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ARS Home » Southeast Area » Canal Point, Florida » Sugarcane Field Station » Research » Publications at this Location » Publication #340757

Research Project: Enhancement of Sugarcane Germplasm for Development of Stress Tolerant, High Yielding Cultivars

Location: Sugarcane Field Station

Title: Development and utilization of 100K SNP array in Saccharum Spp.

Author
item You, Qian
item Yang, Xiping
item Song, Jian
item Islam, Md
item Xu, Liping
item Comstock, Jack
item Wang, Jianping

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: 5/8/2017
Publication Date: 6/16/2017
Citation: You, Q., Yang, X., Song, J., Islam, M.S., Xu, L., Comstock, J.C., Wang, J. 2017. Development and utilization of 100K SNP array in Saccharum Spp.. American Society of Sugar Cane Technologists. ABSTRACT ONLY.

Interpretive Summary: N/A

Technical Abstract: Sugarcane genotyping or fingerprinting has long been a daunting task due to its high polyploidy level with large number of chromosomes. Single nucleotide polymorphisms (SNPs) are very abundant DNA sequence variations in the genome. With the advance of next generation sequencing (NGS) technologies, millions of SNPs were discovered in Sacchharum spp. through NGS enabled target enrichment sequencing and genotyping by sequencing. To develop a high throughput and easy genotyping assay, a 100K SNP array was developed. We selected the SNPs mainly based on two classes. The first class included 68,682 single dose (SD) SNPs based on the genotyping of 37 sugarcane hybrids selected from the world collection of sugarcane and related grasses (WCSRG) through target enrichment sequencing. The second class was comprised of 31, 415 SD SNPs from a small panel of 12 accessions selected from WCSRG, which had proven to be low dosage SNPs (mainly less than 3 copies) in the 37 hybrids. In total, 100, 097 SNPs (121, 806 probe sets) have been implemented on the array with one SNP per 6, 404 bases according to the sorghum genome. To evaluate the 100K sugarcane SNP array, 480 sugarcane clones were isolated and genotyped on the 100K SNP array using the Affymetrix Axiom platform. According to the SNP genotyping calling methods of Axiom Best Practices Genotyping Workflow, SNPs were grouped into six quality classes based on the clustering performance for several quality-control measurements. As a result, a total of 62,761 polymorphic SNP markers were detected with a polymorphic rate of 62.7%. Genotypes of the 62K polymorphic SNPs were called by using superMASSA software. This large amount of SNP markers will allow us to construct a high density genetic map for sugarcane, which will be a critical tool for further gene mapping. This developed SNP array could be a critical and easy assay tool in sugarcane genetics and genomics studies, which will expedite develop of molecular markers and leverage molecular breeding in sugarcane.