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Bassi F.M.,International Center for Agricultural Research in the Dry Areas | Bentley A.R.,The John Bingham Laboratory | Charmet G.,French National Institute for Agricultural Research | Ortiz R.,Swedish University of Agricultural Sciences | Crossa J.,Biometrics and Statistics Unit
Plant Science | Year: 2016

In the last decade the breeding technology referred to as 'genomic selection' (GS) has been implemented in a variety of species, with particular success in animal breeding. Recent research shows the potential of GS to reshape wheat breeding. Many authors have concluded that the estimated genetic gain per year applying GS is several times that of conventional breeding. GS is, however, a new technology for wheat breeding and many programs worldwide are still struggling to identify the best strategy for its implementation. This article provides practical guidelines on the key considerations when implementing GS. A review of the existing GS literature for a range of species is provided and used to prime breeder-oriented considerations on the practical applications of GS. Furthermore, this article discusses potential breeding schemes for GS, genotyping considerations, and methods for effective training population design. The components of selection intensity, progress toward inbreeding in half- or full-sibs recurrent schemes, and the generation of selection are also presented. © 2015 The Authors.


PubMed | International Center for Agricultural Research in the Dry Areas, The John Bingham Laboratory, Biometrics and Statistics Unit, French National Institute for Agricultural Research and Swedish University of Agricultural Sciences
Type: | Journal: Plant science : an international journal of experimental plant biology | Year: 2015

In the last decade the breeding technology referred to as genomic selection (GS) has been implemented in a variety of species, with particular success in animal breeding. Recent research shows the potential of GS to reshape wheat breeding. Many authors have concluded that the estimated genetic gain per year applying GS is several times that of conventional breeding. GS is, however, a new technology for wheat breeding and many programs worldwide are still struggling to identify the best strategy for its implementation. This article provides practical guidelines on the key considerations when implementing GS. A review of the existing GS literature for a range of species is provided and used to prime breeder-oriented considerations on the practical applications of GS. Furthermore, this article discusses potential breeding schemes for GS, genotyping considerations, and methods for effective training population design. The components of selection intensity, progress toward inbreeding in half- or full-sibs recurrent schemes, and the generation of selection are also presented.


PubMed | Aberystwyth University, The John Bingham Laboratory, University of Western Australia, University of Missouri and 19 more.
Type: Journal Article | Journal: Plant biotechnology journal | Year: 2016

Agriculture is now facing the perfect storm of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.


PubMed | The John Bingham Laboratory, University of Bristol, John Innes Center and Affymetrix
Type: Journal Article | Journal: Plant biotechnology journal | Year: 2016

In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheats secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom() genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.


Bentley A.R.,The John Bingham Laboratory | Turner A.S.,John Innes Center | Gosman N.,The John Bingham Laboratory | Leigh F.J.,The John Bingham Laboratory | And 4 more authors.
Plant Breeding | Year: 2011

Differences in photoperiod sensitivity are widely used in wheat breeding to provide adaptation to diverse agronomic environments. Two photoperiod insensitive (PI) mutations in the A genome (Ppd-A1a alleles) were previously identified using near-isogenic lines of tetraploid durum wheat. We show that these Ppd-A1a alleles predominate in modern durum wheat but are absent from wild tetraploid wheat and from conventional hexaploid wheat, suggesting they were selected for improved adaptation during durum cultivation. To increase genetic diversity in hexaploid wheat, synthetic hexaploid wheat lines were developed at CIMMYT by hybridizing elite durum lines with Aegilops tauschii accessions. Ppd-A1a alleles from durum wheat were found in 71.4% of 447 synthetic hexaploids and 9.6% of 115 advanced selections. Backcrosses to hexaploid wheat showed that the durum Ppd-A1a alleles conferred a PI phenotype and that one allele was intermediate between known B and D genome mutations, providing a new source of flowering time variation in hexaploid wheat and the potential for novel combinations of PI alleles. © 2010 Blackwell Verlag GmbH.


