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

Mahsa Mousavi-Derazmahalleh,Dmitry Filatov,David Edwards,James K Hane,Karam B Singh,Jens D Berger,William Erskine,Bruno Nevado,Matthew N Nelson,Bhavna Hurgobin,Lars G Kamphuis,Philipp E Bayer,Andrzej Kilian

doi:10.1007/s00122-017-3045-7

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.Most 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.

Highlights

Agriculture is facing the ‘perfect storm’ of factors that threaten global food security including continued population growth, a rapidly changing climate, reduced water available to agriculture, soil erosion and increasing costs of fertilisers (Abberton et al 2015; Gomiero 2016)
This, together with the recent release of a comprehensive reference genome for narrow-leafed lupin (Hane et al 2017), provides an excellent opportunity to study regional adaptation in wild narrow-leafed lupin within their full native range. To this end, using different genomics and bioinformatics approaches, we addressed the following questions: (1) How does genetic diversity in narrow-leafed lupin vary across its native range? (2) What can we deduce about the demographic history of this species? and (3) Can we detect regions of the genome associated with climatic adaptation? The information will be valuable to understand the origins of a wild crop ancestor such as narrow-leafed lupin, which serves as a model to identify sources of genetic and adaptive diversity to adapt crops to changing environments
Due to the evidence of whole-genome triplication in the genome of narrow-leafed lupin (Hane et al 2017; Kroc et al 2014), we kept those single nucleotide polymorphism (SNP) that had a maximum of three matches in the reference genome (11,690 SNPs remained)

Summary

Introduction

Agriculture is facing the ‘perfect storm’ of factors that threaten global food security including continued population growth, a rapidly changing climate, reduced water available to agriculture, soil erosion and increasing costs of fertilisers (Abberton et al 2015; Gomiero 2016). The human population derives more than 50% of its calorific intake from just three crop species (Awika 2011). This is largely reflected in the concentration of research and breeding investments into major crops, which serves to widen the gap between well-resourced major crop species and minor crops ( known as ‘neglected under-utilised species’). There is a strong need to understand and harness adaptive diversity from the wild ancestors and relatives of crop species (Berger et al 2013; Maxted et al 2012)

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