Genetic Diversity in Narrow-Leafed Lupin Breeding After the Domestication Bottleneck

Abstract

Narrow-leafed lupins (Lupinus angustifolius L.) were fully domesticated as a valuable grain legume crop in Australia during the mid-twentieth century. Pedigree records are available for 31 released varieties and 93 common ancestors from 1967 to 2016, which provides a rare opportunity to study genetic diversity and population inbreeding in a crop following a domestication bottleneck. From the 1930s–1960s, partially domesticated germplasm was exchanged among lupin breeders in eastern and western Europe, Australia, and USA. Mutants of two founder parents contributed to the first fully domesticated narrow-leafed lupin variety “Uniwhite” in 1967. Four Phases of breeding are proposed after domestication in the Australian lupin breeding program: Foundation (1967–1987), First Diversification (1987–1998), Exploitation (1998–2007), and Second Diversification (2007–2016) Phases. Foundation Phase varieties had only two or three founder parents following the domestication bottleneck and high average coefficient of coancestry (f = 0.45). The First Diversification Phase varieties were derived from crosses with wild lupin ecotypes, and varieties in this Phase had lower average coefficient of coancestry (f = 0.27). Population coancestry increased in varieties of the Exploitation Phase (f = 0.39). The rate of inbreeding (ΔF) between the First Diversification and Exploitation Phase (10 years) was 0.09 per cycle, which equates to 9% loss of alleles per cycle due to random drift and low-effective population size (N_e = 5.4), assuming two 5-year cycles. New genetic diversity was introduced in the Second Diversification Phase varieties (f = 0.24) following more crossing with wild lupins. Genetic progress in Australian lupin breeding so far has been substantial with improvements in grain yield and disease resistance, but narrow genetic diversity will limit future genetic progress. The pedigree of the latest varieties includes 39.1% from three founder varieties in the domestication bottleneck and 48.3% from 9 wild ecotypes that survived 50 years of selection. In terms of conservation genetics, the Australian lupin breeding program is a critically endangered population, and subject to excessive random drift. Migration of genetic diversity from wild lupins or exchange with international breeding programs will improve long-term genetic gain and effectiveness of genomic selection.