Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance

Key message GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. Abstract White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.

Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]

In warm-humid ago-ecologies of the world, sorghum [Sorghum bicolor (L.) Moench] production is severely affected by anthracnose disease caused by Colletotrichum sublineolum Henn. New sources of anthracnose resistance should be identified to introgress novel genes into susceptible varieties in resistance breeding programs. The objective of this study was to determine genome-wide association of Diversity Arrays Technology Sequencing (DArTseq) based single nucleotide polymorphisms (SNP) markers and anthracnose resistance genes in diverse sorghum populations for resistance breeding. Three hundred sixty-six sorghum populations were assessed for anthracnose resistance in three seasons in western Ethiopia using artificial inoculation. Data on anthracnose severity and the relative area under the disease progress curve were computed. Furthermore, the test populations were genotyped using SNP markers with DArTseq protocol. Population structure analysis and genome-wide association mapping were undertaken based on 11,643 SNPs with <10% missing data. The evaluated population was grouped into eight distinct genetic clusters. A total of eight significant (P < 0.001) marker-trait associations (MTAs) were detected, explaining 4.86–15.9% of the phenotypic variation for anthracnose resistance. Out of which the four markers were above the cutoff point. The significant MTAs in the assessed sorghum population are useful for marker-assisted selection (MAS) in anthracnose resistance breeding programs and for gene and quantitative trait loci (QTL) mapping.

Assessment of the adaptive potential of strawberry genotypes based on the development of endophytic microbiota and identified R-genes

The paper presents the results of a study of the strawberry genotypes (Fragaria L.) by characteristics of endophytic microbiota and genetic determinants of resistance to fungal pathogens. Highly adaptive genotypes were identified: F. virginiana Duch. ssp. platypetala, F. orientalis Los., F. ovalis Rydb., F. moschata Duch., 298-19-9-43, Urozhaynaya CGL, Flora, Privlekatelnaya and Troitskaya. These strawberry forms are characterized by a high frequency of testing of bacterial microbiota, which suppresses endophytic fungal pathogens. The wild strawberry F. virginiana Duch. ssp. platypetala is characterized by red stele root rot resistance (Rpf1 gene). Strawberry varieties Borovitskaya and Elianny are characterized by anthracnose resistance (Rca2gene).

Occurrence of anthracnose pathogen races and resistance genes in common bean across 30 years in Brazil

Anthracnose caused by Colletotrichum lindemuthianum is one of the most critical diseases in the common bean (Phaseolus vulgaris L.). The characterization and localization of pathogenic fungal races are essential for understanding pathogen population dynamics and recommending strategies to develop resistant cultivars. As resistant genotypes are the most economical and ecologically safe means of controlling plant diseases, there have been efforts to characterize resistance genes in common bean. Several studies using a system of 12 differential bean cultivars have been carried out to monitor anthracnose since 1991, reporting the constant appearance of new fungal races. C. lindemuthianum shows high virulence diversity. The objective of the present study was to review the relationship between C. lindemuthianum races and the common bean pathogenic processes involved in the risk of developing anthracnose disease. As a result, 89 races occurred in Brazil, wherein 73, 65, and 81 of C. lindemuthianum are the most frequent. Furthermore, we built a map with the anthracnose resistance loci, molecular markers, and their respective physical position. The accessibility to the genomes and sequencing technologies permits molecular markers for marker-assisted selection applied to anthracnose-resistant cultivars. This study could be used as a reference for future resistance mapping studies and as a guide for selecting resistance loci in breeding programs aiming to develop common bean cultivars with durable anthracnose resistance.

Optimizing seedling screening method for anthracnose resistance in watermelon

Among three races of Colletotrichum orbiculare, causes of anthracnose of cucurbits, screening for race 2 resistance was studied under greenhouse conditions at various inoculum concentrations and rated plants on different days post inoculation (DPI). The objectives of this study were optimizing inoculum concentration and phenotyping DPI for seedling resistance. Five inoculum concentrations were compared (2.5 x 104, 5 x 104, 1 x 105, 2.5 x 105, and 5 x 105 conidial spore ml-1). Four watermelon genotypes, ‘Black Diamond’, ‘Charleston Gray 133’, PI 543210, PI 189225, and two cucumber genotypes, ‘Marketer’, and ‘H19 Little Leaf’ were evaluated. Disease was recorded on the percentage of cotyledon area lesion (PCL), severity of hypocotyl lesion (SHL), severity of petiole lesion (SPL), percentage of leaf area lesion (PLL), as well as a disease index (INDX) from 5 to 14 DPI. There was a significant difference among genotypes and inoculum concentrations. The resistant PI 189225 was significantly different (P < 0.05) from the highly susceptible PI 543210. Inoculum 1 x 105 spore ml-1 was at par with 5 x 105 and 2.5 x 105 but significantly different from 5 x 104 and 2.5 x 104 for AUDPS PLL, AUDPS INDX, AUDPS SPL, and AUDPS SHL. Inoculum at 1 x 105 spore ml-1 was the most optimal to differentiate germplasm. Genotype plus genotype-by-environment (GGE) biplot showed that PLL was a representative trait. A single PLL rating on 9 DPI would optimize resources for screening a large set of germplasm for anthracnose resistance in a watermelon breeding program.