A multiplex PCR marker distinguishes between a series of four LanFTc1 alleles regulating flowering time in narrow‐leafed lupin (Lupinus angustifolius)

We designed and validated a new multiplex PCR marker which discriminates between four insertion/deletion (INDEL) alleles in the 5′ regulatory region of a major flowering time gene in Lupinus angustifolius, LanFTc1. The four INDEL alleles were the wild‐type allele (ku) in variety ‘Geebung’ (G), a 1,208‐bp deletion allele in accession P22660 (P), a 1,423‐bp deletion allele (Ku) in variety ‘Tanjil’ (T) and a 5,162‐bp deletion allele (Jul) in variety ‘Krasnolistny’ (K). F2 PCR marker genotypes segregated as expected in populations K × G, K × T, P × G and P × T. Heritability of flowering times based on F2:3 parent:offspring correlation was high in K × G (0.81 ± 0.09), P × G (0.76 ± 0.10) and P × T (0.81 ± 0.11) but low in K × T (−0.04 ± 0.15) due to similar early‐flowering phenotypes produced by Ku and Jul. Progeny homozygous for the 1,208‐bp deletion allele resulted in a unique array of mid‐season phenology in the F2, F3 and F4 generations, which may improve agronomic adaptation. This multiplex PCR marker will improve the efficiency of introgression of the new INDELs into future lupin varieties.