Abstract
Key messageGWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin.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.
Highlights
White lupin (Lupinus albus L., 2n = 50) is a grain legume with a high-protein content and various health benefits that shows great potential to complement soybean and meet the growing demand for plant-based protein (Abraham et al 2019; Annicchiarico 2008; Lucas et al 2015)
Strong correlations were observed between these three traits and the overall disease assessment means of threeyear field trials in Switzerland (r > (−)0.8; ESM_5)
The Ethiopian landrace P27175 was resistant in one seed batch (FiBL 39) but susceptible in another (FiBL 19) and showed distinct heterozygosity rates of 0.77% and 32.2%, respectively (ESM_1)
Summary
Cultivation of lupins, is severely compromised by the seed- and air-borne fungal pathogen Colletotrichum lupini, causing lupin anthracnose (Nirenberg et al 2002; Talhinhas et al 2016). Theoretical and Applied Genetics and rain-splash dispersal (secondary infection) can cause total yield loss under favorable conditions (Thomas and Sweetingham 2004; White et al 2008). Colletotrichum lupini is a member of the C. acutatum species complex (clade 1), which contains numerous important plant pathogens (Damm et al 2012). Contrary to the broad host range seen for most members of this complex, C. lupini is host specific to members of the genus Lupinus (Baroncelli et al 2017; Talhinhas et al 2016). The pandemic is caused by a globally dispersed and genetically uniform group (II) of highly aggressive strains originating from South America (Alkemade et al 2021b; Dubrulle et al 2020a). Little is known about the interaction between C. lupini and its host, but a hemibiotrophic lifestyle is considered likely (De Silva et al 2017; Dubrulle et al 2020b)
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