title: GIPS: A Software Guide to Sequencing-Based Direct Gene Cloning in Forward Genetics Studies.
abstract: The Gene Identification via Phenotype Sequencing (GIPS) software considers a range of experimental and analysis choices in sequencing-based forward genetics studies within an integrated probabilistic framework, which enables direct gene cloning from the sequencing of several unrelated mutants of the same phenotype without the need to create segregation populations. GIPS estimates four measurements to help optimize an analysis procedure as follows: (1) the chance of reporting the true phenotype-associated gene; (2) the expected number of random genes that may be reported; (3) the significance of each candidate gene's association with the phenotype; and (4) the significance of violating the Mendelian assumption if no gene is reported or if all candidate genes have failed validation. The usage of GIPS is illustrated with the identification of a rice (Oryza sativa) gene that epistatically suppresses the phenotype of the phosphate2 mutant from sequencing three unrelated ethyl methanesulfonate mutants. GIPS is available at https://github.com/synergy-zju/gips/wiki with the user manual and an analysis example.
authors: State Key Laboratory of Plant Physiology and Biochemistry (H.H., C.M., X.C.) and Institute of Plant Sciences (D.T., Zhi.Z.. C.M.), College of Life Sciences, and Institute of Biochemistry, College of Pharmaceutical Sciences (W.W., Zho.Z., J.Z., X.C.), Zhejiang University, Hangzhou 310058, People's Republic of China;Agricultural Experiment Station, Zhejiang University, Changxing 310058, People's Republic of China (H.H.); andJoint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou 310058, People's Republic of China (X.C.).
authors: Han
authors: H
authors: Hu
authors: State Key Laboratory of Plant Physiology and Biochemistry (H.H., C.M., X.C.) and Institute of Plant Sciences (D.T., Zhi.Z.. C.M.), College of Life Sciences, and Institute of Biochemistry, College of Pharmaceutical Sciences (W.W., Zho.Z., J.Z., X.C.), Zhejiang University, Hangzhou 310058, People's Republic of China;Agricultural Experiment Station, Zhejiang University, Changxing 310058, People's Republic of China (H.H.); andJoint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou 310058, People's Republic of China (X.C.).
authors: Weitao
authors: W
authors: Wang
authors: State Key Laboratory of Plant Physiology and Biochemistry (H.H., C.M., X.C.) and Institute of Plant Sciences (D.T., Zhi.Z.. C.M.), College of Life Sciences, and Institute of Biochemistry, College of Pharmaceutical Sciences (W.W., Zho.Z., J.Z., X.C.), Zhejiang University, Hangzhou 310058, People's Republic of China;Agricultural Experiment Station, Zhejiang University, Changxing 310058, People's Republic of China (H.H.); andJoint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou 310058, People's Republic of China (X.C.).
authors: Zhongxu
authors: Z
authors: Zhu
authors: State Key Laboratory of Plant Physiology and Biochemistry (H.H., C.M., X.C.) and Institute of Plant Sciences (D.T., Zhi.Z.. C.M.), College of Life Sciences, and Institute of Biochemistry, College of Pharmaceutical Sciences (W.W., Zho.Z., J.Z., X.C.), Zhejiang University, Hangzhou 310058, People's Republic of China;Agricultural Experiment Station, Zhejiang University, Changxing 310058, People's Republic of China (H.H.); andJoint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou 310058, People's Republic of China (X.C.).
authors: Jianhua
authors: J
authors: Zhu
authors: State Key Laboratory of Plant Physiology and Biochemistry (H.H., C.M., X.C.) and Institute of Plant Sciences (D.T., Zhi.Z.. C.M.), College of Life Sciences, and Institute of Biochemistry, College of Pharmaceutical Sciences (W.W., Zho.Z., J.Z., X.C.), Zhejiang University, Hangzhou 310058, People's Republic of China;Agricultural Experiment Station, Zhejiang University, Changxing 310058, People's Republic of China (H.H.); andJoint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou 310058, People's Republic of China (X.C.).
authors: Deyong
authors: D
authors: Tan
authors: State Key Laboratory of Plant Physiology and Biochemistry (H.H., C.M., X.C.) and Institute of Plant Sciences (D.T., Zhi.Z.. C.M.), College of Life Sciences, and Institute of Biochemistry, College of Pharmaceutical Sciences (W.W., Zho.Z., J.Z., X.C.), Zhejiang University, Hangzhou 310058, People's Republic of China;Agricultural Experiment Station, Zhejiang University, Changxing 310058, People's Republic of China (H.H.); andJoint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou 310058, People's Republic of China (X.C.).
authors: Zhipeng
authors: Z
authors: Zhou
authors: State Key Laboratory of Plant Physiology and Biochemistry (H.H., C.M., X.C.) and Institute of Plant Sciences (D.T., Zhi.Z.. C.M.), College of Life Sciences, and Institute of Biochemistry, College of Pharmaceutical Sciences (W.W., Zho.Z., J.Z., X.C.), Zhejiang University, Hangzhou 310058, People's Republic of China;Agricultural Experiment Station, Zhejiang University, Changxing 310058, People's Republic of China (H.H.); andJoint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou 310058, People's Republic of China (X.C.) mcz@zju.edu.cn xinchen@zju.edu.cn.
authors: Chuanzao
authors: 0000-0001-5126-2180
authors: C
authors: Mao
authors: State Key Laboratory of Plant Physiology and Biochemistry (H.H., C.M., X.C.) and Institute of Plant Sciences (D.T., Zhi.Z.. C.M.), College of Life Sciences, and Institute of Biochemistry, College of Pharmaceutical Sciences (W.W., Zho.Z., J.Z., X.C.), Zhejiang University, Hangzhou 310058, People's Republic of China;Agricultural Experiment Station, Zhejiang University, Changxing 310058, People's Republic of China (H.H.); andJoint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou 310058, People's Republic of China (X.C.) mcz@zju.edu.cn xinchen@zju.edu.cn.
authors: Xin
authors: 0000-0002-1196-6826
authors: X
authors: Chen
mesh_terms: D003001:Cloning, Molecular; D017343:Genes, Plant; D008967:Molecular Biology / Q000379:methods*; D012275:Oryza / Q000235:genetics; D010641:Phenotype; D012984:Software