Journal Article

Genomic characterization of a nematode tolerance locus in sugar beet

Pucker, Boas, Viehöver, Prisca, Elashry, Abdelnaser, Müller, Andreas E., Schechert, Axel, Sielemann, Katharina, Holtgräwe, Daniela, Orsini, Elena, Schulte, Lukas, Weisshaar, Bernd

2023

Overview

Background Infection by beet cyst nematodes (BCN, Heterodera schachtii ) causes a serious disease of sugar beet, and climatic change is expected to improve the conditions for BCN infection. Yield and yield stability under adverse conditions are among the main breeding objectives. Breeding of BCN tolerant sugar beet cultivars offering high yield in the presence of the pathogen is therefore of high relevance. Results To identify causal genes providing tolerance against BCN infection, we combined several experimental and bioinformatic approaches. Relevant genomic regions were detected through mapping-by-sequencing using a segregating F2 population. DNA sequencing of contrasting F2 pools and analyses of allele frequencies for variant positions identified a single genomic region which confers nematode tolerance. The genomic interval was confirmed and narrowed down by genotyping with newly developed molecular markers. To pinpoint the causal genes within the potential nematode tolerance locus, we generated long read-based genome sequence assemblies of the tolerant parental breeding line Strube U2Bv and the susceptible reference line 2320Bv. We analyzed continuous sequences of the potential locus with regard to functional gene annotation and differential gene expression upon BCN infection. A cluster of genes with similarity to the Arabidopsis thaliana gene encoding nodule inception protein-like protein 7 (NLP7) was identified. Gene expression analyses confirmed transcriptional activity and revealed clear differences between susceptible and tolerant genotypes. Conclusions Our findings provide new insights into the genomic basis of plant-nematode interactions that can be used to design and accelerate novel management strategies against BCN.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agricultural production / Analysis / Animal Genetics and Genomics / Animals / Annotations / Arabidopsis thaliana / Beta vulgaris / Beta vulgaris - genetics / Biomedical and Life Sciences / Climate change / Control / Cultivars / Diseases and pests / DNA sequencing / Gene expression / Gene frequency / Gene mapping / Genes / Genetic aspects / Genetic transcription / Genome resources / Genomes / Genomics / Genotype & phenotype / Genotypes / Genotyping / Health aspects / Infection / Life Sciences / Loci / Mapping-by-sequencing / Microarrays / Microbial Genetics and Genomics / Nematoda / Nematoda - genetics / Nematode diseases of plants / Nematode tolerance / Nematodes / NLP7 / Nucleotide sequence / Nucleotide sequencing / Plant Breeding / Plant Genetics and Genomics / Population genetics / Proteins / Proteomics / Sugar / Sugar beet / Sugar beets / Sugars - metabolism