Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina

Abstract

The poplar rust fungus Melampsora larici-populina causes significant yield reduction and severe economic losses in commercial poplar plantations. After several decades of breeding for qualitative resistance and subsequent breakdown of the released resistance genes, breeders now focus on quantitative resistance, perceived to be more durable. But quantitative resistance also can be challenged by an increase of aggressiveness in the pathogen. Thus, it is of primary importance to better understand the genetic architecture of aggressiveness traits. To this aim, our goal is to build a genetic linkage map for M. larici-populina in order to map quantitative trait loci related to aggressiveness. First, a large progeny of M. larici-populina was generated through selfing of the reference strain 98AG31 (which genome sequence is available) on larch plants, the alternate host of the poplar rust fungus. The progeny's meiotic origin was validated through a segregation analysis of 115 offspring with 14 polymorphic microsatellite markers, of which 12 segregated in the expected 1:2:1 Mendelian ratio. A microsatellite-based linkage disequilibrium analysis allowed us to identify one potential linkage group comprising two scaffolds. The whole genome of a subset of 47 offspring was resequenced using the Illumina HiSeq 2000 technology at a mean sequencing depth of 6X. The reads were mapped onto the reference genome of the parental strain and 144,566 SNPs were identified across the genome. Analysis of distribution and polymorphism of the SNPs along the genome led to the identification of 2580 recombination blocks. A second linkage disequilibrium analysis, using the recombination blocks as markers, allowed us to group 81 scaffolds into 23 potential linkage groups. These preliminary results showed that a high-density linkage map could be constructed by using high-quality SNPs based on low-coverage resequencing of a larger number of M. larici-populina offspring.

Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data

“…Another application is assessing the quality of an assembly ( e.g. , Pernaci et al 2014 ) or ordering scaffolds, such as in the Locus Ordering by Dis-Equilibrium procedure ( Khatkar et al 2010 ). This application of LD is perhaps less well known but is particularly useful for sequencing data, since assemblies are often fragmented or not existent, and has already been used in a study by Tennessen et al (2017) .…”

Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini

“…Taken together, our data suggest that variability in the M. lini genome can be achieved through a high overall recombination rate, consistent with reports of high genetic diversity in natural, sexually reproducing M. lini populations [ 99 ], and an ability of the asexual stage to withstand small- and large-scale chromosomal duplications and deletions, which can both impact upon the virulence phenotype. Several mapping families have been produced for other rust fungi, including the wheat stem rust, poplar rust and pine fusiform rust fungi [ 70 , 100 , 101 ]. Approaches like those described here may facilitate genome analysis and avirulence gene cloning in these rust fungi and other species.…”

Advances in understanding obligate biotrophy in rust fungi

“…A genome‐wide search for single nucleotide polymorphisms or insertion/deletion in rust fungal isolates has enabled the detection of avirulence candidates among secreted protein genes (Cantu et al ., ; Bruce et al ., ; Persoons et al ., ; Upadhyaya et al ., ; Bueno‐Sancho et al ., ; Cuomo et al ., ; Wu et al ., ). Sequencing large volumes of isolates is now possible for relatively low cost, and high‐density genetic maps can be constructed through the resequencing of progenies or by restriction site detection sequencing (RAD‐seq) in rust fungi (Pernaci et al ., ; Anderson et al ., ; Yuan et al ., ). Two recent studies demonstrated the degree to which genomics has impacted the field by combining genomics and resequencing approaches to identify AvrSr35 and AvrSr50 , two P. graminis f. sp.…”