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

Authors: CRAIN, JARED - Kansas State University; Larson, Steven; Dorn, Kevin; KANTARSKI, TRACI - Kansas State University; DEHAAN, LEE - The Land Institute; POLAND, JESSE - Kansas State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/3/2020
Publication Date: 8/12/2020
Citation: Crain, J., Larson, S.R., Dorn, K.M., Kantarski, T., Dehaan, L., Poland, J. 2020. Sequenced-based paternity analysis to improve breeding and identify self-incompatibility loci in intermediate wheatgrass (Thinopyrum intermedium). Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-020-03666-1.
DOI: https://doi.org/10.1007/s00122-020-03666-1

Interpretive Summary: In field crop breeding programs of open-pollinated plant species, uncontrolled random pollination is often used to generate new combinations of gene variants in the breeding population. However, the resulting progeny of these crosses have uncontrolled or uncertain pollen parents. Determining the true pedigrees from these open-pollination blocks is difficult. Using high throughput genotyping datasets from a reference population of intermediate wheatgrass (Thinopyrum intermedium), an open pollinated perennial grain species, we have developed a 'pipeline method' to determine the pedigrees of progeny from an open-pollination breeding scheme with a high degree of confidence. Additionally, this research included a genome-wide association study (GWAS) that enabled the determination of potential effects of gene variants in these parental populations that influence self-incompatibility, or the inability of an individual plant to self pollinate. The GWAS indicated that genes potentially involved in the ability to self pollinate (self incompabilibility (SI) genes) may restrict the combining of specific genotypes thus impacting the future of successful crop genetic improvement.

Technical Abstract: 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 is difficult to keep track of pollen-parent pedigrees. In addition, genetic bottlenecks may limit diversity of self-incompatibility (SI) genes and inhibit many cross combinations. This study investigated the potential of using next-generation sequencing data to assign paternity and impute pedigrees leading to enhanced breeding decisions. Using a reference population of 380 individuals made from controlled crosses of 64 parents, paternity was assigned with 92% agreement using the Cervus program. Using this approach, 90% of 4,158 progeny (n=3,755) from a polycross of 89 parents were assigned paternity. Only 81 of 89 pollen parents were successful with 1,743 unique full-sib families representing 45% of all potential crosses. The number of progeny per successful pollen parent ranged from 1-170, with number of stems per pollen parent significantly correlated to the number of progeny (r = 0.55, p < 0.001). Shannon’s diversity index, assessing the total number and representation of families, was 7.40 compared to an upper possibility of 8.98. Finally, a genome-wide association study (GWAS) of the number of progeny observed from the 89 parents detected significant effects near putative SI genes. These GWAS results suggest that diversity of these SI genes may limit combining of selected genotypes and impact future breeding gains. Male-parent paternity of open crossing blocks can be incorporated within breeding programs to increase efficiency, maintain genetic diversity, and increase the rate of genetic gain.