Identification of sources of resistance to scald (Rhynchosporium commune) and of related genomic regions using genome-wide association in a mapping panel of spring barley.

Barley is an important crop worldwide known for its adaptation to harsh environments and used in multiple forms as feed, food and beverages. Its productivity is affected by major abiotic and biotic stresses. Scald caused by hemibiotrophic fungus Rhynchosporium commune is a major foliar disease in many parts of the world. Host plant resistance is targeted by breeders to efficiently control this disease. An association mapping panel of 316 spring barley genotypes (AM2017) was screened for seedling resistance in greenhouse against three R. commune isolates and for adult plant resistance in three field locations in Morocco. The phenotyping results showed different numbers of entries with resistant and moderately resistant reactions at both seedling and adult plant stages. The reactions differed between the isolates with the highest percentage of resistant genotypes observed for isolate SC-S611 (49.4%) and highest percentage of susceptible genotypes (73.8%) for isolate SC-1122. At adult plant stage, the highest percentage of scald resistant genotypes (64.5%) was observed at Rommani site compared to 56% at Guich site and only 28.8% at Marchouch site. Seven genotypes were resistant at the seedling and adult plant stages. Genome wide association study (GWAS) revealed 102 MTA (15 QTL) at the seedling stage, and 25 MTA (12 QTL) associated with scald resistance at the adult plant stage. In addition, the sequences of 92 out of 102 at SRT, and 24 out of 25 significant SNP markers at APR were located in genomic regions enriched with functional proteins involved in diverse cellular processes including disease resistance. These markers span over all chromosomes with the majority of SNPs located on 3H and 7H. This study has verified 18 QTL reported in previous studies. In addition, it was successful in identifying new sources of resistance and novel genomic regions which could help in enhancing scald resistance in barley breeding programs.

Assessment and modeling using machine learning of resistance to scald (Rhynchosporium commune) in two specific barley genetic resources subsets.

Barley production worldwide is limited by several abiotic and biotic stresses and breeding of highly productive and adapted varieties is key to overcome these challenges. Leaf scald, caused by Rhynchosporium commune is a major disease of barley that requires the identification of novel sources of resistance. In this study two subsets of genebank accessions were used: one extracted from the Reference set developed within the Generation Challenge Program (GCP) with 191 accessions, and the other with 101 accessions selected using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS). These subsets were evaluated for resistance to scald at the seedling stage under controlled conditions using two Moroccan isolates, and at the adult plant stage in Ethiopia and Morocco. The results showed that both GCP and FIGS subsets were able to identify sources of resistance to leaf scald at both plant growth stages. In addition, the test of independence and goodness of fit showed that FIGS filtering approach was able to capture higher percentages of resistant accessions compared to GCP subset at the seedling stage against two Moroccan scald isolates, and at the adult plant stage against four field populations of Morocco and Ethiopia, with the exception of Holetta nursery 2017. Furthermore, four machine learning models were tuned on training sets to predict scald reactions on the test sets based on diverse metrics (accuracy, specificity, and Kappa). All models efficiently identified resistant accessions with specificities higher than 0.88 but showed different performances between isolates at the seedling and to field populations at the adult plant stage. The findings of our study will help in fine-tuning FIGS approach using machine learning for the selection of best-bet subsets for resistance to scald disease from the large number of genebank accessions.

Identification of Resistance Sources and Genome-Wide Association Mapping of Septoria Tritici Blotch Resistance in Spring Bread Wheat Germplasm of ICARDA.

Septoria tritici blotch (STB) of wheat, caused by the ascomycete Zymoseptoria tritici (formerly Mycosphaerella graminicola), is one of the most important foliar diseases of wheat. In Morocco, STB is a devastating disease in temperate wheat-growing regions, and the yield losses can exceed up to 50% under favorable conditions. The aims of this study were to identify sources of resistance to STB in Septoria Association Mapping Panel (SAMP), which is composed of 377 advanced breeding lines (ABLs) from spring bread wheat breeding program of ICARDA, and to identify loci associated with resistance to STB at seedling (SRT) as well as at the adult plant (APS) stages using genome-wide association mapping (GWAM). Seedling resistance was evaluated under controlled conditions with two virulent isolates of STB (SAT-2 and 71-R3) from Morocco, whereas adult plant resistance was assessed at two hot spot locations in Morocco (Sidi Allal Tazi, Marchouch) under artificial inoculation with a mixture of STB isolates. At seedling stage, 45 and 32 ABLs were found to be resistant to 71-R3 and SAT-2 isolates of STB, respectively. At adult plant stage, 50 ABLs were found to be resistant at hot spot locations in Morocco. Furthermore, 10 genotypes showed resistance in both locations during two cropping seasons. GWAM was conducted with 9,988 SNP markers using phenotypic data for seedling and the adult plant stage. MLM model was employed in TASSEL 5 (v 5.2.53) using principal component analysis and Kinship Matrix as covariates. The GWAM analysis indicated 14 quantitative trait loci (QTL) at the seedling stage (8 for isolate SAT-2 and 6 for isolate 71-R3), while 23 QTL were detected at the adult plant stage resistance (4 at MCH-17, 16 at SAT-17, and 3 at SAT-18). SRT QTL explained together 33.3% of the phenotypic variance for seedling resistance to STB isolate SAT-2 and 28.3% for 71-R3, respectively. QTL for adult plant stage resistance explained together 13.1, 68.6, and 11.9% of the phenotypic variance for MCH-17, SAT-17, and SAT-18, respectively. Identification of STB-resistant spring bread wheat germplasm in combination with QTL detected both at SRT and APS stage will serve as an important resource in STB resistance breeding efforts.