus,future studies should focus on diversity of available genetic resources and,particular,wild rice relatives,to reincorporate salinity tolerance traits lost during domestication. 展开更多
关键词 Oryza sativa L. Reactive oxygen species(ROS) Stomatal regulation Membrane transporters Osmotic adjustment Gene network CROSSTALK
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Genetic bases of source-,sink-,and yield-related traits revealed by genome-wide association study in Xian rice 被引量:10
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作者 Yun Wang Yunlong Pang +4 位作者 Kai Chen Laiyuan Zhai Congcong Shen Shu Wang jianlong xu 《The Crop Journal》 SCIE CAS CSCD 2020年第1期119-131,共13页
The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative... The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection. 展开更多
关键词 RICE GWAS Source–sink relationship Quantitative trait loci/locus(QTL) Candidate gene
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Breeding by design for future rice:Genes and genome technologies 被引量:12
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作者 jianlong xu Yongzhong Xing +1 位作者 Yunbi xu Jianmin Wan 《The Crop Journal》 SCIE CSCD 2021年第3期491-496,共6页
1.Introduction Rice is a staple food for 3.2 billion people.The food security threat that shook many Asian countries in 2008 still looms,because farmers are facing the challenge of producing more rice with fewer resou... 1.Introduction Rice is a staple food for 3.2 billion people.The food security threat that shook many Asian countries in 2008 still looms,because farmers are facing the challenge of producing more rice with fewer resources of water,land,and inputs. 展开更多
关键词 BREEDING THREAT producing
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Genetic dissection of rice appearance quality and cooked rice elongation by genome-wide association study 被引量:6
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作者 Xianjin Qiu Jing Yang +6 位作者 Fan Zhang Yanan Niu Xiuqing Zhao Congcong Shen Kai Chen Sheng Teng jianlong xu 《The Crop Journal》 SCIE CSCD 2021年第6期1470-1480,共11页
Appearance and cooked rice elongation are key quality traits of rice. Although some QTL for these traits have been identified, understanding of the genetic relationship between them remains limited. In the present stu... Appearance and cooked rice elongation are key quality traits of rice. Although some QTL for these traits have been identified, understanding of the genetic relationship between them remains limited. In the present study, large phenotypic variation was observed in 760 accessions from the 3 K Rice Genomes Project for both appearance quality and cooked rice elongation. Most component traits of appearance quality and cooked rice elongation showed significant pairwise correlations, but a low correlation was found between appearance quality and cooked rice elongation. A genome-wide association study identified 74 QTL distributed on all 12 chromosomes for grain length, grain width, length to width ratio, degree of endosperm with chalkiness, rice elongation difference, and elongation index. Thirteen regions containing QTL stably expressed in multiple environments and/or exerting pleiotropic effects on multiple traits were detected. By gene-based association analysis and haplotype analysis, 46 candidate genes, including five cloned genes, and 49 favorable alleles were identified for these 13 QTL. The effect of the candidate gene Wx on rice elongation difference was validated by a transgenic strategy. These results shed light on the genetic bases of appearance quality and cooked rice elongation and provide gene resources for improving rice quality by molecular breeding. 展开更多
关键词 Appearance quality Cooked rice elongation Genome-wide association study Candidate gene Favorable allele Quantitative trait locus/loci(QTL)
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Breeding by selective introgression: Theory, practices, and lessons learned from rice 被引量:4
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作者 Fan Zhang Yingyao Shi +2 位作者 Jauhar Ali jianlong xu Zhikang Li 《The Crop Journal》 SCIE CSCD 2021年第3期646-657,共12页
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 genomic... 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 BBD.BBSI 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 selection.Phase(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 backgrounds.Phase(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 markers.Phase(c)has also been implemented by designed QTL pyramiding,resulting in a prototype of BBD in several successful cases.The 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 programs.BBSI 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. 展开更多
关键词 BACKCROSS Trait-specific introgression line Breeding by selective introgression Designed QTL pyramiding
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Selection efficiencies for improving drought/salt tolerances and yield using introgression breeding in rice(Oryza sativa L.) 被引量:2
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作者 Ying Wang Lubiao Zhang +3 位作者 Afif Nafisah Linghua Zhu jianlong xu Zhikang Li 《The Crop Journal》 SCIE CAS 2013年第2期134-142,共9页
