White Lupin Adaptation to Moderately Calcareous Soils: Phenotypic Variation and Genome-Enabled Prediction

Abstract

White lupin is a promising high-protein crop, the cultivation of which is limited by a lack of adaptation to soils that are even just mildly calcareous. This study aimed to assess the phenotypic variation, the trait architecture based on a GWAS, and the predictive ability of genome-enabled models for grain yield and contributing traits of a genetically-broad population of 140 lines grown in an autumn-sown environment of Greece (Larissa) and a spring-sown environment of the Netherlands (Ens) that featured moderately calcareous and alkaline soils. We found large genotype × environment interaction and modest or nil genetic correlation for line responses across locations for grain yield, a lime susceptibility score, and other traits, with the exception of individual seed weight and plant height. The GWAS identified significant SNP markers associated with various traits that were markedly inconsistent across locations, while providing direct or indirect evidence for widespread polygenic trait control. Genomic selection proved to be a feasible strategy, owing to a moderate predictive ability for yield and lime susceptibility in Larissa (the site featuring greater lime soil stress). Other supporting results for breeding programs where the identification of a candidate gene for lime tolerance and the high reliability of genome-enabled predictions for individual seed weight.

Genome-wide association study revealed significant SNPs for anthracnose resistance, seed alkaloids and protein content in white lupin

“…Genomic prediction in white lupin has been shown to be successful for grain yield, drought tolerance, anthracnose resistance and a set of morphological traits (Annicchiarico et al 2023 , 2019 ; Pecetti et al 2023 ; Rychel-Bielska et al 2020 ). In this study, the approach of genomic selection was applied to predict anthracnose resistance, seed alkaloid and protein content phenotype in white lupin.…”

“…The lack of modern breeding tools has hampered until recently the progress of white lupin improvement. The establishment of genetic maps, definition of first molecular markers for key traits (Phan et al 2007 ; Yang et al 2010 ; Rychel-Bielska et al 2020 ; Rychel and Książkiewicz 2019 ; Alkemade et al 2022b ), application of genomic selection (Rychel-Bielska et al 2020 ; Annicchiarico et al 2019 , 2023 ; Pecetti et al 2023 ) and publication of the genome sequence for cultivar Amiga (2 n = 50, 451 Mb) and variants from 39 accessions (Hufnagel et al 2020 , 2021 ) allow now to boost breeding research and marker development for this valuable yet neglected crop.…”