Genome-wide association mapping of resistance to the sorghum aphid in sorghum bicolor

Authors: PUNNURI, SOMASHEKHAR - Fort Valley State University; AYELE, ADDISSU - Fort Valley State University; Harris-Shultz, Karen; Knoll, Joseph - Joe; Coffin, Alisa; Tadesse, Haile; Armstrong, John; WIGGINS, TRAHMAD - Fort Valley State University; LI, HANXIA - University Of Georgia; Sattler, Scott; WALLACE, JASON - University Of Georgia

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/10/2022
Publication Date: 6/15/2022
Citation: Punnuri, S., Ayele, A., Harris-Shultz, K.R., Knoll, J.E., Coffin, A.W., Tadesse, H.K., Armstrong, J.S., Wiggins, T., Li, H., Sattler, S.E., Wallace, J. 2022. Genome-wide association mapping of resistance to the sorghum aphid in sorghum bicolor. Genomics. 114(4). Article 110408. https://doi.org/10.1016/j.ygeno.2022.110408.
DOI: https://doi.org/10.1016/j.ygeno.2022.110408

Interpretive Summary: The sugarcane aphid has been an economically important pest to sorghum since a new biotype invaded the United States in 2013. Multiple sorghum accessions with host plant resistance have been identified but only a region on Chromosome 6 which includes the RMES1 (Resistance to Melanaphis sacchari 1) locus has been associated with resistance. In this study, we utilized a diverse collection of 283 sorghum accessions to identify additional genetic regions that confer sugarcane aphid resistance. Using a combination of field and greenhouse studies as well as data from visual observations and reflectance-based imagery, we consistently identified two regions in the sorghum genome associated with sugarcane aphid resistance. These regions are located on sorghum chromosome 8 at 11,781,182 bp and sorghum chromosome 10 at 2,507,813 bp. Some of the genes in or near these regions are known to function in resistance to diseases, pests, or other stresses, and are likely candidates for further study. Breeding multiple resistance genes into elite sorghum lines will enhance the durability of host resistance to the sugarcane aphid.

Technical Abstract: Since 2013, the sugarcane aphid (SCA), Melanaphis sacchari (Zehntner), has been a serious pest that hampers all types of sorghum production in the U.S. Our understanding of sugarcane aphid resistance in sorghum is limited to knowledge about a few genetic regions on chromosome SBI-06. In this study, a subset of the Sorghum Association Panel (SAP) was used along with some additional lines to identify genetic regions that confer sugarcane aphid resistance. These lines were grown in the field and visually evaluated for SCA resistance during the growing seasons of 2019 and 2020 in Tifton, GA. In 2020, the SAP accessions were also evaluated for SCA resistance in the field using drone-based high throughput phenotyping (HTP) and visual scoring under greenhouse conditions. Plant height and flowering time were also recorded in the field to confirm that our methods were sufficient for identifying known quantitative trait loci (QTL). This study combined phenotypic data from field-based visual ratings, reflectance-based data, and greenhouse evaluations to identify genome-wide associated (GWAS) marker-trait associations (MTA) using genotyping-by-sequencing (GBS) data. Several MTAs were identified for sugarcane aphid-related traits across the genome, with a few common markers that were consistently identified on SBI-08 and SBI-10 for aphid count and plant damage as well as for reflectance indices-based traits on SBI-02, SBI-03, and SBI-05. Candidate genes encoding leucine-rich repeats (LRR), lipoxygenases (LOXs), calmodulins (CAM), WRKY transcription factors, flavonol biosynthesis genes, and 12-oxo-phytodienoic acid reductase are near SNPs that had significant associations with different SCA traits. In this study, plant height and flowering time-related genes were also identified. The total phenotypic variation explained by significant SNPs across SCA-scored traits, plant height, and flowering time ranged from 0 to 74%, while the heritability value ranged from 4 to 74%. These results supported the existing literature, and also revealed several new loci. Markers identified in this study will support marker-assisted breeding for sugarcane aphid resistance.