Sequencing of an Anthracnose‐Resistant Sorghum Genotype and Mapping of a Major QTL Reveal Strong Candidate Genes for Anthracnose Resistance

Abstract

Anthracnose, caused by the fungal pathogen Colletotrichum sublineolum Henn. ex. Sacc. and Trotter 1913, is an economically damaging disease of sorghum [Sorghum bicolor (L.) Moench] in hot and humid production regions of the world. Control of anthracnose is almost exclusively through the use of genetic resistance. To further elucidate genetic resistance to anthracnose, a recombinant inbred line population derived from the cross of BTx623 (susceptible) and SC748‐5 (resistant) was created. A linkage map was constructed using 117 F5 individuals that were genotyped using Digital Genotyping, a genotyping‐by‐sequencing method developed specifically for C4 grasses, on an Illumina GAIIx. The linkage map consists of 619 single nucleotide polymorphism markers and three microsatellites with a total map length of 1269.9 cM. The population was phenotyped for anthracnose in four different environments. Using both composite interval mapping and inclusive composite interval mapping (ICIM), one major quantitative trait locus (QTL) on chromosome 5 was consistently identified as the source of anthracnose resistance in all environments. Sequencing genomic DNA from SC748‐5 and comparison to BTx623 genomic sequence revealed numerous amino acid changes in annotated disease‐resistance genes located in the area under the anthracnose QTL. This suggests that the genetic architecture for anthracnose resistance in SC748‐5 is not under the control of one gene but, more likely, a linkage block containing several resistance genes.

Quantitative Trait Loci Associated with Anthracnose Resistance in Sorghum

“…Leaf tissue from 10‐ to 12‐d‐old seedlings of each genotype was collected and total genomic DNA was extracted using the FastPrep FP120 instrument (Bio 101 Savant) along with the FastDNA Spin Kit (MP Biomedicals) and quantified using a Qubit Fluorometer (Invitrogen). Five hundred nanograms of DNA from each line was digested with the methylation‐sensitive enzyme Fse I (New England BioLabs) and an Illumina template library was made as described by Burrell et al (2015). Standard Illumina protocols were followed for cluster generation from the template and single‐end sequencing was performed on an Illumina GAIIx.…”

“…Hence, a focus of applied breeding programs is to identify multiple genetic resistance sources and then pyramid resistance genes into elite cultivars. Both dominant and recessive sources of genetic resistance to anthracnose have been reported, and resistance loci have been mapped with molecular techniques that include random amplified polymorphic DNA (Boora et al, 1998; Singh et al, 2006), amplified fragment length polymorphisms (AFLPs) (Perumal et al, 2009), simple sequence repeats (Klein et al, 2001; Murali Mohan et al, 2010), complementary DNA‐AFLP transcript profiling in combination with virus‐induced gene silencing (Biruma et al, 2012), and single‐nucleotide polymorphisms (SNPs) (Upadhyaya et al, 2013; Burrell et al, 2015).…”

Sorghum [Sorghum bicolor (L.) Moench] breeding for resistance to leaf and stalk anthracnose, Colletotrichum sublineolum, and improved yield: Progress and prospects

“…Totals of 5186 and 2759 informative SNP markers were identified in the two bi-parental mapping populations used. Burrell et al (2015) created a RIL population of 117 inbred lines, and generated 619 SNP and three microsatellite markers to create a genetic map for QTL analysis. After phenotyping for anthracnose symptoms, they identified a QTL on chromosome 5 that colocalized with the QTL identified by Cuevas et al (2014) and Perumal et al (2009).…”

Dedicated Herbaceous Biomass Feedstock Genetics and Development

“…Sequencing revealed numerous amino acid changes in multiple genes, suggesting that Cg1 is not one resistance gene but a group of several linked resistance genes. This could explain why the resistance to anthracnose conferred by Cg1 appears to be stable across multiple environments [11]. In a separate study, pathotypes of anthracnose from Puerto Rico, Arkansas, and Texas were tested against resistant line SC112-14, and three additional resistance loci were also found on chromosome 5 [21].…”