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Title: Development of an Axiom Sugarcane 100K SNP array for high-resolution genetic map construction and QTL identification

Author
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
item XU, LIPING - Fujian Agricultural & Forestry University
item WANG, JIANPING - University Of Florida

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2019
Publication Date: 7/18/2019
Citation: You, Q., Yang, X., Peng, Z., Islam, M.S., Sood, S.G., Luo, Z., Comstock, J.C., Xu, L., Wang, J. 2019. Development of an Axiom sugarcane 100K SNP array for high-resolution genetic map construction and QTL identification. Journal of Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-019-03391-4.
DOI: https://doi.org/10.1007/s00122-019-03391-4

Interpretive Summary: Next generation sequencing (NGS) enable us to identify thousands of Single nucleotide polymorphisms (SNPs) marker for genotyping and fingerprinting. However, the process requires very precise bioinformatics analysis and filtering process. High throughput SNP array with predefined genomic location could overcome the problem. A 100K SNP array has been developed for facilitating high throughput and easy genotyping service for the sugarcane researcher. We selected the SNPs mainly based on two classes. The first class included 68,682 single dose (SD) SNPs based on 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 based on 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.

Technical Abstract: To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single dose (SD) and 68,648 low dosage (33,277 SD and 35,371 double dose) SNPs were selected and tiled on Affymetrix Axiom 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 one 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 3,514 SD SNP markers spanning 3,336 cM, a map for IND81-146 with 1,518 SD SNP markers spanning 2,615 cM, and a map for CP80-1827 with 562 SD SNP markers spanning 3,073 cM. Quantitative trait loci (QTL) analysis identified a total of 19 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.