Editorial: Genomics-Enabled Crop Genetics

Abstract

Editorial on the Research Topic Genomics-Enabled Crop Genetics In the genomics era, omics-based technologies have unprecedentedly promoted progress in plant biology, from plant growth and development, plant physiology to molecular genetic studies, and system and synthetic biology. While proteomics and metabolomics are becoming prevalent, genomics and transcriptomics are the most popular and widely used platforms for crop studies due to their rapidly decreased costs, improved sequencing quality, a broad spectrum of applications, and well-established bioinformatic tools. Genetic and functional genomic studies in crops, especially those in non-model crops, have been lagged far behind compared to those in model plant species for a couple of reasons. First, some crops can have a large, complex and polyploidy genome, such as wheat (Triticum aestivum) (International Wheat Genome Sequencing Consortium, 2018). Second, while a group of closely related crop species is often comparatively studied or used in breeding programs, they could have distinct genomes and/or ploidy levels, representing further technical challenges for molecular studies. For example, the peanuts include the cultivated peanut (Arachis hypogaes, AABB genome), the wild tetraploid peanut (Arachis monticola, AABB genome) and two wild diploid peanuts, Arachis duranensis (AA genome) and Arachis ipaensis (BB genome) (Bertioli et al., 2016, 2019; Chen et al., 2016, 2019; Lu et al., 2018; Yin et al., 2018, 2019; Zhuang et al., 2019). Another example is the cultivated bananas, which are interspecific or intraspecific hybrids between wild diploid Musa acuminata (AA genome) and Musa balbisiana (BB genome). They have various genotypes, including diploid (AA, BB, and AB), triploid (AAA, AAB, and ABB) and tetraploid (AAAB, AABB, ABBB) variants (D'Hont et al., 2012; Davey et al., 2013; Martin et al., 2016; Wang et al., 2019). Third, for many crops the genomic resources supporting functional studies and molecular breeding are not often available, including high-quality reference genome assemblies, high-density genetic maps, and genomics-characterized populations. Finally, in some crops (such as sorghum), genetic transformation is still challenging, and mutant resources are not well-established. When synergistically integrated with other omics approaches, genomic technologies can be compelling for crop genetics, representing a technological basis to help mitigate or circumvent the challenges mentioned above in crop studies. The papers included in this Research Topic, Genomics-Enabled Crop Genetics, illustrate this concept. The various studies collected in this Research Topic can be summarized into three major aspects: (1) the theme of “Genomic technologies promote germplasm characterization” includes contributions regarding molecular identification, characterization of crop species and accessions with genomics-based methods. (2) The subject of “Genomic technologies enhance crop population genetics” showcases the examples of population genetic studies facilitated by the genomic approaches. (3) The topic of “Genomic technologies enable functional mining of genomic components in crops,” on the other hand, presents the applications in multiple genomic and transcriptomic databases. These resources are comprehensively integrated to generate functional insights into the genomic components, e.g., genes, miRNAs and cis-regulatory elements. This Research Topic includes thirteen original research articles, one hypothesis and theory paper, one opinion paper and one review article, covering the following three aspects. Markers of simple sequence repeats (SSR) or chloroplast DNA are often used to study the phylogenetic relationship between accessions or species within a crop genus. Taking the advantages of RNA-seq that provides sequence information about functional genes in a cost-effective and high-throughput way, Karcı et al. performed transcriptome sequencing of pistachio (Pistacia vera), developed 233 genic SSR markers (gSSR) and studied the phylogenetic relationship using 55 gSSR markers from nine Pistacia species. This study exemplifies RNA-seq as a tool to contribute to the taxonomy of crop species and their relatives. Qiu et al. assembled the five fescue taxa's chloroplast genomes, including three subspecies of Festuca rubra, one Festuca brevipila, and one Festuca ovina, providing resources to screen fescue germplasm accessions and to refine species identification. With the plastid genome information, Qiu et al. reconstructed the phylogenetic relationship of the Festuca-Lolium complex. Synthetic or artificial polyploid hybrid materials within the Triticum genus or Triticum and its relative species represent essential wheat genetic improvement resources. Cytogenetic techniques can help provide insights into crop genomics, guiding further investigations on certain genomic issues. For example, to better characterize the tetraploid wheat-Aegilops ventricosa amphiploid materials, Zhang et al. observed the chromosomal behavior of the progeny plants (AABBD^VD^VN^VN^V) derived from crosses between T. turgidum (AABB) and Aegilops ventricosa (D^VD^VN^VN^V) using multicolor Fluorescence in situ hybridization (mc-FISH), providing insights into the genome stability of allopolyploidization in the wheat group. Genomic-based technologies have enhanced the traditional linkage mapping of quantitative trait loci (QTL) and enabled genome-wide association study (GWAS) by developing hundreds of thousands of markers (single nucleotide polymorphism, SNP, e.g., in most applications). In understudied crops, it is...