Bread wheat is not only an important cereal crop but also a model for study of an allopolyploid plant with a large, highly repetitive genome. Advances in next-generation sequencing (NGS) technology provide needed throughput to conquer the enormous size of the wheat genome. Multiple high quality reference genome sequences will soon be available. Full-scale wheat functional genomics studies are dawning. In this review we highlight the available tools and methodologies for wheat functional genomics research developed with the assistance of NGS technology and recent progress, particularly the concerted effort in generating multiple reference genomes, strategies to attain genome-wide genetic variation, genome-wide association studies, mutant population generation, and NGS-supported gene cloning and functional characterization. These resources and platforms lay a solid foundation for wheat research, leading to a new era of wheat functional genomics that will bridge the gap between genotype and phenotype. Dissection of wheat genomes and gene functions should assist in genomics-assisted selection and facilitate breeding of elite varieties for sustainable agriculture in China and the world.

Common wheat is an important and widely cultivated food crop throughout the world. Much progress has been made in regard to wheat genome sequencing in the last decade. Starting from the sequencing of single chromosomes/chromosome arms whole genome sequences of common wheat and its diploid and tetraploid ancestors have been decoded along with the development of sequencing and assembling technologies. In this review, we give a brief summary on international progress in wheat genome sequencing, and mainly focus on reviewing the effort and contributions made by Chinese scientists.

Genome editing is one of the most promising biotechnologies to improve crop performance. Common wheat is a staple food for mankind. In the past few decades both basic and applied research on common wheat has lagged behind other crop species due to its complex, polyploid genome and difficulties in genetic transformation. Recent breakthroughs in wheat transformation permit a revolution in wheat biotechnology. In this review, we summarize recent progress in wheat genetic transformation and its potential for wheat improvement. We then review recent progress in plant genome editing, which is now readily available in wheat. We also discuss measures to further increase transformation efficiency and potential applications of genome editing in wheat. We propose that, together with a high quality reference genome, the time for efficient genetic engineering and functionality studies in common wheat has arrived.

As a cool season crop, wheat (Triticum aestivum L.) has an optimal daytime growing temperature of 15 °C during the reproductive stage. With global climate change, heat stress is becoming an increasingly severe constraint on wheat production. In this review, we summarize recent progress in understanding the molecular mechanisms of heat tolerance in wheat. We firstly describe the impact of heat tolerance on morphology and physiology and its potential effect on agronomic traits. We then review recent discoveries in determining the genetic and molecular factors affecting heat tolerance, including the effects of phytohormone signaling and epigenetic regulation. Finally, we discuss integrative strategies to improve heat tolerance by utilization of existing germplasm including modern cultivars, landraces and related species.

Wheat is one of the most important food crops, and its yield is seriously restricted by high salinity and other abiotic stresses. Many attempts have been made to elucidate the major physiological processes associated with salt tolerance and to identify the genes controlling the processes. In this review, the major role of high-affinity potassium transporter (HKT) genes in enhancing the salt tolerance of wheat is summarized. The link between maintenance of reactive oxygen species (ROS) homeostasis and salt tolerance through a comprehensive study of a wheat introgression line is examined, and the contribution of a set of genes involved in this process is depicted. New research strategies to uncover the mechanisms underlying salt tolerance in wheat based on recent advances in omics will be discussed.

Fusarium head blight (FHB) or scab caused by Fusarium graminearum is a major threat to wheat production in China as well as in the world. To combat this disease, multiple efforts have been carried out internationally. In this article, we review our long-time effort in identifying the resistance genes and dissecting the resistance mechanisms by both forward and reverse genetics approaches in the last two decades. We present recent progress in resistance QTL identification, candidate functional gene discovery, marker-assisted improvement of FHB resistant varieties, and findings in investigating association of signal molecules, such as Ca⁺⁺, SA, JA, and ET, with FHB response, with the assistance from rapidly growing genomics platforms. The information will be helpful for designing novel and efficient approaches to curb FHB.

