Wheat genomics and breeding: bridging the gap.

Abstract

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, until very recently efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species due to its large polyploid genome. However, an international public-private effort spanning nine years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat genome assembly in 2017. Shortly thereafter, in 2020, the genome of assemblies of additional fifteen global wheat accessions were released. Wheat has now entered into the pan-genomic era where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays capable of genotyping hundreds of wheat lines using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up a new horizon for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits including grain yield, yield-related traits, end-use quality and resistance to biotic and abiotic stresses. We also enlisted several reported candidate and cloned candidate genes responsible for the aforesaid traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits through the use of (i) clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) mediated gene-editing, (ii) positional cloning methods, and of genomic selection. Finally, we make recommendations on the utilization of genomics for the next-generation wheat breeding and provide a practical example of using the latest, in silico bioinformatics tools that were based on the wheat reference genome sequence.

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm

“…Resistance to the viral vectors, such as bird cherryoat aphid (Rhopalosiphum padi) and English grain aphid (Sitobion avenae), has been identified in T. boeoticum, Ae. tauschii, T. araraticum, and T. dicoccoides [226].…”

Past, Current and Future of Wheat Diseases in Kenya

“…These limitations are being overcome by improving already available techniques to form next-generation sequencing (NGS) [98]. With next-generation sequencing (NGS) technologies, SNP markers have been discovered in wheat, which is a good choice due to their abundance in the genome as they are distributed across all the wheat chromosomes [99]. These technologies offer easier means to map…”

Applications and Potential of Genome-Editing Systems in Rice Improvement: Current and Future Perspectives

“…Improving plant disease resistance through classical breeding approaches, such as back crossing breeding, multiline breeding, and stacking of resistance (R) gene/s, is a lengthy and tedious process that consumes years [54,55]. Whereas, targeting of different susceptibility (S) factors and gene/s through the CRISPR/Cas9 system has fast-forwarded the development of broad-spectrum disease resistance within a year [12,[56][57][58][59][60].…”