Genetic analysis of sorghum (Sorghum bicolor (L.) Moench ssp.) for resistance to anthracnose (Colletotrichum sublineolum) and grain mold diseases

Abstract

Fungal diseases, such as anthracnose and grain mold pose significant challenges to the production and productivity of sorghum. Favored by warm and humid conditions, sorghum Anthracnose (Colletotrichum sublineolum) is among the most devastating diseases of sorghum that can cause yield losses of up to 50% in susceptible cultivars. It can attack all above-ground parts including foliage, stalk, panicle, and grain. The severity of infection depends on the genotype, the pathotype, and the environment. Grain mold is another major sorghum disease that is prevalent under warm and wet conditions that occur during grain development. This disease is caused by one or more genera of fungi of which Aspergillus and Fusarium are the most common. Breeding efforts have focused on the development of resistant varieties that can reduce the impact of these diseases. Conventional breeding supported by genomic tools may enhance this effort and accelerate the release of new resistant cultivars. To contribute to this endeavor three experiments were initiated and executed. This dissertation thus presents the results of a comprehensive investigation into enhancing resistance to sorghum anthracnose and grain mold diseases through genomic selection, genome-wide association studies (GWAS), and combining ability analysis. The first chapter explores the utilization of genomic selection techniques to improve anthracnose and grain mold resistance in sorghum through prediction using genomic estimated breeding values (GEBVs). Through the integration of advanced genomic tools and phenotypic data, we demonstrated the potential for accurately predicting resistance levels in sorghum lines, that may facilitate the development of more resilient cultivars. During the 2015 and 2016 cropping seasons, a study was conducted in Bako, Ethiopia, involving 946 sorghum accessions obtained from the gene bank. These accessions were examined for resistance to sorghum leaf anthracnose (Colletotrichum sublineolum) and grain mold. Genotyping of these accessions was performed using the genotype-by-sequencing (GBS) method, resulting in the generation of 410,717 high-quality SNP markers. To investigate the impact of SNP density on prediction accuracy, the markers were pruned using TASSEL software, maintaining marker distances of 1,000 bp, 50,000 bp, 75,000 bp, and 100,000 bp between them. The analysis involved varying the size of the training population from 10% to 90% at intervals of 10%. Principal component analysis was carried out to assess the genetic relatedness patterns among the sorghum accessions. For anthracnose resistance, we obtained a prediction accuracy of 0.38 and 0.45 for the 10% and 90% training population sizes respectively for the 2016 data. A prediction accuracy of 0.38 and 0.41 were recorded for grain mold at 10% and 80% training population sizes. In the second experiment, a GWAS study was conducted to identify key genomic regions and candidate genes associated with sorghum anthracnose resistance. Our analysis unveiled the presence of Single Nucleotide Polymorphisms (SNPs) on several chromosomes, specifically chromosomes 1, 2, 3, 4, 6, 8, and 10. Notably, chromosomes 8 and 1 exhibited a higher abundance of significant SNPs. Chromosome 8 displayed the most pronounced genetic associations, with nine specific loci (S8_16230498, S8_16389715, S8_37466666, S8_39664335, S8_42468301, S8_42983043, S8_43776246, S8_7908407, and S8_570182) having significant associations with anthracnose disease reaction. Similarly, we identified multiple loci on chromosome 1 (S1_20098885, S1_49271328, S1_49271328, S1_49454848, S1_50111275, S1_50294000, S1_50533418, S1_30455882, and S1_50721682) that also have significant association with the disease. Chromosome 2 revealed two significant loci (S2_55407842 and S2_69275221), while only one locus on chromosome 3 (S3_53970498) showed significant association. Two loci each on chromosomes 4 (S4_62789639, S4_7538383) and chromosome 6, (S6_25755784, and S6_55783758) were shown to have significant association with the disease. By leveraging high-throughput genotyping data and extensive phenotypic evaluations, this research provides valuable insights into the genetics of anthracnose resistance, offering a foundation for marker-assisted breeding efforts. The third experiment explored the combining ability of sorghum lines for anthracnose resistance. By assessing the genetic interactions among different sorghum parental lines, this study elucidated the potential for breeding strategies that harness the complementary genetic contributions of parental lines to enhance resistance traits in the progeny. We conducted the experiment across five different environments and collected data on various agronomic traits, including flowering time (DTF), plant height (PTH), panicle weight (PKW), grain yield per panicle (GYP), hundred-grain weight (HGW), and resistance to anthracnose (ANT). Our findings indicated that there were significant variations in trait reactions across different replicates and environmental conditions, particularly for PTH, GYP, and ANT due to notable environmental effects. The entry effect, which represents the contributions of different parental lines and hybrid combinations, was highly significant for all traits we examined. Additionally, the interaction between male and female parents (M vs. F) showed a high level of significance specifically for ANT. A negative significant correlation was observed between panicle weight and anthracnose and grain yield per panicle and anthracnose. Through our combining ability analysis, we were able to identify the genetic contributions of various genotypes. Notably, certain parents such as R245, R604, R633, A539, and A553 exhibited high general combining ability (GCA) for anthracnose resistance. Furthermore, some hybrid combinations like A539 × R669, A527 × R672, A531 × R672, A539 × R588 demonstrated highly significant specific combining ability (SCA) effects for anthracnose resistance. These findings provide valuable insights for breeders, enabling them to make well-informed decisions when designing breeding strategies. Collectively, this thesis represents a multidisciplinary approach to addressing the pressing issue of anthracnose and grain mold resistance in sorghum. The findings contribute to the development of more resilient sorghum cultivars, thus supporting global food security and sustainable agriculture practices.