Catherine J. Howarth

Aberystwyth University | AU · Institute of Biological, Environmental and Rural Sciences

Genomic prediction has mostly been used in single environment contexts, largely ignoring genotype x environment interaction, which greatly affects the performance of plants. However, in the last decade, prediction models including marker x environment (MxE) interaction have been developed. We evaluated the potential of genomic prediction in red clo...

Powdery mildew, caused by the biotrophic fungus Blumeria graminis DC. f. sp. avenae , is a widespread disease of oats, especially in the temperate regions of Western and Central Europe, and the use of resistant varieties is the most sustainable way to ensure stable yields. Therefore, the identification of robust and effective resistance to powdery...

Context Several high-quality reference genomes for oat (Avena sativa L. and relatives) have been published, with the prospect of many additional whole-genome assemblies emerging in the near future. Aims This has necessitated an effort by the International Oat Nomenclature Committee (IONC; all co-authors on this paper) to devise a universal system f...

This poster explains the functioning of the stay-green trait in sorghum

The poster explains the maintenance of yield in stay-green sorghums.

This poster demonstrated that introgressed stay-green QTL functions in a senescent background.

The Pc54 oat line carries the crown rust resistance gene Pc54 and an unknown gene effective against powdery mildew. In this study, two recombinant inbred line (RIL) populations were developed to identify the genomic locations of the two genes and produce lists of molecular markers with a potential for marker-assisted selection. The RILs and parents...

Most oat grains destined for human consumption must possess the ability to pass through an industrial de-hulling process with minimal breakage and waste. Uniform grain size and a high groat to hull ratio are desirable traits related to milling performance. The purpose of this study was to characterize the genetic architecture of traits related to m...

The extent to which the quality and yield of plant varieties are influenced by the environment is important for their successful uptake by end users particularly as climatic fluctuations are resulting in environments that are highly variable from one growing season to another. The genotype-by-environment interaction (GEI) of milling quality and yie...

Key message Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. Abstract During the twentieth century, oat landraces have increasing...

Oats (Avena sativa L.) are a healthy food, being high in dietary fibre (e.g. β-glucans), antioxidants, minerals, and vitamins. Understanding the effect of variety and crop management on nutritional quality is important. The response of four oat varieties to increased nitrogen levels was investigated across multiple locations and years with respect...

A barrier to the adoption of genomic prediction in small breeding programs is the initial cost of genotyping material. Although decreasing, marker costs are usually higher than field trial costs. In this study we demonstrate the utility of stratifying a narrow‐base biparental oat population genotyped with a modest number of markers to employ genomi...

Oat (Avena sativa L.), ranking sixth in world cereal production, is primarily produced as a multipurpose crop for grain, pasture, and forage or as a rotation crop in many parts of the world. Recent research has elevated its potential dietary value for human nutrition and health care. Oats are well adapted to a wide range of soil types and can perfo...

Introduction Oats (Avena sativa L.) are a whole grain cereal recognised for their health benefits and which are cultivated largely in temperate regions providing both a source of food for humans and animals, as well as being used in cosmetics and as a potential treatment for a number of diseases. Oats are known as being a cereal source high in diet...

Although oat cultivation around the Mediterranean basin is steadily increasing, its yield in these regions lags far behind those of Northern Europe. This results mainly from the poor adaptation of current oat cultivars to Mediterranean environments. Local landraces may act as reservoirs of favorable traits that could contribute to increase oat resi...

Figure S1 The density of markers in the updated consensus map, based on (a) TL‐haplotype loci and (b) GBS‐SNPs. Figure S2 Mean chromosome haplotype diversity of the three subpopulations. Figure S3 Haplotype diversity of the full set of lines (a), the spring set (b), and the southern set (c) infered using the TL‐haplotype markers. Figure S4 The s...

Appendix S4 The input file used for the Haplotag analysis of the 4657 lines.

Appendix S1 The list of 4657 taxa genotyped and the consensus map. Appendix S2 The genotype data of the 950 lines used to update the consensus map (full data available by accessing haplotag.aowc.ca/SM3_OC_placement_RAW_merged.zip) Appendix S3 Significant GWAS hits of the different comparisons.

