Pat Heslop-Harrison

University of Leicester | LE · Department of Genetics

Background Molecular cytogenetics, utilizing DNA probes, serves as a critical tool for mapping genes to the physical structures of chromosomes. Methods In this study, we examined three Allium species: A. cepa L., A. sativum L., and A. fistulosum L., using in situ hybridization to localize 45S rDNA and 5S rDNA genes. Results We observed variation...

Satellite DNAs are highly repetitive, tandemly arranged sequences, typically making up large portions (> 20%) of the eukaryotic genome. Most satDNAs are fast evolving and changes in their abundance and nucleotide composition may be related to genetic incompatibilities between species. Here, we used Illumina paired-end sequencing raw data and graph-...

Lectin receptor-like kinases (LecRLKs) are membrane-bound receptor genes found in many plant species. They are involved in perceiving stresses and responding to the environment. Oat (Avena sativa; 2n = 6x = 42) are an important food and forage crop with potential in drought, saline, or alkaline soils. Here, we present a comprehensive genome-wide an...

Beta-glucan is a noncellulosic polysaccharide linked by β-(1,3) and β-(1,4) glycosidic bonds, mainlydistributed in the endosperm and aleurone layer of cereal crop grains with the synthesis in the Golgi apparatus,transportation to the plasma membrane by vesicles, and deposition in the cell wall. Beta-glucan is effective inreducing cholesterol and bl...

Flavonoids in Musaceae are involved in pigmentation and stress responses, including cold resistance, and are a component of the healthy human diet. Identification and analysis of the sequence and copy number of flavonoid biosynthetic genes are valuable for understanding the nature and diversity of flavonoid evolution in Musaceae species. In this st...

Introduction: The mapping of the satellite DNA on chromosomes is vital to understanding the distribution and evolution of repetitions in the genome since these chromosomal studies have shown the origin, evolutionary mode, and function of repetitive sequences. This study aimed to prospect the satellitome and determine its location in the genome of...

The genus Aubrieta Adan. (Brassicaceae) is widely distributed and diverged across different elevations. The genome components and organization of this plant are still less understood. Tandemly repeated sequences were examined in whole genome raw reads of four Aubrieta species using Next Generation Sequencing (NGS) and bioinformatics techniques. Six...

Epistasis refers to nonallelic interaction between genes that cause bias in estimates of genetic parameters for a phenotype with interactions of two or more genes affecting the same trait. Partitioning of epistatic effects allows true estimation of the genetic parameters affecting phenotypes. Multigenic variation plays a central role in the evoluti...

Diploid wild oat Avena longiglumis has nutritional and adaptive traits which are valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly siz...

Hibiscus rosa-sinensis L. (Hibiscus, Malvaceae) is an ornamental species grown widely in landscape plantings. We collected leaves from a plant on an urban sidewalk near a market in Guangzhou that showed multiple symptoms of leaf rolling, deformation and chlorosis. Initial evaluation by electron microscopy using negative staining of dip preparations...

Background and Aims The grass genus Urochloa (Brachiaria) sensu lato includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America, and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis...

Flavonoids in Musaceae are involved in pigmentation and stress responses, including pathogen defense and UV protection, and are a component of the healthy human diet. Identification and analysis of the sequence and copy number of flavonoid biosynthetic genes are valuable for understanding the nature and diversity of flavonoid evolution in Musaceae...

Background The BOP (Bambusoideae, Oryzoideae, and Pooideae) clade of the Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2n = 24; genome size 389 Mb) and Brachypodium, Brachypodium distachyon (2n = 10; 271 Mb). We exploit chromosome-scale genome assemblies to show the nature of genomic expansion, structural va...

A total of 139 triticale × wheat progenies (including recombinant inbred lines and doubled haploids) were developed indigenously. Screening at cytogenetic level using genomic in situ hybridization and fluorescence in situ hybridization revealed maximum progenies (48%) carrying 1RS.1BL translocation. D-R genome substitution ranging from 1 to 7 chrom...

We report the results of a structured expert elicitation to identify the most likely types of potential food system disruption scenarios for the UK, focusing on routes to civil unrest. We take a backcasting approach by defining as an end-point a societal event in which 1 in 2000 people have been injured in the UK, which 40% of experts rated as “Pos...

Introduction The garden petunia, Petunia hybrida (Solanaceae) is a fertile, diploid, annual hybrid species (2n=14) originating from P. axillaris and P. inflata 200 years ago. To understand the recent evolution of the P. hybrida genome, we examined tandemly repeated or satellite sequences using bioinformatic and molecular cytogenetic analysis. Meth...

