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Dynamic Intra-Japonica Subspecies Variation and Resource Application

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Molecular Plant 2012年第1期5卷 218-230页

作者： Haiyan Lin Peng Xia rod A.wing Qifa Zhang Meizhong Luo National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Arizona Genomics Institute University of ArizonaTucsonAZ 85721USA

We constructed a physical map of O. sativa ssp. japonica cv. ZH11 and compared it and its random sample sequences with the Nipponbare RefSeq derived from the same subspecies. This comparison showed that the two japonica genomes were highly syntenic but revealed substantial differences in terms of structural variations, rates of substitutions and indels, and transposable element content. For example, contractions/expansions as large as 450 kb and repeat sequences that were present in high copy numbers only in ZH11 were detected. In tri-alignment regions using the indica variety 93-11 sequence as an outgroup, we found that：（1） the substitution rates of the two japonica-indica inter- subspecies comparison combinations were close but almost a magnitude higher than the substitution rate between the japonica rice varieties ZH11 and Nipponbare; （2） of the substitutions found between ZH11 and Nipponbare, 47.2% occurred in ZH11 and 52.6% in Nipponbare; （3） of the indels found between ZH11 and Nipponbare, the indels that occurred in ZH11 were 15.8 times of those in Nipponbare. Of the indels that occurred in ZH11, 75.67% were insertions and 24.33% deletions. Of the indels that occurred in Nipponbare, 48.23% were insertions and 51.77% were deletions. The ZH11 com- parative map covered four Nipponbare physical gaps, detected assembly errors in the Nipponbare sequence, and was integrated with the FSTs of a large ZH11 T-DNA insertion mutant library. ZH11 BAC clones can be browsed, searched, and obtained at our website, http：//***.

关键词： Physical map comparative genomics Japonica Oryza rice BAC.

The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice

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Molecular Plant 2008年第5期1卷 839-850页

作者： Chuanzhu Fana Yong Zhang Yeisoo Yu Steve Rounsley Manyuan Long rod A. wing Arizona Genomics Institute Department of Plant Sciences University of Arizona Tucson AZ 85721 USA Department of Ecology and Evolution University of Chicago Chicago IL 60637 USA BIO5 Institute for Collaborative Research University of Arizona Tucson AZ 85721 USA

Despite general observations of non-random genomic distribution of new genes, it is unclear whether or not new genes preferentially occur in certain genomic regions driven by related molecular mechanisms. Using 1.5 Mb of genomic sequences from short arms of chromosome 3 of Oryza glaberrima and O. punctata, we conducted a comparative genomic analysis with the reference O. sativa ssp. japonica genome. We identified a 60-kb segment located in the middle of the subtelomeric region of chromosome 3, which is unique to the species O. sativa. The region contained gene duplicates that occurred in Asian cultivated rice species that diverged from the ancestor of Asian and African cultivated rice one million years ago （MYA）. For the 12 genes and one complete retrotransposon identified in this segment in O. sativa ssp. japonica, we searched for their parental genes. The high similarity between duplicated paralogs further supports the recent origination of these genes. We found that this segment was recently generated through multiple independent gene recombination and transposon insertion events. Among the 12 genes, we found that five had chimeric gene structures derived from multiple parental genes. Nine out of the 12 new genes seem to be functional, as suggested by Ka/Ks analysis and the presence of cDNA and/or MPSS data. Furthermore, for the eight transcribed genes, at least two genes could be classified as defense or stress response-related genes. Given these findings, and the fact that subtelomeres are associated with high rates of recombination and transcription, it is likely that subtelomeres may facilitate gene recombination and transposon insertions and serve as hot spots for new gene origination in rice genomes.

关键词： comparative genomics gene duplication Oryza sativa subtelomere new genes.

Ortholog Alleles at Xa3/Xa26 Locus Confer Conserved Race-Specific Resistance against Xanthomonas oryzae in Rice

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Molecular Plant 2012年第1期5卷 281-290页

作者： Hong-Jing Li Xiang-Hua Li Jing-Hua Xiao rod A.wing Shi-Ping Wang National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Huazhong Agricultural UniversityWuhan 430070China Arizona Genomics Institute School of Plant SciencesBIO5 InstituteUniversity of ArizonaTucsonAZ 85721USA

The rice disease resistance （R） gene Xa3/Xa26 （having also been named Xa3 and Xa26） against Xanthomonas oryzae pv. oryzae （Xoo）, which causes bacterial blight disease, belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar （Oryza sativa L.）. This family encodes leucine-rich repeat （LRR） receptor kinase- type proteins, Here, we show that the orthologs （alleles） of Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3, from wild Oryza spe- cies O. officinalis （CC genome） and O. minuta （BBCC genome）, respectively, were also R genes against Xoo. Xa3/Xa26-2 and Xa3/Xa26-3 conferred resistance to 16 of the 18 Xoo strains examined. Comparative sequence analysis of the Xa3/Xa26 families in the two wild Oryza species showed that Xa3/Xa26-3 appeared to have originated from the CC genome of O. minuta. The predicted proteins encoded by Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3 share 91-99% sequence identity and 94-99% sequence similarity. Transgenic plants carrying a single copy of Xa3/Xa26, Xa3/Xa26-2, or Xa3PXa26-3, in the same genetic background, showed a similar resistance spectrum to a set of Xoo strains, although plants carrying Xa3/Xa26-2 or Xa3/Xa26-3 showed lower resistance levels than the plants carrying Xa3/Xa26. These results suggest that the Xa3/Xa26 locus predates the speciation of A and C genome, which is approximately 7.5 million years ago. Thus, the resistance spec- ificity of this locus has been conserved for a long time.

