Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Carolina Sansaloni,Paul Shaw,Juan Burgueño,José Crosa,Bruno Santos,Jaime Campos,Marianne Bänziger ,Jorge Franco,Cristóbal Uauy ,César Petroli ,Jason Carling,Lawrence Percival‐Alwyn ,Thomas Payne,Mario Cáccamo ,Sebastian Raubach,Carlos Guzmán ,Carolina Saint Pierre,Gordon Stephen,Kate Dreher,Andrzej Kilian,Ahmed Amri,Benjamin Kilian,Peter Wenzl,Iain Milne,Sukhwinder Singh,Huihui Li,David Marshall,Zakaria Kehel,K.v Pixley

doi:10.1038/s41467-020-18404-w

Abstract

Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseqTM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs.

Highlights

IntroductionThe analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection
Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population
We characterized the genetic diversity of 79,191 accessions from the CIMMYT and ICARDA germplasm banks: 56,342 domesticated wheat hexaploids, 18,946 domesticated wheat tetraploids, and 3903 crop wild relatives (CWR)

Summary

Introduction

The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs. Since its domestication >10,000 years ago, wheat cultivars have increased yields and adapted to a number of different climates and growing conditions7–10 This success, has resulted in a reduction of the genetic diversity in the elite gene pool, This limits the development of new wheat varieties required to sustainably address the demands of the growing world population in a backdrop of climate changes, and abiotic and biotic stresses. The Seeds of Discovery initiative (SeeD; http://seedsofdiscovery.org/), which aims to facilitate the effective use of genetic diversity of wheat and maize, has characterized nearly 80,000 accessions from two of the world’s largest wheat germplasm banks: (i) CIMMYT, which hosts 140,812 wheat accessions, and (ii) the International Center for Agricultural Research in the Dry Areas (ICARDA), with

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