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With 1 figure and 4 tables Abstract Marker-assisted selection (MAS) is desirable for breeding non-shattering pods in narrow-leafed lupin and for facilitating the process of broadening the gene pool of existing domesticated Australian lupin cultivars. In this study, we developed a molecular marker using a strategy to incorporate the validation step during the candidate marker identification step by microsatellite-anchored fragment length polymorphisms (MFLP). Three MFLP polymorphisms showing banding patterns consistent with pod-shattering phenotypes on the 12 representative F8 recombinant inbred lines (RILs) were identified as candidate markers linked to lentus. One of these three markers matching the lentus phenotypes on representative cultivars and wild accessions was selected and converted into a co-dominant PCR-based marker, named LeLi. When marker LeLi was applied to 25 cultivars released in Australia and 125 wild core accessions of the Australian Lupin Collection, an overall matching rate of 60.67% was found assuming correct determination of the phenotypes. This newly developed marker is simple PCR-based and co-dominant and can be used for MAS in current lupin breeding in Western Australia.

Wild plants of Lupinus angustifolius avoid extinction in a drought year by production of seeds with coats that are impermeable to water, preventing germination of a large percentage of the seed in any given year. Domesticated cultivars of this species carry the recessive gene mollis, making the seed coat permeable to water and, in turn promoting good crop establishment in the year of sowing. A dominant microsatellite-anchored fragment length polymorphism candidate marker was identified as being tightly linked to mollis in a population of recombinant inbred lines derived from domesticated and wild-type parents. The candidate marker was excised from the gel, amplified by PCR, sequenced and extended beyond the SSR end of the original MseI-SSR fragment. Two single nucleotide polymorphisms were found within this extended sequence. Specific primers were designed to create a marker 209 bp long. PCR products of these primers run on a single strand conformation polymorphism gel resolved in a co-dominant fashion. This marker will be used in marker-assisted selection for mollis when introgressing wild material into lupin breeding programmes.

Wild types of Lupinus angustifolius require vernalization to promote flowering. Modern domesticated cultivars carry the early-flowering gene Ku which removes this requirement. A microsatellite-anchored fragment length polymorphism marker was identified as co-segregating with the Ku gene in a recombinant inbred line (RIL) population derived from a domesticated x wild-type cross. DNA sequencing showed that the marker contained a 7 bp insertion/deletion polymorphism, as well as a single nucleotide polymorphism. A pair of sequence-specific primers was designed and successfully converted the size polymorphism into a simple polymerase chain reaction based co-dominant marker. This marker is closely linked to the Ku gene, as it co-segregates with the Ku phenotyping in a population consisting of 106 RILs.