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BackgroundGenomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability.ResultsUsing these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set.ConclusionUsing a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0613-z) contains supplementary material, which is available to authorized users.

Prior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, which has a time and labour cost. It can also be inferred from family means, although the spread in days to heading within families demands roguing in first generation synthetics. Another option is to predict heading date from molecular markers. In this study we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Opportunities exist to develop a cheap assay to sequence a small number of regions in linkage disequilibrium with heading date QTL in thousands of samples. Simultaneous use of these markers in non-linkage based marker-assisted selection approaches, such as paternity testing, should enhance the utility of such an approach.

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BackgroundPerennial ryegrass is a cool-season grass species from the family Poaceae and is widely cultivated in temperate regions because it exhibits rapid growth and establishment, and possesses high forage quality. The extension of the growing season in Ireland in spring and autumn is a breeding target to make farming more profitable since a grass-fed diet based on grazing is the cheapest way of nutrition for ruminants.MethodsFifty-seven perennial ryegrass accessions were screened for their ability to grow under typical Irish spring conditions as taken from long term temperature records in controlled climate chambers. They were grown in low temperature (8 °C/2 °C day/night) and control conditions (15 °C/8 °C day/night) in three consecutive independent experiments. Fresh weight, height, chlorophyll content and electrolyte leakage were measured, and these parameters were used to rank plant performance under low temperature growth conditions.ResultsThe results showed that height, yield and electrolyte leakage are excellent measures for the impact of cold stress tolerance. Little variation in growth was seen under cold stress, but a wide variety of responses were observed under control conditions.DiscussionOur results suggest that cold stress is under tight physiological control. Interestingly, the various genotypes responded differentially to more amenable control conditions, indicating that a quick response to more amenable growth conditions is a better target for breeding programmes.