JIA-2018-09
1977 YANG Hai-long et al. Journal of Integrative Agriculture 2018, 17(9): 1972–1978 kernel composition in the nested association mapping and inbred association panels. Plant Physiology , 158 , 824–834. Cornelis S, Gansemans Y, Deleye L, Deforce D, Van Nieuwerburgh F. 2017. Forensic SNP genotyping using nanopore MinION sequencing. Scientific Reports , 7 , 41759. Davey J W, Hohenlohe P A, Etter P D, Boone J Q, Catchen J M, and Blaxter M L. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics , 12 , 499–510. Earl D A. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources , 4 , 359–361. Feltus F A, Wan J, Schulze S R, Estill J C, Jiang N, Paterson A H. 2004. An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments. Genome Research , 14 , 1812–1819. Flint-Garcia S A, Thuillet A C, Yu J, Pressoir G, Romero S M, Mitchell S E, Doebley J, Kresovich S, Goodman M M, Buckler E S. 2005. Maize association population: A high- resolution platform for quantitative trait locus dissection. The Plant Journal , 44 , 1054–1064. Gore M A, Chia J-M, Elshire R J, Sun Q, Ersoz E S, Hurwitz B L, Peiffer J A, McMullen M D, Grills G S, Ross-Ibarra J. 2009. A first-generation haplotype map of maize. Science , 326 , 1115–1117. He J, Zhao X, Laroche A, Lu Z X, Liu H, Li Z. 2014. Genotyping- by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science , 5 , 484. Hoisington D, Khairallah M, Reeves T, Ribaut J M, Skovmand B, Taba S, Warburton M. 1999. Plant genetic resources: What can they contribute toward increased crop productivity. Proceedings of the National Academy of Sciences of the United States of America , 96 , 5937–5943. Jakobsson M, Rosenberg N A. 2007. CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics , 23 , 1801–1806. Jiao Y, Zhao H, Ren L, Song W, Zeng B, Guo J, Wang B, Liu Z, Chen J, Li W. 2012. Genome-wide genetic changes during modern breeding of maize. Nature Genetics , 44 , 812–815. Kopelman N M, Mayzel J, Jakobsson M, Rosenberg N A, Mayrose I. 2015. Clumpak: A program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources , 15 , 1179–1191. LaFramboise T. 2009. Single nucleotide polymorphism arrays: A decade of biological, computational and technological advances. Nucleic Acids Research , 37 , 4181–4193. Lam H M, Xu X, Liu X, Chen W, Yang G, Wong F L, Li M W, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun S S, Zhang G. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics , 42 , 1053–1059. Larkin M A, Blackshields G, Brown N P, Chenna R, McGettigan P A, McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D, Gibson T J, Higgins D G. 2007. Clustal Wand Clustal X version 2.0. Bioinformatics , 23 , 2947–2948. Lee T H, Guo H, Wang X, Kim C, Paterson A H. 2014. SNPhylo: A pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics , 15 , 162. Li Y H, Zhou G, Ma J, Jiang W, Jin L G, Zhang Z, Guo Y, Zhang J, Sui Y, Zheng L, Zhang S S, Zuo Q, Shi X H, Li Y F, Zhang W K, Hu Y, Kong G, Hong H L, Tan B, Song J, et al . 2014. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nature Biotechnology , 32 , 1045–1052. Liu K, Goodman M, Muse S, Smith J S, Buckler E, Doebley J. 2003. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics , 165 , 2117–2128. Liu K, Muse S V. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics , 21 , 2128–2129. Lorenz A, Hoegemeyer T. 2013. The phylogenetic relationships of US maize germplasm. Nature Genetics , 45 , 844–845. Matsuoka Y, Vigouroux Y, Goodman M M, Sanchez J, Buckler E, Doebley J. 2002. A single domestication for maize shown by multilocus microsatellite genotyping. Proceedings of the National Academy of Sciences of the United States of America , 99 , 6080–6084. McNally K L, Childs K L, Bohnert R, Davidson R M, Zhao K, Ulat V J, Zeller G, Clark R M, Hoen D R, Bureau T E. 2009. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America , 106 , 12273–12278. Mohammadi S, Prasanna B. 2003. Analysis of genetic diversity in crop plants-salient statistical tools and considerations. Crop Science , 43 , 1235–1248. Nielsen R, Paul J S, Albrechtsen A, Song Y S. 2011. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics , 12 , 443–451. Peakall R, Smouse P E. 2006. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Resources , 6 , 288–295. Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M. 1998. Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theoretical and Applied Genetics , 97 , 1248–1255. Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu M V. 2013. An overview of STRUCTURE: Applications, parameter settings, and supporting software. Frontiers in Genetics , 4 , 98. Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics , 155 , 945–959. Pritchard J K, Wen X, and Falush D. 2009. Documentation for structure software: Version 2.3. Department of Human Genetics, University of Chicago, Chicago, USA.
Made with FlippingBook
RkJQdWJsaXNoZXIy MzE3MzI3