Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species

Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice.

Effect of Seasonal Drought on the Agronomic Performance of Four Banana Genotypes (Musa spp.) in the East African Highlands

Banana (Musa spp.), a perennial (sub-)tropical crop, suffers from seasonal droughts, which are typical of rain-fed agriculture. This study aimed at understanding the effect of seasonal drought on early growth, flowering and yield traits in bananas grown in the East African highlands. A field experiment was set up in North Tanzania using four genotypes from different geographical origins and two different ploidy levels. The treatments considered were exclusively rain-fed versus rain supplemented with irrigation. Growth in plant girth and leaf area were promising traits to detect the early effect of water deficit. Seasonal drought slowed down vegetative growth, thus significantly decreasing plant girth, plant height and the number of suckers produced when compared to irrigated plants. It also delayed flowering time and bunch maturity and had a negative effect on yield traits. However, the results depended on the genotype and crop cycle and their interaction with the treatments. “Nakitengwa”, an East African highland banana (EAHB; AAA genome group), which is adapted to the region, showed sensitivity to drought in terms of reduced bunch weight and expected yield, while “Cachaco” (ABB genome group) showed less sensitivity to drought but had a poorer yield than “Nakitengwa”. Our study confirms that seasonal drought has a negative impact on banana production in East Africa, where EAHBs are the most predominant type of bananas grown in the region. We also show that a drought-tolerant cultivar not adapted to the East African highlands had a low performance in terms of yield. We recommend a large-scale screening of diploid bananas to identify drought-tolerant genotypes to be used in the improvement of locally adapted and accepted varieties.

Effective resistance to powdery mildew in Aegilops L. accessions

Background. Powdery mildew (Blumeria graminis (DC.) E.O. Speer f. sp. tritici Em. Marchal) is widespread and harmful in all regions of bread wheat cultivation. Severe development of powdery mildew leads to a decrease in the number and weight of grains. Growing resistant cultivars is the most environmentally friendly and economically profitable method to protect wheat from the disease. Development of such cultivars requires a search for new donors of effective genes controlling the resistance. To expand the genetic diversity of wheat for resistance to B. graminis, wild relatives of Triticum aestivum L., including Aegilops L. spp., are widely used. The aim of this work was to characterize seven Aegilops spp. for effective seedling and adult plant resistance to powdery mildew.Materials and methods. The material of the study consisted of 437 accessions representing 7 Aegilops spp. (Ae. speltoides Tausch, Ae. caudata L., Ae. biuncialis Vis., Ae. tauschii Coss., Ae. cylindrica Host, Ae. crassa Boiss. and Ae. ventricosa Tausch) from the collection of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR, St. Petersburg). Juvenile resistance was studied when the seedlings were inoculated with the agent of powdery mildew under controlled laboratory conditions; the adult plant resistance, after artificial inoculation of the plants and under natural infection in the fields of Pushkin and Pavlovsk Laboratories of VIR. Complex populations of the B. graminis agent were used for inoculation. The types of response to infection were scored 10 days after inoculation according to a conventional scale.Results and conclusions. As a result of the tests, susceptibility to powdery mildew was shown in all Aegilops accessions of the D-genome group; all the studied representatives of Ae. speltoides, Ae. caudata and Ae. biuncialis were highly resistant to powdery mildew.

Multi Locus View : An Extensible Web Based Tool for the Analysis of Genomic Data

MotivationTracking and understanding data quality, analysis and reproducibility are critical concerns in the biological sciences. This is especially true in genomics where Next Generation Sequencing (NGS) based technologies such as ChIP-seq, RNA-seq and ATAC-seq are generating a flood of genome-scale data. These data-types are extremely high level and complex with single experiments capable of mapping ten to hundreds of thousands of biologically meaningful events across the genome. However, such data are usually processed with automated tools and pipelines, generating tabular outputs and static visualizations. These are difficult to interact with and require substantial bioinformatic skills to manipulate and query. Similarly, interpretation is normally made at a high level without the ability to visualise the underlying data in detail and so the complexity and quality of the real underlying biological signal is lost. Also genomics datasets require integration with other genomics datasets to be properly interpreted and this integration with multiple tracks again requires substantial bioinformatics skills and is difficult to visualise across multiple pertinent datasets. Conventional genome browsers do allow for the detailed visualisation of multiple tracks but are limited to browsing single locations and do not allow for interactions with the dataset as a whole. MLV has been developed to allow users to fluidly interact with genomics datasets at multiple scales, from complete metadata labelled and clustered populations to detailed representations of individual elements. It has inbuilt tools to integrate signals across multiple datasets and to perform dimensionality reduction and clustering analysis based on the extracted signal, allowing for the high-level analysis of complex datasets while maintaining visualisation of the fine grain structure of the data. MLV’s ability to visualise clustering within the data combined with efficient tools for large-scale tagging of individual elements makes it a unique tool for the generation of annotated datasets for modern machine learning approaches.ResultsMulti Locus View (MLV) is a web based tool for the visualisation, analysis and annotation of Next Generation Sequencing data sets. The user is able to browse the raw data, cluster, and combine the data with other analysis. Intuitive filtering and visualisation then enables the user to quickly locate and annotate regions of interest. User datasets can then be shared with other users or made public for quick assessment from the academic community. MLV is publically available at https://mlv.molbiol.ox.ac.uk and the source code is available at https://github.com/Hughes-Genome-Group/mlv