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) dev... 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 Hainan.Thirdly, 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. 展开更多
关键词 BACKCROSS BREEDING High YIELD DROUGHT TOLERANCE Salt TOLERANCE SELECTION efficiency
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QTL underlying iron and zinc toxicity tolerances at seedling stage revealed by two sets of reciprocal introgression populations of rice(Oryza sativa L.) 被引量:1
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作者 Huan Liu Aijaz Soomro +6 位作者 Yajun Zhu Xianjin Qiu Kai Chen Tianqing Zheng Longwei Yang Danying Xing jianlong xu 《The Crop Journal》 SCIE CAS CSCD 2016年第4期280-289,共10页
Iron and zinc are two trace elements that are essential for rice. But they are toxic at higher concentrations, leading to severe rice yield losses especially in acid soils and inland valleys. In this study, two recipr... Iron and zinc are two trace elements that are essential for rice. But they are toxic at higher concentrations, leading to severe rice yield losses especially in acid soils and inland valleys. In this study, two reciprocal introgression line(IL) populations sharing the same parents were used with high-density SNP bin markers to identify QTL tolerant to iron and zinc toxicities. The results indicated that the japonica variety 02,428 had stronger tolerance to iron and zinc toxicities than the indica variety Minghui 63. Nine and ten QTL contributing to iron and zinc toxicity tolerances,respectively, were identified in the two IL populations. The favorable alleles of most QTL came from 02,428. Among them, q FRRDW2, q ZRRDW3, and q FRSDW11 appeared to be independent of genetic background. The region C11S49–C11S60 on chromosome 11 harbored QTL affecting multiple iron and zinc toxicity tolerance-related traits, indicating partial genetic overlap between the two toxicity tolerances. Our results provide essential information and materials for developing excellent rice cultivars with iron and/or zinc tolerance by marker-assisted selection(MAS). 展开更多
关键词 RICE Reciprocal INTROGRESSION lines IRON TOLERANCE Zinc TOLERANCE Quantitative trait locus/loci(QTL)
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Genetic background effects on QTL and QTL × environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice 被引量:1
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作者 Xiaoqian Wang Yunlong Pang +6 位作者 Jian Zhang Qiang Zhang Yonghong Tao Bo Feng Tianqing Zheng jianlong xu Zhikang Li 《The Crop Journal》 SCIE CAS 2014年第6期345-357,共13页
QTLs for quantitative traits are influenced by genetic background(GB) and environment.Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection(MAS)... QTLs for quantitative traits are influenced by genetic background(GB) and environment.Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection(MAS). In this study, QTLs and QTL × environment interactions affecting grain yield per plant(GY) and its component traits, filled grain number per panicle(FGN), panicle number per plant(PN) and 1000-grain weight(TGW) across six environments were dissected using two sets of reciprocal introgression lines(ILs) derived from the cross Lemont × Teqing and SNP genotypic data. ANOVA indicated that the differences among genotypes and environments within each set of ILs were highly significant for all traits. A total of 72 distinct QTLs for GY and its component traits including 15 for GY, 25 for FGN, 18 for PN, and 29 for TGW were detected over the six environments. Most QTLs(87.4%) showed significant QTL × environment interactions(QEIs) and appeared to be more or less environment-specific. Among 72 QTLs, 15(20.8%) QTLs and 12(16.7%) QEIs were commonly identified in both backgrounds, indicating QTL especially QEI for yield and its component traits had strong GB effects. Four QTL regions affecting GY and its component traits, including S1269707–S4288071, S16661497–S17511092, and S35861863–S36341768 on chromosome 3, and S4134205–S7643153 on chromosome 5, were detected in both backgrounds and coincided with cloned genes for yield-related traits. These regions can be the targeted in rice breeding for high yield potential through MAS. Application of QTL main effects and their environmental interaction effects in MAS was discussed in detail. 展开更多
关键词 Quantitative TRAIT LOCUS YIELD potential Marker-assisted selection Genetic background QTL × environment interaction
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Genetic mechanism of heterosis for rice milling and appearance quality in an elite rice hybrid 被引量:1
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作者 Hui You Sundus Zafar +6 位作者 Fan Zhang Shuangbing Zhu Kai Chen Congcong Shen Xiuqin Zhao Wenzhong Zhang jianlong xu 《The Crop Journal》 SCIE CSCD 2022年第6期1705-1716,共12页
