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| 1 | The landscape of gene-CDS-haplotype diversity in rice:Properties,population organization,footprints of domestication and breeding,and implications for genetic improvement显示文摘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. | Fan Zhang Chunchao Wang Min Li Yanru Cui Yingyao Shi Zhichao Wu Zhiqiang Hu Wensheng Wang Jianlong Xu Zhikang Li | 2021 | Molecular Plant2021，14，5： | 5 |
| 2 | Breeding by selective introgression: Theory, practices, and lessons learned from rice显示文摘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. | Fan Zhang Yingyao Shi Jauhar Ali Jianlong Xu Zhikang Li | 2021 | The Crop Journal2021，9，3： | 3 |
| 3 | Simultaneous improvement and genetic dissection of grain yield and its related traits in a backbone parent of hybrid rice ( Oryza sativa L.) using selective introgression显示文摘 | Hongjun Zhang Hui Wang Yiliang Qian Jiafa Xia Zefu Li Yingyao Shi Linghua Zhu Jauhar Ali Yongming Gao Zhikang Li | 2013 | Molecular Breeding2013，，1： | 1 |
| 4 | Characterization of intermolecular interaction between cyanidin-3-glucoside and bovine serum albumin: Spectroscopic and molecular docking methods显示文摘 | SHI Jiehua WANG Jing ZHU Yingyao | 2013 | Luminescence2013，，： | 1 |
| 5 | Characterization of interaction between isoliquiritigenin and bovine serum albumin: Spectroscopic and molecular docking methods显示文摘 | SHI Jiehua WANG Jing ZHU Yingyao | 2014 | Journal of Luminescence2014，145，： | 1 |
| 6 | Can health technology assessments assist the global campaign against poverty?显示文摘Although a key tenant of the Sustainable Development Goals is to achieve universal health coverage,the global drug gap persists-cver a third of the global population lack access to essential medicines.Without access to affordable drugs,people have worse health outcomes,higher medical expenses,and productivity loss,pushing them into poverty.Health technology assessments(HTAs)offer an opportunity to decrease the global drug gap and increase access to essential medicines by overcoming barriers to medicine access.These barriers include drug procurement,drug affordability for payers and patients,a patienfs ability to obtain essential medicines,and health system capacity.Using HTAs can therefore close the global drug gap by increasing access to affordable essential medicines.In turn,people have better health outcomes,spend less money on medical care,and can have better productivity.Ultimately,use of HTAs can lift the population out of poverty and force fewer people into poverty by creating better health outcomes at affordable prices. | Debra Renee Winberg Ye Lu Yingyao Chen Lizheng Shi | 2021 | Global Health Journal2021，5，3： | 1 |
| 7 | Stress-Activated Protein Kinase OsSAPK7 Regulates Salt- Stress Tolerance by Modulating Diverse Stress-Defensive Responses in Rice显示文摘Soil salinity is an environmental threat limiting rice productivity.Identification of salinity tolerance genes and exploitation of their mechanisms in plants are vital for crop breeding.In this study,the function of stress-activated protein kinase 7(OsSAPK7),a SnRK2 family member,was characterized in response to salt stress in rice.Compared with variety 9804,OsSAPK7-overexpression plants had a greater survival rate,increased chlorophyll and proline contents,and superoxide dismutase and catalase activities at the seedling stage under salt-stress conditio ns,as well as decreased sodium potassium ratio(Na+/K+)and malondialdehyde contents.After salt stress,the OsSAPK7 knockout plants had lower survival rates,in creased Na^K*ratios and malomdiadehyde contents,and decreased physiological parameters compared with 9804.These changes in transgenic lines suggested that OsSAPK7 increased the salt tolerance of rice by modulating ion homeostasis,redox reactions and photosynthesis.The results of RNA-Seq indicated that genes involved in redox-dependent signaling pathway,photosynthesis and zeatin synthesis pathways were significantly down-regulated in the OsSAPK7 knockout line compared with 9804 un der salt-stress conditio n,which con firmed that OsSAPK7 positively regulated salt tolera nee by modulating diverse stress-defe nsive resp on ses in rice.These findings provided novel in sights for the genetic improvement of rice and for understanding the regulatory mechanisms of salt-stress toleranee. | ZENG Dan WANG Chunchao XIE Junpin ZHANG Fan LU Jialing SHI Xiaorong SHI Yingyao ZHOU Yongli | 2021 | Rice science2021，28，6： | 0 |
| 8 | Rice3K56 is a high-quality SNP array for genome-based genetic studies and breeding in rice(Oryza sativa L.)显示文摘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. | Chaopu Zhang Min Li 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 | 2023 | The Crop Journal2023，11，3： | 0 |
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