Location: Soil Management and Sugarbeet Research
Title: A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium Yellows resistance QTLAuthor
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Submitted to: DNA Research
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 7/8/2024 Publication Date: N/A Citation: N/A Interpretive Summary: Sugar beet is the source of over half of domestic sugar production in the United States. Multiple pests and pathogens cause substantial yield losses across the major regions of beet sugar production. Improved sugar beet disease resistance is a critical tool for enhancing the long-term resiliency of this industry. USDA-ARS scientists in Fort Collins, CO and Stoneville, MS utilized cutting edge DNA mapping technologies to develop the most complete map of the sugar beet genome to date. The researchers used this new resource to identify a new region of the sugar beet genome responsible for resistance to the disease Fusarium Yellows. This new resistance trait can be used by breeders to improve sugar beet resistance to this important disease. The methods and genome database developed by the ARS team will be critical for the discovery resistance traits for other important diseases. Technical Abstract: Sugar beet (Beta vulgaris L.) is a global source for table sugar and animal fodder. Here we report a highly contiguous and haplotype phased genome assembly and annotation for sugar beet line FC309. Both assembled haplomes for FC309 represent the largest and most contiguous assembled beet genomes reported to date, as well as gene annotations sets that capture over 1500 additional protein-coding loci compared to prior beet genome annotations. These new genomic resources were used to identify novel quantitative trait loci (QTL) for Fusarium Yellows resistance from the FC309 genetic background using an F2 mapping-by-sequencing approach. The highest QTL signals were detected on Chromosome 3, spanning approximately 10Mbp in both haplomes. A parallel transcriptome profiling experiment identified candidate genes within the Chromosome 3 QTL with plausible roles in disease response, including NBS-LRR genes with expression trends suggestive of their role as causal resistance genes. Investigation of genetic variants in these candidate genes found one major disease resistance protein contained high effect variants of interest. Collectively, the genomic resources for FC309 presented here be foundational tool for comparative genomics, mapping other traits in the FC309 background, and as a reference genome for other beet studies due to its contiguity, completeness, and high-quality gene annotations. |
