Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax

Liqiang He; Yao Sui; Yanru Che; Huixian Wang; Khalid Y Rashid; Sylvie Cloutier; Frank M You

doi:10.3389/fpls.2023.1229457

Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax

Front Plant Sci. 2023 Oct 25:14:1229457. doi: 10.3389/fpls.2023.1229457. eCollection 2023.

Authors

Liqiang He^#^{1

2}, Yao Sui^#², Yanru Che^#², Huixian Wang², Khalid Y Rashid¹, Sylvie Cloutier¹, Frank M You¹

Affiliations

¹ Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
² School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China.

^# Contributed equally.

Abstract

Introduction: Flax (Linum usitatissimum L.) is an economically important crop due to its oil and fiber. However, it is prone to various diseases, including pasmo caused by the fungus Septoria linicola.

Methods: In this study, we conducted field evaluations of 445 flax accessions over a five-year period (2012-2016) to assess their resistance to pasmo A total of 246,035 single nucleotide polymorphisms (SNPs) were used for genetic analysis. Four statistical models, including the single-locus model GEMMA and the multi-locus models FarmCPU, mrMLM, and 3VmrMLM, were assessed to identify quantitative trait nucleotides (QTNs) associated with pasmo resistance.

Results: We identified 372 significant QTNs or 132 tag QTNs associated with pasmo resistance from five pasmo resistance datasets (PAS2012-PAS2016 and the 5-year average, namely PASmean) and three genotypic datasets (the all SNPs/ALL, the gene-based SNPs/GB and the RGA-based SNPs/RGAB). The tag QTNs had R² values of 0.66-16.98% from the ALL SNP dataset, 0.68-20.54%from the GB SNP dataset, and 0.52-22.42% from the RGAB SNP dataset. Of these tag QTNs, 93 were novel. Additionally, 37 resistance gene analogs (RGAs)co-localizing with 39 tag QTNs were considered as potential candidates for controlling pasmo resistance in flax and 50 QTN-by-environment interactions(QEIs) were identified to account for genes by environmental interactions. Nine RGAs were predicted as candidate genes for ten QEIs.

Discussion: Our results suggest that pasmo resistance in flax is polygenic and potentially influenced by environmental factors. The identified QTNs provide potential targets for improving pasmo resistance in flax breeding programs. This study sheds light on the genetic basis of pasmo resistance and highlights the importance of considering both genetic and environmental factors in breeding programs for flax.

Keywords: GWAS; SNP; flax; multi-locus model; pasmo.

Copyright © 2023 Yao Sui, Yanru Che, Huixian Wang, and His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada for the contribution of Liqiang He, Khalid Y. Rashid, Sylvie Cloutier and Frank M. You.

Grants and funding

This study was supported by Genome Canada and other industrial stakeholders for the Total Utilization Flax GENomics (TUFGEN) project, Agriculture Development Fund for Diverse Field Crop Cluster project in genomics and molecular markers to identify resistance genes in flax, Hainan Provincial Natural Science Foundation of China (No. 323RC422 and No. 321RC1148), and the Hainan University Startup Fund (KYQD(ZR)-21027).