Sequencing Based Identification of Resistance Genes in Lolium multiflorum

Lolium multiflorum (Italian ryegrass) is an important fodder grass of temperate regions. Harvest may be severely reduced due to infections with the wilt causing bacterium Xanthomonas translucens pv. graminis (Xtg) or the crown rust fungus Puccinia coronata (Pc).

Exploitation of naturally occurring resistance in breeding programs may be facilitated by genomic markers linked to disease resistance against these pathogens.

Previously, a major Quantitative Trait Locus (QTL) was found in a bi-parental mapping population explaining up to 84% of resistance against Xtg. To learn more about this genomic region, the parental DNA of this cross and pools of DNA of the most resistant and most susceptible quartile of the progeny were sequenced using the Illumina Hiseq2000 platform. The reads of the resistant parent were assembled into 1.3x10⁵ contiguous sequences, serving as a reference for the identification of single nucleotide polymorphisms (SNPs). 18x10⁶ SNPs were called between the parents,  12x10⁶ of these could be covered with the reads from the pools. Thereby, 16 parental scaffolds enriched in SNPs covered by reads from the resistant pool could be determined. Comparison of these sequences with databases revealed homologies to resistance related sequences from various grass species such as the serine/threonine-protein kinase-like protein CCR4-like gene of Brachypodium.

A nested association mapping (NAM) cross of Lolium perenne, genotyped by sequencing, was characterized for Xtg and Pc resistance, leading to several candidate genes including LRR-containing proteins and transcriptions factors.

High resolution melt (HRM) curve analysis will reveal whether these candidate genes map into the QTL region.