Introduction: The garden petunia, Petunia hybrida (Solanaceae) is a fertile, diploid, annual hybrid species (2n=14) originating from P. axillaris and P. inflata 200 years ago. To understand the recent evolution of the P. hybrida genome, we examined tandemly repeated or satellite sequences using bioinformatic and molecular cytogenetic analysis. Meth...

Cytological preparations from cell nuclei are required to count the number of chromosomes (including determining ploidy or aneuploidy), to investigate their morphology and organization. The results are valuable for genetic and evolutionary studies, and in breeding programs to understand species relationships, polyploidy, and potential introgression...

Loss and damage from climate change have risen to a prominent position on the international agenda. At COP27 in 2022, the Conference of the Parties (COP) to the UN Framework Convention on Climate Change (UNFCCC) ratified a decision to establish a loss and damage fund to compensate low- and middle-income countries that are suffering negative impacts...

Background and Aims: The grass genus Urochloa (Brachiaria) includes forage crops that are important for beef and dairy industries in tropical and subtropical Africa, South America, and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis, and M. ma...

Chromosomes have been studied since the late nineteenth century in the disciplines of cytology and cytogenetics. Analyzing their numbers, features, and dynamics has been tightly linked to the technical development of preparation methods, microscopes, and chemicals to stain them, with latest continuing developments described in this volume. At the e...

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characteriz...

Background: Avena longiglumis Durieu (2n = 2x = 14) is a wild relative of cultivated oat (Avena sativa, 2n = 6x = 42) with good agronomic and nutritional traits. The plant mitochondrial genome has a complex organization and carries genetic traits of value in exploiting genetic resources, not least male sterility alleles used to generate F1 hybrid...

The 1958 Delaney amendment to the Federal Food Drug and Cosmetics Act prohibited food additives causing cancer in animals by appropriate tests. Regulators responded by adopting chronic lifetime cancer tests in rodents, soon challenged as inappropriate, for they led to very inconsistent results depending on the subjective choice of animals, test des...

Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, disc...

Background Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. M...

Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex...

The genus Aubrieta Adan. (Brassicaceae) is widely distributed and diverges across different elevations. We aimed to study aspects of the genome organization and components to understand evolution and differentiation. Endogenous pararetroviruses (EPRVs) were examined in whole-genome of four Aubrieta species using high-throughput DNA sequencing and b...

Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic...

Background Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns, are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the Brassicas, but occur frequently in wild specie...

Endogenous viral elements of the Caulimoviridae family have been registered in different plant families as integrants. As one of the Asteraceae family, Taraxacum has been studied here to find endogenous pararetroviruses (EPRVs), including its three different agamospecies genomes. Three different agamospecies genomes of Taraxacum O978, A978, and S3,...

Background: Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. We aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction. Methods: We explored...

Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in the tropical and subtropical regions of Africa and Asia. In this study, we aimed to investigate the genomic organization and characterize some of the repetitive DNA sequences in this species. Due to the apomictic propagation, various aneuploid genotypes are found,...

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characteris...

Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x =7, genomes of oats show frequent intergenomi...

Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is a...

Meriz goat is a native goat breed found along the northern boundary of the Iraqi Kurdistan region near the center of species diversity and domestication. This economically important breed is distinguished by its production of fine hair, high persistence, and ability to thrive in harsh environmental conditions. Although the phenotype and productive...

Background and aims Tandemly repeated DNA and transposable elements represent most of the DNA in higher plant genomes. High-throughput sequencing allows a survey of the DNA in a genome, but whole-genome assembly can miss a substantial fraction of highly repeated sequence motifs. Chrysanthemum nankingense (2n = 2x = 18; genome size = 3.07 Gb; Astera...

Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in tropical and subtropical regions of Africa and Asia. In this work, we aim to investigate the genomic organization and characterize the nature of repetitive DNA sequences in this species. Because of the apomictic propagation, various aneuploid genotypes are found a...

Background Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. Findings Using Oxford Nanopore Technologies, ch...

Endogenous retroviruses (ERVs) represent genomic components of retroviral origin that are found integrated in the genomes of various species of vertebrates. These genomic elements have been widely characterized in model organisms and humans. However, composition and abundances of ERVs have not been categorized fully in all domestic animals. The adv...

Endogenous retroviruses (ERVs) represent genomic components of retroviral origin that are found integrated in the genomes of various species of vertebrates. These genomic elements have been widely characterized in model organisms and humans. However, composition and abundances of ERVs have not been categorized fully in all domestic animals. The adv...

Background Oat ( Avena sativa , 2 n =6 x =42) is an important crop, and with its wild relatives including A. longiglumis (ALO, 2 n =6 x =14), has advantageous agronomic and nutritional traits. A de-novo chromosome-level ALO genome assembly was made to investigate diversity and structural genome variation between Avena species and other Poaceae in a...

