Genome‐Wide Association Mapping of Anthracnose (Colletotrichum sublineolum) Resistance in the U.S. Sorghum Association Panel

Abstract

The productivity and profitability of sorghum [ (L.) Moench] is reduced by susceptibility to fungal diseases, such as anthracnose ( P. Henn.). A limited number of resistant accessions are present in the temperate-adapted germplasm; other exotic sources of resistance are not currently available for breeding programs. Among 335 accessions available to breeders from a previously genotyped sorghum association panel (SAP), we found that 75 were resistant to anthracnose. A phylogenetic analysis of these accessions showed high genetic diversity and multiple resistance sources. Genome-wide association scans (GWAS) were conducted using 268,289 single-nucleotide polymorphisms to identify loci associated with anthracnose resistance. Using logistic regressions for binary measures of resistance responses, we identified three loci within a region on chromosome 5 that have been previously associated with three sources of anthracnose resistance. A GWAS limited to Caudatum germplasm identified an association with a region on chromosome 1 and with the same previous region on chromosome 5. Candidate genes within these loci were related to R-gene families, signaling cascades, and transcriptional reprogramming, suggesting that the resistance response is controlled by multiple defense mechanisms. The strategic integration of exotic resistant germplasm into the SAP is needed to identify additional rare resistance alleles via GWAS.

Conserved defense responses between maize and sorghum to Exserohilum turcicum

“…Several resources have been developed for genomewide association mapping in sorghum [22,28,29]. Association mapping has been used in sorghum for diverse traits and has been successfully used to identify genes that are known to underlie given traits [30,31]. Here we used the SCP because all lines flower in central Illinois, and plant height is relatively uniform.…”

Genomic Dissection of Anthracnose (Colletotrichum sublineolum) Resistance Response in Sorghum Differential Line SC112-14

“…Approximately ten C. sublineolum-colonized seeds were placed into the leaf whorl of 30-45 day-old-plants. The anthracnose resistance responses of the lines were determined approximately 30-45 days after flowering (harddough stage to physiological maturity) using the scale described by , which has been proven successful for identifying anthracnose resistance loci (Ramasamy et al 2009;Felderhoff et al 2016;Cuevas et al 2018;Cuevas et al 2019). Each single-row plot was visually inspected for presence of anthracnose disease and the most infected plant was used to determine the disease score based on a 1-5 scale, where 1 = no symptoms or chlorotic flecks in the plot; 2 = hypersensitive reaction, but no acervuli present in the plot; 3 = infected bottom leaves with acervuli formation in at least one plant within the plot; 4 = necrotic lesions with acervuli observed on bottom leaves and spreading to middle leaves in at least one plant within the plot; and 5 = most leaves necrotic due to infection, including infection of the flag leaf in at least one plant within the plot.…”

“…Genome-wide association analysis within the anthracnose resistance locus Three previous GWAS analyses for anthracnose resistance response in the sorghum association panel (SAP) (Cuevas et al 2018;Prom et al 2019), and NPGS Ethiopian collection (Cuevas et al 2019) were combined to conduct an association analysis limited to the 276 SNPs present in the resistance locus on chromosome 5 (65.17 to 65.64 Mb). A total of 280 accessions from SAP have been evaluated against pathotypes from Puerto Rico, Georgia and Texas, U.S.A. of which 35 accessions were found to be resistant across locations.…”

“…Genome-wide association studies (GWAS) for anthracnose resistance response using the SAP and a core-set of the NPGS Ethiopian collections identified candidate genes within QTL intervals previously identified on chromosomes 5 and 9. Based on the anthracnose resistance response in the SAP observed in Puerto Rico and Georgia (U.S.A.), three loci were identified within a 12-Mb region on chromosome 5 that may match the loci identified in SC112-14, SC414-12E, and SC748-5 (Cuevas et al 2018). Nevertheless, these three loci only explained 56% of the observed phenotypic variation, implying the presence of other resistance sources in the panel.…”

“…The sorghum association panel (SAP) is comprised of 149 U.S. breeding lines and 228 lines adapted to temperate regions and was assembled to capture the majority of genetic diversity present in sorghum germplasm and breeding programs (Casa et al 2008). Among 335 accessions from the SAP evaluated against pathotypes from Puerto Rico, Texas and Georgia, 37 were resistant to all tested pathotypes of anthracnose (Cuevas et al 2018;Prom et al 2019). Unfortunately, the lack of information on the genetic control of resistance in these sources has limited their use in breeding programs.…”