scholarly journals Mapping-by-Sequencing via MutMap Identifies a Mutation in ZmCLE7 Underlying Fasciation in a Newly Developed EMS Mutant Population in an Elite Tropical Maize Inbred

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 281 ◽  
Author(s):  
Quan Hong Tran ◽  
Ngoc Hong Bui ◽  
Christian Kappel ◽  
Nga Thi Ngoc Dau ◽  
Loan Thi Nguyen ◽  
...  
Keyword(s):  
Point Mutations ◽  
Gene Discovery ◽  
Forward Genetics ◽  
Tropical Maize ◽  
Mapping Procedure ◽  
The Public ◽  
Rapid Mapping ◽  
Maize Varieties ◽  
Comparable Quality ◽  
Mapping By Sequencing

Induced point mutations are important genetic resources for their ability to create hypo- and hypermorphic alleles that are useful for understanding gene functions and breeding. However, such mutant populations have only been developed for a few temperate maize varieties, mainly B73 and W22, yet no tropical maize inbred lines have been mutagenized and made available to the public to date. We developed a novel Ethyl Methanesulfonate (EMS) induced mutation resource in maize comprising 2050 independent M2 mutant families in the elite tropical maize inbred ML10. By phenotypic screening, we showed that this population is of comparable quality with other mutagenized populations in maize. To illustrate the usefulness of this population for gene discovery, we performed rapid mapping-by-sequencing to clone a fasciated-ear mutant and identify a causal promoter deletion in ZmCLE7 (CLE7). Our mapping procedure does not require crossing to an unrelated parent, thus is suitable for mapping subtle traits and ones affected by heterosis. This first EMS population in tropical maize is expected to be very useful for the maize research community. Also, the EMS mutagenesis and rapid mapping-by-sequencing pipeline described here illustrate the power of performing forward genetics in diverse maize germplasms of choice, which can lead to novel gene discovery due to divergent genetic backgrounds.

scholarly journals ATP-dependent Clp protease subunit C1, HvClpC1, is a strong candidate gene for barley variegation mutant luteostrians as revealed by genetic mapping and genomic re-sequencing

2021 ◽  
Author(s):  
Mingjiu Li ◽  
Ganggang Guo ◽  
Hélène Pidon ◽  
Michael Melzer ◽  
Alberto R. Prina ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Mapping ◽  
Candidate Gene ◽  
Gene Discovery ◽  
Plant Morphology ◽  
Mutation Breeding ◽  
Forward Genetics ◽  
Next Generation ◽  
Mapping By Sequencing ◽  
Generation Sequencing

AbstractImplementation of next-generation sequencing in forward genetic screens greatly accelerated gene discovery in species with larger genomes, including many crop plants. In barley, extensive mutant collections are available, however, the causative mutations for many of the genes remains largely unknown. Here we demonstrate how a combination of low-resolution genetic mapping, whole-genome resequencing and comparative functional analyses provides a promising path towards candidate identification of genes involved in plastid biology and / or photosynthesis, even if genes are located in recombination poor regions of the genome. As a proof of concept, we simulated the prediction of a candidate gene for the recently cloned variegation mutant albostrians (HvAST / HvCMF7) and adopted the approach for suggesting HvClpC1 as candidate gene for the yellow-green variegation mutant luteostrians.Author SummaryForward genetics is an approach of identifying a causal gene for a mutant phenotype and has proven to be a powerful tool for dissecting the genetic control of biological processes in many species. A large number of barley mutants was generated in the 1940s to 1970s when mutation breeding programs flourished. Genetic dissection of the causative mutations responsible for the phenotype, however, lagged far behind, limited by lack of molecular markers and high-throughput genotyping platforms. Next-generation sequencing technologies have revolutionized genomics, facilitating the process of identifying mutations underlying a phenotype of interest. Multiple mapping-by-sequencing or cloning-by-sequencing strategies were established towards fast gene discovery. In this study, we used mapping-by-sequencing to identify candidate genes within coarsely delimited genetic intervals, for two variegation mutants in barley – luteostrians and albostrians. After testing the approach using the example of the previously cloned albostrians gene HvAST, the gene HvClpC1 could be delimited as candidate gene for luteostrians. The mapping-by-sequencing strategy implemented here is generally suited for surveying barley mutant collections for phenotypes affecting fundamental processes of plant morphology, physiology and development.

scholarly journals Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Sirlene Viana de Faria ◽  
Leandro Tonello Zuffo ◽  
Wemerson Mendonça Rezende ◽  
Diego Gonçalves Caixeta ◽  
Hélcio Duarte Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Breeding Program ◽  
Tropical Maize ◽  
Maize Breeding ◽  
Breeding Programs ◽  
The Public ◽  
Maize Inbred Lines

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

scholarly journals Investigating the Type of Gene Action Conditioning Tolerance to Aluminum (Al) Toxicity in Tropical Maize

