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The Genomic Variation of 3,000 diverse Rice (Oryza sativa L.)Accessions:Discoveries And Applications In Rice Improvement

The Genomic Variation of 3,000 diverse Rice (Oryza sativa L....

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2018中国作物学会学术年会

作者：黎志康 Fan Zhang Whensheng Wang Ramil Mauleon Zhiqiang Hu Dmytro Chebotarov Shuaishuai Tai Zhichao Min Li Tianqing Zheng Roven Rommel Fuentes Locedie Mansueto Dario Copetti Millicent Sanciangco Kevin Christian Palis Jianlong Xu Chen Sun Hongliang Zhang Binying Fu Yongming Gao Xiuqin Zhao Fei Shen Xiao Cui Hong Yu Zichao Li Miaolin Chen Jeffery Detras Yongli Zhou Xinyuan Zhang Yue Zhao Dave Kudrna Chunchao Wang Rui Li Ben Jia Jinyuan Lu Xianchang He Zhaotong Dong Jiabao Xu Yanhong Li Miao Wang Jianxin Shi Jing Li Dabing Zhang Seunhee Lee Wushu Hu Alexander Poliakov Inna Dubchak Victor Jun Ulat Frances Nikki Borja John Robert Mendoza Jauhar Ali Ming Yang Yongchao Niu Zhen Yue Ma.Elizabeth B.Naredo Jayson Talag Xueqiang Wang Jinjie Li Xiaodong Fang Ye Yin Jean-Christophe Glaszmann Jianwei Zhang Jiayang Li Ruaraidh Sackville Hamilton Rod A.Wing Chaochun Wei Jue Ruan Gengyun Zhang Kenneth L.Mcnally Nickolai Alexandrov Hei Leung Hei Institute of Crop Sciences Chinese Academy of Agricultural Sciences Shenzhen Institute for Innovative Breeding Chinese Academy of Agricultural Sciences International Rice Research Institute School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai Center for Bioinformation Technology BGI Genomics BGI-Shenzhen Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Anhui Agricultural University Arizona Genomics Institute School of Plant SciencesUniversity of Arizona China Agricultural University Institute of Genetics and Developmental Biology Chinese Academy of Sciences Lawrence Berkeley National Laboratory

Asian cultivated rice(Oryza sativa L.) is the staple food for the half world population with rich within species *** analyses of the genome resequencing data of a core collection of 3,010 rice accessions revealed four important aspects of the genomic diversity within ***,over 42 million SNPs and >3 million small InDels were discovered against five reference ***,we discovered more than 90,000 structural(>100 bps) variations(SVs) when compared with the Geng reference genome,consisting primarily of small-sized deletions and translocations,plus many duplications and *** SVs accounted for significant portion of the rice genome and involved most(～80%) rice ***,we discovered >12,000 full-length novel protein-coding genes plus 9000+ novel genes of partial sequences that are absent in the Nipponbare reference *** rice pan genome consists of ～62%core genes/gene families that are present in all rice lines,and ～38%distributed genes that are present only some of rice ***,using large-effect SNPs and InDels of all loci in the PG,a rice functional haplotype database was *** SNP,PG and SV variation clearly resolve the 3,010 rice accessions into two major subspecies,Xian(indica) and Geng(japonica),plus Aus and Aro groups and multiple subpopulations within Xian and *** reduced diversity was found in genomic regions where over 1,000 agronomically important and domestication-related genes *** efforts have been taken to identify and mine genes/QTLs/alleles associated with a wide range of important traits in rice using the 3 k materials and SNP *** demonstrate how the results of the 3 k RGP could be used in rice improvement,genomic constitutions of 476 BC F introgression lines(ILs) from our breeding program were constructed using high-quality reference genomes of their 9 parents and the 3 k RGP *** compared with their recurrent parent,Huang-hua-

关键词： Rice genome diversity population structure pan genomes genomics-based breeding by design

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Genomic diversity Comparison among Multi-Strains of the Sinorhizobium meliloti by CGH Microarray

Genomic Diversity Comparison among Multi-Strains of the Sino...

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全国寄生虫学与热带医学学术研讨会

作者：郭虹孙晟徐建平 Key Laboratory Hainan Medical CollegeHaikouHainan ProvinceP.R.China 571101 Center for Environmental Genomics Department of BiologyMcMaster UniversityHamiltonOntarioCanada L8S 4K1

Microarray based comparative genomic hybridization(CGH) have been used to study genomic diversity in ten Sinorhizobium meliloti strains by comparing with a sequenced lab model strain Rm1021(reference strain).The strains used in this study(tester strains) originated from different ET types,different plant host and various geographic *** genome-wide *** Rm1021 Sm6k-oligonucleotide chips were used for the two colors CGH *** of *** showed considerable diversity in gene content(variable present ORFs,VAP-absent or VAP-duplicate):In VAP-absent group,total 2154 ORFs were considered absent in at least one of the natural strains tested compared to *** ratio of absent ORFs to all ORFs annotated on pSymA was significantly higher than that of on pSymB and chromosome. The percentage of absent divergent genes in the tester strains varied from 1.51%to 6.35;58.34%of all absent ORFs was considered as highly diversity for absent in more than two natural *** the VAP-duplicate group,total 1904 ORFs were considered duplicate in at least one of the natural strains *** number of duplicate genes varied greatly in the individual strains, from 0.27%up to 8.56%.52.86%of all duplicate ORFs were considered as highly diversity. The relationships among genome size,the number of absent ORF,and the number of duplicated ORF were analyzed and *** potential ecological significance was also discussed by comparing the mummer of absent/duplicated ORFs with the host species,geographic origin,ET types of tester *** variation was found in functional categories corresponding to each replicon genome.

关键词： CGH Microarray genome diversity Sinorhizobium meliloti

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