关键词： Bacterial blight broad-spectrum resistance durable resistance Oryza officinalis Oryza minuta Oryza sativa.

Preparation of high molecular weight （HMW） genomic DNA from tea plant （Camellia sinensis） for BAC library construction

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Journal of Agricultural Science and Technology 2009年第1期3卷 1-10页

作者： LIN Jin-ke Dave Kudrna rod A wing Arizona Genomics Institute Department of Plant Sciences The University of Arizona Tucson AZ 85721 USA Department of Tea Sciences Fujian Agriculture and Forestry University Fuzhou 350002 China

A bacterial artificial chromosome （BAC） library is an invaluable resource tool to initiate tea plant genomics research, and the preparation of high molecular weight （HMW） genomic DNA is a crucial first step for constructing a BAC Library. In order to construct a BAC library for enhancing tea plant genomics research, a new method for the preparation of tea pant high molecular weight （HMW） genomic DNA must be developed due to young tea plant leaves and shoots are notably rich in both tea polyphenols and tea polysaccharides. In this paper, a modified method for preparing high quality tea plant HMW genomi~ DNA was optimized, and the quality of tea plant genomic DNA was evaluated. The results were as follows： Critical indicators of HMW DNA preparation were the appearance of the smooth nuclei in solution （as opposed to sticky-gummy） before agarose plug solidification, non-dark colored nuclei plugs after lysis with an SDS/proteinase K solution, and the quality and quantity of HMW DNA fragments after restriction enzyme digestion. Importantly, 1% dissolved PVP-40 and 1% un-dissolved PVP-40 during the nuclei extraction steps, in conjunction with the removal of PVP-40 from the plug washing and nuclei lysis steps, were critical for achieving HWM tea plant DNA suitable for BAC library construction. Additionally, a third PFGE fraction selection step to eliminate contaminating small DNA fragments. The modifications provided parameters that may have prevented deleterious interactions from tea polyphenols and tea polysaccharides. The HMW genomic DNA produced by this new modified method has been used to successfully construct a large-insert tea plant BAC library, and thus may be suitable for BAC library construction from other plant species that contain similarly interfering compounds.

关键词： tea plant bacterial artificial chromosome library BAC clone tea polyphenols high molecular weight genomic DNA preparation Camellia sinensis

Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion

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Molecular Plant 2014年第4期7卷 642-656页

作者： Julie Jacquemin Jetty S.S. Ammiraju Georg Haberer Dean D. Billheimer Yeisoo Yu Liana C. Liu Luis F. Rivera Klaus Mayer Mingsheng Chen rod A. wing Arizona Genomics Institute School of Plant Sciences University of Arizona Tucson AZ 85721 USA MIPS/IBIS Helmholtz Center Munich Ingoistaedter Landstrasse 1 85764 Neuherberg Germany Arizona Statistics Consulting Laboratory School of Plant Sciences University of Arizona Tucson AZ 85721 USA State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences 8eijing 100101 China

In analyzing gene families in the whole-genome sequences available for O. sativa （AA）, O. glaberrima （AA）, and O. brachyantha （FF）, we observed large size expansions in the AA genomes compared to FF genomes for the superfamilies F-box and NB-ARC, and five additional families： the Aspartic proteases, BTB/POZ proteins （BTB）, Glutaredoxins, Trypsin a-amylase inhibitor proteins, and Zf-Dof proteins. Their evolutionary dynamic was investigated to understand how and why such important size variations are observed between these closely related species. We show that expansions resulted from both amplification, largely by tandem duplications, and contraction by gene losses. For the F-box and NB-ARC gene families, the genes conserved in all species were under strong purifying selection while expanded orthologous genes were under more relaxed purifying selection. In F-box, NB-ARC, and BTB, the expanded groups were enriched in genes with little evidence of expression, in comparison with conserved groups. We also detected 87 loci under positive selection in the expanded groups. These results show that most of the duplicated copies in the expanded groups evolve neutrally after duplication because of functional redundancy but a fraction of these genes were preserved following neofunctionalization. Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection.

关键词： gene family expansion Oryza tandem duplication duplicated gene evolution.

Two reference genomes of indica rice and their implications for rice research and breeding applications

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Two reference genomes of indica rice and their implications ...

