This Special Issue on ‘Advances in Cereal Crops Breeding’ comprises 10 papers covering a wide range of subjects, including the expression-level investigation of genes in terms of salinity stress adaptations and their relationships with proteomics in rice, the use of genetic analysis to assess the general combining ability (GCA) and specific combining ability (SCA) in promising hybrids of maize, the use of DNA markers based on PCR in rice, the identification of quantitative trait loci (QTLs) in wheat and simple sequence repeats (SSR) in rice, the use of single-nucleotide polymorphisms (SNP) in a genome-wide association study (GWAS) in cereals, and Nanopore direct RNA sequencing of related with LTR RNA retrotransposon in triticale prior to the genomic selection of heterotic maize hybrids.

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Repetitive DNA is ubiquitous in eukaryotic genomes, and, in many species, comprises the bulk of the genome. Repeats include transposable elements that can self-mobilize and disperse around the genome, and tandemly-repeated satellite DNAs that increase in copy number due to replication slippage and unequal crossing over. Despite their abundance, repetitive DNA is often ignored in genomic studies due to technical challenges in their identification, assembly, and quantification. New technologies and methods are now providing the unprecedented power to analyze repetitive DNAs across diverse taxa. Repetitive DNA is of particular interest because it can represent distinct modes of genome evolution. Some repetitive DNA forms essential genome structures, such as telomeres and centromeres, which are required for proper chromosome maintenance and segregation, whereas others form piRNA clusters that regulate transposable elements; thus, these elements are expected to evolve under purifying selection. In contrast, other repeats evolve selfishly and produce genetic conflicts with their host species that drive adaptive evolution of host defense systems. However, the majority of repeats likely accumulate in eukaryotes in the absence of selection due to mechanisms of transposition and unequal crossing over. Even these neutral repeats may indirectly influence genome evolution as they reach high abundance. In this Special Issue, the contributing authors explore these questions from a range of perspectives.

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What controls the different rates of evolution to give rise to conserved and divergent proteins and RNAs? How many trials until evolution can adapt to physiological changes? Every organism has arisen through multiple molecular changes, and the mechanisms that are employed (mutagenesis, recombination, transposition) have been an issue left to the elegant discipline of evolutionary biology. But behind the theory are realities that we have yet to ascertain: How does an evolving cell accommodate its requirements for both conserving its essential functions, while also providing a selective advantage? In this volume, we focus on the evolution of the eukaryotic telomere, the ribo-nuclear protein complex at the end of a linear chromosome. The telomere is an example of a single chromosomal element that must function to maintain genomic stability. The telomeres of all species must provide a means to avoid the attrition from semi-conservative DNA replication and a means of telomere elongation (the telomere replication problem). For example, telomerase is the most well-studied mechanism to circumvent telomere attrition by adding the short repeats that constitutes most telomeres. The telomere must also guard against the multiple activities that can act on an unprotected double strand break requiring a window (or checkpoint) to compensate for telomere sequence loss as well as protection against non-specific processes (the telomere protection problem). This volume describes a range of methodologies including mechanistic studies, phylogenetic comparisons and data-based theoretical approaches to study telomere evolution over a broad spectrum of organisms that includes plants, animals and fungi. In telomeres that are elongated by telomerases, different components have widely different rates of evolution. Telomerases evolved from roots in archaebacteria including splicing factors and LTR-transposition. At the conserved level, the telomere is a rebel among double strand breaks (DSBs) and has altered the function of the highly conserved proteins of the ATM pathway into an elegant means of protecting the chromosome end and maintaining telomere size homeostasis through a competition of positive and negative factors. This homeostasis, coupled with highly conserved capping proteins, is sufficient for protection. However, far more proteins are present at the telomere to provide additional species-specific functions. Do these proteins provide insight into how the cell allows for rapid change without self-destruction?

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