NDLI: Development of a maize 55 K SNP array with improved genome coverage for molecular breeding

Content Provider	Springer Nature Link
Author	Xu, Cheng Ren, Yonghong Jian, Yinqiao Guo, Zifeng Zhang, Yan Xie, Chuanxiao Fu, Junjie Wang, Hongwu Wang, Guoying Xu, Yunbi Li, Ping Zou, Cheng
Copyright Year	2017
Abstract	With the decrease of cost in genotyping, single nucleotide polymorphisms (SNPs) have gained wide acceptance because of their abundance, even distribution throughout the maize (Zea mays L.) genome, and suitability for high-throughput analysis. In this study, a maize 55 K SNP array with improved genome coverage for molecular breeding was developed on an Affymetrix® Axiom® platform with 55,229 SNPs evenly distributed across the genome, including 22,278 exonic and 19,425 intronic SNPs. This array contains 451 markers that are associated with 368 known genes and two traits of agronomic importance (drought tolerance and kernel oil biosynthesis), 4067 markers that are not covered by the current reference genome, 734 markers that are differentiated significantly between heterotic groups, and 132 markers that are tags for important transgenic events. To evaluate the performance of 55 K array, we genotyped 593 inbred lines with diverse genetic backgrounds. Compared with the widely-used Illumina® MaizeSNP50 BeadChip, our 55 K array has lower missing and heterozygous rates and more SNPs with lower minor allele frequency (MAF) in tropical maize, facilitating in-depth dissection of rare but possibly valuable variation in tropical germplasm resources. Population structure and genetic diversity analysis revealed that this 55 K array is also quite efficient in resolving heterotic groups and performing fine fingerprinting of germplasm. Therefore, this maize 55 K SNP array is a potentially powerful tool for germplasm evaluation (including germplasm fingerprinting, genetic diversity analysis, and heterotic grouping), marker-assisted breeding, and primary quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) for both tropical and temperate maize.
Starting Page	1
Ending Page	12
Page Count	12
File Format	PDF
ISSN	13803743
Journal	Molecular Breeding
Volume Number	37
Issue Number	3
e-ISSN	15729788
Language	English
Publisher	Springer Netherlands
Publisher Date	2017-02-16
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Maize Single nucleotide polymorphism (SNP) 55 K SNP array DNA fingerprinting Molecular breeding Plant Sciences Plant Genetics & Genomics Plant Pathology Plant Physiology Biotechnology
Content Type	Text
Resource Type	Article
Subject	Genetics Plant Science Molecular Biology Biotechnology Agronomy and Crop Science

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