Genetic Diversity Analysis of Selected Sugarcane (Saccharum spp. Hybrids) Varieties Using DArT-Seq Technology
Erin B. Bello1*, Jhun Laurence S. Rasco1, Pamella Marie D. Sendon1,
Fe M. Dela Cueva1, Antonio G. Lalusin2, and Antonio C. Laurena1
1Institute of Plant Breeding, College of Agriculture and Food Science,
University of the Philippines Los Baños, Los Baños 4031 Philippines
2Institute of Crop Science, College of Agriculture and Food Science,
University of the Philippines Los Baños, Los Baños 4031 Philippines
Sugarcane is an economically important crop grown for sugar and bioethanol. Most commercial varieties are hybrids of the noble cane Saccharum officinarum and its wild relative S. spontaneum. Sugarcane breeding in the Philippines is focused on the development of new varieties with higher sucrose content and resistance to major fungal diseases. Evaluation of parents for crossing depends on the knowledge of the genetic diversity of the available sugarcane germplasm. In this study, the genetic diversity of 54 local and foreign sugarcane varieties selected from the local germplasm was evaluated through genotyping-by-sequencing (GBS) using diversity arrays technology (DArT). Single nucleotide polymorphisms (SNPs) and silico-DArT (presence/absence) dominant markers were developed using DArT-Seq method, which employs genome complexity reduction method using methylation-sensitive restriction enzymes (REs) and high-throughput next-generation sequencing (NGS). Polymorphism information content (PIC) values of resulting SNP markers range from 0.009 to 0.5 with an average of 0.195, while Silico-DArT markers have PIC values from 0.02 to 0.5 with an average of 0.271. Silico-DArT markers were considered more informative based on higher average reproducibility, call rate, and PIC values. Cluster analysis and principal coordinate analysis using scoring data from SNP and silico-DArT markers showed low-sucrose varieties grouping separately from commercial hybrids developed in the Philippines. However, observed genetic distances among varieties genotyped indicate moderate to high genetic relatedness within the local germplasm, especially among commercially-available varieties in the country. DArT-Seq genotyping was successfully used in analysis of genetic diversity among current commercial varieties and can be a useful tool in the evaluation of new breeding materials for the development of more improved varieties.
Sugarcane is an economically important crop cultivated for sugar and bioethanol production in tropical and subtropical countries. The sugarcane industry is a major component of the Philippines’ agriculture sector, with more than 400,000 hectares of land allocated for sugarcane cultivation alone (SRA 2018). Modern sugarcane varieties were primarily derived from interspecific hybrids of two Saccharum species – the domesticated S. officinarum, the “noble cane,” and its wild relative, S. spontaneum. S. officinarum (2n = 80) had been historically domesticated for its high sugar content, but its susceptibility to diseases led breeders to introgress resistance genes to its genome from the vigorous S. spontaneum (2n = 40–128). Early hybrids were repeatedly back-crossed to S. officinarum to recover high sugar content in its stalks. Continuous hybridizations through the last century resulted to modern varieties with chromosome numbers ranging from 100 to 120, with 70–80% of the genome derived from S. officinarum, 20% from S. spontaneum, and the rest as recombinants of the two. Thus, high polyploidy and aneuploidy – in addition to the presence of highly repetitive sequences – are characteristic of the genome of modern sugarcane varieties (Metcalfe et al. 2015). . . . . read more
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