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Anthracnose susceptibility and ill-adapted flowering time severely affect  Lupinus luteus  yield, which has high seed protein content, is excellent for sustainable agriculture, but requires genetic improvement to fulfil its potential. This study aimed to (1) develop a genetic map; (2) define collinearity and regions of synteny with  Lupinus angustifolius ; and (3) map QTLs/candidate genes for anthracnose resistant and flowering time. A few linkage groups/genomic regions tended to be associated with segregation distortion, but did not affect the map. The developed map showed collinearity, and syntenic regions with  L. angustifolius . Major QTLs were mapped in syntenic regions. Alleles from the wild parent and cultivar, explained 75% of the phenotypic variance for anthracnose resistance and 83% for early flowering, respectively. Marker sequences flanking the QTLs showed high homology with the  Lanr1  gene and  Flowering-locus-T  of  L. angustifolius . This suggests orthologous genes for both traits in the  L. luteus  genome. The findings are remarkable, revealing the potential to combine early flowering/anthracnose resistant in fulfilling yield capacity in  L. luteus , and can be a major strategy in the genetic improvement and usage of this species for sustainable protein production. Allele sequences and PCR-marker tagging of these genes are being applied in marker assisted selection.

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Genetic and comparative mapping of Lupinus luteus L. highlight syntenic regions with major orthologous genes controlling anthracnose resistance and flowering time