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 bi-parental fungal populations, no genetic linkage map has been developed for P. tritici-repentis 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.

Pyrenophora tritici-repentis是一种子囊菌真菌，会导致小麦出现棕褐色斑点。该病害在全球范围内分布，可导致小麦产量和质量的显着损失。真菌病原体在性质上是同种的，这意味着它可以通过自交进行有性繁殖，在麦茬上产生假壳，以便季节性生存。由于同源性排除了双亲真菌种群的发展，因此没有为P. tritici-repentis开发遗传连锁图用于真菌毒力基因的定位和基于定位的克隆。在这项工作中，我们通过删除两个亲本分离株 86-124（种族 2）和 AR CrossB10（新种族）中的每一个中的一个交配型基因来创建两个异源菌株，并在它们之间开发了双亲真菌种群。将两个亲本分离株的基因组序列草图与 Pt-1C-BFP 参考序列进行比对，以挖掘单核苷酸多态性 (SNP)。总共开发了 225 个 SNP 标记用于对整个群体进行基因分型。此外，还开发了 75 个简单序列重复和两个基因标记并用于基因分型。由此产生的连锁图由 13 个连锁群组成，遗传距离为 5,075.83 cM。因为亲本分离株 AR CrossB10 是一个新种族并产生 Ptr ToxC，从头组装成重叠群。在连锁图的帮助下，大多数重叠群进一步锚定在染色体中。AR CrossB10 与 M4 参考基因组的全基因组比较揭示了一些染色体重排。遗传连锁图和新的 AR CrossB10 基因组序列是在P. tritici-repentis 中进行基因克隆的宝贵工具。