Zikhali M.,John Innes Center | Leverington-Waite M.,John Innes Center | Fish L.,John Innes Center | Simmonds J.,John Innes Center | And 6 more authors.
Molecular Breeding | Year: 2014

Vernalization, photoperiod and the relatively poorly defined earliness per se (eps) genes regulate flowering in plants. We report here the validation of a major eps quantitative trait locus (QTL) located on wheat 1DL using near isogenic lines (NILs). We used four independent pairs of NILs derived from a cross between Spark and Rialto winter wheat varieties, grown in both the field and controlled environments. NILs carrying the Spark allele, defined by QTL flanking markers Xgdm111 and Xbarc62, consistently flowered 3–5 days earlier when fully vernalized relative to those with the Rialto. The effect was independent of photoperiod under field conditions, short days (10-h light), long days (16-h light) and very long days (20-h light). These results validate our original QTL identified using doubled haploid (DH) populations. This QTL represents variation maintained in elite north-western European winter wheat germplasm. The two DH lines used to develop the NILs, SR9 and SR23 enabled us to define the location of the 1DL QTL downstream of marker Xgdm111. SR9 has the Spark 1DL arm while SR23 has a recombinant 1DL arm with the Spark allele from Xgdm111 to the distal end. Our work suggests that marker assisted selection of eps effects is feasible and useful even before the genes are cloned. This means eps genes can be defined and positionally cloned in the same way as the photoperiod and vernalization genes have been. This validation study is a first step towards fine mapping and eventually cloning the gene directly in hexaploid wheat. © 2014, The Author(s).


PubMed | The John Bingham Laboratory and John Innes Center
Type: Journal Article | Journal: Molecular breeding : new strategies in plant improvement | Year: 2014

Vernalization, photoperiod and the relatively poorly defined earliness


PubMed | The John Bingham Laboratory, Roslin Institute and University of Cambridge
Type: | Journal: Applied & translational genomics | Year: 2016

Most agriculturally significant crop traits are quantitatively inherited which limits the ease and efficiency of trait dissection. Multi-parent populations overcome the limitations of traditional trait mapping and offer new potential to accurately define the genetic basis of complex crop traits. The increasing popularity and use of nested association mapping (NAM) and multi-parent advanced generation intercross (MAGIC) populations raises questions about the optimal design and allocation of resources in their creation. In this paper we review strategies for the creation of multi-parent populations and describe two complementary


PubMed | John Innes Center, Affymetrix, The John Bingham Laboratory, RAGT Seeds and 2 more.
Type: | Journal: Plant biotechnology journal | Year: 2016

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819571 previously characterized wheat markers, here we describe the identification of 35143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom


PubMed | The John Bingham Laboratory
Type: Journal Article | Journal: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik | Year: 2014

We show the application of association mapping and genomic selection for key breeding targets using a large panel of elite winter wheat varieties and a large volume of agronomic data. The heightening urgency to increase wheat production in line with the needs of a growing population, and in the face of climatic uncertainty, mean new approaches, including association mapping (AM) and genomic selection (GS) need to be validated and applied in wheat breeding. Key adaptive responses are the cornerstone of regional breeding. There is evidence that new ideotypes for long-standing traits such as flowering time may be required. In order to detect targets for future marker-assisted improvement and validate the practical application of GS for wheat breeding we genotyped 376 elite wheat varieties with 3,046 DArT, single nucleotide polymorphism and gene markers and measured seven traits in replicated yield trials over 2years in France, Germany and the UK. The scale of the phenotyping exceeds the breadth of previous AM and GS studies in these key economic wheat production regions of Northern Europe. Mixed-linear modelling (MLM) detected significant marker-trait associations across and within regions. Genomic prediction using elastic net gave low to high prediction accuracies depending on the trait, and could be experimentally increased by modifying the constituents of the training population (TP). We also tested the use of differentially penalised regression to integrate candidate gene and genome-wide markers to predict traits, demonstrating the validity and simplicity of this approach. Overall, our results suggest that whilst AM offers potential for application in both research and breeding, GS represents an exciting opportunity to select key traits, and that optimisation of the TP is crucial to its successful implementation.

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