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.

Quantitative Control of Early Flowering in White Lupin (Lupinus albus L.)

“…Together with the previously published markers [ 26 , 29 , 30 ], the final set used for genotyping of white lupin germplasm collection consisted of 50 markers which enabled us to track all major QTLs of flowering time and 29 white lupin homologs of flowering induction pathway genes ( Supplementary Tables S4 and S5 ). Novel alleles (not present in the parental lines of mapping population) were identified for markers FTc1-F4 (16 lines), CO-F1 (2 lines), TP56963 (two lines), MFT-FT3-F1 (one line), and TP114357 (one line).…”

“…In the L. albus mapping population, several QTL loci for time to flowering were identified hitherto, including five QTLs confirmed in at least two years of observations [ 24 , 25 , 26 ]. Following the construction of a high-density reference linkage map, sequence-defined markers flanking these QTLs were developed [ 26 , 29 ]. Moreover, recent research highlighted candidate genes for four QTLs, namely GIGANTEA ( GI ) for the QTL1, FLOWERING LOCUS T homolog a1 ( FTa1 ) for the QTL2, SEPALLATA 3 ( SEP3 ) for the QTL4 and FRIGIDA3 ( FRI3 ) for the QTL5 [ 30 ].…”

“…Introduction of preferred alleles on one-by-one basis can be inefficient, due to epistatic interactions between major components of flowering regulatory network [ 90 ]. Phenotyping studies revealed that white lupin germplasm collection has variability of many agronomic traits, including, besides time to flowering, winter survival, pod fertility, pod wall proportion, number of leaves on the main stem, several yield related traits and anthracnose resistance [ 11 , 12 , 13 , 29 , 91 , 92 , 93 , 94 ]. Despite relatively small genotype sample size (83 landraces and eight varieties), genomic prediction for grain yield, winter plant survival and onset of flowering provided prospective output, manifested by model-based predictive ability values as high as 0.84–0.86 [ 10 ].…”

“…The white lupin germplasm collection which was subjected to phenotyping of flowering time and vernalization responsiveness, was also genotyped with PCR-based markers. The set of markers included markers for flowering time QTLs developed in this study as well as previously published markers designed for white lupin homologs of flowering control genes [ 30 ] and those developed for the anthracnose resistance QTL localized at the linkage group ALB02 overlapping with the flowering time QTL1 [ 29 ]. Young 5 week-old leaves were collected from plants cultivated in greenhouse and immediately frozen under liquid nitrogen.…”

“…Quantitative trait loci (QTL) mapping, based on the same mapping population, revealed the presence of two major QTLs for anthracnose resistance, located in the linkage groups ALB02 and ALB04, as well as five major QTLs for flowering time, two of them located in the linkage group ALB02 (including one overlapping with the major anthracnose resistance locus), another two in the linkage group ALB13, and one in the linkage group ALB16 [ 24 , 25 , 26 ]. The white lupin molecular toolbox has been recently supplemented with PCR-based markers suitable for tracking Ethiopian alleles of major anthracnose resistance loci, alkaloid locus pauper and main candidate genes controlling flowering induction [ 29 , 30 , 31 ]. Interestingly, white lupin breeders revealed that joining of early flowering with anthracnose resistance in the progeny descending from the cross between Kiev Mutant and P27174 was ineffective, however, replacement of the Ukrainian donor of early flowering by the other (French) thermoneutral germplasm made this process much more feasible [ 22 , 32 ].…”