Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize
- 439 Downloads
The development of a high-throughput genotyping platform with high quality, flexibility, and affordable genotyping cost is critical for marker-assisted breeding. In this study, a genotyping by target sequencing (GBTS) platform was developed in maize, which can be realized for a small number of markers (several to 5 K) through multiplex PCR (GenoPlexs) and for a large number of markers (1 to 45 K) through in-solution capture. The later was used for development of four SNP marker panels (GenoBaits Maize) containing 20 K, 10 K, 5 K, and 1 K markers. Two genotype panels, one consisting 96 representative worldwide maize inbred lines and the other containing 387 breeding lines developed in our maize breeding programs, were used to test and validate the developed marker panels. First, a 20 K SNP panel, with markers evenly distributed across maize genome, was developed from a 55 K SNP array with improved genome coverage. From this single marker panel, 20 K, 10 K, 5 K, and 1 K SNP markers can be generated by sequencing the samples at the average sequencing depths of 50×, 20×, 7.5×, and 2.5×, respectively. Highly consistent marker genotypes were obtained between the four marker panels and the 55 K array (over 95%) and between two biological replications (over 98%). Also, highly consistent phylogenetic relationships were generated by using four marker panels and two genotype panels, providing strong evidence for the reliability of SNP markers and GBTS genotyping platform. Cost-benefit analysis indicated that the genotypic selection cost based on the GBTS in maize was lower than phenotypic selection, allowing GBTS an affordable genotyping platform for marker-assisted breeding. Integration of this affordable genotyping platform with other breeding platforms and open-source breeding network would greatly facilitate the molecular breeding activities in small- and medium-size companies and developing countries. The four marker panels could be used for many fields of marker application, including germplasm evaluation, genetic mapping, marker-assisted selection (including genomic selection), and plant variety protection.
KeywordsMaize Single nucleotide polymorphism(SNP) Genotyping by target sequencing(GBTS) Molecular breeding Marker-assisted selection
This research is supported by the National Key Research and Development Program of China (2016YFD0101201 and 2017YFD0101201) and the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences (CAAS) (CAAS-XTCX2016009), and Research activities of CIMMYT staff were supported by the Bill and Melinda Gates Foundation and the CGIAR Research Program MAIZE.
- Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS (2003) Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 68:69–78CrossRefGoogle Scholar
- Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner EM, Joets J, Le Paslier MC, McMullen MD, Montalent P, Rose M, Schön CC, Sun Q, Walter H, Martin OC, Falque M (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One 6:e28334CrossRefGoogle Scholar
- Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q, Li JY, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967CrossRefGoogle Scholar
- Lu Y, Yan J, Guimarães CT, Taba S, Hao Z, Gao S, Chen S, Li J, Zhang S, Vivek BS, Magorokosho C, Mugo S, Makumbi D, Parentoni SN, Shah T, Rong T, Crouch JH, Xu Y (2009) Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet 120:93–115CrossRefGoogle Scholar
- Rousselle Y, Jones E, Charcosset A, Moreau P, Robbins K, Stich B, Knaak C, Flament P, Karaman Z, Martinant JP, Fourneau M, Taillardat A, Romestant M, Tabel C, Bertran J, Ranc N, Lespinasse D, Blanchard P, Kahler A, Chen J, Kahler J, Dobrin S, Warner T, Ferris R, Smith S (2015) Study on essential derivation in maize: III. Selection and evaluation of a panel of single nucleotide polymorphism loci for use in European and North American germplasm. Crop Sci 55:1170–1180CrossRefGoogle Scholar
- Schlötterer C, Tobler R, Kofler R, Nolte V (2014) Sequencing pools of individuals—mining genome-wide polymorphism data without big funding. Nucleic Acids Res 15:749–763Google Scholar
- Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Bio/Technology 7:257–264Google Scholar
- Unterseer S, Bauer E, Haberer G, Seidel M, Knaak C, Ouzunova M, Meitinger T, Strom TM, Fries R, Pausch H, Bertani C, Davassi A, Mayer KF, Schön CC (2014) A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array. BMC Genomics 15:823CrossRefGoogle Scholar
- Xu Y (2003) Developing marker-assisted selection in plant breeding hybrid rice. Plant Breed Rev 23:73–174Google Scholar