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

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

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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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