Fast-Forwarding Genetic Gain Li, Huihui; Rasheed, Awais; Hickey, Lee T. ...
Trends in plant science,
03/2018, Volume:
23, Issue:
3
Journal Article
Peer reviewed
Open access
‘Speed breeding’ enables scientists to exploit gene bank accessions and mutant collections for an unparalleled rapid gene discovery and gene deployment. Combining speed breeding and other ...leading-edge plant breeding technologies with strategic global partnerships, has the potential to achieve the genetic gain targets required to deliver our future crops.
Adult-plant resistance (APR) is a type of genetic resistance in cereals that is effective during the later growth stages and can protect plants from a range of disease-causing pathogens. Our ...understanding of the functions of APR-associated genes stems from the well-studied wheat-rust pathosystem. Genes conferring APR can offer pathogen-specific resistance or multi-pathogen resistance, whereby resistance is activated following a molecular recognition event. The breeding community prefers APR to other types of resistance because it offers broad-spectrum protection that has proven to be more durable. In practice, however, deployment of new cultivars incorporating APR is challenging because there is a lack of well-characterised APRs in elite germplasm and multiple loci must be combined to achieve high levels of resistance. Genebanks provide an excellent source of genetic diversity that can be used to diversify resistance factors, but introgression of novel alleles into elite germplasm is a lengthy and challenging process. To overcome this bottleneck, new tools in breeding for resistance must be integrated to fast-track the discovery, introgression and pyramiding of APR genes. This review highlights recent advances in understanding the functions of APR genes in the well-studied wheat-rust pathosystem, the opportunities to adopt APR genes in other crops and the technology that can speed up the utilisation of new sources of APR in genebank accessions.
Key message
This review explores how speed breeding protocols that hasten plant growth and development could be applied to shorten breeding cycles and accelerate research activities in orphan crops.
...There is a growing need for the agri-food sector to sustainably produce larger quantities of higher-quality food, feed and fuel using fewer resources, within the context of changing agroclimatic conditions. Meeting this challenge will require the accelerated development and dissemination of improved plant varieties and substantial improvement of agricultural practices. Speed breeding protocols that shorten plant generation times can hasten breeding and research to help fulfil the ever-increasing demands. Global agri-food systems rely on a relatively small number of plant species; however, there are calls to widen the scope of globally important crops to include orphan crops, which are currently grown and used by the world’s poorest people or marketed as niche products for affluent consumers. Orphan crops can supply global diets with key nutrients, support economic development in the world’s poorest regions, and bolster the resilience of the global agri-food sector to biotic and abiotic stresses. Little research effort has been invested in orphan crops, with farmers growing landraces that are sourced and traded through poorly structured market systems. Efforts are underway to develop breeding resources and techniques to improve orphan crops. Here, we highlight the current efforts and opportunities to speed breed orphan crops and discuss alternative approaches to deploy speed breeding in the less-resourced regions of the world. Speed breeding is a tool that, when used together with other multidisciplinary R&D approaches, can contribute to the rapid creation of new crop varieties, agricultural practices and products, supporting the production and utilisation of orphan crops at a commercial scale.
Breeding crops to feed 10 billion Hickey, Lee T; N Hafeez, Amber; Robinson, Hannah ...
Nature biotechnology,
07/2019, Volume:
37, Issue:
7
Journal Article
Peer reviewed
Open access
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.
Farmers around the world have recently experienced significant crop losses due to severe heat and drought. Such extreme weather events and the need to feed a rapidly growing population have raised ...concerns for global food security. While plant breeding has been very successful and has delivered today's highly productive crop varieties, the rate of genetic improvement must double to meet the projected future demands. Here we discuss basic principles and features of crop breeding and how modern technologies could efficiently be explored to boost crop improvement in the face of increasingly challenging production conditions.
Fast-forward breeding for a food-secure world Varshney, Rajeev K.; Bohra, Abhishek; Roorkiwal, Manish ...
Trends in genetics,
December 2021, 2021-12-00, 20211201, Volume:
37, Issue:
12
Journal Article
Peer reviewed
Open access
Crop production systems need to expand their outputs sustainably to feed a burgeoning human population. Advances in genome sequencing technologies combined with efficient trait mapping procedures ...accelerate the availability of beneficial alleles for breeding and research. Enhanced interoperability between different omics and phenotyping platforms, leveraged by evolving machine learning tools, will help provide mechanistic explanations for complex plant traits. Targeted and rapid assembly of beneficial alleles using optimized breeding strategies and precise genome editing techniques could deliver ideal crops for the future. Realizing desired productivity gains in the field is imperative for securing an adequate future food supply for 10 billion people.
The rapid advances in plant genome sequencing and phenotyping have enhanced trait mapping and gene discovery in crops.Increasing adoption of machine learning algorithms is crucial to derive meaningful inferences from complex multidimensional phenotyping data.Emerging breeding approaches like optimal contribution selection, alone or in combination with genomic selection, will enhance the genetic base of breeding programs while accelerating genetic gain.Integrating speed breeding with new-age genomic breeding technologies holds promise to relieve the long-standing bottleneck of lengthy crop breeding cycles.Haplotype-based breeding, genomic prediction, and genome editing will hasten targeted assembly of superior alleles in future cultivars for sustainable agricultural development and long-term food security.