Genome group classification and diversity analysis of talas and rutai banana, two local cultivars from East Kalimantan, based on morphological characters

Sunaryo W, Mulyadi A, Nurhasanah. 2019. Genome group classification and diversity analysis of talas and rutai banana, two local cultivars from East Kalimantan, based on morphological characters. Biodiversitas 20: 2355-2367. Talas and rutai banana are two local cultivars grown in East Kalimantan and long-time used as dessert or cooking bananas for traditional food and cakes, but unfortunately, their taxonomic and genetic status are still little known. This study was conducted to explore their taxonomic and genetic status through morphological observation, genomic group classification and diversity analysis of talas and rutai banana compared to other recognized and identified bananas in Indonesia, i.e., liar/monyet, Ambon, tanduk and klutuk banana. In total 108 morphological characters were observed on site of growing area using the “Descriptors for Banana (Musa spp.)” morphological indicators. The genome group classification was carried out using Simmonds and Shepherd scoring system toward fifteen key banana characters. The diversity analysis was performed using Hierarchy Cluster Analysis at MINITAB 17.1 software based on the selected characters of the highest Principal Component Analysis (PCA) values. The morphological observation showed that the characters of talas and rutai banana are much closely related to those of belonging to M. acuminata although some characters showed balbisiana-type. In addition, liar/monyet and klutuk banana morphological characters were exactly matched with the M. acuminata and M. balbisiana accessions. Furthermore, most of Ambon banana morphological characters are similar to M. acuminata, but tanduk banana had a combination characters between M. acuminate and M. balbisiana. The genome group classification showed that talas and rutai banana are the AAB genotype, while liar/monyet, Ambon, tanduk, and klutuk were grouped into AA, AAA, AB, and BB genotype, respectively. The diversity analysis showed that talas and rutai banana have a very high similarity about 75% and closed related to AA/AAA genotype i.e., liar/monyet and Ambon with similarities level of 45%.

Mitochondrial genome reorganization provides insights into the relationship between oribatid mites and astigmatid mites (Acari: Sarcoptiformes: Oribatida)

Oribatida s.l. represents one of the most species-rich mite lineages, including two recognized groups: oribatid mites (Oribatida s.s., non-astigmatan oribatids) and astigmatid mites (Astigmata). However, the relationship between these two groups has been debated. Here, we sequenced the complete mitochondrial (mt) genome of one oribatid mite and one astigmatid mite, retrieved complete mt genomes of three oribatid mites, and compared them with two other oribatid mites and 12 astigmatid mites sequenced previously. We find that gene orders in the mt genomes of both oribatid mites and astigmatid mites are rearranged relative to the hypothetical ancestral arrangement of the arthropods. Based on the shared derived gene clusters in each mt genome group, rearranged mt genomes are roughly divided into two groups corresponding to each mite group (oribatid mites or astigmatid mites). Phylogenetic results show that Astigmata nested in Oribatida. The monophyly of Astigmata is recovered, while paraphyly of Oribatida s.s. is observed. Our results show that rearranged gene orders in the mt genomes characterize various lineages of oribatid mites and astigmatid mites, and have potential phylogenetic information for resolving the high-level (cohort or supercohort) phylogeny of Oribatida.

NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control

ABSTRACTWith decreasing cost of next-generation sequencing (NGS), we are observing a rapid rise in the volume of ‘big data’ in academic research, healthcare and drug discovery sectors. The present bottleneck for extracting value from these ‘big data’ sets is data processing and analysis. Considering this, there is still a lack of reliable, automated and easy to use tools that will allow experimentalists to assess the quality of the sequenced libraries and explore the data first hand, without the need of investing a lot of time of computational core analysts in the early stages of analysis.NGseqBasic is an easy-to-use single-command analysis tool for chromatin accessibility (ATAC, DNaseI) and ChIP sequencing data, providing support to also new techniques such as low cell number sequencing and Cut-and-Run. It takes in fastq, fastq.gz or bam files, conducts all quality control, trimming and mapping steps, along with quality control and data processing statistics, and combines all this to a single-click loadable UCSC data hub, with integral statistics html page providing detailed reports from the analysis tools and quality control metrics. The tool is easy to set up, and no installation is needed. A wide variety of parameters are provided to fine-tune the analysis, with optional setting to generate DNase footprint or high resolution ChIP-seq tracks. A tester script is provided to help in the setup, along with a test data set and downloadable example user cases.NGseqBasic has been used in the routine analysis of next generation sequencing (NGS) data in high-impact publications 1,2. The code is actively developed, and accompanied with Git version control and Github code repository. Here we demonstrate NGseqBasic analysis and features using DNaseI-seq data from GSM689849, and CTCF-ChIP-seq data from GSM2579421, as well as a Cut-and-Run CTCF data set GSM2433142, and provide the one-click loadable UCSC data hubs generated by the tool, allowing for the ready exploration of the run results and quality control files generated by the tool.AvailabilityDownload, setup and help instructions are available on the NGseqBasic web site http://userweb.molbiol.ox.ac.uk/public/telenius/NGseqBasicManual/external/Bioconda users can load the tool as library “ngseqbasic”. The source code with Git version control is available in https://github.com/Hughes-Genome-Group/NGseqBasic/[email protected]

