Capturing Wheat Phenotypes at the Genome Level

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, 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 9 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 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, 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 Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for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 new opportunities 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 focus on reported candidate genes cloned and linked to 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 and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.

Identification and validation of quantitative trait loci for chlorophyll content of flag leaf in wheat under different phosphorus treatments

“…The donor of the wheat D genome is the species of Aegilops tauschii . Previous research has revealed that the D genome of wheat plays a crucial role in stress tolerance ( Mirzaghaderi and Mason, 2019 ; Hussain et al., 2022 ). In this study, the two major chlorophyll QTLs with the highest phenotypic contribution rate were identified on chromosome 4D, and there was no previously reported chlorophyll content QTLs in same interval, suggesting that Qchl.saw-4D.1 and Qchl.saw-4D.2 may be novel major QTL.…”

Wheat Omics: Advancements and Opportunities

“…Advancement in NGS technologies has propelled a massive wave of scientific discoveries, providing enormous modern genomic tools and resources for wheat genetic improvement and bringing a paradigm shift in breeding methods [ 14 ]. Innovations have been made in the development of efficient genotyping platforms in wheat which could be combined with physical maps for rapid gene discovery [ 15 , 16 , 17 ].…”

“…The availability of millions of SNPs in wheat has opened vistas of new gene discoveries using genome-wide association studies (GWAS) [ 14 , 73 ]. As of today, more than 3000 marker-trait associations are known for a plethora of agronomic traits in wheat which have been compiled into 141 meta-QTLs [ 74 ].…”

Finding the LMA needle in the wheat proteome haystack

“…The industry will equally benefit from these latest scientific developments since processing companies, markets and food industries demand not only high yielding and resistant varieties, but also those with specific end-use qualities (1,3). Market requirements have influenced wheat breeding as not to neglect essential protein content and quality.…”

“…Common bread wheat ( Triticum aestivum L .) is the dominant crop in temperate regions, currently covering more than 220 million hectares worldwide, exceeding 749 million tons in production annually (1) and predicted to reach 835 million tons by 2030 (2). From the most primitive form of wheat 10,000 years ago in the Fertile Crescent to the species currently grown all over the world, desirable characteristics have been selected and improved upon by human societies (3).…”