Chromosome-Wide Characterization of Intragenic Crossover in Shiitake Mushroom, Lentinula edodes

• Published in: Journal of fungi (Basel) Vol. 7; no. 12; p. 1076
• Main Authors: Gong, Wenbing, Shen, Nan, Zhang, Lin, Bian, Yinbing, Xiao, Yang
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 15.12.2021; MDPI
• Subjects: Chromosomes; cis- and trans-loci; Communication; Gene mapping; Genetic crosses; Genetic diversity; Genomes; Haplotypes; hotspots; intragenic crossover; Lentinula edodes; Meiosis; Mushrooms; Quantitative trait loci; Recombination; Single-nucleotide polymorphism; Transcription; cis- and trans-loci; intragenic crossover; hotspots; Lentinula edodes
• ISSN: 2309-608X; 2309-608X
• DOI: 10.3390/jof7121076

Meiotic crossover plays a critical role in generating genetic variations and is a central component of breeding. However, our understanding of crossover in mushroom-forming fungi is limited. Here, in , we characterized the chromosome-wide intragenic crossovers, by utilizing the single-nucleotide polymorphisms (SNPs) datasets of an F haploid progeny. A total of 884 intragenic crossovers were identified in 110 single-spore isolates, the majority of which were closer to transcript start sites. About 71.5% of the intragenic crossovers were clustered into 65 crossover hotspots. A 10 bp motif (GCTCTCGAAA) was significantly enriched in the hotspot regions. Crossover frequencies around mating-type A (MAT-A) loci were enhanced and formed a hotspot in . Genome-wide quantitative trait loci (QTLs) mapping identified sixteen crossover-QTLs, contributing 8.5-29.1% of variations. Most of the detected crossover-QTLs were co-located with crossover hotspots. Both - and -QTLs contributed to the nonuniformity of crossover along chromosomes. On chr2, we identified a QTL hotspot that regulated local, global crossover variation and crossover hotspot in . These findings and observations provide a comprehensive view of the crossover landscape in , and advance our understandings of conservation and diversity of meiotic recombination in mushroom-forming fungi.