Genomics and Applied Biology 2024, Vol.15, No.1, 8-11 http://bioscipublisher.com/index.php/gab 8 Scientific Review Open Access A New Chapter in Sugarcane Genomics: Constructing the R570 Reference Genome and the Future of Agricultural Biotechnology MayWang , JimFang Hainan Institute of Tropical Agricultural Resources, Sanya, 572024, China Corresponding email: whmj919@gmail.com Genomics and Applied Biology, 2024, Vol.15, No.1 doi: 10.5376/gab.2024.15.0002 Received: 20 Nov., 2023 Accepted: 22 Dec., 2023 Published: 5 Jan., 2024 Copyright © 2024 Wang and Fang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wang M., and Fang J., 2024, A new chapter in sugarcane genomics: constructing the R570 reference genome and the future of agricultural biotechnology, Genomics and Applied Biology, 15(1): 8-11 (doi: 10.5376/gab.2024.15.0002) A paper titled "The Complex Polyploid Genome Architecture of Sugarcane" by A.L. Healey, O. Garsmeur, J.T. Lovell, et al., from institutions including the Hudson Alpha Institute for Biotechnology, CIRAD, and the University of Queensland, was published in the journal Nature on March 27, 2024. This research successfully constructed a polyploid reference genome for the sugarcane (Saccharum spp.) variety R570. As the highest-yielding crop worldwide, sugarcane is a crucial source of sugar and biomass production. Despite certain successes in adapting to new environments and pathogens through traditional breeding methods, the increase in sugarcane's sugar yield has plateaued in recent years. By generating a polyploid reference genome for the R570 variety, this study fills a gap in the lack of high-quality reference genomes for modern sugarcane varieties, marking an important step forward for biotechnological advancements in sugarcane. 1 Experimental Data Analysis The study employed a range of cutting-edge genomics technologies, including high-throughput Illumina sequencing, high-accuracy PacBio HiFi sequencing, and precise chromosome flow sorting, to successfully construct a high-continuity reference genome for the sugarcane variety R570. The genome size is estimated at 10Gb, reflecting the characteristic traits of a modern hybrid variety created through the breeding of two primary parent species of sugarcane: Saccharum officinarum and Saccharum spontaneum. Furthermore, the genome annotation work identified 194,593 genes, significantly enriching our understanding of the complex polyploid genome structure of sugarcane and providing valuable resources for exploring the genetic diversity and functional genomics of sugarcane. The size of this genome and the number of genes reflect the genetic complexity and richness of sugarcane as a significant agricultural and bioenergy plant, laying a solid foundation for further molecular breeding, genetic improvement, and disease prevention research. Figure 1 illustrates the pedigree and genome structure of the hybrid sugarcane R570. From Figure 1a, it is seen that R570 is a sugarcane variety approximately 4 meters in height. Figure 1b details the breeding pedigree of R570, where pie charts show the genome contributions from wild sugarcane (red) and sweet sugarcane (blue) to R570. The asterisks "*" represent the diploid chromosome transmission in the first two generations, and the "+" indicates the first generation of hybrids. Although the exact pedigrees of ‘R331’ and ‘Co213’ are unknown, they are estimated to be BC2F2 and BC2:BC1 F1, respectively. Figure 1c shows R570 chromosomes prepared after in situ hybridization with wild sugarcane-specific probes, with the red parts marking the chromosomes from wild sugarcane. Figure 1d is the karyotype of R570, with colors corresponding to those in figure 1b. This information helps researchers understand the complex polyploid genome structure of R570 hybrid sugarcane. Figure 2 presents the genome assembly information for the sugarcane variety R570. Figure 2a is a schematic of the main assembly of the R570 genome, showing that each homologous chromosome has about 12 chromosome copies, but almost identical haplotypes are folded in the genome assembly due to backcrossing and 2n+n chromosome transmission (indicated by different colored shadows). Figure 2b shows the one-to-one orthologous
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