Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium)

Jared Crain,Lee DeHaan,Traci Hagedorn,Jesse Poland,Kevin Dorn,Steve Larson

doi:10.1007/s00122-020-03666-1

Abstract

Key MessagePaternity assignment and genome-wide association analyses for fertility were applied to aThinopyrum intermediumbreeding program. A lack of progeny between combinations of parents was associated with loci near self-incompatibility genes.In outcrossing species such as intermediate wheatgrass (IWG, Thinopyrum intermedium), polycrossing is often used to generate novel recombinants through each cycle of selection, but it cannot track pollen-parent pedigrees and it is unknown how self-incompatibility (SI) genes may limit the number of unique crosses obtained. This study investigated the potential of using next-generation sequencing to assign paternity and identify putative SI loci in IWG. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using Cervus software. Using this approach, 80% of 4158 progeny (n = 3342) from a polycross of 89 parents were assigned paternity. Of the 89 pollen parents, 82 (92%) were represented with 1633 unique full-sib families representing 42% of all potential crosses. The number of progeny per successful pollen parent ranged from 1 to 123, with number of inflorescences per pollen parent significantly correlated to the number of progeny (r = 0.54, p < 0.001). Shannon’s diversity index, assessing the total number and representation of families, was 7.33 compared to a theoretical maximum of 8.98. To test our hypothesis on the impact of SI genes, a genome-wide association study of the number of progeny observed from the 89 parents identified genetic effects related to non-random mating, including marker loci located near putative SI genes. Paternity testing of polycross progeny can impact future breeding gains by being incorporated in breeding programs to optimize polycross methodology, maintain genetic diversity, and reveal genetic architecture of mating patterns.

Highlights

Perennial grain crops are posited to provide ecosystem services, such as reduced nitrate leaching and less soil erosion, as well as nutrition for the growing human population (Glover et al 2010)
The remaining true errors totaled approximately 4% (15 of 380) and included a parent that had no relationship with the recorded parent in 13 instances, and two of the mismatches were assigned to pollen donors that had a full-sibling or closer relationship according to the recorded parent pedigrees
This study used single nucleotide polymorphic (SNP) markers generated from low coverage GBS data to assign paternity

Summary

Introduction

Perennial grain crops are posited to provide ecosystem services, such as reduced nitrate leaching and less soil erosion, as well as nutrition for the growing human population (Glover et al 2010). The inferred origins of the polyploid T. intermedium genome have not been entirely consistent but are understood to be an allohexaploid with three distinct subgenomes (Chen et al 1998; Tang et al 2000; Mahelka et al 2011; Wang et al 2015). It is clear from linkage mapping experiments that IWG shows disomic inheritance patterns similar to allohexaploid wheat (Kantarski et al 2016). Further clarification of genome relationships between IWG and its diploid relatives is being obtained from the T. intermedium Genome Sequencing Project (http://phytozome.jgi.doe.gov/)

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