Appendix S4 The input file used for the Haplotag analysis of the 4657 lines.

The sections in this article are Quantitative Traits – What They are and How They are Mapped Biomarkers of the Senescence Process Correlated Developmental Events as Second‐Order Senescence Traits G × E and the Contribution of Biotic and Abiotic Factors Case Studies Exploitation of QTL Mapping for Senescence Traits QTL , Senescence, Ageing an...

In a de-novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker-density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-l...

Downy mildew (DM) of pearl millet, caused by fungus Sclerospora graminicola, is the most destructive disease of pearl millet which can cause grain yield losses up to 60%. Also referred to as ‘green ear’, this disease is widely distributed in temperate and tropical areas of the world and is especially important in India and Africa. In an earlier stu...

The Collaborative Oat Research Enterprise (CORE) was initiated in 2009 and ran until approximately 2014. It consisted of a set of coordinated projects, funded investigators, and collaborators who were united by an over-arching goal of developing modern tools for genomics and molecular breeding in oat. Principle outcomes of the CORE included: (1) se...

Key message: Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS a...

The genetic variability of 28 sorghum genotypes of known senescence phenotype was investigated using 66 SSR markers well-distributed across the sorghum genome. The genotypes of a number of lines from breeding programmes for stay-green were also determined. This included lines selected phenotypically for stay-green and also RSG 03123, a marker-assis...

Six hundred thirty five oat lines and 4,561 SNP loci were used to evaluate population structure, linkage disequilibrium (LD) and genotype-phenotype association with heading date. The first five principal components (PC) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PC nor the cross-validation errors from K=1 to 2...

Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (~12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density c...

Association mapping is becoming a more and more popular approach to identify genes responsible for quantitative variation of complex traits with agronomical importance. Recent advances in genomic tools such as high-throughput sequencing technologies and high-density single nucleotide polymorphism (SNP) genotyping, allow for development of powerful...

Global mean surface temperature has increased by 0.6oC to 0.9oC between 1906 and 2005 and is predicted to increase by 1.5oC to 2.2oC by 2030 and by 3.7oC to 4.8oC degrees over the next 100 years (Hoffman, 2013). Agriculture is extremely susceptible to climate change. For example, higher temperatures can inhibit photosynthesis, disturb pollination a...

Flowering time varies between and within species, profoundly influencing reproductive fitness in wild plants and productivity in crop plants. The time of flowering, therefore, is an important statistic that is regularly collected as part of breeding programs and phenotyping experiments to facilitate comparison of genotypes and treatments. Its autom...

Diseases caused by crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) are among the most important constraints for the oat crop. Breeding for resistance is one of the most effective, economical, and environmentally friendly means to control these diseases. The purpose of this work was to identify elite...

Oats are a low input crop, grown in high rainfall areas in Northern Europe but with origins in arid zones, mostly likely in central Turkey. The crop is increasingly grown for human use, greatly increasing its value, or as a beneficial component of cereal rotations. A collaboration between IBERS (UK), IPBB and KARI (Kazakhstan) and KSUAF (Turkey) ai...

In this study, genetic diversity among 177 oat (Avena sativa L.) accessions including both white and red oat landraces and 36 commercial cultivars was studied for simple sequence repeat (SSR) loci. Thirty-one genomic and expressed sequence tags (EST)-derived primer pairs were selected according to high polymorphism from an initial 66 SSR batch. Mar...

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP d...

Biotic stresses such as rust and powdery mildew constitute major constraints for oat crops. Efficient utilization of genetic resources in breeding programs might be greatly facilitated by proper information generated by genetic studies. However, linkage mapping studies are restricted to specific genetic backgrounds limiting their usefulness. To ove...

