Two reference genomes of indica rice and their implications for rice research and breeding applications
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- 英文论文题名：Two reference genomes of indica rice and their implications for rice research and breeding applications
- 论文作者：Qifa Zhang ; Jianwei Zhang ; Lingling Chen ; Feng Xing ; Rod Wing
- 英文论文作者：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 Sciences ; University of Arizona
- 年：2016
- 作者机构：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 Sciences,University of Arizona;
- 英文论文关键词：Oryza sativa ssp ; indica ; reference genome ; heterosis
- 会议召开时间：2016-10-09
- 会议录名称：2016年全国植物生物学大会摘要集
- 语种：英文
- 分类号：S511
- 学会代码：ZGZO
- 会议名称：2016年全国植物生物学大会
- 会议地点：中国湖北武汉
- 主办单位：中国遗传学会、中国细胞生物学学会、中国植物学会、中国植物生理与植物分子生物学学会、中国作物学会
- 学会名称：中国植物学会
- 页数：1
- 文件大小：842k
- 原文格式：D
- 会议级别：全国
摘要
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 system,will serve as an excellent model for further characterization of the biological basis of heterosis.
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 system,will serve as an excellent model for further characterization of the biological basis of heterosis.
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 system,will serve as an excellent model for further characterization of the biological basis of heterosis.
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