Genome-wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.)

Authors: YANG, XIPING - University Of Florida; LUO, ZILIANG - University Of Florida; Todd, James; Sood, Sushma; WANG, JIANPING - University Of Florida

Submitted to: Plant Methods
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/12/2019
Publication Date: 3/20/2020
Citation: Yang, X., Luo, Z., Todd, J.R., Sood, S.G., Wang, J. 2020. Genome-wide association study of multiple yield traits in a diversity panel of polyploid sugarcane (Saccharum spp.). Plant Methods. https://doi.org/10.1002/tpg2.20006.
DOI: https://doi.org/10.1002/tpg2.20006

Interpretive Summary: Sugarcane is an important economic crop, contributing up to 80% of sugar and approximately 60% of bio-fuel globally. To meet the increased demand for sugar and bio-fuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits using conventional and/or molecular approaches. In this study, we evaluated and analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the “world collection of sugarcane and related grasses”. Genome-wide association studies (GWAS) between the markers and traits were conducted with dosages and gene actions taken into consideration. In total, 217 non-redundant markers and 225 candidate genes were identified to be significantly associated with the yield traits. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel, characterized 282 ROHs, and found that the occurrence of ROH in the genome were non-random, and probably under selection. ROHs were associated with total weight and dry weight, and high ROHs resulted in decrease of the two traits.

Technical Abstract: Background: Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of bio-fuel globally. To meet the increased demand for sugar and bio-fuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance by providing genetic resources, and fundamental information for crop improvement. Results: In this study, we evaluated and analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the “world collection of sugarcane and related grasses”. By genotyping the sugarcane diversity panel using target enrichment sequencing (TES), we identified a large number of sequence variants in sugarcane. Genome-wide association studies (GWAS) between the markers and traits were conducted with dosages and gene actions taken into consideration. In total, 217 non-redundant markers and 225 candidate genes were identified to be significantly associated with the yield traits. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel, characterized 282 ROHs, and found that the occurrence of ROH in the genome were non-random, and probably under selection. ROHs were associated with total weight and dry weight, and high ROHs resulted in decrease of the two traits. Conclusions: We performed GWAS in a representative sugarcane diversity panel, and the current study was substantially improved by applying TES and GWASpoly, allowing us to differentiate all genotypes of sequence variants in sugarcane, and to do GWAS with six different models regarding different gene actions. We identified hundreds of DNA markers and candidate genes associated with the nine yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement on yield traits. For the first time, we studied ROH in sugarcane, and our results suggested that genomic inbreeding has led to negative impacts on sugarcane yield. This research provided valuable and novel genomic resources and tools for sugarcane breeding programs, and empowered GWAS analyses in this polyploid species.