Skim sequencing: an advanced NGS technology for crop improvement

Kumar, Pardeep; Choudhary, Mukesh; Jat, Bahadur Singh; Kumar, Bhupender; Singh, Vishal; Kumar, Virender; Singla, Deepak; Rakshit, Sujay

doi:10.1007/s12041-021-01285-3

Cited by 17 publications

(9 citation statements)

References 73 publications

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“…The complete nucleotide sequence of the cp genome of U. laevis was determined through HTS “skim sequencing” ( Kumar et al, 2021 ). Using 864,534 high-quality plastid reads, the cpDNA of one individual (Fsw1) was de novo assembled with a depth coverage of 815×.…”

Section: Resultsmentioning

confidence: 99%

Novel Insights Into Refugia at the Southern Margin of the Distribution Range of the Endangered Species Ulmus laevis

et al. 2022

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Riparian ecosystems, in long-time developed regions, are among the most heavily impacted by human activities; therefore, the distribution of tree riparian species, such as Ulmus laevis, is highly affected. This phenomenon is particularly relevant at the margins of the natural habitat of the species, where populations are small and rare. In these cases, it is difficult to distinguish between relics or introductions, but it is relevant for the restoration of natural habitats and conservation strategies. The aim of this study was to study the phylogeography of the southern distribution of the species. We sequenced the entire chloroplast (cp) genomes of 54 individuals from five sampled populations across different European regions to highlight polymorphisms and analyze their distribution. Thirty-two haplotypes were identified. All the sampled populations showed private haplotypes that can be considered an indicator of long-term residency, given the low mutation rate of organellar DNA. The network of all haplotypes showed a star-like topology, and Serbian haplotypes were present in all branches. The Balkan population showed the highest level of nucleotide and genetic diversity. Low genetic differentiation between populations was observed but we found a significant differentiation among Serbia vs. other provenances. Our estimates of divergent time of U. laevis samples highlight the early split of above all Serbian individuals from other populations, emphasizing the reservoir role of white elm genetic diversity of Serbian population.

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Section: Resultsmentioning

confidence: 99%

Novel Insights Into Refugia at the Southern Margin of the Distribution Range of the Endangered Species Ulmus laevis

et al. 2022

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“…For example, sequencing of sub-sampled loci ( 43 ) has been widely used in phylogenomics studies for cost-effective large-scale genotyping. Skim sequencing ( 44 ) is another low-coverage WGS approach. Target enrichment sequencing investigates specific genomic elements via pre-defined probe sequences ( 45 ).…”

Section: Genomics and Transcriptomics Datamentioning

confidence: 99%

Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

Deng,

Naithani,

Kumari

et al. 2023

Database

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Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021–22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.

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“…With GBS approaches, the rapid discovery of sequence-based molecular markers has been successful in constructing high-density genetic maps in maize, oat, chickpea, and ramie ( Chen et al., 2014 ; Huang et al., 2014 ; Jaganathan et al., 2015 ; Liu et al., 2017 ). Consequently, GBS is becoming more common in genetic mapping studies, genome-wide association studies, genomic selection, polyploidy studies, and genetic diversity and phylogeny studies ( He et al., 2014 ; Limborg et al., 2016 ; Chung et al., 2017 ; Kumar et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing

Jin

Yang

et al. 2023

Front. Plant Sci.

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Rice is a major food crop that sustains approximately half of the world population. Recent worldwide improvements in the standard of living have increased the demand for high-quality rice. Accurate identification of quantitative trait loci (QTLs) for rice grain quality traits will facilitate rice quality breeding and improvement. In the present study, we performed high-resolution QTL mapping for rice grain quality traits using a genotyping-by-sequencing approach. An F2 population derived from a cross between an elite japonica variety, Koshihikari, and an indica variety, Nona Bokra, was used to construct a high-density genetic map. A total of 3,830 single nucleotide polymorphism markers were mapped to 12 linkage groups spanning a total length of 2,456.4 cM, with an average genetic distance of 0.82 cM. Seven grain quality traits—the percentage of whole grain, percentage of head rice, percentage of area of head rice, transparency, percentage of chalky rice, percentage of chalkiness area, and degree of chalkiness—of the F2 population were investigated. In total, 15 QTLs with logarithm of the odds (LOD) scores >4 were identified, which mapped to chromosomes 6, 7, and 9. These loci include four QTLs for transparency, four for percentage of chalky rice, four for percentage of chalkiness area, and three for degree of chalkiness, accounting for 0.01%–61.64% of the total phenotypic variation. Of these QTLs, only one overlapped with previously reported QTLs, and the others were novel. By comparing the major QTL regions in the rice genome, several key candidate genes reported to play crucial roles in grain quality traits were identified. These findings will expedite the fine mapping of these QTLs and QTL pyramiding, which will facilitate the genetic improvement of rice grain quality.

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Skim sequencing: an advanced NGS technology for crop improvement

Cited by 17 publications

References 73 publications

Novel Insights Into Refugia at the Southern Margin of the Distribution Range of the Endangered Species Ulmus laevis

Novel Insights Into Refugia at the Southern Margin of the Distribution Range of the Endangered Species Ulmus laevis

Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing

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