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ARS Home » Southeast Area » Canal Point, Florida » Sugarcane Field Station » Research » Publications at this Location » Publication #363321

Research Project: Development of High-Yielding, Stress Tolerant Sugarcane Cultivars Using Agronomic, Genetic, and Molecular Approaches

Location: Sugarcane Field Station

Title: Developing and applying sugarcane 100K SNP array for sugarcane genetic map construction and QTL identification

item YOU, QIAN - University Of Florida
item YANG, XIPING - University Of Florida
item PENG, ZE - University Of Florida
item Islam, Md
item Sood, Sushma
item LUO, ZILIANG - University Of Florida
item COMSTOCK, JACK - Retired ARS Employee
item XU, LIPING - Fujian Agriculture And Forest University
item WANG, JIANPING - University Of Florida

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: 6/22/2019
Publication Date: 12/20/2019
Citation: You, Q., Yang, X., Peng, Z., Islam, M.S., Sood, S.G., Luo, Z., Comstock, J.C., Xu, L., Wang, J. 2019. Developing and applying sugarcane 100K SNP array for sugarcane genetic map construction and QTL identification. American Society of Sugar Cane Technologists. 39:34.

Interpretive Summary: N/A

Technical Abstract: Genotyping high polyploidy sugarcane has been a challenging task for sugarcane genetic studies. To accelerate genetic studies in sugarcane, a customized sugarcane100K single nucleotide polymorphism (SNP) array was developed. The 100,097 SNPs markers were selected from approximately 4.5 million SNPs called from target enrichment sequencing of 300 sugarcane accessions in the world collection of sugarcane and related grass species through a serial of criteria, with a focus on single dose (SD) or low dosage SNPs to be tiled on Affymetrix SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This newly developed array was used to genotype 469 sugarcane clones, including a F1 population derived from interspecific cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. High-density linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3,482 SD SNP markers spanning 3,336 cM, a map for IND81-146 with 1,513 SD SNP markers spanning 2,615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3,651 cM. Quantitative trait loci (QTL) analysis identified a total of 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high throughput genotyping in highly polyploid sugarcane.