Tools for Chrysanthemum genetic research and breeding: Is genotyping-by-sequencing (GBS) the best approach?

Abstract

Chrysanthemum, which belongs to the Asteraceae family, is a floriculture crop with ornamental, industrial, and medicinal value. Chrysanthemum breeding programs have generated genetic linkage maps and identified molecular markers for important traits. Chrysanthemum species have a complex genetic background, and several studies on Chrysanthemum species have been published in the last 3 decades. The Chrysanthemum genome was published by Amway Botanical RD however, the molecular breeding of Asteraceae is not well studied yet. Next-generation sequencing (NGS) technologies, genotyping-by-sequencing (GBS), and association mapping have facilitated the identification of novel genetic markers. Chrysanthemum species have a very large genome and include diploid and polyploid species (such as allohexaploids) with complex hereditary features such as self-incompatibility systems and inbreeding depression. The development of NGS technologies allowed the advance of high-throughput DNA sequencing for detecting and single nucleotide polymorphisms (SNP) in various plant species. Through NGS, a large number of SNPs detected via whole-genome sequencing can be used as markers in breeding and genetic studies. While SNP markers allow rapid analyses, contribute to the low cost of genome-wide scans, and are sequenced by numerous efficient platforms in diverse genetic backgrounds, GBS can be advantageous for the study of gene function, genetic variation, and heredity, specifically in modern plant breeding. In addition, GBS can reduce genome complexity, allowing SNP discovery and genotyping of sequences without a reference genome. This review focuses on the tools used for genomic research and breeding in Chrysanthemum, and discusses the processes in SNP development and study of the evolutionary processes in Chrysanthemum species.