Wild species related to agricultural crops (crop wild relatives, or CWR) can increase the adaptive capacity of agricultural systems around the world. They represent a large pool of genetic diversity from which to draw new allelic variation required in breeding programs. Crop wild relatives have been extremely valuable in adapting crop varieties to changing disease pressures, farming practices, market demands, and climatic conditions. Unfortunately, CWR are a threatened resource and measures need to be taken to protect them, both in the wild and in genebanks. Here, we review how wild species have contributed to the development of improved crop varieties and where efforts must be concentrated to harness their value in the future. Drawing on the results of an extensive literature search, a series of 14 expert consultation meetings, and in-depth interview with experts on 24 crops, we document the role that CWR play in modern crop breeding. We discuss (i) their past and current use, (ii) advanced breeding methods and technologies that promise to facilitate the continued use of CWR, and (iii) what constraints continue to hinder increased use of CWR in breeding. H. Dempewolf, B. Kilian, and L. Guarino, Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany; H. Dempewolf, and G. Baute, Univ. of British Columbia, Dep. of Botany, 6270 University Blvd., Vancouver, BC Canada; J. Anderson, Univ. of Hawaii at Manoa, Dep. of Tropical Plant & Soil Sciences, 3190 Maile Way, Honolulu, Hawaii 96822; C. Smith, Univ. of Waterloo, Dep. of Environment and Resource Studies, 200 University Ave. W., Waterloo, ON N2L 3G1, Canada. Received 15 Oct. 2016. Accepted 15 Dec. 2016. *Corresponding author (hannes.dempewolf@croptrust.org). Assigned to Associate Editor Stella Kantartzi. Abbreviations: CSSL, chromosome segment substitution line; CWR, crop wild relative; MAS, marker-assisted selection; QTL, quantitative trait locus; SNP, single-nucleotide polymorphism; WGS, wholegenome shotgun sequence. Published in Crop Sci. 57:1070–1082 (2017). doi: 10.2135/cropsci2016.10.0885 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA This is an open access article distributed under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Published June 16, 2017

Past and Future Use of Wild Relatives in Crop Breeding

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1%, and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al., 2012) and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segregating population derived from a Golden Promise x Morex cross (Liu et al., 2014) and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions. Manual adjustment of the cluster files used by the interpreting software for genotype scoring improved results substantially, but migration of cluster files between sites led to a deterioration of results, suggesting that local adjustment of cluster files is required on a site-per-site basis. Information relating to the markers on the chip is available online at https://ics.hutton.ac.uk/50k (email: barleysnpchip@hutton.ac.uk).

/pdf/development-and-evaluation-of-a-barley-50k-iselect-snp-array-234xkgkwrm.pdf

Development and Evaluation of a Barley 50k iSelect SNP Array.

Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In the present study we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterisation of the association between HEs and PAVs in B. napus at the pangenome level. This article is protected by copyright. All rights reserved.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.12867

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

Designing Future Crops: Genomics-Assisted Breeding Comes of Age

Key message
TheBrassica napusIllumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploidB. napusand its progenitor diploid genomes.

/pdf/a-high-density-snp-genotyping-array-for-brassica-napus-and-271i5udumd.pdf

A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome

Wing Cheung

Papers

A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome