High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Bárbara Hufnagel ,William Marande ,L Pons Marqués ,Romain Guyot ,André Marques ,Matthew N Nelson ,Alexandre Soriano ,Sébastien Carrère ,Martín Crespi ,Sandrine Arribat ,Veit Schubert ,Fernando Geu‐Flores ,Jean Keller ,Thomas Blein ,Patrick Doumas ,Delphine Aimé ,Hélène Bergès ,Jérôme Salse ,Cécile Huneau ,Karine Gallardo ,Jemma L Taylor ,Fanchon Divol ,Pierre-Marc Delaux ,Jérôme Gouzy ,Erika Sallet ,Malika Laguerre ,Davide Mancinotti ,Benjamin Péret

doi:10.1038/s41467-019-14197-9

Abstract

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.

Highlights

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds
White lupin (Lupinus albus L.) is a pulse that originates from the Mediterranean region, its center of origin is believed to be Greece, Western Turkey and southern Balkans where wild ‘graecus’ types still persist[4]
We provide a comparison of soil exploration capacity between a cultivated and a wild accession, highlighting the early establishment of lateral and cluster roots in the modern cultivar

Summary

Introduction

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. White lupin (Lupinus albus L.) is a pulse that originates from the Mediterranean region, its center of origin is believed to be Greece, Western Turkey and southern Balkans where wild ‘graecus’ types still persist[4] This crop is recognized as a traditional food due to its very high protein content (between 30 and 40% of the whole seed)[5]. WL cultivation has the potential to solve several issues related to the future of European protein supply due to its high quality seeds (very high levels of proteins, high levels of tocopherols, lowest glycemic index of consumed grains, high dietary fiber content, gluten-free, low oil, and minimal starch)[5,7,8,9] It is a crop with low need for phosphate fertilizers due to its highly adapted root system[10] and no need of nitrogen input as a legume. We provide a list of candidate genes present in the pauper locus, which is a common QTL controlling the accumulation of toxic alkaloids in WL seeds

Methods

Results

Conclusion