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Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize

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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.

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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.

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Correspondence to Jianan Zhang or Yunbi Xu.

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Supplementary Fig. 1

Distribution of minor allele frequency (MAF) for maize 20 K SNP marker panel as revealed by 96 representative inbred lines (96-genotype panel) (PDF 263 kb)

Supplementary Fig. 2

Distribution of polymorphic information contents (PICs) for four marker panels using 96 representative inbred lines (96-genotype panel) (PDF 284 kb)

Supplementary Fig. 3

Distribution of gene diversity (GD) as revealed by 96 maize inbred lines (96-genotype panel) and four marker panels (PDF 295 kb)

Supplementary Fig. 4

Distribution of polymorphic rates as revealed by 96 maize inbred lines (96-genotype panel) and four marker panels (PDF 284 kb)

Supplementary Fig. 5

Phylogenetic trees constructed using 387 maize breeding lines and 96 representative maize inbred lines (483 genotypes) (PDF 1883 kb)

Supplementary Table 1

The 96 diverse maize inbred lines (96-genotype panel) were used in this study (XLSX 14 kb)

Supplementary Table 2

The 387 breeding lines (387-genotype panel) selected from the ongoing breeding programs at CAAS (XLSX 24 kb)

Supplementary Table 3

Pairwise differences among eight heterotic groups of maize inbred lines as revealed by four marker panels. The lower diagonal are the average genetic distances between groups. The diagonal cells are pairwise nucleotide diversities within groups (XLSX 13 kb)

Supplementary Table 4

The field cost involved in phenotypic selection across three experimental stations in China (XLSX 14 kb)

Supplementary Table 5

Savings that can be achieved by marker-assisted selection for Fusarium verticillioides ear rot across three experimental stations in China (XLSX 13 kb)

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Guo, Z., Wang, H., Tao, J. et al. Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize. Mol Breeding 39, 37 (2019).

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