Rapid advances in "next-generation" DNA sequencing technology have brought the US$1000 human (Homo sapiens) genome within reach while providing the raw sequencing output for researchers to revolutionize the way populations are genotyped. To capitalize on these advancements, genotypingby-sequencing (GBS) has been developed as a rapid and robust approach for reduced-representation sequencing of multiplexed samples that combines genome-wide molecular marker discovery and genotyping. The fl exibility and low cost of GBS makes this an excellent tool for many applications and research questions in plant genetics and breeding. Here we address some of the new research opportunities that are becoming more feasible with GBS. Furthermore, we highlight areas in which GBS will become more powerful with the continued increase of sequencing output, development of reference genomes, and improvement of bioinformatics. The ultimate goal of plant biology scientists is to connect phenotype to genotype. In plant breeding, the genotype can then be used to predict phenotypes and select improved cultivars. Furthering our understanding of the connection between heritable genetic factors and the resulting phenotypes will enable genomics-assisted breeding to exist on the scale needed to increase global food supplies in the face of decreasing arable land and climate change.

Plant breeding and genetics research is an inherently data‐driven enterprise. Typical experiments and breeding nurseries can contain thousands of unique entries and programs will often evaluate tens of thousands of plots each year. To function efficiently on this scale, electronic data management becomes essential. Many research programs, however, continue to operate by scribing and transcribing massive amounts of data on paper field books. While effective, this form of data management places heavy burdens on human resources, decreases data integrity, and greatly limits future utilization of data and the ability to expand the breeding program. To help address these constraints, we have developed an open‐source application for electronic data capture that runs on consumer‐grade Android tablets. By focusing on a simple, stand‐alone application with an intuitive and customized interface, we attempt to decrease both the technological and cost barriers that hinder adoption of electronic data management in breeding programs. The simplicity of Field Book allows adoption of the technology without a steep learning curve. With low‐cost, accessible solutions, the vision of one handheld per breeder can become a reality for breeding programs around the world. Transformational capacity in electronic data collection and management will be essential to realizing a contemporary green revolution.

Motivation Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. Availability and implementation More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.

Key message The first cytological characterization of the 2NvS segment in hexaploid wheat; complete de novo assembly and annotation of 2NvS segment; 2NvS frequency is increasing 2NvS and is associated with higher yield. Abstract The Aegilops ventricosa 2NvS translocation segment has been utilized in breeding disease-resistant wheat crops since the early 1990s. This segment is known to possess several important resistance genes against multiple wheat diseases including root knot nematode, stripe rust, leaf rust and stem rust. More recently, this segment has been associated with resistance to wheat blast, an emerging and devastating wheat disease in South America and Asia. To date, full characterization of the segment including its size, gene content and its association with grain yield is lacking. Here, we present a complete cytological and physical characterization of this agronomically important translocation in bread wheat. We de novo assembled the 2NvS segment in two wheat varieties, ‘Jagger’ and ‘CDC Stanley,’ and delineated the segment to be approximately 33 Mb. A total of 535 high-confidence genes were annotated within the 2NvS region, with > 10% belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families. Identification of groups of NLR genes that are potentially N genome-specific and expressed in specific tissues can fast-track testing of candidate genes playing roles in various disease resistances. We also show the increasing frequency of 2NvS among spring and winter wheat breeding programs over two and a half decades, and the positive impact of 2NvS on wheat grain yield based on historical datasets. The significance of the 2NvS segment in wheat breeding due to resistance to multiple diseases and a positive impact on yield highlights the importance of understanding and characterizing the wheat pan-genome for better insights into molecular breeding for wheat improvement.

One major and three minor QTLs for resistance to pre-harvest sprouting (PHS) were identified from a white wheat variety "Danby." The major QTL on chromosome 3A is TaPHS1, and the sequence variation in its promoter region was responsible for the PHS resistance. Additive × additive effects were detected between two minor QTLs on chromosomes 3B and 5A, which can greatly enhance the PHS resistance. Pre-harvest sprouting (PHS) causes significant losses in yield and quality in wheat. White wheat is usually more susceptible to PHS than red wheat. Therefore, the use of none grain color-related PHS resistance quantitative trait loci (QTLs) is essential for the improvement in PHS resistance in white wheat. To identify PHS resistance QTLs in the white wheat cultivar "Danby" and determine their effects, a doubled haploid population derived from a cross of Danby × "Tiger" was genotyped using genotyping-by-sequencing markers and phenotyped for PHS resistance in two greenhouse and one field experiments. One major QTL corresponding to a previously cloned gene, TaPHS1, was consistently detected on the chromosome arm 3AS in all three experiments and explained 21.6-41.0% of the phenotypic variations. A SNP (SNP-222) in the promoter of TaPHS1 co-segregated with PHS in this mapping population and was also significantly associated with PHS in an association panel. Gene sequence comparison and gene expression analysis further confirmed that SNP-222 is most likely the causal mutation in TaPHS1 for PHS resistance in Danby in this study. In addition, two stable minor QTLs on chromosome arms 3BS and 5AL were detected in two experiments with allele effects consistently contributed by Danby, while one minor QTL on 2AS was detected in two environments with contradicted allelic effects. The two stable minor QTLs showed significant additive × additive effects. The results demonstrated that pyramiding those three QTLs using breeder-friendly KASP markers developed in this study could greatly improve PHS resistance in white wheat.