Colinearity of SNP loci mapping to chromosomes 9D and 15A. (TIF)

A 21-chromosome anchored consensus map of oat. (TIF)

Correspondence of consensus chromosomes with published KO linkage groups. (DOCX)

SNP deletion analysis of monosomic hybrid stocks representing chromosomes 6C and 9D. (TIF)

Details for regions of sequence similarity between SNP markers on 21 chromosomes from an oat consensus map and chromosomes from the sequenced genomes of Brachypodium distachyon and Oryza sativa . (XLSX)

Pedigree data for 20 genotypes selected for transcriptome sequencing and SNP identification and for 109 genotypes selected to represent genetic diversity in North American oat germplasm. (XLSX)

Consensus map and component maps from six bi-parental mapping populations, including original SNP genotype calls for component mapping populations. (XLSX)

Sequences for in silico SNP assays analyzed with the GoldenGate genotyping platform. (XLSX)

Oats are a low input cereal widely grown across the world as both a grain and forage crop. Significant areas of production are in Northern Europe and North America and also in China and Australia. Although a traditional crop in many countries, in the last 50 years there has been a significant shift in oat production as a consequence of changing agr...

Pearl millet is grown as a grain and stover crop by the poorest farmers in the harshest cropping environments of South Asia and Sub Saharan Africa. It has excellent tolerance to environmental stresses and has high nutritional and therapeutic food value. Soil fertility, biotic (Striga, downy mildew) and abiotic stresses exacerbated by weather and cl...

The powdery mildew and rust fungi are highly successful pathogens that pose a constant threat to UK cereals where infection may drastically reduce grain quality and yield. The fungi are biotrophic, feeding on living plant cells, depriving the plant of nutrients and causing premature leaf senescence. Genetic host resistance offers disease control th...

Wild relatives of crop species are a rich source of valuable traits for crop improvement but the challenge is how to successfully access such genetic variation without negative effects on crop production. Diploid, tetraploid and hexaploid relatives of the cultivated oat (Avena sativa L.) have been shown to display resistance to a wide range of dise...

Image segmentation is a fundamental yet challenging step during image analysis. In this paper we propose a novel method for choosing the number of labels during automatic image segmentation. It minimizes an objective function based on the number of labels, the segmentation errors, and consistency of labels between neighboring pixels. An experimenta...

Genetic diversity studies are an important tool to be exploited by breeding programs. However, one of the factors that have limited their success in applying results to breeding is that most genomic studies have been conducted in populations derived from a bi-parental cross and hence, the identified markers often turn out to be unique to a specific...

Howarth, C. J., Cowan, A. A., Leggett, J. M., Valentine, J. (2005). Using molecular mapping to access and understand valuable traits in wild relatives of oats. In: E. Lipman; L. Maggioni; H. Kn?pffer; R. Ellis; J.M. Leggett; G. Kleijer; I. Faberov?; A. Le Blanc (compilers). ECPGR Cereal Genetic Resources in Europe: Report of a Cereals Network: Firs...

Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity A...

RONO: 10962A, 10075A; BB/H009582/1; RD2008-3566 Sponsorship: BBSRC; HGCA; DEFRA

Quantitative trait loci (QTL) analysis of resistance to three foliar diseases, viz. target leaf spot, zonate leaf spot and drechstera leaf blight was undertaken in sorghum using 168 F7 recombinant inbred lines derived from a cross between '296B' (resistant) and 'IS18551' (susceptible) parents. The genomic region flanked by plant colour locus (Plcor...

Drought stress during the reproductive stage is one of the most important environmental factors reducing the grain yield and yield stability of pearl millet. A QTL mapping approach has been used in this study to understand the genetic and physiological basis of drought tolerance in pearl millet and to provide a more-targeted approach to improving t...

Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is saliniz...

List of markers. Complete listing of DArT markers and associated clones showing marker clusters (bins) based on scores, map positions, and clone similarity based on sequence assembly.

List of varieties. Inventory of 182 oat varieties and accessions used in DArT marker development and diversity analysis.

Map comparison. Expanded version of 'Kanota' × 'Ogle' 2008 DArT map showing increased density of DArT markers with annotated comparisons to the previous map [9].

Cluster analysis of orthogonal varieties. This is a high-resolution multi-page version of Figure 6.

Pedigree clusters. UPGMA cluster analysis of pedigree distances (D) among 182 oat varieties not orthogonal across all three discovery arrays.

