Joris A. Alkemade, Nelson Nazzicari, Monika M. Messmer, Paolo Annicchiarico, Barbara Ferrari, Ralf T. Voegele, Maria R. Finckh, Christine Arncken & Pierre Hohmann

Theoretical and Applied Genetics; March 2022; vol. 135: 1011–1024

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.

See: https://link.springer.com/article/10.1007/s00122-021-04014-7

Figure 3: Manhattan and corresponding Q–Q plots by MLM showing SNP association with anthracnose resistance. a, b Disease score (standardized area under the disease progress curve (sAUDPC)). c, d Relative lesion size (%). e, f Relative shoot fresh weight. Upper dashed line indicates Bonferroni corrected LOD threshold of 4.96 (P = 1.08E-05), and lower dotted line indicates fixed LOD threshold of 4.3 (P = 5.00E-05).