Development of hybrid rice with high yield and grain quality is a goal of rice breeding.To investigate the genetic mechanism of heterosis for rice milling and appearance quality in indica/xian rice,QTL mapping was con... Development of hybrid rice with high yield and grain quality is a goal of rice breeding.To investigate the genetic mechanism of heterosis for rice milling and appearance quality in indica/xian rice,QTL mapping was conducted using 1061 recombinant inbred lines(RILs)derived from a cross of the xian rice cultivars Quan 9311B(Q9311B)and Wu-shan-si-miao(WSSM),and a backcross F_(1)(BC_(1)F_(1)) population developed by crossing the RILs with Quan 9311A(Q9311A),combined with phenotyping in two environments.The F_(1) hybrid(Q9311A×WSSM)showed various degrees of heterosis for milling and appearance quality.A total of 142 main-effect QTL(M-QTL)and 407 pairs of epistatic QTL(E-QTL)were identified for five milling and appearance quality traits and grain yield per plant(GYP)in the RIL,BC_(1)F_(1) and mid-parental heterosis(H_(MP)) populations.Differential detection of QTL in three populations revealed that most additive loci detected in the RILs did not show heterotic effects,but some of them did contribute to BC_(1)F_(1) trait performance.Unlike heterosis of GYP,single-locus overdominance and epistasis were the main contributors to heterosis for milling and appearance quality.Epistasis contributed more to the heterosis for milling quality than to that for appearance quality.Three(four)QTL regions harboring opposite(consistent)directions of favorable allele effects for GYP and grain quality were identified,indicating the presence of partial genetic overlaps between GYP and grain quality.Three strategies are proposed to develop hybrid rice with high yield and good grain quality:1)pyramiding favorable alleles with consistent directions of gene effects for GYP and grain quality at the M-QTL on different chromosomes;2)introgressing favorable alleles for GYP and grain quality into the parents and then pyramiding and fixing these additive effects in hybrids;and 3)pyramiding overdominant and dominant loci and minimizing or eliminating underdominant loci from the parents. 展开更多
关键词 Milling and appearance quality Quantitative trait locus/loci(QTL) HETEROSIS Hybrid rice Pyramiding breeding
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Developing green super rice varieties with high nutrient use efficiency by phenotypic selection under varied nutrient conditions 被引量:1
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作者 Zilhas Ahmed Jewel Jauhar Ali +5 位作者 Yunlong Pang Anumalla Mahender Bart Acero Jose Hernandez jianlong xu Zhikang Li 《The Crop Journal》 SCIE CAS CSCD 2019年第3期368-377,共10页
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 conditions.In the present study, we followed an e... 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 conditions.In 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 donor.Starting 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 parents.Significant trait variations were observed between the treatments and ILs.Positive 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 conditions.Out of 230 ILs,12 were identified as promising under two or more nutrient deficiency conditions.The 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 conditions.The promising ILs can be useful resources for molecular genetic dissection and understanding the physiological mechanisms of NuUE. 展开更多
关键词 Nutrient use efficiency Grain yield NITROGEN PHOSPHORUS Green super rice
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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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作者 Muhiuddin Faruquee Qiang Zhang +7 位作者 Lubiao Zhang Linyun xu Wensheng Wang Jiansan Chen jianlong xu Zhikang Li Binying Fu Tianqing Zheng 《The Crop Journal》 SCIE CSCD 2021年第2期400-411,共12页
Dominant early heading(DEH)in rice(Oryza sativa L.)is of interest in both breeding and genetics.The genetic mechanisms underlying DEH have remained largely unclear.We have developed a near-isogenic DEH line without yi... Dominant early heading(DEH)in rice(Oryza sativa L.)is of interest in both breeding and genetics.The genetic mechanisms underlying DEH have remained largely unclear.We 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 background.We conducted a pilot genetic investigation under both short-day(SD)and long-day(LD)conditions.The DEH line harbored only 1.06%variation in the genome sequence relative to MH63.The variants were distributed throughout the genome.Using 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 condition.Joint 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_229.An InDel marker,ZMEH_1,was designed based on the variation between DEH_229 and MH63 within this region.It 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 population.This study reveals the genetic complexity of DEH in the near-isogenic line and may provide useful material and marker information for plant molecular breeding. 展开更多
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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Effects of Exogenousα-Ketoglutaric Acid on 2-Acetyl-1-Pyrroline,Yield Formation and Grain Quality Characters of Aromatic Rice
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作者 Bin Du Qixia Wu +5 位作者 Shuochen Jiang Dingyue Zhang Yue Qiao Yimei Xie jianlong xu Jianqiang Zhu 《Phyton-International Journal of Experimental Botany》 SCIE 2021年第2期437-447,共11页
