Identification of Broad Spectrum Anthracnose Resistance QTL in Sorghum By Whole Genome Sequencing

Anthracnose is one of the most devastating diseases of sorghum (Sorghum bicolor (L.) Moench), caused by the fungal pathogen Collectotrichum sublineolum. We explored the natural variation in sorghum germplasm to identify anthracnose resistant sorghum genotypes. In the present study, we identified a sorghum line of East African origin which was resistant to about ten C. sublineolum isolates. To determine the genetic bases of this anthracnose resistance, a recombinant inbred (RIL) population of 209 lines was generated by crossing the resistant and susceptible sorghum lines and subsequent selfing for many generations. Among these, 50 resistant and 50 susceptible RI individuals were selected based on repeated disease assays on plants inoculated with C. sublineolum in greenhouse experiments. Analysis of whole genome sequences of the resistant and susceptible lines identified QTL for C. sublineolum resistance which  maps to about 8Mb region of chromosome 7 (P < 0.05). A total of 11,170 sequence variations, including 9,567 SNPs, 755 insertions, and 848 deletions, were identified in the QTL region. To increase the success of the gene identification effort, we conducted RNA-seq analysis of the parental lines after mock or fungal inoculation. In the QTL region, the expression of a total of 21 genes were significantly changed after inoculation with C. sublineolum between the resistant and parental lines, including 9 genes which were up-regulated in the resistant line and 12 genes that were down-regulated in the susceptible lines. Further analysis is being conducted to identify the specific sequence change underlying the differences between the resistant and susceptible lines. The RNA-seq coupled with the genomic sequence data are being explored to identify the specific gene underlying this broad spectrum resistance. Future work will validate the resistance gene through the identification and analysis of additional alleles and conducting molecular and functional studies on the resistance gene. Ultimately, this knowledge will be used for improving anthracnose resistance in sorghum.