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Genomic selection has the potential to accelerate genetic gain in perennial ryegrass breeding, provided complex traits such as forage yield can be predicted with sufficient accuracy. In this study, we compared modelling approaches and feature selection strategies to evaluate the accuracy of genomic prediction models for seasonal forage yield production. Overall, model selection had limited impact on predictive ability when using the full data set. For a baseline genomic best linear unbiased prediction model, the highest mean predictive accuracy was obtained for spring grazing (0.78), summer grazing (0.62) and second cut silage (0.56). In terms of feature selection strategies, using uncorrelated single‐nucleotide polymorphisms (SNPs) had no impact on predictive ability, allowing for a potential decrease of the data set dimensions. With a genome‐wide association study, we found a significant SNP marker for spring grazing, located in the genic region annotated as coding for an enzyme responsible for fucosylation of xyloglucans—major components of the plant cell wall. We also presented an approach to increase interpretability of genomic prediction models with the use of Gene Ontology enrichment analysis. Approaches for feature selection will be relevant in development of low‐cost genotyping platforms in support of routine and cost‐effective implementation of genomic selection. This study evaluated the accuracy of genomic prediction models for seasonal forage yield production in perennial ryegrass. Using uncorrelated single‐nucleotide polymorphism (SNPs) improved model accuracy, while selecting SNPs based on their concordance across different experiments reduced it. These findings could help develop low‐cost genotyping platforms for routine and cost‐effective implementation of genomic selection.

Abstract: Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potato.

Simple sequence repeat (SSR) markers are potentiallyvaluable tools for plant breeding. The objectives ofthe work reported here were to search the EMBL andGenbank databases for the presence of SSR-containingsequences from the genus Capsicum, to assess thefrequency of different motifs, and to examine thepolymorphism of selected markers in a panel ofgenotypes, including 10 Capsicumspp. and 1tomato and 1 potato genotype. Fifty-eightmicrosatellites with different motifs were found inCapsicumsequences. A subset of twelve of thesewere selected for the polymorphism survey using PCRprimers flanking the SSR. Polymorphisms between Capsicumlines can be detected with 5 of these primerpairs. PCR products of the predicted size were alsoamplified with three primer pairs in potato and oneprimer pair in tomato. The study also showed thatshorter microsatellites could be valuable markers inCapsicum.

The application of AFLPs, RAPDs and SSRs to examine genetic relationships in the primary northwestern European cultivated potato gene pool was investigated. Sixteen potato cultivars were genotyped using five AFLP primer combinations, 14 RAPD primers, and 17 database-derived SSR primer pairs. All three approaches successfully discriminated between the 16 cultivars using a minimum of one assay. Similarity matrices produced for each marker type on the basis of Nei and Li coefficients showed low correlations when compared with different statistical tests. Dendrograms were produced from these data for each marker system. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, or EMR) and the amount of polymorphism detected (diversity index, or DI). AFLPs had the highest EMR, and SSRs the highest DI. A single parameter, marker index (MI), which is the product of DI and EMR, was used to evaluate the overall utility of each marker system. The use of these PCR-based marker systems in potato improvement and statutory applications is discussed. Abbreviations: PCR, polymerase chain reaction; AFLP, amplified fragment length polymorphism; RAPD, randomly amplified polymorphic DNA; DNA, deoxyribonucleic acid; EMR, effective multiplex ratio; DI, diversity index; MI, marker index; RFLP, restriction fragment length polymorphism.