The improvement of grain quality in aromatic rice is very important for farmer to increase their income.Present study was conducted with a two-year field experiment and three aromatic rice cultivars in order to study ... The improvement of grain quality in aromatic rice is very important for farmer to increase their income.Present study was conducted with a two-year field experiment and three aromatic rice cultivars in order to study the effects of exogenousα-ketoglutaric acid on yield formation,grain quality characters and the biosynthesis of 2-acetyl-1-pyrroline(2-AP,key component of aromatic rice’s fragrance)in aromatic rice.At heading stage,0.50 mmol L^(-1)(T1)and 1.00 mmol L^(-1)(T2)α-ketoglutaric acid solutions were overhead sprinkle to aromatic rice plants,respectively while the treatment which was overhead sprinkled with distilled water was set as control(CK).The results showed that 17.34%-33.04%and 21.39%-34.74%higher grain 2-AP contents were recorded in T1 and T2 treatments,respectively.Compared with CK,T1 and T2 treatments significantly reduced the transcript level of gene BADH2 which is related to the 2-AP biosynthesis in aromatic rice.3.86%-7.51%higher grain protein contents and 1.15%-3.37%higher head rice rates were also recorded inα-ketoglutaric acid treatments than CK.Moreover,T1 and T2 treatments remarkably decreased the chalky rice rate,chalkiness and grain amylose content.However,there was no remarkable difference in grain yield and related trails(effective panicle number,grain number per panicle,seed-setting rate and 1000-grain weight)among CK,T1 and T2 treatments.In conclusion,application of exogenousα-ketoglutaric acid enhanced 2-AP biosynthesis and improved grain quality of aromatic rice. 展开更多
关键词 α-ketoglutaric acid aromatic rice CHALKINESS protein 2-acetyl-1-pyrroline
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The basic helix-loop-helix transcription factor gene,OsbHLH38,plays a key role in controlling rice salt tolerance 被引量:5
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作者 Fengping Du Yinxiao Wang +8 位作者 Juan Wang Yingbo Li Yue Zhang Xiuqin Zhao jianlong xu Zhikang Li Tianyong Zhao Wensheng Wang Binying Fu 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2023年第8期1859-1873,共15页
The plant hormone abscisic acid(ABA)is crucial for plant seed germination and abiotic stress tolerance.However,the association between ABA sensitivity and plant abiotic stress tolerance remains largely unknown.In this... The plant hormone abscisic acid(ABA)is crucial for plant seed germination and abiotic stress tolerance.However,the association between ABA sensitivity and plant abiotic stress tolerance remains largely unknown.In this study,436 rice accessions were assessed for their sensitivity to ABA during seed germination.The 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 ecotypes.The upland-Geng accessions were most sensitive to ABA.Genome-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 sensitivity.Comprehensive functional analyses using knockout and overexpression transgenic lines revealed that OsbHLH38 expression was responsive to multiple abiotic stresses.Overexpression 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.Moreover,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 responsiveness.These results demonstrated that OsbHLH38 is a key regulator in plant abiotic stress tolerance. 展开更多
关键词 abscisic acid genome-wide association analysis RICE SALTTOLERANCE SEEDGERMINATION
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The rice OsV4 encoding a novel pentatricopeptide repeat protein is required for chloroplast development during the early leaf stage under cold stress 被引量:20
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作者 Xiaodi Gong Qianqian Su +5 位作者 Dongzhi Lin Quan Jiang jianlong xu Jianhui Zhang Sheng Teng Yanjun Dong 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2014年第4期400-410,共11页
Pentatricopeptide repeat (PPR) proteins, charac- terized by tandem arrays of a 35 amino acid motif, have been suggested to play central and broad roles in modulating the expression of organelle genes in plants. Howe... Pentatricopeptide repeat (PPR) proteins, charac- terized by tandem arrays of a 35 amino acid motif, have been suggested to play central and broad roles in modulating the expression of organelle genes in plants. However, the molecular mechanisms of most rice PPR genes remains unclear. In this paper, we isolated and characterized a temperature-conditional virescent mutant, OsV4, in rice (Oryza sativa cultivar Jiahual (WT, japonica rice variety)). The mutant displays albino phenotype and abnormal chloroplasts at the three leaf stage, which gradually turns green after the four leaf stage at a low temperature (20℃). But the mutant always develops green leaves and well-developed chloroplasts at a high temperature (32℃). Genetic and molecular analyses uncovered that OsV4 encodes a novel chloroplast-targeted PPR protein including four PPR motifs. Further investigations show that the mutant phenotype is associated with changes in chlorophyll content and chloroplast development. The OsV4 transcripts only accumulate to high levels in young leaves, indicating that its expression is tissue-specific. In addition, transcript levels of some ribosomal components and plastid- encoded polymerase-dependent genes are dramatically re- duced in the albino mutants grown at 20℃. These findings suggest that OsV4 plays an important role during early chloroplast development under cold stress in rice. 展开更多
