Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing

Zander, Manuel; Patel, Dhwani A.; Wouw, Angela P. Van de; Lai, Kaitao; Lorenc, Michał T.; Campbell, Emma; Hayward, Alice; Edwards, David; Raman, Harsh; Batley, Jacqueline

doi:10.1007/s10142-013-0324-5

Cited by 25 publications

(48 citation statements)

References 52 publications

(63 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous work (Chapter 3; Rouxel et al, 2011;Zander et al, 2013;Grandaubert et al, 2014b;Patel et al, 2015) has led us to understand that the Australian blackleg population is highly diverse.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, Dilmaghani et al (2012) proposed from minisatellite marker results that two genetically different populations of blackleg are present in Western Canada. Zander et al (2013) conducted a small scale population diversity study using SNPs, whose successful results were used as a foundation for the large-scale study described in Patel et al (2015) (Chapter 3).…”

Section: Population Diversitymentioning

confidence: 99%

“…These were chosen from the list of 21,814 SNPs described in Zander et al (2013). The SNP prediction was conducted using…”

Section: Illumina Goldengate Assaymentioning

confidence: 99%

“…isolates Lm-1 and Lm-2 (Zander et al, 2013). Approximately 100 bp of sequence on either side of the SNP was scrutinized to ensure that no degenerate bases or other polymorphisms were present.…”

Section: Illumina Goldengate Assaymentioning

confidence: 99%

“…The SNPs were chosen to cover the expanse of supercontigs on which SNP changes were detected (Zander et al, 2013). The 27 supercontigs chosen for SNP selection represented 96.7% of the total SNP changes detected in the L. maculans genome (Zander et al, 2013). Sample preparation for the Illumina GoldenGate assay was performed according to the Illumina GoldenGate Genotyping Assay guide (Catalogue No.…”

Section: Illumina Goldengate Assaymentioning

confidence: 99%

See 4 more Smart Citations

Population diversity and genomics of the fungal pathogen of canola Leptosphaeria maculans

Patel¹

View full text Add to dashboard Cite

Canola (Brassica napus) is an important agricultural crop in Australia. Its value as an agricultural commodity has dramatically increased over the past few years to >$2000 million (AUD) in 2015.However, the production of this prosperous crop is threatened by up to 34 different pests, including fungal, bacterial and viral pathogens. Diseases caused by these pathogens lead to substantial crop losses that collectively amount to $130 million (AUD) each year. Leptosphaeria maculans (blackleg) is a ubiquitous ascomycete fungus that is the major causal agent of disease on canola plants. It is called blackleg due to its necrotrophic effects that cause stem canker at the base of the stem during the last stages of infection. When canola was first introduced to Australia as an agricultural crop in the 1970s, blackleg disease led to almost 90% crop losses, threatening to drive the nascent canola industry in Australia to the ground. In recent years, crop losses still amount to $76.6 million (AUD) per annum. Therefore, it is imperative to devise methods to control the devastating effects of this pathogen to protect this economically significant crop. In order to do so, we must decipher the genomic content that drives this pathogen to cause large-scale infections in the field.Blackleg disease is a major concern not only in Australia, but also in other parts of the world such as Europe and Canada. Over the past few years, scientists have made significant advances in decoding the genome of this pathogen. It has been established that L. maculans interacts in a genefor-gene manner with its host. It is composed of disease-causing avirulence (Avr) genes that are specifically recognised by the corresponding resistance (R) gene in the host plant. The specific location and characterisation of the Avr genes AvrLm1, AvrLm6, AvrLm4-7, AvrLm11, AvrLmJ1, AvrLm2 and AvrLm3 has been determined. Furthermore, the reference genome for this pathogen was sequenced in 2011. The reference genome based on the strain v23.1.3 is 45.12 Mb and is scaffolded onto 76 supercontigs. It was reported to be bipartite in nature, composed of AT and GCrich blocks and riddled with truncated copies of transposable elements (TEs) that were affected by Repeat-Induced Point (RIP) mutations. The availability of a reference genome has greatly assisted in designing bioinformatics tools to analyse the genomic content of this pathogen. Here we contribute to the growing pool of knowledge of blackleg genomics.This thesis begins by shedding light on the population diversity of this pathogen in Australia. We used Single Nucleotide Polymorphisms (SNPs) and sampled a large variety of isolates from different canola-growing regions across Australia. We were able to conclude that the Australian blackleg population is panmictic in nature, where members of the population interact randomly with one another, leading to high diversity via sexual reproduction. Increased genetic diversity amongst the population contributes significantly to increase the evolutionary potential of thi...

show abstract

Section: Discussionmentioning

confidence: 99%