Investigation of SNP molecular markers in the sucrose synthesis genes of sugarcane using Restriction Site Associated DNA Sequencing (RAD-seq)

Abstract

At present, Breeding sugarcane varieties to achieve good and desirable characteristics has not been as successful as it should be, for the most part, sugarcane breeding still uses conventional breeding methods in which the breeders with the desired characteristics are mixed. Using the external appearance, it takes a long period for the selection of sugarcane varieties that have characteristics that are suitable for agricultural use for farmers. Single-nucleotide polymorphism (SNP) marker is important resources for marker-assisted selection by Restriction site Associated DNA Sequencing (RAD-Seq). The molecular markers can be used to determine species identity, Detection the hybrid varieties and Classification the related species. Here, we performed restriction-site-associated DNA sequencing (RAD-seq.) on 16 sugarcane varieties such as UT17 LK92-11 KK07-250 KK09-0857 UT15 KK09-0939 K88-92 KK07-599 KK08-059 DOA-NS1 KK09-0941 DOA-KK3 DOA-KK4 KK07-037 KK09-0844 and Si Samrong1 which were collected at Khon Kaen Field Crops Research Center (KKFCRC). An average of 1.9 million SNPs and 23,000 INDELs were identified from each individual.Then, we constructed the maximum likelihood phylogenetic tree based on SNPs data and revealed that the grouping is in association with the sugar content levels or commercially extractable sucrose (C.C.S.) content of sugarcane varieties in group 1 were of 9-12 and group 2 were 13-15. In addition to the results of sucrose synthesis genes clustering, implicating the remarkable effectiveness and potential applications in genetic analysis and breeding techniques for sugarcane varieties and other agricultural crops.