2019 ◽  
pp. 1-8
Author(s):  
Victoria Ndeke ◽  
Langa Tembo
Keyword(s):  
Root Length ◽  
Aluminum Toxicity ◽  
Gene Action ◽  
Abiotic Factors ◽  
Al Toxicity ◽  
High Yield ◽  
Small Scale ◽  
Tropical Maize ◽  
Maize Varieties ◽  
Small Scale Farmers

Maize is a third important cereal crop in the world after wheat and rice. In Zambia, it is an important staple crop. Its production is however hampered by both biotic and abiotic factors. Among the abiotic factors, Aluminum (Al) toxicity causes high yield losses and is directly linked to acidic soils. Application of lime can ameliorate this problem, but it is expensive for small scale farmers. Developing maize varieties that are tolerant to Al toxicity is cheaper and feasible for small scale farmers. The purpose of this research was to investigate the type of gene action conditioning tolerance to aluminum toxicity in tropical maize.  Eleven inbred lines were mated in an 8 male (4 moderately tolerant and 4 susceptible) x 3 female (resistant) North Carolina Design II. Results revealed that general combining ability (GCA) effects due to both males and females were highly significant (P≤ 0.001) for root biomass. The shoot length GCA effects due to both male and female respectively were significant (P≤ 0.01). Similarly, the GCA effects due to females and males for root length were significant, P≤ 0.01 and P≤ 0.05 respectively. The genotype CML 511 had the most desirable significant GCA effect value (1.40) for root length among the male lines while CML 538 had the most desirable significant GCA effect value (0.92) among the female lines. The baker’s ratio for root length was found to be 0.49 implying that both additive and non-additive gene action were important in conditioning aluminum toxicity tolerance in tropical maize.

scholarly journals Quantifying Influences on Intragenomic Mutation Rate

2020 ◽  
Vol 10 (8) ◽  
pp. 2641-2652
Author(s):  
Helmut Simon ◽  
Gavin Huttley
Keyword(s):  
Point Mutations ◽  
Population Based ◽  
Genomic Diversity ◽  
Ensembl Database ◽  
Sequence Context ◽  
The Public ◽  
Recombination Hotspots ◽  
Strand Asymmetry ◽  
The Impact ◽  
Central Base

We report work to quantify the impact on the probability of human genome polymorphism both of recombination and of sequence context at different scales. We use population-based analyses of data on human genetic variants obtained from the public Ensembl database. For recombination, we calculate the variance due to recombination and the probability that a recombination event causes a mutation. We employ novel statistical procedures to take account of the spatial auto-correlation of recombination and mutation rates along the genome. Our results support the view that genomic diversity in recombination hotspots arises largely from a direct effect of recombination on mutation rather than predominantly from the effect of selective sweeps. We also use the statistic of variance due to context to compare the effect on the probability of polymorphism of contexts of various sizes. We find that when the 12 point mutations are considered separately, variance due to context increases significantly as we move from 3-mer to 5-mer and from 5-mer to 7-mer contexts. However, when all mutations are considered in aggregate, these differences are outweighed by the effect of interaction between the central base and its immediate neighbors. This interaction is itself dominated by the transition mutations, including, but not limited to, the CpG effect. We also demonstrate strand-asymmetry of contextual influence in intronic regions, which is hypothesized to be a result of transcription coupled DNA repair. We consider the extent to which the measures we have used can be used to meaningfully compare the relative magnitudes of the impact of recombination and context on mutation.

scholarly journals Mapping-by-sequencing accelerates forward genetics in barley

2014 ◽  
Vol 15 (6) ◽  
pp. R78 ◽  
Author(s):  
Martin Mascher ◽  
Matthias Jost ◽  
Joel-Elias Kuon ◽  
Axel Himmelbach ◽  
Axel Aßfalg ◽  
...  
Keyword(s):  
Forward Genetics ◽  
Mapping By Sequencing

scholarly journals Public Streets for Multicultural Use: Exploring the Relationship between Cultural Background, Built Environment, and Social Behaviour

2021 ◽  
Author(s):  
◽  
Maryam Lesan
Keyword(s):  
Cultural Diversity ◽  
Public Space ◽  
Public Spaces ◽  
Success Factor ◽  
Main Concern ◽  
Cultural Backgrounds ◽  
Mapping Procedure ◽  
The Public ◽  
Spatial Design ◽  
Design Characteristics