Obligate biotrophic fungi cause serious and widespread diseases of crop plants, but are challenging to investigate because they cannot be cultured in vitro. The two economically important groups of biotrophic fungi parasitizing wheat are the rust and powdery mildew pathogens, but their obligate biotrophic lifestyles and pathogenicity mechanisms are not well understood at the molecular level. With the advent of next generation sequencing technology, increasing numbers of pathogen genomes are becoming available. Research in plant pathology has entered a new genomics era. This review summarizes recent progress in understanding the biology and pathogenesis of biotrophic fungal pathogens attacking wheat based on pathogen genomics. We particularly focus on the three wheat rust and the powdery mildew fungi in regard to genome sequencing, avirulence gene cloning, effector discovery, and pathogenomics. We predict that coordinated study of both wheat and its pathogens should reveal new insights in biotrophic adaptation, pathogenicity mechanisms, and population dynamics of these fungi that will assist in development of new strategies for breeding wheat varieties with durable resistance.

Wheat is the most widely cultivated staple food crop, and multiple types of food derivatives are processed and consumed globally. Wheat grain quality (WGQ) is central to food processing and nutritional value, and is a decisive factor for consumer acceptance and commercial value of wheat cultivars. Hence, improvement in WGQ traits is top priority for both conventional and molecular wheat breeding. In this review we will focus on two important WGQ traits, grain milling and end-use, and will summarize recent progress in China. Chinese scientists have invested substantial effort in molecular genetic and genomic analysis of these traits and their effects on end-use properties. The insights and resources generated have contributed to the understanding and improvement of these traits. As high-quality genomics information and powerful genome engineering tools are becoming available for wheat, more fundamental breakthroughs in dissecting the molecular and genomic basis of WGQ are expected. China will strive to make further significant contributions to the study and improvement of WGQ in the genomics era.

The common wheat landrace Chinese Spring (CS) was made famous by the work of Ernie Sears, a great cytogenetist, who developed a number of CS-based aneuploid series that were used to identify individual wheat chromosomes. Based on this, a standard karyotype and nomenclature system was developed for wheat chromosomes that allowed wheat researchers to analyze and manipulate the wheat genome with unprecedented precision and efficiency. Nevertheless, not much is known about the utilization of CS at its hometown, Chengdu in Sichuan province, during early wheat breeding activity. In this review, we follow the speculation that CS is a selection from the Cheng-du-guang-tou (CDGT) landrace. We provide a description of how CDGT became a founder landrace for wheat breeding activities in early times. We show that CDGT-derived varieties were reinforced genetically by crosses to six more exotic parents. These varieties remained the major elite cultivar for several decades. Later, synthetic hexaploid wheats were introduced into the breeding program, firstly using those from CIMMYT and later using materials produced with local tetraploid wheat and goat grass. Finally, we discuss the strategies and future directions to improve wheat yield and resistance through an expanded genetic basis, especially by recapturing lost genetic variations from landraces and related wild species, a process that may set an example for wheat breeders in China and elsewhere.

Stripe rust (yellow rust), caused by Puccinia striiformis f. sp. tritici (PST), is one of the most devastating fungal diseases in common wheat (Triticum aestivum L.) in China and worldwide. Resistance breeding is the most effective strategy to control diseases in crop plants. Chinese wheat lines Mengmai 58 and Huaiyang 1 are highly resistant to PST race CYR34 (V26) at the adult plant stage. To genetically map the underlying resistance genes we developed segregating populations by crossing Mengmai 58 and Huaiyang 1 with the susceptible cultivar Nongda 399. The stripe rust resistances in Mengmai 58 and Huaiyang 1 were both controlled by single dominant genes, provisionally designated YrMM58 and YrHY1, respectively. Bulked segregant RNA-Seq (BSR-Seq) analysis showed that YrMM58 and YrHY1 were located in the same distal ~ 16 Mb region on chromosome 2AS. Comparative genomics analysis with the physical map of Aegilops tauschii proved useful for developing additional markers to saturate the genetic linkage map. YrMM58 and YrHY1 were mapped to the distal end of chromosome arm 2AS, with the closest marker WGGB148 being 7.7 cM and 3.8 cM from the resistance gene, which was considered to be Yr17. These markers can be used in marker-assisted selection.