Location: Sugarcane Research
Title: Selecting Single-dose Single Nucleotide Polymorphism (SNP) Markers for Accurate Identification of Sugarcane Clones (Saccharum spp. hybrids) Using KASP GenotypingAuthor
Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only Publication Acceptance Date: 12/2/2024 Publication Date: N/A Citation: N/A Interpretive Summary: Since 2005, fluorescence-labeled Microsatellite (SSR) DNA markers and their genotyping method have been developed and routinely used in the Louisiana sugarcane industry to construct molecular identities of crossing parents, breeding lines, and foreign introductions. These molecular identities are archived in a sugarcane molecular identity database, which has been utilized to ensure the correct clones are involved in sugarcane breeding, micro-propagation, and field research projects, as well as to promote sugarcane genetics and genomics research. However, the SSR-based method is laborious, expensive, and requires manual scoring of DNA fingerprints. In this study, we selected and validated a low-density SNP array (including 118 single-dose SNPs), which is sufficient to distinguish among 188 samples from 80 sugarcane clones (Saccharum spp. hybrids) held at the USDA-ARS Sugarcane Research Unit in Houma, LA. Validated through Kompetitive Allele-Specific PCR (KASP) assays, this SNP panel accurately detected all duplicated samples included in this study, with genotyping results fully compatible with those from SSR genotyping. Moreover, the SNP genotyping data enabled the reconstruction of pedigree relationships among the 80 sugarcane clones tested, revealing insights into the genetic background of the improved Louisiana sugarcane clones. This low-density SNP array therefore provides a high-throughput alternative to the SSR genotyping method currently used by the U.S. sugarcane industry. Technical Abstract: Since 2005, fluorescence-labeled Microsatellite (SSR) DNA markers and their genotyping method have been developed and routinely used in the Louisiana sugarcane industry to construct molecular identities of crossing parents, breeding lines, and foreign introductions. These molecular identities are archived in a sugarcane molecular identity database, which has been utilized to ensure the correct clones are involved in sugarcane breeding, micro-propagation, and field research projects, as well as to promote sugarcane genetics and genomics research. However, the SSR-based method is laborious, expensive, and requires manual scoring of DNA fingerprints. In this study, we selected and validated a low-density SNP array (including 118 single-dose SNPs), which is sufficient to distinguish among 188 samples from 80 sugarcane clones (Saccharum spp. hybrids) held at the USDA-ARS Sugarcane Research Unit in Houma, LA. Validated through Kompetitive Allele-Specific PCR (KASP) assays, this SNP panel accurately detected all duplicated samples included in this study, with genotyping results fully compatible with those from SSR genotyping. Moreover, the SNP genotyping data enabled the reconstruction of pedigree relationships among the 80 sugarcane clones tested, revealing insights into the genetic background of the improved Louisiana sugarcane clones. This low-density SNP array therefore provides a high-throughput alternative to the SSR genotyping method currently used by the U.S. sugarcane industry. |