Genome-Wide Association Mapping of Crown and Brown Rust Resistance in Perennial Ryegrass.

Mattia Fois,Torben Asp,Marta Malinowska,Morten Greve,Andrea Bellucci,Anja Karine Ruud

doi:10.3390/genes13010020

Abstract

A population of 239 perennial ryegrass (Lolium perenne L.) genotypes was analyzed to identify marker-trait associations for crown rust (Puccinia coronata f. sp. lolii) and brown rust (Puccinia graminis f. sp. loliina) resistance. Phenotypic data from field trials showed a low correlation (r = 0.17) between the two traits. Genotypes were resequenced, and a total of 14,538,978 SNPs were used to analyze population structure, linkage disequilibrium (LD), and for genome-wide association study. The SNP heritability (h2SNP) was 0.4 and 0.8 for crown and brown rust resistance, respectively. The high-density SNP dataset allowed us to estimate LD decay with the highest possible precision to date for perennial ryegrass. Results showed a low LD extension with a rapid decay of r2 value below 0.2 after 520 bp on average. Additionally, QTL regions for both traits were detected, as well as candidate genes by applying Genome Complex Trait Analysis and Multi-marker Analysis of GenoMic Annotation. Moreover, two significant genes, LpPc6 and LpPl6, were identified for crown and brown rust resistance, respectively, when SNPs were aggregated to the gene level. The two candidate genes encode proteins with phosphatase activity, which putatively can be induced by the host to perceive, amplify and transfer signals to downstream components, thus activating a plant defense response.

Highlights

Perennial ryegrass (Lolium perenne L.) is predominantly used as a forage crop in Europe, New Zealand, and temperate regions of Japan, Australia, South Africa, and SouthAmerica due to its high productivity and high nutritional value in terms of palatability and digestibility [1]
The aims of this study were (i) to resequence a diploid perennial ryegrass population to generate a high-density single nucleotide polymorphism (SNP) marker set, (ii) to identify markers associated with crown rust resistance (CRR), and brown rust resistance (BRR) using genome-wide association mapping, and (iii) to identify candidate genes that potentially play a role in the resistance to the two diseases
The resequencing of a diploid perennial ryegrass population phenotyped for crown and brown rust resistance produced a large and complex dataset employed in a genomewide association study

Summary

Introduction

Perennial ryegrass (Lolium perenne L.) is predominantly used as a forage crop in Europe, New Zealand, and temperate regions of Japan, Australia, South Africa, and SouthAmerica due to its high productivity and high nutritional value in terms of palatability and digestibility [1]. The infection, common from July to October, is followed by sporulation, which causes several breaks on the leaf surface leading to increased transpiration, reduced watersoluble carbohydrate (WSC), and plant vigor. Crown rust infection can lower yield by up to 56%, along with reduced thousand-seed weight [4,5], negatively affecting perennial ryegrass seed production. Since both dry matter digestibility and efficient rumen fermentation are influenced by WSC concentration [6,7], crown rust infection likely affects both factors, reducing palatability and favoring saprophytes [8], which might threaten animal health

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