Abstract
Key messageThis study revealed that the western Mediterranean provided the founder population for domesticated narrow-leafed lupin and that genetic diversity decreased significantly during narrow-leafed lupin domestication.The evolutionary history of plants during domestication profoundly shaped the genome structure and genetic diversity of today’s crops. Advances in next-generation sequencing technologies allow unprecedented opportunities to understand genome evolution in minor crops, which constitute the majority of plant domestications. A diverse set of 231 wild and domesticated narrow-leafed lupin (Lupinus angustifolius L.) accessions were subjected to genotyping-by-sequencing using diversity arrays technology. Phylogenetic, genome-wide divergence and linkage disequilibrium analyses were applied to identify the founder population of domesticated narrow-leafed lupin and the genome-wide effect of domestication on its genome. We found wild western Mediterranean population as the founder of domesticated narrow-leafed lupin. Domestication was associated with an almost threefold reduction in genome diversity in domesticated accessions compared to their wild relatives. Selective sweep analysis identified no significant footprints of selection around domestication loci. A genome-wide association study identified single nucleotide polymorphism markers associated with pod dehiscence. This new understanding of the genomic consequences of narrow-leafed lupin domestication along with molecular marker tools developed here will assist plant breeders more effectively access wild genetic diversity for crop improvement.
Highlights
The ancestral origin of crop species is one of the primary questions in plant domestication
For the Fst and genome-wide association study (GWAS) analyses, we used a subset of 38,948 SNP markers that was mapped to pseudo-chromosomes and 11,690 SNPs were utilised for phylogeny, population structure and linkage disequilibrium studies
Phylogenetic analysis clearly distinguished wild from domesticated accessions, and four wild accessions from the western Mediterranean (P22839 and P22829 from Portugal, P22770 from Spain and P22845 from Morocco) were basal to the domesticated accessions (Fig. 1)
Summary
The ancestral origin of crop species is one of the primary questions in plant domestication. Current distribution of wild progenitors of crops often provides a reliable indicator of where domestication occurred. Unravelling fundamental stages in the evolution of domesticated plants is another keystone of domestication research. This includes isolating and characterising domestication genes, inferring historic population bottlenecks and gene flow based on extant patterns of genetic diversity and the accumulation of yield- and quality-related minor genes. The emergence of new genomic tools has both revolutionised the precision of these studies and extended their breadth beyond the major staple crop species (Emshwiller 2006; Gepts 2014; Larson et al 2014; Mousavi-Derazmahalleh et al 2018a)
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