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

Abstract

Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum, is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.

The inheritance of anthracnose (Colletotrichum sublineola) resistance in sorghum differential lines QL3 and IS18760

“…Remarkably, the proteins encoded by this cluster of six R -genes also have amino acid sequence similarity (> 70%) with proteins encoded by another R -gene cluster at the distal end of chromosome 9 ( Sobic09G013000 , Sobic09G013100 and Sobic09G013300 ), which has been previously associated with anthracnose resistance response 19 , 25 . Moreover, the resistance response of anthracnose-differential line SC112-14 against AMP-048 could not be associated to either genomic region, while the resistance response against the other seven pathotypes was determined by a 34 kb genomic region on chromosome 5 31 . The interaction among effectors produced by AMP-048 and proteins encoded by some of the genes in this R -gene cluster might be associated with the activation of the plant immune system, while resistance alleles for this R -gene cluster are absent in SC112-14.…”

“…The results confirmed that anthracnose resistance response depend on the C. sublineola population present at each location. Multiple studies have shown that anthracnose resistance responses observed in the greenhouse failed under field conditions 28 , 31 , 33 . Small changes in the environmental conditions in the field can favor a greater anthracnose disease pressure to which the plant can respond through a combination of pathogen recognition, activation of the plant immune system and activation of specific metabolic pathways that lead to the production of defense compounds.…”

“…The large diversity of C. sublineola pathotypes within populations in the field causes a large variation in the resistance response among different sorghum genotypes 28 . Inheritance studies of anthracnose resistance response based on field conditions have identified genomic regions containing R -genes, transcription factors and defense-related proteins, suggesting the interaction of multiple defense mechanisms 25 , 26 , 30 , 31 . If multiple R -genes are involved in the defense against different field pathotypes, it is not possible to detect these genomic regions due to the lack of a clear inheritance pattern in a mapping population.…”

“…For instance, in greenhouse evaluations, the lines SC414-12E and SC112-14 were susceptible against some C. sublineola isolates from Georgia and Texas 28 . However, both lines showed a broader resistance response across locations during field evaluations 26 , 31 . In contrast, RTx2536 was shown to be susceptible to anthracnose in the field, but showed resistance against some isolates in the greenhouse.…”

“…Inheritance studies of three anthracnose-differential lines under field conditions (SC748-5, SC112-14 and SC414-12E) identified three major loci located at the distal region of chromosome 5 26 , 30 , 31 , and comparative analysis determined that each line contained independent resistance loci. The resistance locus of SC112-14 was fine mapped to a 34-kb genomic region harboring five genes involved in plant immune resistance response instead of pathogen pattern recognition.…”