Genome-wide association mapping of anthracnose (Colletotrichum sublineolum) resistance in NPGS Ethiopian sorghum germplasm

Authors: Cuevas, Hugo; Prom, Louis; Cruet-Burgos, Clara

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/28/2019
Publication Date: 9/1/2019
Citation: Cuevas, H.E., Prom, L.K., Cruet-Burgos, C. 2019. Genome-wide association mapping of anthracnose (Colletotrichum sublineolum) resistance in NPGS Ethiopian sorghum germplasm. G3, Genes/Genomes/Genetics. 9(9): 2879-2885. https://doi.org/10.1534/g3.119.400350.
DOI: https://doi.org/10.1534/g3.119.400350

Interpretive Summary: Anthracnose (Colletotrichum sublineolum) is becoming the major disease of sorghum [Sorghum bicolor (L.) Moench] in warm and humid sorghum production regions of the world. The most cost-effective and environmentally benign way to control anthracnose is through incorporation of resistance genes. Therefore, a core-set of 322 NPGS Ethiopian accessions were evaluated for anthracnose to identify 165 resistance accessions. Genome-wide association scan identified two loci on chromosome 5 and 9 that explained 51% of the variation, indicating other undetected loci are present. Inheritance study found loci in chromosome 9 have a dominant mode of action making it suitable for seed hybrid production. The integration of these anthracnose resistance accessions into breeding programs should aid in the development of new anthracnose resistant varieties.

Technical Abstract: The National Plant Germplasm System (NPGS) Ethiopian sorghum [Sorghum bicolor (L.) Moench] collection of the United States is an important genetic resource for sorghum improvement. Anthracnose (Colletotrichum sublineolum) is one of the most harmful fungal diseases in humid sorghum production regions. Although multiple resistance sources have been identified in temperate-adapted germplasm present in the Sorghum Association Panel (SAP); these identified resistance loci only explain a limited portion of the variation, while exotic sources of resistance are not currently available for breeding programs. Thus, a core set of 335 NPGS Ethiopian accessions previously genotyped was evaluated to identify 165 resistant to anthracnose. To identify loci associated with anthracnose resistance, the genotypic and anthracnose response data of both NPGS Ethiopian germplasm and the SAP were merged and genome-wide association scans (GWAS) conducted using 219,037 single-nucleotide polymorphisms (SNPs) and 617 accessions. The integration of NPGS Ethiopian germplasm with SAP allowed the detection of a locus in chromosome 9 present in the SAP at low frequency; while increased the detection power for a previously identified locus in chromosome 5. Both loci explain 60% of the observed resistance response in NPGS Ethiopian accessions indicating the presence of other resistance loci. A candidate gene search in chromosome 9 locus yielded three R-genes clustered within a 47 kb region. Inheritance study based on two F2 populations determined chromosome 9 locus has a dominant mode of action that can be beneficial for sorghum hybrid production. The integration of NPGS exotic germplasm is needed to identify additional rare resistance alleles in the SAP, and to determine which NPGS exotic accessions might be enclosing new sources of resistance