Characterizing untapped Ethiopian barley agrobiodiversity to identify novel targets for molecular breeding

Modern crop varieties, including those genetically improved by either conventional or molecular approaches, have been developed to maximize agricultural yields. Their superior traits, however, often depend on the use of large quantities of agricultural inputs, including fertilizers, phytochemicals, and water. When optimal growing conditions are not met, the performance of these varieties may become sub-par insofar they lack traits of local adaptation. Traditional crop varieties, including landraces maintained in smallholder farming systems, have a great potential in transferring resilience traits to modern varieties aiming at combining yield stability with local adaption. This study aims at characterizing the genetic basis of traits of agronomic interest in Ethiopian barley landraces (Hordeum vulgare L.), and untapped reservoir of alleles that may be relevant for breeding. It does so by using an interconnected multi-parental advanced generation intercross (iMAGIC) population, a novel multi-parental design characterized by a high mapping resolution and power. Five hundred iMAGIC lines, including the founder lines, were previously cultivated and phenotyped at two locations in Ethiopia (Dabat and Geregera) for two consecutive years (2022 and 2023). Collected phenotypes include phenological, agronomic, and post-harvest data. In order to identify genomic loci associated with phenotypic best linear unbiased predictions (BLUPs), we performed a genome wide association study (GWAS) by running the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model using a genomic association and predicted integrated tool (GAPIT_3.1.0). Here we identified quantitative trait nucleotides (QTNs) associated with well-known genes, such as flowering-time genes PHOTOPERIOD-H1 (PPD-H1) and VRN-H3, row-type gene SIX-ROWED SPIKE1 (VRS1), and semi-dwarfing gene Sdw1. According to our analyses, VRS1 has a pleiotropic effect on numerous phenotypic BLUPs beyond row-type. Finally, we have identified a gene on chromosome 6H, which is contained in a QTL hotspot known to play a fundamental role in agronomically relevant complex traits.