Date of Award
8-2023
Document Type
Thesis
Degree Name
Master of Science (MS)
Department
Plant and Environmental Science
Committee Chair/Advisor
Dr. Richard E. Boyles III
Committee Member
Dr. Sandra E. Branham
Committee Member
Dr. Christopher A. Saski
Committee Member
Dr. Guido Schnabel
Abstract
Anthracnose of sorghum (causal agent: Colletotrichum sublineola) is the most detrimental disease of sorghum (Sorghum bicolor) worldwide, significantly reducing grain yield. This study includes a literature review of the disease and a meta-analysis of genome-wide association studies (GWAS) of anthracnose-resistance in sorghum as means to elucidate genetic sources of the trait. The meta-analysis includes genotypic and phenotypic data from 5 unique studies and 1,071 sorghum lines. Original genotyping-by-sequencing data from were obtained primarily from National Center for Biotechnology Information’s Sequence Read Archive (NCBI-SRA) and prepared and processed using the Tassel 5 GBS v2. pipeline. Phenotypic data were standardized across studies by reconciling different disease-rating scales and generating BLUPs based on standardized disease ratings. GWAS models were produced using the GAPIT3 R package. Two SNPs, S05_65194648 and S09_1173266, were statistically significant across multiple models. The site on chromosome 5 may be associated with the previously identified Cg1 locus for anthracnose resistance, and the position lies within the transcript for an F-box domain which is a protein structure linked to disease resistance in many crops. Similarly, the site on chromosome 9 was identified as a candidate SNP in one of the composite studies, and it lies within the transcript for a leucine-rich P-loop, also associated with plant defense. The results of this study bring confidence to existing and novel candidate loci for anthracnose resistance on the sorghum genome, while challenges of the analysis highlight the importance of data management in a post-GWAS era of plant-breeding.
Recommended Citation
Behnke, Mary-Frances, "Identifying Genetic Sources of Anthracnose Resistance in Global Sorghum Lines" (2023). All Theses. 4151.
https://tigerprints.clemson.edu/all_theses/4151