Ricardo Humberto Ramirez-Gonzalez

John Innes Centre · Department of Crop Genetics

The identification of genetic markers linked to genes of agronomic importance is a major aim of crop research and breeding programmes. Here, we identify markers for Yr15, a major disease resistance gene for wheat yellow rust, using a segregating F2 population. After phenotyping, we implemented RNA sequencing (RNA-Seq) of bulked pools to identify si...

The design of genetic markers is of particular relevance in crop breeding programs. Despite many economically important crops being polyploid organisms, the current primer design tools are tailored for diploid species. Bread wheat, for instance, is a hexaploid comprising of three related genomes and the performance of genetic markers is diminished...

Insights from the annotated wheat genome Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consort...

Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide population. Exploiting natural variation for the genetic improvement of crops plays a central role in increasing productivity. Although current genomic technologies can be used for high-throughput identification of genetic variation, methods for effici...

Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports a...

Breeding crops resilient to climate change is urgently needed to help ensure food security. A key challenge is to harness genetic diversity to optimise adaptation, yield, stress resilience and nutrition. We examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection of bread wheat ( Triticum aestivum ), a major global cere...

Wheat blast, caused by the fungus Magnaporthe oryzae, threatens global cereal production since its emergence in Brazil in 1985 and recently spread to Bangladesh and Zambia. Here we demonstrate that the AVR-Rmg8 effector, common in wheat-infecting isolates, is recognised by the gene Pm4, previously shown to confer resistance to specific races of Blu...

Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres...

Brassicas are important crops susceptible to significant losses caused by disease: thus, breeding resistant lines can mitigate the effects of pathogens. MAMPs (microbe-associated molecular patterns) are conserved molecules of pathogens that elicit host defence responses known as pattern-triggered immunity (PTI). Necrosis & Ethylene-inducing peptide...

Significance Wheat is a globally important food crop that suffers major yield losses due to outbreaks of severe disease. A better mechanistic understanding of how wheat responds to pathogen attack could identify new strategies for enhancing disease resistance. Here, we discover six pathogen-induced biosynthetic pathways that share a common regulato...

Background Polyploidy, especially allopolyploidy, which entails merging divergent genomes via hybridization and whole-genome duplication (WGD), is a major route to speciation in plants. The duplication among the parental genomes (subgenomes) often leads to one subgenome becoming dominant over the other(s), resulting in subgenome asymmetry in gene c...

Wheat is one of the most widely grown food crops in the world. However, it succumbs to numerous pests and pathogens that cause substantial yield losses. A better understanding of biotic stress responses in wheat is thus of major importance. Here we identify previously unknown pathogen-induced biosynthetic pathways that produce a diverse set of mole...

Background Transcriptomics is being increasingly applied to generate new insight into the interactions between plants and their pathogens. For the wheat yellow (stripe) rust pathogen ( Puccinia striiformis f. sp. tritici , Pst ) RNA-based sequencing (RNA-Seq) has proved particularly valuable, overcoming the barriers associated with its obligate bio...

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome¹, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecul...

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies....

Abstract Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologou...

Legumes tend to be nodulated by competitive rhizobia that do not maximize nitrogen (N 2 ) fixation, resulting in suboptimal yields. Rhizobial nodulation competitiveness and effectiveness at N 2 fixation are independent traits, making their measurement extremely time-consuming with low experimental throughput. To transform the experimental assessmen...

Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. The recent release of high-quality reference sequences for these crops underpin...

Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat (Triticum aestivum) cultivar Chinese Spring reference genome allows...

Background: Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are oft...

To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind,...

To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind,...

Wheat grain development is a robust biological process that largely determines grain quality and yield. In this study, we investigated the grain transcriptome of winter wheat cv. Xiaoyan-6 at four developmental stages (5, 10, 15, and 20 days post-anthesis), using high-throughput RNA sequencing (RNA-Seq). We identified 427 grain-specific transcripti...

In Triticeae endosperm (e.g. wheat and barley), starch granules have a bimodal size distribution (with A- and B-type granules) whereas in other grasses the endosperm contains starch granules with a unimodal size distribution. Here, we identify the gene, BGC1 (B-GRANULE CONTENT 1), responsible for B-type starch granule content in Aegilops and wheat....

Polyploidization has played an important role in plant evolution. However, upon polyploidization, the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to st...

Polyploidization has played an important role in plant evolution. However, upon polyploidization the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to sta...

Previously, we identified a quantitative trait locus on the group 4 chromosomes of Aegilops and bread wheat that controls B-type starch-granule content. Here, we identify a candidate gene by fine-mapping in Aegilops and confirm its function using wheat TILLING mutants. This gene is orthologous to the FLOURY ENDOSPERM 6 (FLO6) gene of rice and barle...

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 is often stored on multiple systems. As analyses of interest i...

Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought...

Number of reads generated and mapped for each sample using Kallisto. (A) Wheat samples were pseudoaligned against the Chinese Spring RefSeqv1.0+UTR transcriptome reference. (B) Wheat–rye hybrids and triticale samples were pseudoaligned against a wheat+rye transcriptome constructed in silico by combining the Chinese Spring RefSeqv1.0+UTR transcripto...

Genes differentially expressed among samples and total number of expressed genes (EG) in this study. (A) High confidence (HC) wheat genes. (B) Low confidence (LC) wheat genes. (C) Rye genes.

(A) Functional annotation of DEGs up-regulated in wheat–rye hybrids vs. triticale (both containing Ph1). (B) Functional annotation of DEGs down-regulated in wheat–rye hybrids vs. triticale (both containing Ph1).