Rice Gene Index:A comprehensive pan-genome database for comparative and functional genomics of Asian rice

2016年全国植物生物学大会

作者： Qifa Zhang Jianwei Zhang Lingling Chen Feng Xing rod wing National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Arizona Genomics Institute and BIO5 Institute School of Plant SciencesUniversity of Arizona

Asian cultivated rice consists of two subspecies: Oryza sativa ssp. indica and O. sativa ssp. japonica. Indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse. Although a reference genome of the japonica rice Nipponbare was published in 2005 and has remained the highest quality crop genome sequence for more than a decade,lack of reference genome for indica rice has hindered the progress of rice research. Previous studies established that indica rice can be divided into two major varietal groups,Ind I and Ind II,independently bread and widely cultivated in China and Southeast Asia. Using a BAC-by-BAC strategy and PAC Bio sequencing technique,we generated reference genome sequences for two indica rice lines,Zhenshan 97 and Minghui 63,which represent Ind I and Ind II groups,respectively. The sequences were assembled into 237(Zhenshan 97) and 181(Minghui 63) contigs,with an accuracy >99.99%,and covered 90.6% and 93.2% of their estimated genome sizes. Our comparative analyses of these two indica genomes uncovered surprising structural differences,especially with respect to inversions,translocations,presence/absence variations and segmental duplications. These analyses clearly indicated the necessity of having multiple reference genomes for understanding natural variation in rice,which also have general implications for understanding intra-specific variations of organisms with complex genomes including plants and animals. In particular,hybrids produced from crosses between these two indica varietal groups usually show strong heterosis,which has provided basis for successful utilization of hybrid rice in China and several other countries. Zhenshan 97 and Minghui 63 are the parents of a leading hybrid Shanyou 63 that has been widely grown in China for over 30 years. The availability of these two reference genomes,combined with data from more than 20 years of genetic analyses of the Zhenshan 97,Minghui 63,and the hybrid syst

关键词： Oryza sativa ssp indica reference genome heterosis

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Molecular Plant 2023年第5期16卷 798-801页

作者：于志超陈永明周勇张雨露李梦圆欧阳亦聃 Dmytro Chebotarov Ramil Mauleon 赵虎谢为博 Kenneth L.McNally rod A.wing 郭伟龙张建伟 National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and Utilization(MOE)and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Center for Desert Agriculture Biological and Environmental Sciences&Engineering Division(BESE)King Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Saudi Arabia International Rice Research Institute(IRRI) Los Ban˜osLaguna 4031Philippines Arizona Genomics Institute School of Plant SciencesUniversity of ArizonaTucsonAZ 85721USA

Dear Editor,Asian rice(Oryza sativa)is the staple food for half the world and is a model crop that has been extensively *** contributes20%of calories to the human diet(Stein et al.,2018).With the increase in global population and rapid changes in climate,rice breeders need to develop new and sustainable cultivars with higher yields,healthier grains,and reduced environmental footprints(wing et al.,2018).Since the first gold-standard reference genome of rice variety Nipponbare was published(International Rice Genome Sequencing Project,2005),an increasing number of rice accessions have been sequenced,assembled,and annotated with global ***,a single reference genome is obviously insufficient to perform the genetic difference analysis for rice ***,the pan-genome has been proposed as a solution,which allows the discovery of more presence-absence variants compared with single-reference genome-based studies(Zhao et al.,2018).Over the past years,several databases,such as RAP-db(https://***),RGAP(http://***),and Gramene(https://***),have long-term served rice genomic research by providing information based on one or a series of individual reference *** integrate and utilize the genomic information of multiple accessions,we performed comparative analyses and established the user-friendly Rice Gene Index(RGI;https://***)*** is the first gene-based pan-genome database for rice.

关键词： sativa comprehensive cultivar

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植物基因组作图

生物技术通报 1993年第10期9卷 8-10页

作者： Andrew H.Paterson rod A.wing 孙雷心

前言由精典遗传学利用分子生物学工具和生物统计学方法合成的一种新概念——基因组作图——是一种研究植物生物学的有效方法。基因组图谱来源于传统的遗传连锁分析,用最新技术帮助对负责简单或复杂表型的基因进行定位作图。植物因增代... 详细信息

前言由精典遗传学利用分子生物学工具和生物统计学方法合成的一种新概念——基因组作图——是一种研究植物生物学的有效方法。基因组图谱来源于传统的遗传连锁分析,用最新技术帮助对负责简单或复杂表型的基因进行定位作图。植物因增代时间短、易于产生大量群体、及其人工杂交的可控制性使之非常适宜进行基因组作图。广泛收集植物在形态学、生理学及发育方面的变异体,为基因研究提供了丰富的资源。图谱克隆(map-based cloning) (即根据图谱位置克隆构成可识别表型的基因)

关键词：基因组作图遗传连锁位置克隆生物统计学方法增代时间基因连锁基因组大小 cloning 基因研究引物扩增

Dissect the rice immune system using a whole-genome sequenced mutant population

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Dissect the rice immune system using a whole-genome sequence...