A Third Type of Resistance to Cydia pomonella Granulovirus in Codling Moths Shows a Mixed Z-Linked and Autosomal Inheritance Pattern

ABSTRACT Different isolates of Cydia pomonella granulovirus (CpGV) are used worldwide to control codling moth larvae (Cydia pomonella) in pome fruit production. Two types of dominantly inherited field resistance of C. pomonella to CpGV have been recently identified: Z-chromosomal type I resistance and autosomal type II resistance. In the present study, a CpGV-resistant C. pomonella field population (termed SA-GO) from northeastern Germany was investigated. SA-GO individuals showed cross-resistance to CpGV isolates of genome group A (CpGV-M) and genome group E (CpGV-S), whereas genome group B (CpGV-E2) was still infective. Crossing experiments between individuals of SA-GO and the susceptible C. pomonella strain CpS indicated the presence of a dominant autosomal inheritance factor. By single-pair inbreeding of SA-GO individuals for two generations, the genetically more homogenous strain CpRGO was generated. Resistance testing of CpRGO neonates with different CpGV isolates revealed that isolate CpGV-E2 and isolates CpGV-I07 and -I12 were resistance breaking. When progeny of hybrid crosses and backcrosses between individuals of resistant strain CpRGO and susceptible strain CpS were infected with CpGV-M and CpGV-S, resistance to CpGV-S appeared to be autosomal and dominant for larval survivorship but recessive when success of pupation of the hybrids was considered. Inheritance of resistance to CpGV-M, however, is proposed to be both autosomal and Z linked, since Z linkage of resistance was needed for pupation. Hence, we propose a further type III resistance to CpGV in C. pomonella, which differs from type I and type II resistance in its mode of inheritance and response to CpGV isolates from different genome groups. IMPORTANCE The baculovirus Cydia pomonella granulovirus (CpGV) is registered and applied as a biocontrol agent in nearly all pome fruit-growing countries worldwide to control codling moth caterpillars in an environmentally friendly manner. It is therefore the most widely used commercial baculovirus biocontrol agent. Since 2005, field resistance of codling moth to CpGV products has been observed in more than 40 field plantations in Europe, threatening organic and integrated apple production. Knowledge of the inheritance and mechanism(s) of resistance is indispensable for the understanding of host response to baculovirus infection on the population level and the coevolutionary arms race between virus and host, as well as for the development of appropriate resistance management strategies. Here, we report a codling moth field population with a new type of resistance, which appears to follow a highly complex inheritance in regard to different CpGV isolates.

Evidence for a Second Type of Resistance against Cydia pomonella Granulovirus in Field Populations of Codling Moths

ABSTRACTCydia pomonella granulovirus (CpGV) is an important biocontrol agent for the codling moth (CM) in organic and integrated apple production worldwide. Previously, Z chromosome-linked dominant resistance in at least 38 CM field populations in Europe was reported, threatening organic apple production. Growers responded by switching to a different resistance-breaking isolate of CpGV that could control these populations. Here, we report a nonuniform response of different CM field populations to CpGV isolates from CpGV genome groups A to E. Even more strikingly, one field population, NRW-WE, was resistant to all known CpGV genome groups except group B. Single-pair crossing experiments with a susceptible strain, followed by resistance testing of the F1offspring, clearly indicated cross-resistance to CpGV isolates that had been considered to be resistance breaking. This finding provides clear evidence of a second, broader type of CpGV resistance with a novel mode of inheritance that cannot be fully explained by Z-linkage of resistance.IMPORTANCECpGV is registered and used in virtually all commercial apple growing areas worldwide and is therefore the most widely used baculovirus biocontrol agent. Recently, resistance to CpGV products was reported in different countries in Europe, threatening organic growers who rely almost exclusively on CpGV products. This resistance appeared to be targeted against a 24-bp repeat in thepe38gene in isolate CpGV-M of genome group A, which had been used commercially for many years. On the other hand, resistance could be broken by CpGV isolates from CpGV genome groups B to E. Here, we report clear evidence of a second type of field resistance that is also directed against resistance-breaking isolates of CpGV genome groups C, D, and E and which appears not to be targeted against CpGVpe38. Therefore, we propose to differentiate between type I resistance, which is targeted againstpe38of CpGV genome group A, and a novel type II resistance with an unknown molecular target. This finding stresses the need for further adoption of resistance management strategies for CpGV, since growers cannot rely solely on the use of resistance-breaking CpGV isolates.