Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.).

BACKGROUND: Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between 'Criollo de Morellos-334' (CM-334), a resistant landrace from Mexico, and 'Early Jalapeno', a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. RESULTS: Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. CONCLUSIONS: Results support the genetic complexity of the P. capsici-Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

Etiology of Alternaria Leaf Spot of Cotton in Southern New Mexico.

Alternaria leaf spot (caused by Alternaria spp.) is one of the most common foliar diseases of cotton (Gossypium spp.) and occurs in most cotton-growing regions of the world. In surveys of commercial cotton fields, Alternaria leaf spot has increased in prevalence and incidence in southern New Mexico due to favorable environmental conditions in recent years. Incidence, severity, and etiology of leaf spot of cotton in southern New Mexico were determined. Fourteen cotton fields with plants exhibiting leaf spot symptoms were evaluated in October and November 2016, when plants were at late growth stage. Disease incidence was 100% in 13 of the fields, and averaged 70% in the 14th field. Average disease severity index for all fields ranged from 21.5 to 87.0. For identification of the causal agent, 14 isolates (one from each field) were characterized based on morphological features and PCR using universal primers ITS4/ITS5 and primers targeting the plasma membrane ATPase gene. Colonies of all 14 isolates were olive green with distinct white margins and relatively small spores when compared with reference isolates of large-spored species. All 14 isolates were identified as A. alternata. The fungus grew on potato dextrose agar from 5 to 35°C, and optimum growth occurred at temperatures between 20 and 30°C. Cotton plants inoculated with selected isolates of A. alternata displayed symptoms similar to those observed under field conditions. This is the first report of A. alternata as a causal agent of Alternaria leaf spot on cotton in southern New Mexico.