In many cultivated crop species there is limited genetic variation available for the development of new higher yielding varieties adapted to climate change and sustainable farming practises. The distant relatives of crop species provide a vast and largely untapped reservoir of genetic variation for a wide range of agronomically important traits that can be exploited by breeders for crop improvement. In this paper, in what we believe to be the largest introgression programme undertaken in the monocots, we describe the transfer of the entire genome of Festuca pratensis into Lolium perenne in overlapping chromosome segments. The L. perenne/F. pratensis introgressions were identified and characterised via 131 simple sequence repeats and 1612 SNPs anchored to the rice genome. Comparative analyses were undertaken to determine the syntenic relationship between L. perenne/ F. pratensis and rice, wheat, barley, sorghum and Brachypodium distachyon. Analyses comparing recombination frequency and gene distribution indicated that a large proportion of the genes within the genome are located in the proximal regions of chromosomes which undergo low/very low frequencies of recombination. Thus, it is proposed that past breeding efforts to produce improved varieties have centred on the subset of genes located in the distal regions of chromosomes where recombination is highest. The use of alien introgression for crop improvement is important for meeting the challenges of global food supply and the monocots such as the forage grasses and cereals, together with recent technological advances in molecular biology, can help meet these challenges.

The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro-evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post-meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge.

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Molecular genetic markers are tools that provide an opportunity to assist crop breeders in the development of new cultivars. They can be used as a proxy for costly or difficult‐to‐phenotype traits, enabling the screening of germplasm in a more efficient and robust way. The approach of using molecular markers in breeding programs is not new, and the key aim when developing such markers is to identify loci that are in linkage disequilibrium with the trait of interest. However, interesting developments in the technology underpinning contemporary crop genetics, such as next‐generation sequencing and high‐density genotyping platforms, can be translated and applied to crop breeding, potentially improving this process. Key Concepts Genetic loci in linkage disequilibrium with a trait of interest can be used to design molecular markers for breeding. Large numbers of single‐nucleotide polymorphisms (SNPs) enable marker discovery when mapping the trait, with coverage of around one marker per 2 cM to map a trait for marker‐assisted selection (MAS) in crops. A much smaller number can be used for tracking preferred alleles during the breeding process. A denser set of markers than those used in MAS would be needed for genomic selection.