Multi-Allelic Haplotype-Based Association Analysis Identifies Genomic Regions Controlling Domestication Traits in Intermediate Wheatgrass

Prabin Bajgain,James A Anderson

doi:10.3390/agriculture11070667

Abstract

Intermediate wheatgrass (IWG) is a perennial forage grass undergoing a rigorous domestication as a grain crop. As a young grain crop, several agronomic and domestication traits need improvement for IWG to be relevant in current agricultural landscapes. This study genetically maps six domestication traits in the fourth cycle IWG breeding population at the University of Minnesota: height, seed length, seed width, shattering, threshability, and seed mass. A weak population structure was observed and linkage disequilibrium (r2) declined rapidly: 0.23 mega base pairs at conventional r2 value of 0.2. Broad-sense heritabilities were overall high and ranged from 0.71–0.92. Association analysis was carried out using 25,909 single SNP markers and 5379 haplotype blocks. Thirty-one SNP markers and 17 haplotype blocks were significantly associated with the domestication traits. These associations were of moderate effect as they explained 4–6% of the observed phenotypic variation. Ten SNP markers were also detected by the haplotype association analysis. One SNP marker on Chromosome 8, also discovered in haplotype block analysis, was common between seed length and seed mass. Increasing the frequency of favorable alleles in IWG populations via marker-assisted selection and genomic selection is an effective approach to improve IWG’s domestication traits.

Highlights

Intermediate wheatgrass [IWG, Thinopyrum intermedium (Host) Barkworth & D.R.Dewey subsp. intermedium, 2n = 6x = 42] is a perennial forage grass species currently under domestication as a new grain crop [1]
MN in 2019 and 2020 for multiple agronomic and domestication traits, of which we focus our association analysis on six important domestication traits: (1) plant height, (2) seed length, (3) seed width, (4) shattering, (5) free grain threshing, and (6) seed mass measured in terms of thousand kernel weight (TKW)
Allele calling using the IWG reference genome v2.1 resulted in discovery of 4,782,922 genome-wide Single nucleotide polymorphism (SNP) markers in the UMN_C4 population

Summary

Introduction

The crop was recently adopted by multiple breeding programs in an attempt to domesticate it as a food crop. The University of Minnesota (UMN) started its IWG domestication program in 2011 from 2,560 individuals that were derived 66 mother plants of the third recurrent selection cycle at The Land Institute in Salina, KS, USA [7]. Between 2011 and 2020, the UMN IWG breeding program has completed four selection cycles and extensive progress has been made in improving these traits. This progress throughout the years enabled the breeding program to release the first synthetic IWG cultivar for grain production, MN-Clearwater, in 2019 [8]

Methods

Results

Conclusion