Representation of the ratio of coverage along all chromosomes using Box plots. (A) Box plot comparing wheat–rye hybrids and triticale, both containing the Ph1 locus. (B) Box plot comparing wheat in the presence and absence of Ph1. (C) Box plot comparing wheat–rye in the presence and absence of Ph1. (D) Box plot comparing triticale in the presence a...

Chromosome coverage plots of triticale containing Ph1 (Ph1+) (three samples pooled together) vs. each individual sample of triticale lacking Ph1 (Ph1-). Heatmaps show that each triticale sample lacking Ph1 is different. Several deletions (visualized in dark blue) are common to all three samples, but other deletions and chromosomes rearrangements ar...

Number of DEG among samples using different thresholds in the presence (Ph1+) and absence (Ph1-) of the Ph1 locus. (A) Number of wheat DEGs. (B) Number of rye DEGs. The first number in every column title represents the p-adj filter (>0.05, >0.01 or >0.001). The 2FC indicates that genes were up or down-regulated over twofolds.

(A) Gene ontology (GO) classification of DEGs up-regulated in wheat–rye hybrids vs. triticale (both containing the Ph1 locus). (B) Gene ontology (GO) classification of DEGs down-regulated in wheat–rye hybrids vs. triticale (both containing the Ph1 locus). (C) GO Slim classification of DEGs down-regulated in wheat–rye hybrids vs. triticale (both con...

Functional annotation of the 33 DEGs shared by all samples lacking Ph1 vs. all samples containing Ph1, and which are not located in any of the common deletions present in all samples lacking Ph1.

Principal component analysis (PCA) of samples analyzed in this study. Three biological replicates were produced per genotype. (A) PCA for the six wheat samples, three containing the Ph1 locus (Ph1+) and three lacking it (Ph1-). The x and y axis represent the two principal components of the total variance, 73 and 12%, respectively. (B) PCA for 12 wh...

Morphology of whole plants (A) and spikes (B) of triticale containing the Ph1 locus (Ph1+) and lacking it (Ph1-). Plant and spike morphology of all triticale containing Ph1 was perfectly normal; however, every triticale lacking Ph1, was morphologically different, some exhibiting very abnormal phenotypes.

Number of cleaned reads generated and mapped for each sample. The RNA-seq data were aligned to the RefSeqv1.0 assembly using HISAT with strict mapping options to reduce the noise caused by reads mapping to the incorrect regions.

Chromosome coverage plots of wheat containing Ph1 (Ph1+) (three samples pooled together) vs. each individual sample of wheat lacking Ph1 (Ph1-). Heatmaps show that each wheat sample lacking Ph1 is different. Several deletions (visualized in dark blue) are common to all three samples, but other deletions and chromosomes rearrangements are different...

Chromosome configuration of nine newly synthesized triticale both containing the Ph1 locus (Ph1+) and lacking it (Ph1-). No inter-genomic recombination was detected in the presence of Ph1.

Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high...

‘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...

Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high...

Background: Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. Results:...

To meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in crop breeding. One way this can be achieved is through 'speed breeding' (SB), which shortens the breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carri...

Background: Transposable elements (TEs) are ubiquitous components of genomes and they are the main contributors to genome evolution. The reference sequence of the hexaploid bread wheat (Triticum aestivum L.) genome enabled for the first time a comprehensive genome-wide view of the dynamics of TEs that have massively proliferated in the A, B, and D...

Disease resistance genes encoding intracellular immune receptors of the nucleotide-binding and leucine-rich repeat (NLR) class of proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR encoding genes. The availability of the hexaploid wheat cultivar Chinese Spring reference genome now allows...

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an asse...

Significance Pasta and bread wheat are polyploid species that carry multiple copies of each gene. Therefore, loss-of-function mutations in one gene copy are frequently masked by functional copies on other genomes. We sequenced the protein coding regions of 2,735 mutant lines and developed a public database including more than 10 million mutations....

Ash trees (genus Fraxinus, family Oleaceae) are widespread throughout the Northern Hemisphere, but are being devastated in Europe by the fungus Hymenoscyphus fraxineus, causing ash dieback, and in North America by the herbivorous beetle Agrilus planipennis. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucesters...

Advances in genome sequencing and assembly technologies are generating many high quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimised data types and an asse...

The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have r...

The majority of RNA-seq expression studies in plants remain underutilised and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyse and visualise this data. We have developed expVIP, an expression Visualisation and Integration Platform, which allows easy analysis of RNA-seq data combined w...

Targeted Induced Local Lesions in Genomes (TILLING) is a reverse genetics approach to identify novel sequence variation in genomes, with the aims of investigating gene function and/or developing useful alleles for breeding. Despite recent advances in wheat genomics, most current TILLING methods are low to medium in throughput, being based on PCR am...

The use of next generation sequencing (NGS) to identify novel viral sequences from eukaryotic tissue samples is challenging. Issues can include the low proportion and copy number of viral reads and the high number of contigs (post-assembly), making subsequent viral analysis difficult. Comparison of assembly algorithms with pre-assembly host-mapping...

Key message: Markers closely flanking a Type 1 FHB resistance have been produced and the potential of combining this with Type 2 resistances to improve control of FHB has been demonstrated. Two categories of resistance to Fusarium head blight (FHB) in wheat are generally recognised: resistance to initial infection (Type 1) and resistance to spread...

bio-samtools is a Ruby language interface to SAMtools, the highly popular library that provides utilities for manipulating high-throughput sequence alignments in the Sequence Alignment/Map format. Advances in Ruby, now allow us to improve the analysis capabilities and increase bio-samtools utility, allowing users to accomplish a large amount of ana...

Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f....