Harnessing landrace diversity empowers wheat breeding.

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker-trait associations. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security.

Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement.

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

Creation and judicious application of a wheat resistance gene atlas.

Disease-resistance (R) gene cloning in wheat (Triticum aestivum) has been accelerated by the recent surge of genomic resources, facilitated by advances in sequencing technologies and bioinformatics. However, with the challenges of population growth and climate change, it is vital not only to clone and functionally characterize a few handfuls of R genes, but also to do so at a scale that would facilitate the breeding and deployment of crops that can recognize the wide range of pathogen effectors that threaten agroecosystems. Pathogen populations are continually changing, and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily bread. To meet this challenge, we propose the creation of a wheat R-gene atlas by an international community of researchers and breeders. The atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens, such as wheat rusts, blotch diseases, powdery mildew, and wheat blast. We present a costed proposal detailing how the interacting molecular components governing disease resistance could be captured from both the host and the pathogen through biparental mapping, mutational genomics, and whole-genome association genetics. We explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat, as well as their wild relatives and major pathogens, and discuss how the atlas could inform a dynamic, durable approach to R-gene deployment. Set against the current magnitude of wheat yield losses worldwide, recently estimated at 21%, this endeavor presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.

Breeding crops to feed 10 billion.

Crop improvements can help us to meet the challenge of feeding a population of 10 billion, but can we breed better varieties fast enough? Technologies such as genotyping, marker-assisted selection, high-throughput phenotyping, genome editing, genomic selection and de novo domestication could be galvanized by using speed breeding to enable plant breeders to keep pace with a changing environment and ever-increasing human population.

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research.

'Speed breeding' (SB) shortens the breeding cycle and accelerates crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.