Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations

Gorjanc et al. BMC Genomics (2016) 17:30 DOI 10.1186/s12864-015-2345-z RESEARCH ARTICLE Open Access Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations Gregor Gorjanc1,2* , Janez Jenko2,3, Sarah J. Hearne4 and John M. Hickey2 Abstract Background: The limited genetic diversity of elite maize germplasms raises concerns about the potential to breed for new challenges. Initiatives have been formed over the years to identify and utilize useful diversity from landraces to overcome this issue. The aim of this study was to evaluate the proposed designs to initiate a pre-breeding program within the Seeds of Discovery (SeeD) initiative with emphasis on harnessing polygenic variation from landraces using genomic selection. We evaluated these designs with stochastic simulation to provide decision support about the effect of several design factors on the quality of resulting (pre-bridging) germplasm. The evaluated design factors were: i) the approach to initiate a pre-breeding program from the selected landraces, doubled haploids of the selected landraces, or testcrosses of the elite hybrid and selected landraces, ii) the genetic parameters of landraces and phenotypes, and iii) logistical factors related to the size and management of a pre-breeding program. Results: The results suggest a pre-breeding program should be initiated directly from landraces. Initiating from testcrosses leads to a rapid reconstruction of the elite donor genome during further improvement of the prebridging germplasm. The analysis of accuracy of genomic predictions across the various design factors indicate the power of genomic selection for pre-breeding programs with large genetic diversity and constrained resources for data recording. The joint effect of design factors was summarized with decision trees with easy to follow guidelines to optimize pre-breeding efforts of SeeD and similar initiatives. Conclusions: Results of this study provide guidelines for SeeD and similar initiatives on how to initiate pre-breeding programs that aim to harness polygenic variation from landraces. Keywords: Maize, Landrace, Diversity, Pre-breeding, Genomic selection Background This paper uses stochastic simulation to evaluate designs for initiating maize pre-breeding programs that harness polygenic variation from landrace populations for later incorporation into elite maize breeding populations. Today’s elite maize germplasms have lower genetic variance than progenitor populations [1–3], because they were sourced from a limited set of ancestral populations [4, 5] and to a smaller extent due to recent selection [6]. * Correspondence: 1 Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia 2 The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK Full list of author information is available at the end of the article Such a reduced genetic variance limits the potential to breed for new market demands, new pathogens, and changing environments [7–11]. These breeding goals would be easier to address if the vast genetic variation of progenitor populations would be accessible to breeders in a form they could use in their breeding programs (e.g., see [12] and references within). Extensive genetic variation is available in the diverse maize landrace populations around the globe [1–3] as a result of the open-pollinated reproductive system of maize and variation in its components [13], introgression from wild relatives [14], seed exchange between farmers, mutation, drift, and mild selection operating © 2016 Gorjanc et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Gorjanc et al. BMC Genomics (2016) 17:30 over a range of environments and time [13, 15, 16]. Some landraces are well adapted to extreme environments and it is likely they contain favorable alleles that could be used as a genetic resource to enrich the elite germplasms [17]. To use these resources breeders need to bridge the wide performance gap between landrace and elite germplasms, as landraces tend to have low performance, as well as high heterogeneity and negative genetic load. This process can be accelerated by using existing composite or recurrent selection populations, or even inbred lines derived from local landraces [12, 18]. A recent initiative to characterize and use a part of the untapped variation in landraces is Seeds of Discovery (SeeD; http://seedsofdiscovery.org) funded mostly by the Mexican government through the Sustainable Modernization of Traditional Agriculture program (MasAgro; http://masagro.mx). SeeD aims to identify and enable use of favorable variation from landraces to develop bridging germplasm with 75 % or more elite and 25 % or less landrace genome (Fig. 1). This bridging germplasm is planned to provide donor lines carrying novel, landrace-derived genetic variation, to breed for high value characteristics such as nutritional quality, heat and drought tolerance, disease resistance, and tolerance to soil infertility. To this end the breeder’s core of 4,000+ maize landrace accessions from the germplasm bank housed at the International Maize and Wheat Improvement Center (CIMMYT) were genotyped with many markers and phenotyped for testcross performance (http://seedsofdiscovery.org). This resource provides one foundation for harnessing favorable variation from landraces. Since the traits targeted by SeeD are predominantly polygenic e.g., [11, 19], data generated from this population can be approached both by genome-wide association mapping and by genomic selection. Genome-wide association mapping has and continues to be used in SeeD to highlight genomic regions with sizeable associations. Once Page 2 of 15 such regions are identified and underlying alleles characterized, a limited number can be introgressed into elite germplasms following established forward breeding procedures [20–23]. Genomic selection offers an alternative paradigm where favorable genetic variation can be targeted across the whole genome and deleterious variation deselected, without focusing on few genomic regions, which is of particular value for traits of higher genetic complexity. In the context of a pre-breeding program genomic selection could be used to enrich the starting germplasm (from here onwards called as the pre-bridging germplasm) with favorable polygenic varia (...truncated)