Aarhus Universitets segl

Selection of rye (Secale cereale L.) for powdery mildew and leaf rust resistance through phenotyping, target sequencing, and association genetics

Publikation: Bog/antologi/afhandling/rapportPh.d.-afhandling

  • Nikolaj Meisner Vendelbo
Despite decades of declining rye acreage in Northern and Eastern Europe, rye remains an important crop in the European agriculture. Since the introduction of rye hybrids in 1990s breeding efforts have primarily focused on addressing the inherent issues of male-fertility restoration and ergot susceptibility in the predominant hybrid rye breeding gene pools Petkus and Carsten. As a consequence breeding for resistance towards the foliar diseases powdery mildew and leaf rust were concurrently given a lower priority. Capable of causing considerable grain yield and quality losses we investigated the genetics underlying resistance to powdery mildew and leaf rust in a Gülzow-based hybrid rye (Secale cereale L.) elite breeding germplasm distinct from the Petkus and Carsten. In the project commencement a population study of the germplasm was conducted, confirming a strong genetic separation of parental populations suited for hybrid breeding. The investigation, however, revealed a considerable discrepancy in the genetic characteristics of parental populations, emphasizing the need for addressing a low level of genetic diversity in the non-restorer germplasm (NRG) and cytoplasmic-male sterile (CMS) population. For the investigation of resistance a subset of 190 Nordic Seed hybrid rye breeding lines were genotyped on the state-of-the-art 600K high-density single nucleotide polymorphism array and phenotyped in field, and the restorer population (n = 101) in a greenhouse trial. In contrast to the Petkus and Carsten gene pools we observed a high level and diverse spectra of leaf rust resistance in both parental populations. Using genome-wide association study (GWAS) we identified a novel leaf rust resistance (R) gene on chromosome arm 7RS and five quantitative trait loci (QTLs) on chromosome arms 1RS, 1RL, 2RL, 5RL, and 7RS. Using k-mer association genetics coupled with resistance gene enrichment and sequencing (AgRenSeq) we, furthermore, identified four candidate leaf rust R genes, of which one co-localized with Pr3 and the identified QTL on chromosome arm 1RS. For powdery mildew, as a result of a low level of natural infection in the field trials, a greenhouse trial was conducted using distinct field populations as inoculum leading to observation of a moderate level of resistance in the NRG&CMS population and low level of resistance in the restorer population. Using GWAS a we identified a novel powdery mildew R gene on chromosome arm 7RL.
On basis of the Danish official trials records during the past 25 years and current projections of powdery mildew on Triticeae under near-future climate conditions in Northern Europe, these suggest a likely minor role of powdery mildew as a biotic stress factor in rye. While powdery mildew is not a bygone threat, it is likely to be confined to sporadic years, or geographical regions, with conducive climatic conditions or certain agricultural practices. In contrast, leaf rust is becoming a biotic stress factor of growing importance in rye with current projections concurring on an augmented effect of climatic changes on leaf rust on Triticeae in Northern and Eastern Europe. The increase in restrictions, prohibitions and environmental taxation on the use of pesticide as a result of the rising political incentive on a sustainable transition of agricultural practices in the EU emphasizes the need for improving the low level of leaf rust resistance in released hybrid rye cultivars. On basis of our findings the Gülzow germplasm, therefore, constitute a valuable genetic resource for addressing this potential demand. In order to improve the quality of markers for successful implementation of marker assisted selection and/or marker assisted backcrossing strategies for discovered leaf rust R genes and QTLs we propose (i) separation of GWAS on parental populations due to large discrepancy in linkage disequilibrium, (ii) increasing sample size and marker density for GWAS on the restorer population, (iii) establishment of multi-parent advanced generation inter-cross population(s) for discovery of less prevalent leaf rust R genes and slow rusting QTLs, and (iv) use of candidate leaf rust R gene sequences for potential development of high quality functional markers.
In addition to the study of powdery mildew and leaf rust resistance in the germplasm a investigation of the genetics underlying the Gülzow fertility control was likewise done. By GWAS on a biparental mapping population we identified a novel Gülzow-type major restoration of male-fertility gene on chromosome arm 3RL. Using the recent ‘Lo7’ rye reference genome we identified a mitochondrial transcription termination factor co-expressed in two Gülzow-type hybrids during flowering as a likely candidate gene. With no previous record of a major restoration of male-fertility gene in fertility control systems of rye on chromosome arm 3RL nor on syntenic regions in barley and wheat our finding constitute a novel discovery with potential value for implementation in other Triticeae hybrid breeding systems
ForlagAarhus Universitet
Antal sider231
StatusUdgivet - dec. 2021

Note vedr. afhandling

Forsvar: 6. december 2021<br/>Termination date: 03.01.2022


  • Secale cereale L., Puccinia recondita f. sp. secalis, Blumeria graminis f.sp. secalis, leaf rust, powdery mildew, hybrid breeding, fertility control system, male-fertility restoration, population study, GWAS

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