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ARS Home » Southeast Area » Canal Point, Florida » Sugarcane Field Station » Research » Publications at this Location » Publication #349230

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

Location: Sugarcane Field Station

Title: Developing 100K Affymetrix Axiom SNP Array for Polyploid Sugarcane

Author
item YOU, QIAN - University Of Florida
item YANG, XIPING - University Of Florida
item SONG, JIAN - University Of Florida
item Islam, Md
item Comstock, Jack
item XU, LIPING - Fujian Agricultural & Forestry University
item WANG, JIANPING - University Of Florida

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/6/2018
Publication Date: 1/13/2018
Citation: You, Q., Yang, X., Song, J., Islam, M.S., Comstock, J.C., Xu, L., Wang, J. 2018. Developing 100K Affymetrix Axiom SNP Array for Polyploid Sugarcane. Plant and Animal Genome Conference. 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 genomes. With the advance of next generation sequencing (NGS) technologies, several millions of SNPs were discovered in Sacchharum spp. through NGS enabled target enrichment sequencing and genotyping by sequencing. To create a high throughput and easy genotyping assay, a 100K SNP array was developed. We selected the SNPs mainly based on two datasets. The first dataset was comprised of 1.2 M non-redundant from a small panel of 12 accessions selected from the world collection of sugarcane and related grasses (WCSRG) through target enrichment sequencing, and 31,415 (2.6%) single dose (SD) SNPs were selected. The second dataset included 3.4 M non-redundant SNPs based on genotyping of 37 sugarcane hybrids selected from WCSRG through target enrichment sequencing, and 68,682 (2.0%) low dosage SNPs (mainly = two copies) were selected. In total, 100,097 SNPs (121,860 probesets) have been implemented on the array with one SNP per 6,404 bases according to sorghum genome. To evaluate the 100K sugarcane SNP array, a bi-parental population of 314 progeny and a diversity panel of 13 sugarcane accessions were genotyped with the newly developed array using Affymetrix Axiom platform. According to the SNP genotyping calling methods of Axiom Best Practices Genotyping Workflow, SNPs were sorted into six quality classes based on the clustering performance. As a result, a total of 62,761 polymorphic SNPs were detected with a polymorphic rate of 62.7%, of which 19,325 SNPs from three quality classes with clear two or three clusters (poly high resolution no minor homozygote, and call rate below threshold) can be utilized for further analysis. This large amount of SNP markers allowed us to construct a high density genetic map for sugarcane, which will be a critical tool for further gene mapping. This SNP array will leverage high throughput genotyping and molecular breeding in sugarcane with minimal effort.