<p>Public space is the domain of interest for urban planners and designers and the most important type of public space is streets. Public spaces, and particularly busy streets in urban centres, provide opportunities for people to meet, often by chance. As cities become increasingly multi-cultural in population the use and nature of public space reflects this. The best public spaces cater to the needs of all who use them and in multicultural societies this also means they must meet the expectations of people from different cultures.  Many scholars have challenged the tendency for streets to be conceived of as movement channels, often at the expense of their use as social space. Streets have traditionally catered to a broad array of activities including walking, cycling and standing. Streets that facilitate such activities are preferred by the public. Streets in multicultural societies are also where people from different ethnic backgrounds find opportunities to interact.  When public spaces are successful, they will increase opportunities to participate in communal activities. Spatial design is a critical success factor for streets; a goal for urban designers must be to create spaces where people from different social and cultural backgrounds value the public spaces they have access to. As cities become more multicultural the challenge is to design and manage spaces that appeal to the breadth of cultures that are represented in the population. Such public spaces are described in the literature as being more public. However, there is presently little information to help planners and designers to realise streets that appeal to people having different socio-cultural backgrounds. The research aims to identify those characteristics that will promote and maintain cultural diversity in the context of neighbourhood commercial streets in New Zealand’s multi-cultural society.  The research is undertaken in two stages. “Stage One” makes use of ethnographic fieldwork as a basic method, complimented by structured field observations using a behavioural mapping procedure, and surveys of users of the streets. This stage provides data on specific streets and their usage through three case studies. Stage Two” utilises online surveys that generated data in relation to street visualizations. This stage seeks to understand what design characteristics and furniture arrangements are associated with stationary, social and gathering activities of people and to define design characteristics of footpath spaces preferred by each cultural group and all groups collectively.  The main conclusion from this research is that retail activities remain the main concern of people in multi-cultural streets. Management and higher level planning of retail activities on the streets could encourage and motivate possible tenants in order to enrich the retail assortment of the street and provide a means for social and cultural diversity. In addition to business activities, spatial design characteristics are found to have an influence on people’s behaviour and activity. The findings of this research suggest that retail and business activities, together with the design and skilful management of the public areas, could support a broader range of static and social activities among people of various cultural backgrounds. The thesis makes recommendations for urban planners and designers based on the findings of the research.</p>

scholarly journals Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis

2019 ◽  
Vol 47 (21) ◽  
pp. e140-e140
Author(s):  
David Wilson-Sánchez ◽  
Samuel Daniel Lup ◽  
Raquel Sarmiento-Mañús ◽  
María Rosa Ponce ◽  
José Luis Micol
Keyword(s):  
Point Mutations ◽  
Sequencing Depth ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Genetic Screens ◽  
Induced Mutations ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Forward Genetic Screens ◽  
Mapping By Sequencing

Abstract Forward genetic screens have successfully identified many genes and continue to be powerful tools for dissecting biological processes in Arabidopsis and other model species. Next-generation sequencing technologies have revolutionized the time-consuming process of identifying the mutations that cause a phenotype of interest. However, due to the cost of such mapping-by-sequencing experiments, special attention should be paid to experimental design and technical decisions so that the read data allows to map the desired mutation. Here, we simulated different mapping-by-sequencing scenarios. We first evaluated which short-read technology was best suited for analyzing gene-rich genomic regions in Arabidopsis and determined the minimum sequencing depth required to confidently call single nucleotide variants. We also designed ways to discriminate mutagenesis-induced mutations from background Single Nucleotide Polymorphisms in mutants isolated in Arabidopsis non-reference lines. In addition, we simulated bulked segregant mapping populations for identifying point mutations and monitored how the size of the mapping population and the sequencing depth affect mapping precision. Finally, we provide the computational basis of a protocol that we already used to map T-DNA insertions with paired-end Illumina-like reads, using very low sequencing depths and pooling several mutants together; this approach can also be used with single-end reads as well as to map any other insertional mutagen. All these simulations proved useful for designing experiments that allowed us to map several mutations in Arabidopsis.

scholarly journals Ethylene signaling mediates host invasion by parasitic plants

2020 ◽  
Vol 6 (44) ◽  
pp. eabc2385
Author(s):  
Songkui Cui ◽  
Tomoya Kubota ◽  
Tomoaki Nishiyama ◽  
Juliane K. Ishida ◽  
Shuji Shigenobu ◽  
...  
Keyword(s):  
Point Mutations ◽  
Parasitic Plants ◽  
Forward Genetics ◽  
Ethylene Signaling ◽  
Cell Proliferation And Differentiation ◽  
Proliferation And Differentiation ◽  
Meristematic Activity ◽  
Signaling Inhibitors ◽  
Signaling Components ◽  
Host Invasion

Parasitic plants form a specialized organ, a haustorium, to invade host tissues and acquire water and nutrients. To understand the molecular mechanism of haustorium development, we performed a forward genetics screening to isolate mutants exhibiting haustorial defects in the model parasitic plant Phtheirospermum japonicum. We isolated two mutants that show prolonged and sometimes aberrant meristematic activity in the haustorium apex, resulting in severe defects on host invasion. Whole-genome sequencing revealed that the two mutants respectively have point mutations in homologs of ETHYLENE RESPONSE 1 (ETR1) and ETHYLENE INSENSITIVE 2 (EIN2), signaling components in response to the gaseous phytohormone ethylene. Application of the ethylene signaling inhibitors also caused similar haustorial defects, indicating that ethylene signaling regulates cell proliferation and differentiation of parasite cells. Genetic disruption of host ethylene production also perturbs parasite invasion. We propose that parasitic plants use ethylene as a signal to invade host roots.

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