Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin

Abstract

Key messageThis first pan-Mediterranean analysis of genetic diversity in wild narrow-leafed lupin revealed strong East–West genetic differentiation of populations, an historic eastward migration, and signatures of genetic adaptation to climatic variables.AbstractMost grain crops suffer from a narrow genetic base, which limits their potential for adapting to new challenges such as increased stresses associated with climate change. Plant breeders are returning to the wild ancestors of crops and their close relatives to broaden the genetic base of their crops. Understanding the genetic adaptation of these wild relatives will help plant breeders most effectively use available wild diversity. Here, we took narrow-leafed lupin (Lupinus angustifolius L.) as a model to understand adaptation in a wild crop ancestor. A set of 142 wild accessions of narrow-leafed lupin from across the Mediterranean basin were subjected to genotyping-by-sequencing using Diversity Arrays Technology. Phylogenetic, linkage disequilibrium and demographic analyses were employed to explore the history of narrow-leafed lupin within the Mediterranean region. We found strong genetic differentiation between accessions from the western and eastern Mediterranean, evidence of an historic West to East migration, and that eastern Mediterranean narrow-leafed lupin experienced a severe and recent genetic bottleneck. We showed that these two populations differ for flowering time as a result of local adaptation, with the West flowering late while the East flowers early. A genome-wide association study identified single nucleotide polymorphism markers associated with climatic adaptation. Resolving the origin of wild narrow-leafed lupin and how its migration has induced adaptation to specific regions of the Mediterranean serves as a useful resource not only for developing narrow-leafed lupin cultivars with greater resilience to a changing climate, but also as a model which can be applied to other legumes.Electronic supplementary materialThe online version of this article (10.1007/s00122-017-3045-7) contains supplementary material, which is available to authorized users.

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin

“…Additionally, while early phenotypic studies suggested the Aegean region as the diversity centre of wild narrow-leafed lupin (Clements and Cowling 1994), we recently showed that the western Mediterranean is the centre of genetic diversity. We also demonstrated a strong east–west differentiation among wild narrow-leafed lupin across Mediterranean basin and historic migration from west to east (Mousavi-Derazmahalleh et al 2018b). …”

“…Distribution of wild accessions along the two different lines (Fig. 2) is due to the west/east division of wild samples which was discovered in our previous study (Mousavi-Derazmahalleh et al 2018b). As with the phylogeny result (Fig.…”

“…While narrow-leafed lupin is predominantly a self-pollinated species, different rates of natural cross-pollination (from 0 to 11.95%), in particular through honey bees, have been reported for samples from different geographical regions (Forbes et al 1971). This indicates gene flow between wild and domesticated narrow-leafed lupin, which is due to either random cross-pollination or previously observed west/east migration patterns (Mousavi-Derazmahalleh et al 2018b). …”

“…1). This high level of congruity with geographic origin may reflect the low-level migration between the eastern and western Mediterranean, as shown by Mousavi-Derazmahalleh et al (2018b). While narrow-leafed lupin is predominantly a self-pollinated species, different rates of natural cross-pollination (from 0 to 11.95%), in particular through honey bees, have been reported for samples from different geographical regions (Forbes et al 1971).…”

“…Details of wild accessions were described by Mousavi-Derazmahalleh et al (2018b). Domesticated accessions are from seven countries (Australia, Belarus, Germany, Poland, Russia, Ukraine and South Africa), which cover all the major breeding programmes of narrow-leafed lupin.…”