TY  - JA
AU  - Nan Wang
AU  - Yibing Yuan
AU  - Hui Wang
AU  - Diansi Yu
AU  - Yubo Liu
AU  - Ao Zhang
AU  - Gowda,M.
AU  - Nair,S.K.
AU  - Zhuanfang Hao
AU  - Yanli Lu
AU  - San Vicente,F.M.
AU  - Prasanna,B.M.
AU  - Xinhai Li
AU  - Xuecai Zhang
TI  - Applications of genotyping-by-sequencing (GBS) in maize genetics and breeding
SN  - 2045-2322
PY  - 2020///
CY  - London (United Kingdom)
PB  - Nature Publishing Group, 
KW  - Maize
KW  - AGROVOC
KW  - Plant breeding
KW  - Plant Genetics
N1  - Peer review; Open Access; MCRP; FP2
N2  - Genotyping-by-Sequencing (GBS) is a low-cost, high-throughput genotyping method that relies on restriction enzymes to reduce genome complexity. GBS is being widely used for various genetic and breeding applications. In the present study, 2240 individuals from eight maize populations, including two association populations (AM), backcross first generation (BC1), BC1F2, F2, double haploid (DH), intermated B73 × Mo17 (IBM), and a recombinant inbred line (RIL) population, were genotyped using GBS. A total of 955,120 of raw data for SNPs was obtained for each individual, with an average genotyping error of 0.70%. The rate of missing genotypic data for these SNPs was related to the level of multiplex sequencing: ~ 25% missing data for 96-plex and ~ 55% for 384-plex. Imputation can greatly reduce the rate of missing genotypes to 12.65% and 3.72% for AM populations and bi-parental populations, respectively, although it increases total genotyping error. For analysis of genetic diversity and linkage mapping, unimputed data with a low rate of genotyping error is beneficial, whereas, for association mapping, imputed data would result in higher marker density and would improve map resolution. Because imputation does not influence the prediction accuracy, both unimputed and imputed data can be used for genomic prediction. In summary, GBS is a versatile and efficient SNP discovery approach for homozygous materials and can be effectively applied for various purposes in maize genetics and breeding
UR  - https://hdl.handle.net/10883/20965
T2  - Scientific Reports
DO  - https://doi.org/10.1038/s41598-020-73321-8
ER  -