DNA Sequences. FASTA formatted DNA sequence data containing 2670 vector-trimmed sequences corresponding to 2573 unique DArT clones, and 490 consensus sequences from an assembly of the above.

Marker mapping data. Molecular marker data set (in Mapmaker [35] format) including all DArT scores as well as framework marker scores (from [9]) for a set of 80 RIL progenies from the 'Kanota' × 'Ogle' mapping population.

Framework Molecular Map of KxO. Framework version of a molecular marker map in Kanota × Ogle with integrated DArT markers. This is a high-resolution version of the cartoon map presented in Figure 4.

Detailed map placements. HTML version of the new 'Kanota' × 'Ogle' DArT framework map, listing approximate placement for additional markers, including more recently published markers.

Cluster analysis of all varieties. UPGMA cluster analysis of germplasm diversity based on 182 oat varieties, including those that were not orthogonal across all three discovery arrays.

BLAST identity. Potential clone identity based on BLAST for non-redundant set of 1774 DArT clone sequences (consensus and singletons).

Marker diversity data. Non-redundant DArT marker data set for the germplasm diversity study, containing a full set of data from 1295 non-redundant markers and 182 oat varieties, and a nearly orthogonal set with 1295 markers and 134 varieties.

Potentially duplicated markers. List of 156 DArT markers for which there is some evidence that the marker may map to more than one locus. Three types of evidence are explained in the table legend.

Clusters with and without potentially duplicated markers. Analysis of orthogonal diversity data by "Fanny" routine in statistical package 'R'. Fanny finds fuzzy clusters at a given cluster number, 'K'. These analyses were performed with K = 40 on the complete data set (134 × 1295), and, for comparison, on the same data set with potentially duplicat...

Background: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based o...

Howarth, C. J. (2005). Genetic improvement of growth and survival at high temperature. Pages 277-300 in: Ashraf, M.; Harris, P. J. C. (Eds), Abiotic stresses: plant resistance through breeding and molecular approaches. The Haworth Press Inc., New York.

The already available comprehensive genome sequence information of model crops along with the transcriptomic resource from other crops provides an excellent opportunity for comparative genome analysis. We studied the synteny between each of the four major sorghum staygreen quantitative trait loci (QTL) regions with that in the rice genome and attem...

The breeding of modern oat varieties for specific end uses would be greatly enhanced by the use of marker assisted selection. We have developed a genetic linkage map using a combination of microsatellite and DArT markers using a population derived from a cross between two winter oats, Buffalo and Tardis. The use of DArT markers enables meta-QTL ana...

Sponsorship SEERAD, BBSRC RONO: AC03130

The scientific and economic significance of plant senescence means that much effort has been made to understand the processes involved and to devise means of manipulating them agriculturally. During the past few years there has been considerable progress in this regard, especially in the molecular, genetic and genomic aspects. Senescence has a trem...

KEYWORDS: Pennisetum glaucum • genetic diversity • SSR • ICRISAT Genetic diversity among 70 maintainers and two pollinators of sub-Saharan and Indian origin was studied for simple sequence repeat (SSR) loci using 34 primer pairs. A total of 213 alleles were detected with an average of 6.26 alleles per locus. Polymorphic information content (PIC) ra...

Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is saliniz...

Pearl millet marker-assisted selection (MAS) programs targeting adaption to variable postflowering moisture environments would benefit from quantitative trait loci (QTLs) that improve grain yield across the full range of postflowering moisture conditions, rather that just in drought-stressed environments. This research was undertaken to identify su...

Pearl millet [Pennisetum glaucum (L.) R. Br.] is the sixth most important cereal globally after maize, rice, wheat, barley and sorghum. It is grown as a dual-purpose food grain and fodder crop in the hottest, driest regions of sub-Saharan Africa and South Asia where dryland agriculture is practiced. In these marginal crop livestock production envir...

HHB 67, released in 1990 by CCS Haryana Agricultural University, is one such single-cross pearl millet hybrid. HHB 67 is highly popular because of its extra-early maturity (it needs less than 65 days from sowing to grain maturity) and is now grown on over 500?000 ha in Haryana and Rajasthan, India. Recent surveys have indicated that this hybrid is...