Hibiscus rosa-sinensis L. (Hibiscus, Malvaceae) is an ornamental species grown widely in amenity plantings. We collected leaves on an urban roadside pavement (sidewalk) near a market in Guangzhou which showed multiple symptoms of leaf rolling, deformation and chlorosis. Initial evaluation by electron microscopy using negative staining of drip prepa...

Enset (Ensete ventricosum) is a multipurpose crop extensively cultivated in southern and southwestern Ethiopia for human food, animal feed, and fiber. It has immense contributions to the food security and rural livelihoods of 20 million people. Several distinct enset landraces are cultivated for their uses in traditional medicine. These landraces a...

Sequencing technology and bioinformatics tools enable us to generate and analyses whole genome sequences of Brassica crops and wild relatives. High quality assembled references genome for the Brassica species are available, aiding downstream genome scale analysis such as variant calling, chromosomal rearrangement, translocations, repetitive DNA div...

Structural variations (SVs) are a major contributor of genetic diversity and phenotypic variations, however their prevalence and functions in domestic animals are largely unexplored. Here, we assembled 26 haplotype-resolved genome assemblies from 13 genetically diverse sheep breeds using PacBio HiFi sequencing. We then constructed an ovine graph pa...

Background and Aims Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment , often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome...

Background Ensete glaucum (2 n = 2 x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana ( Musa ). A high-quality reference genome sequence of E. glaucum offers a vital genomic resource for functional and evolutionary studies of Ensete , the Musaceae, and more widely in the Zingiberales. Findings Using...

Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been...

The EU chemicals strategy for sustainability (CSS) asserts that both human health and the environment are presently threatened and that further regulation is necessary. In a recent Guest Editorial, members of the German competent authority for risk assessment, the BfR, raised concerns about the scientific justification for this strategy. The comple...

The interest in Robertsonian fusion chromosomes (Rb fusions), sometimes referred to as Robertsonian translocations, derives from their impact on mammalian karyotype evolution, as well from their influence on fertility and disease. The formation of a Rb chromosome necessitates the occurrence of double strand breaks in the pericentromeric regions of...

Background and aims: The C4 Urochloa spp (syn. Brachiaria) and Megathyrsus maximus (syn. Panicum maximum) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease amount of land required per unit produc...

Background and Aims: Urochola (syn. Brachiaria, and including some Panicum and Megathyrus) is a genus of tropical and subtropical grasses widely sown as forage to feed ruminants in the tropics. A better understanding of the diversity among Urochola spp. allow us to leverage its varying ploidy levels and genome composition to accelerate its improvem...

We are presenting the complete mitogenomes of eight fish species/cytotypes from Neotropical region belonging to the Astyanax and Psalidodon genus: A. aeneus, A. altiparanae, P. fasciatus (from two locations - Upper Paraná and São Francisco river basins), A. lacustris, P. rivularis (two cytotypes) and P. rioparanaibano. We perform the whole-genome s...

Key message Heavy doses of gamma irradiation can reduce linkage drag by disrupting large sized alien translocations and promoting exchanges between crop and wild genomes. Abstract Resistance to mustard aphid (Lipaphis erysimi) infestation was significantly improved in Brassica juncea through B. juncea-B. fruticulosa introgression. However, linkage...

Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. We aimed to develop an optimized approach to dete...

Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse transcriptase and share a common origin with retroviruses and LTR retrotransposons, presumably dating back 1.6 billion years and illustrating the transition from an RNA to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA synthesis oc...

Switchgrass (Panicum virgatum L.) is a promising biofuel crop and one of the dominant species in North American tallgrass prairies. It grows rapidly, reaching up to 2.7 m, and planted fields remain productive for 15 years. The large, highly repetitive, and highly heterozygous genome of the generally tetraploid species have always been challenging f...

We aimed to develop an optimized approach to determine ploidy for dried leaf material in a germplasm collection of a tropical forage grass group, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now,...

Background and Aims Diploid and polyploid Urochloa (including Brachiaria , Panicum and Megathyrsus species) C 4 tropical forage grasses originating from Africa and now planted worldwide are important for food security and the environment, often being planted in marginal lands. We aimed to characterize the nature of their genomes, the repetitive DNA...

Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. It is difficult to distinguish Brassica chromosomes as they are small and morphologically similar. We aimed to develop a genome-sequence based cytogenetic toolkit for repr...

The C4 Urochloa spp (syn. Brachiaria ) and Megathyrsus maximus (syn. Panicum maximum ) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease amount of land required per unit production and enhanced li...