Enhancing Crop Domestication Through Genomic Selection, a Case Study of Intermediate Wheatgrass.

Jared Crain,Xiaofei Zhang,Prabin Bajgain,Lee Dehaan,James Anderson,Jesse Poland

doi:10.3389/fpls.2020.00319

Abstract

Perennial grains could simultaneously provide food for humans and a host of ecosystem services, including reduced erosion, minimized nitrate leaching, and increased carbon capture. Yet most of the world’s food and feed is supplied by annual grains. Efforts to domesticate intermediate wheatgrass (Thinopyrumn intermedium, IWG) as a perennial grain crop have been ongoing since the 1980’s. Currently, there are several breeding programs within North America and Europe working toward developing IWG into a viable crop. As new breeding efforts are established to provide a widely adapted crop, questions of how genomic and phenotypic data can be used among sites and breeding programs have emerged. Utilizing five cycles of breeding data that span 8 years and two breeding programs, University of Minnesota, St. Paul, MN, and The Land Institute, Salina, KS, we developed genomic selection (GS) models to predict IWG traits. Seven traits were evaluated with free-threshing seed, seed mass, and non-shattering being considered domestication traits while agronomic traits included spike yield, spikelets per inflorescence, plant height, and spike length. We used 6,199 genets – unique, heterozygous, individual plants – that had been profiled with genotyping-by-sequencing, resulting in 23,495 SNP markers to develop GS models. Within cycles, the predictive ability of GS was high, ranging from 0.11 to 0.97. Across-cycle predictions were generally much lower, ranging from −0.22 to 0.76. The prediction ability for domestication traits was higher than agronomic traits, with non-shattering and free threshing prediction abilities ranging from 0.27 to 0.75 whereas spike yield had prediction abilities ranging from −0.22 to 0.26. These results suggest that progress to reduce shattering and increase the percent free-threshing grain can be made irrespective of the location and breeding program. While site-specific programs may be required for agronomic traits, synergies can be achieved in rapidly improving key domestication traits for IWG. As other species are targeted for domestication, these results will aid in rapidly domesticating new crops.

Highlights

80% of the world’s calories are provided by annual crops (Pimentel et al, 2012), with only three crops, maize (Zea mays), wheat (Triticum aestivum), and rice (Oryza sativa), providing nearly 60% of human calorie consumption
Given the need for new crops and the challenges associated with developing perennial crops, this study focused on (1) How data from diverse sites and breeding programs could be combined to improve prediction abilities of models for enhanced selection decisions, (2) The ability of genomic selection (GS) to accurately predict traits across a range of environments and traits, with emphasis on differences between domestication and agronomic traits, and (3) How insights gained from intermediate wheatgrass (IWG) breeding could be applied to other potential new crops undergoing domestication
Genomic selection was used in the The Land Institute (TLI)-C7 generation, and a training population consisting of 1,179 genets from approximately 4,000 genotyped genets, was planted in the fall of 2017

Summary

Introduction

80% of the world’s calories are provided by annual crops (Pimentel et al, 2012), with only three crops, maize (Zea mays), wheat (Triticum aestivum), and rice (Oryza sativa), providing nearly 60% of human calorie consumption (fao.org). Intermediate wheatgrass is native to Eastern Europe and the Mediterranean region (Tsvelev, 1983) and was introduced into the United States for erosion control and forage purposes in 1932 (Vogel and Jensen, 2001). This species was selected for domestication as a grain crop in the 1980’s from an evaluation of nearly 100 perennial grasses based on its seed size, vigorous growth habit, and potential for mechanical harvest, among other desirable characteristics, at the Rodale Institute, Kutztown, PA (Wagoner, 1990). Products made from IWG grain are being sold under the trade name Kernza in limited markets (DeHaan and Ismail, 2017)

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Results

Discussion

Conclusion