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

Abstract

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.

Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata)

“…The “statgenGWAS” v.1.0.5 R package (van Rossum 2020 ) was utilized to perform GWAS on all traits. This package utilizes a linear mixed model (LMM) and has been used in several studies (Brzozowsk et al 2021 ; Alkemade et al 2022 ). With the statgenGWAS package, the genetic relationships between the cabbage accessions were calculated and a kinship matrix was created to correct for population structure.…”

Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose

“…Virulence tests were performed on white lupin cultivar Feodora and Andean lupin landraces LUP17 and LUP100 with C. lupini isolates JA01 (II), CBS19225 (I), RB121 (I), and JA23 (IV) through stem‐wound inoculation as described by (Alkemade, Messmer, Arncken, et al, 2021 ). The method was shown to highly correlate with three‐year field trials in Switzerland (Alkemade, Nazzicari, et al, 2022 ). Disease scores ranging from 1 (nonpathogenic) and 2 (low virulence) to 9 (highly virulent; Alkemade, Messmer, Arncken, et al, 2021 ) were taken 3, 7, and 10 days postinoculation (dpi) and the sAUDPC was calculated (Jeger & Viljanen‐Rollinson, 2001 ).…”

“…Virulence tests were performed on white lupin cultivar Feodora and Andean lupin landraces LUP17 and LUP100 with C. lupini isolates JA01 (II), CBS19225 (I), RB121 (I), and JA23 (IV) through stemwound inoculation as described by (Alkemade, Messmer, Arncken, et al, 2021). The method was shown to highly correlate with threeyear field trials in Switzerland (Alkemade, Nazzicari, et al, 2022).…”

“…As no effective sustainable treatment is available yet (Alkemade, Arncken, et al, 2022 ), host resistance would be the most desired solution. Recent studies identified three resistance genes in blue lupin (Fischer et al, 2015 ; Yang et al, 2004 , 2008 ) and one candidate gene and two major quantitative trait loci in white lupin (Alkemade, Nazzicari, et al, 2022 ; Książkiewicz et al, 2017 ). To aid resistance breeding in lupin crops, a better understanding of C. lupini population structure and evolution is required as different populations may vary in geographic distribution and differ in pathogenicity, virulence, or other biological traits.…”

“…As no effective sustainable treatment is available yet (Alkemade, Arncken, et al, 2022), host resistance would be the most desired solution. Recent studies identified three resistance genes in blue lupin (Fischer et al, 2015;Yang et al, 2004Yang et al, , 2008 and one candidate gene and two major quantitative trait loci in white lupin (Alkemade, Nazzicari, et al, 2022;Książkiewicz et al, 2017).…”