Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.)

Abstract

White lupin (Lupinus albus L.) is a high-protein grain legume crop, grown since ancient Greece and Rome. Despite long domestication history, its cultivation remains limited, partly because of susceptibility to anthracnose. Only some late-flowering, bitter, low-yielding landraces from Ethiopian mountains displayed resistance to this devastating disease. The resistance is controlled by various genes, thereby complicating the breeding efforts. The objective of this study was developing tools for molecular tracking of Ethiopian resistance genes based on genotyping-by-sequencing (GBS) data, envisaging linkage mapping and genomic selection approaches. Twenty GBS markers from two major quantitative trait loci (QTLs), antr04_1/antr05_1 and antr04_2/antr05_2, were converted to PCR-based markers using assigned transcriptome sequences. Newly developed markers improved mapping resolution around both anthracnose resistance loci, providing more precise QTL estimation. PCR-based screening of diversified domesticated and primitive germplasm revealed the high specificity of two markers for the antr04_1/antr05_1 locus (TP222136 and TP47110) and one for the antr04_2/antr05_2 locus (TP338761), highlighted by simple matching coefficients of 0.96 and 0.89, respectively. Moreover, a genomic selection approach based on GBS data of a recombinant inbred line mapping population was assessed, providing an average predictive ability of 0.56. These tools can be used for preselection of candidate white lupin germplasm for anthracnose resistance assays.

Keywords: Anthracnose resistance; Genomic selection; Marker-assisted selection; Quantitative trait; White lupin.

Fig. 1

Major QTLs for anthracnose resistance in white lupin. Linear plots show LOD values (threshold 3.5); rectangles, LOD-based QTL ranges (LOD 2.0 and 1.0 below the maximum value), whereas bar graphs visualize corresponding linkage group fragments. Names of markers included into PCR-based assay are bold faced. Colors correspond to QTL assays: interval mapping, IM, blue (antr04, the first year) and green (antr05, the second year); composite interval mapping, CIM, pink (antr04) and red (antr05). Linkage groups and LOD graphs are drawn to scale

Fig. 2

Linkage disequilibrium pattern observed for PCR-based markers from ALB02 (a) and ALB04 (b) linkage groups. The set of 107 white lupin lines originating from 22 countries (81 primitive populations and landraces and 26 domesticated) was used to estimate R² values

Fig. 3

Predictive ability of ridge regression BLUP models as measured by Pearson’s correlation between true and predicted values as a function of the maximum allowed missing rate for single SNP markers, for three anthracnose disease resistance scores from the first year (antr04), the second year (antr05), and mean from both years (antr_avg). Values are derived through 10-fold cross-validations and averaged over 50 repetitions