Development of a genome-wide genetic linkage map in the wheat pathogen Pyrenophora tritici-repentis and its utilization in genome assembling and comparison

Authors: KARIYAWASAM, GAYAN - North Dakota State University; WYATT, NATHAN - Orise Fellow; SHI, GONGJUN - North Dakota State University; LIU, SANZHEN - North Dakota State University; YAN, CHANGHUI - North Dakota State University; MA, YONGCHAO - North Dakota State University; ZHONG, SHAOBIN - North Dakota State University; RASMUSSEN, JACK - North Dakota State University; MOOLHUIJZEN, PAULA - Curtin University; MOFFAT, CAROLINE - Curtin University; Friesen, Timothy; LIU, ZHAOHUI - North Dakota State University

Submitted to: Fungal Genetics and Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/28/2021
Publication Date: 5/17/2021
Citation: Kariyawasam, G.K., Wyatt, N., Shi, G., Liu, S., Yan, C., Ma, Y., Zhong, S., Rasmussen, J.B., Moolhuijzen, P., Moffat, C.S., Friesen, T.L., Liu, Z. 2021. Development of a genome-wide genetic linkage map in the wheat pathogen Pyrenophora tritici-repentis and its utilization in genome assembling and comparison. Fungal Genetics and Biology. 152:103571. https://doi.org/10.1016/j.fgb.2021.103571.
DOI: https://doi.org/10.1016/j.fgb.2021.103571

Interpretive Summary: Tan spot is an economically important disease of wheat throughout the world. Understanding the genetics of virulence in the causal pathogen is a critical component in controlling this disease and this understanding has been hampered by the inability to make crosses in the pathogen. Here we describe a new population generated using a novel sexual crossing method involving two parents that differ in virulence. Full genome sequences of the two parents were generated and used to mine for molecular markers that were used to generate a genetic linkage map. This map will be useful in identifying the chromosomal locations of genes contributing to tan spot disease on wheat. This understanding of pathogen virulence is critical to germplasm development and the release of cultivars that harbor resistance to this important disease. In addition to being used by wheat geneticists and breeders, this information will also be used by other pathologists working with similar pathogens.

Technical Abstract: Pyrenophora tritici-repentis is an ascomycete fungus that causes tan spot of wheat. The disease has a worldwide distribution and can cause significant yield and quality losses in wheat production. The fungal pathogen is homothallic in nature, which means it can undergo sexual reproduction by selfing to produce pseudothecia on wheat stubble for seasonal survival. Since homothallism precludes the development of biparental fungal populations, no genetic linkage map has been developed for P. triticirepentis for mapping and map-based cloning of fungal virulence genes. In this work, we created two heterothallic strains by deleting one of the mating type genes in each of two parental isolates 86-124 (race 2) and AR CrossB10 (a new race) and developed a bi-parental fungal population between them. The draft genome sequences of the two parental isolates were aligned to the Pt-1c-BFP reference sequence to mine single nucleotide polymorphisms (SNPs). A total of 225 SNP markers were developed for genotyping the entire population. Additionally, 75 simple sequence repeat, and two gene markers were also developed and used in the genotyping. The resulting linkage map consisted of 13 linkage groups spanning 5,075.83 cM in genetic distance. Because the parental isolate AR CrossB10 is a new race and produces Ptr ToxC, it was sequenced using long-read sequencing platforms and de novo assembled into contigs. The majority of the contigs were further anchored into chromosomes with the aid of the linkage maps. The whole genome comparison of AR CrossB10 to the reference genome of M4 revealed a few chromosomal rearrangements. The genetic linkage map and the new AR CrossB10 genome sequence are valuable tools for gene cloning in P. tritici-repentis .