Marker-Assisted Selection (MAS) in Crop Plants

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Background

Global climate change, reductions in arable land, and food security demands that plant breeding will continue to play an imperative role in feeding 9 billion people sustainably by 2050. In order to face this challenge, modern plant breeding will necessitate the adoption of new technologies and practices to boost production of cultivated plants by capturing or generating more favorable genetic diversity. In crop plants, the majority of agronomically important traits are quantitatively inherited, controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). The most common approach to pre-breeding is to use genetic mapping to identify QTLs for key phenotypic variation followed by introgressing those QTLs into the elite gene pool with marker-assisted selection (MAS), which can enhance the selection criteria of phenotypes comparing to conventional breeding with the selection of genes. As the cost of genotyping continues to decline, the use of genotyping-by-sequencing (GBS) technologies or whole genome re-sequencing, coupled with the release of the genome sequences of plant species have permitted the development of dense arrays of single nucleotide polymorphisms (SNPs) covering the entire genome, which have in turn paved the way to genome-wide association studies (GWAS). Meanwhile, fine mapping guided by genome sequences of many plant species have facilitated the exploration of functional genes; in addition, pan-genomes constructed from various available resources such as the reference sequence and its variants, raw reads and haplotype reference panels provide a new perspective on QTL locations and potential molecular targets for plant breeding. Similarly, new approaches to marker-trait association analyses such as quantitative trait locus sequencing (QTL-seq) and quantitative trait gene sequencing (QTG-seq) that are based on bulked-segregant analysis (BSA) and whole-genome resequencing will help accelerate QTL fine-mapping and identification of the causal genes. In conclusion, the tools and strategies for MAS in modern plant breeding have been expanding in recent years. By embracing a broad array of conventional and new molecular techniques, modern plant breeding has a bright future in delivering new crop cultivars to keep our food, fiber and biobased economy diverse and safe.

With this research topic, we aim to cover current knowledge, technology, and approaches that facilitate MAS in plant breeding. Recent advances in genotyping technologies together with comparative and functional genomics approaches are broadening QTL conception to expression QTL (eQTL), protein QTL (pQTL), splicing QTL (sQTL), metabolites QTL (mQTL), and methylation QTL (meQTL), et al. Advances in statistics, molecular biology, quantitative and population genetics, genomics, phenomics and other -omics, et al., would help explore more functional genes based on QTL mapping, which would offer the potential of transforming MAS in plant breeding programs toward a data-rich and evidence-based process and improving the efficiency.

We welcome Original Research, Review and Methods contributions on current knowledge and approaches facilitating plant breeding under (but not limited to) the following categories:
1) Innovations in QTL mapping methods in plant breeding.
2) Exploration of functional genes in crop plants.
3) Marker-assisted selection (MAS) based on QTLs or functional genes in crop plants.
4) Application of MAS in crops especially with complex genomes (i.e. sugarcane, lily, etc.) or long selection cycle (i.e. loblolly pine, pecan, etc.).
5) Pan-genomes and their applications in plant breeding.

Please note: Frontiers in Plant Science does not accept solely descriptive studies - studies which report responses to treatments and descriptive reports of ‘Omics studies will not be considered if they do not progress biological understanding of these responses.

Keywords: plant breeding, marker-assisted selection (MAS), functional genes, whole genome re-sequencing, quantitative trait locus sequencing (QTL-seq), pan-genomes

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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