关键词 Chloroplast development pentatricopeptide repeat plastid-encoded polymerase RICE virescent
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From Green Super Rice to green agriculture:Reaping the promise of functional genomics research 被引量:13
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作者 Sibin Yu Jauhar Ali +26 位作者 Shaochuan Zhou Guangjun Ren Huaan Xie jianlong xu Xinqiao Yu Fasong Zhou Shaobing Peng Liangyong Ma Dingyang Yuan Zefu Li Dazhou Chen Ruifeng Zheng Zhigang Zhao Chengcai Chu Aiqing You Yu Wei Susong Zhu Qiongyao Gu Guangcun He Shigui Li Guifu Liu Changhua Liu Chaopu Zhang Jinghua Xiao Lijun Luo Zhikang Li Qifa Zhang 《Molecular Plant》 SCIE CAS CSCD 2022年第1期9-26,共18页
Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge.Here,we review the concept and practices of Gree... Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge.Here,we review the concept and practices of Green Super Rice(GSR)that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture.The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources,functional gene discoveries,and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving,environmentally friendly crop production systems.We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agricul-ture and better nourish the world population. 展开更多
关键词 RICE functional genomics Green Super Rice genomic breeding nutritious crops sustainable agriculture
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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 被引量:16
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作者 Fan Zhang Chunchao Wang +7 位作者 Min Li Yanru Cui Yingyao Shi Zhichao Wu Zhiqiang Hu Wensheng Wang jianlong xu Zhikang Li 《Molecular Plant》 SCIE CAS CSCD 2021年第5期787-804,共18页
Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of rice.We characterized the gene-coding sequence-haplotype(gcHap)diversity of 45963 rice genes in 3010 rice ... Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of rice.We characterized the gene-coding sequence-haplotype(gcHap)diversity of 45963 rice genes in 3010 rice accessions.With 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 genes.We found that 39218 rice genes carry>255179 major gcHaps of potential functional importance.Most(87.5%)of the detected gcHaps were specific to subspecies or populations.The 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 sativa.Past 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 subspecies.Low 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 gcHaps.The gcHap data were demonstrated to have greater power than SNPs for the detection of causal genes that affect complex traits.The rice gcHap diversity dataset generated in this study would facilitate rice basic research and improvement in the future. 展开更多
关键词 gene-CDS-haplotype diversity functional alleles genome-wide selection signals evolution
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Oligolayered Ti3C2Tx MXene towards high performance lithium/sodium storage 被引量:7
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作者 Xiaolan Song Hui Wang +11 位作者 Shengming Jin Miao Lv Ying Zhang Xiaodong Kong Hongmei xu Ting Ma Xinyuan Luo Hengfeng Tan Dong Hu Chaoyong Deng Xinghua Chang jianlong xu 《Nano Research》 SCIE EI CAS CSCD 2020年第6期1659-1667,共9页
Nano Research volume 13,pages1659–1667(2020)Cite this article 232 Accesses 3 Citations Metrics details Abstract 2D MXenes are highly attractive for achieving ultrafast and stable lithium/sodium storage due to their g... Nano Research volume 13,pages1659–1667(2020)Cite this article 232 Accesses 3 Citations Metrics details Abstract 2D MXenes are highly attractive for achieving ultrafast and stable lithium/sodium storage due to their good electric conductivity and abundant redox active sites.While,effective strategies for scalable preparation of oligolayered MXenes are still under exploration.Herein,oligolayered Ti3C2Tx MXene is successfully obtained after conventional synthesis of multilayered Ti3C2 and subsequent delamination process via an organic solvent of tetramethyl-ammonium hydroxide(TMAOH).Comprehensive electrochemical study reveals that surface-controlled redox reaction dominated the charge storage behavior of oligolayered Ti3C2Tx with fast reaction kinetics.Impressively,the obtained oligolayered Ti3C2Tx exhibits excellent lithium/sodium storage performance,featured for a high specific capacity of 330 mAhg^−1 at 1.0 Ag^−1 after 800 cycles for lithium storage and 280 mAhg^−1 at 0.5 Ag^−1 after 500 cycles for sodium storage.Such impressive performance will advance the development of oligolayered Ti3C2Tx based materials for lithium/sodium storage and even broaden their application into energy storage. 展开更多
关键词 oligolayered Ti3C2Tx MXene DELAMINATION lithium ion battery sodium ion battery pseudocapacitance contribution
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