Key message
The efficiency of phenotype-based assessments of plant variety protection and registration could be improved by the integration of DNA-based testing. We review the current and proposed ...models in the era of next-generation breeding.
The current plant variety protection system relies on morphological description of plant varieties. Distinctness, uniformity, and stability (DUS) assessments determine whether a new variety is distinguishable from common knowledge varieties and exhibits sufficient phenotypic uniformity and stability during two independent growing cycles. However, DUS assessment can be costly, time-consuming and often restricted to a relatively small number of traits that can be influenced by environmental conditions. This calls for the adoption of a DNA-based system which is endorsed by the International Union for the Protection of New Varieties of Plants (UPOV). This could enable examiners to deploy trait-specific DNA markers in DUS testing as well as using such genetic markers to manage reference collections. Within UPOV’s system, breeders can freely use protected varieties in breeding programs. However, breeders of protected varieties may seek sharing in ownership of essentially derived varieties once it is proven that they, with the exception of a few distinctive DUS trait(s), conform to parental varieties in essential characteristics. As well as their complementary role in DUS testing, DNA markers have been known as a good replacement of morphological traits in defining boundaries between independently and essentially derived varieties. With the advent of new breeding technologies that allow minor modification in varieties with outcomes of specific merit or utility, detecting distinctness between varieties may become increasingly challenging. This, together with the ever-increasing number of varieties with which to compare new candidate varieties, supports the potential utility of using DNA-based approaches in variety description.
Stem rust (SR) or black rust caused by Puccinia graminis f. sp. tritici is one of the most common diseases of wheat (Triticum aestivum L.) crops globally. Among the various control measures, the most ...efficient and sustainable approach is the deployment of genetically resistant cultivars. Traditionally, wheat breeding programs deployed genetic resistance in cultivars, but unknowingly this is often underpinned by a single seedling resistance gene, which is readily overcome by the pathogen. Nowadays, adult plant resistance (APR) is a widely adopted form of rust resistance because more durable mechanisms often underpin it. However, only a handful of SR APR genes are available, so breeders currently strive to combine seedling and APR genes. Phenotyping adult wheat plants for resistance to SR typically involves evaluation in the field. But establishing a rust nursery can be challenging, and screening is limited to once a year. This slows down research efforts to isolate new APR genes and breeding of genetically resistant cultivars.In this study, we report a protocol for rapid evaluation of adult wheat plants for resistance to stem rust. We demonstrate the technique by evaluating a panel of 16 wheat genotypes consisting of near isogenic lines (NILs) for known Sr genes (i.e., Sr2, Sr33, Sr45, Sr50, Sr55, Sr57, and Sr58) and three landraces carrying uncharacterized APR from the N. I. Vavilov Institute of Plant Genetic Resources (VIR). The method can be completed in just 10 weeks and involves two inoculations: first conducted at seedling stage and a second at the adult stage (using the same plants). The technique can detect APR, such as that conferred by APR gene Sr2, along with pseudo-black chaff (the morphological marker). Phenotyping can be conducted throughout the year, and is fast and resource efficient. Further, the phenotyping method can be applied to screen breeding populations or germplasm accessions using local or exotic races of SR.
Designer Roots for Future Crops Voss-Fels, Kai P.; Snowdon, Rod J.; Hickey, Lee T.
Trends in plant science,
November 2018, 2018-11-00, 20181101, Volume:
23, Issue:
11
Journal Article
Peer reviewed
Despite the importance of roots, they have largely been ignored by modern crop research and breeding. We discuss important progress in crop root research and highlight how the context-dependent ...optimisation of below- and above-ground plant components provides opportunities to improve future crops in the face of increasing environmental fluctuations.
The optimal root system architecture (RSA) of a crop is context dependent and critical for efficient resource capture in the soil. Narrow root growth angle promoting deeper root growth is often ...associated with improved access to water and nutrients in deep soils during terminal drought. RSA, therefore is a drought-adaptive trait that could minimize yield losses in regions with limited rainfall. Here, GWAS for seminal root angle (SRA) identified seven marker-trait associations clustered on chromosome 6A, representing a major quantitative trait locus (
) which also displayed high levels of pairwise LD (
= 0.67). Subsequent haplotype analysis revealed significant differences between major groups. Candidate gene analysis revealed loci related to gravitropism, polar growth and hormonal signaling. No differences were observed for root biomass between lines carrying hap1 and hap2 for
, highlighting the opportunity to perform marker-assisted selection for the
locus and directly select for wide or narrow RSA, without influencing root biomass. Our study revealed that the genetic predisposition for deep rooting was best expressed under water-limitation, yet the root system displayed plasticity producing root growth in response to water availability in upper soil layers. We discuss the potential to deploy root architectural traits in cultivars to enhance yield stability in environments that experience limited rainfall.
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