Doori Park1, Su-Hyun Park2,3, Youn Shic Kim2, Beom-Soon Choi4, Ju-Kon Kim5, Nam-Soo Kim6,7, Ik-Young Choi8. 1. Department of Molecular Bioscience, Kangwon National University, Chuncheon, South Korea. 2. Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, South Korea. 3. Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA. 4. Phyzen Genomics Institute, Seongnam, South Korea. 5. Graduate School of International Agricultural Technology and Crop Biotech Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, South Korea. jukon@snu.ac.kr. 6. Department of Molecular Bioscience, Kangwon National University, Chuncheon, South Korea. kimnamsu@kangwon.ac.kr. 7. Institute of Bioscience and Biomedical Sciences, Kangwon National University, Chuncheon, South Korea. kimnamsu@kangwon.ac.kr. 8. Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea. choii@kangwon.ac.kr.
Abstract
BACKGROUND: As the transformation process can induce mutations in host plants, molecular characterization of the associated genomic changes is important not only for practical food safety but also for understanding the fundamental theories of genome evolution. OBJECTIVES: To investigate a population-scale comparative study of the genome-wide spectrum of sequence variants in the transgenic genome with the variations present in 3000 rice varieties. RESULTS: On average, we identified 19,273 SNPs (including Indels) per transgenic line in which 10,729 SNPs were at the identical locations in the three transgenic rice plants. We found that these variations were predominantly present in specific regions in chromosomes 8 and 10. Majority (88%) of the identified variations were detected at the same genomic locations as those in natural rice population, implying that the transgenic induced mutations had a tendency to be common alleles. CONCLUSION: Genomic variations in transgenic rice plants frequently occurred at the same sites as the major alleles found in the natural rice population, which implies that the sequence variations occur within the limits of a biological system to ensure survival.
BACKGROUND: As the transformation process can induce mutations in host plants, molecular characterization of the associated genomic changes is important not only for practical food safety but also for understanding the fundamental theories of genome evolution. OBJECTIVES: To investigate a population-scale comparative study of the genome-wide spectrum of sequence variants in the transgenic genome with the variations present in 3000 rice varieties. RESULTS: On average, we identified 19,273 SNPs (including Indels) per transgenic line in which 10,729 SNPs were at the identical locations in the three transgenic rice plants. We found that these variations were predominantly present in specific regions in chromosomes 8 and 10. Majority (88%) of the identified variations were detected at the same genomic locations as those in natural rice population, implying that the transgenic induced mutations had a tendency to be common alleles. CONCLUSION: Genomic variations in transgenic rice plants frequently occurred at the same sites as the major alleles found in the natural rice population, which implies that the sequence variations occur within the limits of a biological system to ensure survival.
Authors: Ray Ming; Shaobin Hou; Yun Feng; Qingyi Yu; Alexandre Dionne-Laporte; Jimmy H Saw; Pavel Senin; Wei Wang; Benjamin V Ly; Kanako L T Lewis; Steven L Salzberg; Lu Feng; Meghan R Jones; Rachel L Skelton; Jan E Murray; Cuixia Chen; Wubin Qian; Junguo Shen; Peng Du; Moriah Eustice; Eric Tong; Haibao Tang; Eric Lyons; Robert E Paull; Todd P Michael; Kerr Wall; Danny W Rice; Henrik Albert; Ming-Li Wang; Yun J Zhu; Michael Schatz; Niranjan Nagarajan; Ricelle A Acob; Peizhu Guan; Andrea Blas; Ching Man Wai; Christine M Ackerman; Yan Ren; Chao Liu; Jianmei Wang; Jianping Wang; Jong-Kuk Na; Eugene V Shakirov; Brian Haas; Jyothi Thimmapuram; David Nelson; Xiyin Wang; John E Bowers; Andrea R Gschwend; Arthur L Delcher; Ratnesh Singh; Jon Y Suzuki; Savarni Tripathi; Kabi Neupane; Hairong Wei; Beth Irikura; Maya Paidi; Ning Jiang; Wenli Zhang; Gernot Presting; Aaron Windsor; Rafael Navajas-Pérez; Manuel J Torres; F Alex Feltus; Brad Porter; Yingjun Li; A Max Burroughs; Ming-Cheng Luo; Lei Liu; David A Christopher; Stephen M Mount; Paul H Moore; Tak Sugimura; Jiming Jiang; Mary A Schuler; Vikki Friedman; Thomas Mitchell-Olds; Dorothy E Shippen; Claude W dePamphilis; Jeffrey D Palmer; Michael Freeling; Andrew H Paterson; Dennis Gonsalves; Lei Wang; Maqsudul Alam Journal: Nature Date: 2008-04-24 Impact factor: 49.962