Abstract
Key messageSNPs and candidate genes associated with bacterial wilt resistance in Italian ryegrass were identified by sequencing the parental plants and pooled F1 progeny of a segregating population.Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grass species in temperate regions. Its yield, quality and persistency can significantly be reduced by bacterial wilt, a serious disease caused by Xanthomonas translucens pv. graminis. Although a major QTL for bacterial wilt resistance has previously been reported, detailed knowledge on underlying genes and DNA markers to allow for efficient resistance breeding strategies is currently not available. We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F1 individuals was pooled and sequenced using the Illumina HiSeq 2000 platform. Allele frequencies of 18 × 106 single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP™ markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance. This study highlights the power of pooled DNA sequencing to efficiently target binary traits in biparental mapping populations. It delivers genome sequence data, SNP markers and potential candidate genes which will allow to implement marker-assisted strategies to fix bacterial wilt resistance in outcrossing breeding populations of Italian ryegrass.
Highlights
High-yielding forage grasses are major components of temperate grasslands worldwide, providing an important feed source for sustainable ruminant livestock production (Humphreys et al 2010)
The de novo assembly of M2289 had a slightly higher number of complete BUSCOs and a lower number of missing BUSCOs (80.5% and 11.0% compared to 75.5% and 13.9% in Adret2, respectively), both assemblies provide a solid basis for single nucleotide polymorphisms (SNP) discovery in the Xanthomonas translucens pv. graminis (Xtg)-ART mapping population
We demonstrate the efficacy of next-generation sequencing (NGS)-based pooled DNA sequencing to enrich with sequence information a previously identified QTL region harboring an important source of bacterial wilt resistance in Italian ryegrass
Summary
High-yielding forage grasses are major components of temperate grasslands worldwide, providing an important feed source for sustainable ruminant livestock production (Humphreys et al 2010). Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grasses, mainly used for hay and silage production and valued for its high palatability and biomass yield (Bernard et al 2002). Biomass yield of Italian ryegrass can be severely reduced by various bacterial and fungal pathogens. The most important bacterial pathogen of Italian ryegrass is Xanthomonas translucens pv. Graminis (Xtg), which causes bacterial wilt on a range of forage grass species including ryegrasses and fescues (Egli et al 1975). Yield losses are reported to range between 20% in field swards (Schmidt and Nuesch 1980) and up to 80% in experimental setups after leaf inoculation (Wang and Sletten 1995).
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