Genomic DNA extraction from the plant leaves using the CTAB method

Masoodi, Khalid Z.; Lone, Sameena Maqbool; Rasool, Rovidha Saba

doi:10.1016/b978-0-12-824449-4.00007-4

Cited by 13 publications

(6 citation statements)

References 2 publications

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“…Hengxing shrimp compound feed was used throughout the whole process and the same management was carried out during the breeding period. The genomic DNA of water, biofloc, and intestinal samples was extracted by the cetyltrimethylammonium bromide (CTAB) method (Khalid et al, 2021) and the purity and concentration of DNA was measured by agar gel electrophoresis. DNA samples were diluted to 1 µg/µl with sterile water.…”

Section: Sample Collection and Extraction Of Total Dna Of Microbial Floramentioning

confidence: 99%

Metagenomic Analysis of Bacterial Communities and Antibiotic Resistance Genes in Penaeus monodon Biofloc-Based Aquaculture Environments

Chen

Zhao

et al. 2022

Front. Mar. Sci.

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Biofloc technology (BFT) is one of the most promising technologies in global aquaculture for the purpose of improving water quality, waste treatment, and disease prevention in intensive aquaculture systems. However, characterization of the microbial species and antibiotic resistance potentially present in biofloc-based aquaculture environments is needed. In this study, we used high-throughput sequencing technology to comprehensively compare the bacterial communities in mariculture ponds of Penaeus monodon (P. monodon), by testing of water, biofloc, and intestine of P. monodon. Operational taxonomic units (OTUs) cluster analysis showed that the nine samples tested divided into 45 phyla and 457 genera. Proteobacteria was the dominant bacteria in water, biofloc and prawn intestine. In biofloc and intestine, the Ruegeria (2.23–6.31%) genus represented the largest proportion of bacteria, with Marivita (14.01–20.94%) the largest group in water. Microbial functional annotation revealed that in all the samples, genes encoding metabolism were predominant. The antibiotic resistance gene annotation showed the highest absolute abundance of patB, adeF, OXA-243, and Brucella_suis_mprF from Proteobacteria. PatB (11.33–15.01%), adeF (15.79–18.16%), OXA-243 (35.65%), and Brucella_suis_mprF (10.03%) showed the highest absolute abundance of antibiotic resistance genes in water, biofloc, and intestines, respectively. These findings may greatly increase our understanding of the characteristics of the microbiota of shrimp biofloc-based aquaculture systems and the complex interactions among shrimp, ambient microflora, and environmental variables. It provides a reference basis for policy on breeding, environmental safety, and maintaining food safety in the production of P. monodon.

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Section: Sample Collection and Extraction Of Total Dna Of Microbial Floramentioning

confidence: 99%

Metagenomic Analysis of Bacterial Communities and Antibiotic Resistance Genes in Penaeus monodon Biofloc-Based Aquaculture Environments

Chen

Zhao

et al. 2022

Front. Mar. Sci.

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“…Meanwhile, leaves were collected from two parents. DNA extraction was performed from leaves using the CTAB method ( Masoodi et al, 2021 ). The concentration of the extracted DNA was detected using the Qubit fluorometer (Thermo Fisher Scientific).…”

Section: Methodsmentioning

confidence: 99%

QTL-seq analysis identified the genomic regions of plant height and days to heading in high-latitude rice

Wang,

Li,

Zhang

et al. 2024

Front. Genet.

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Introduction: Rice (Oryza sativa L.) is one of the most extensive crops in the world. China’s Heilongjiang Province is the northernmost rice-growing region in the world. However, rice cultivars suitable for growth in low-latitude regions may not mature normally due to their distinct climate and short frost-free period. It is necessary to precisely determine the frost-free period for each region to make the best use of the rice growth stage so as to ensure the maturity and yield of different rice cultivars in Heilongjiang Province. The time span of the heading stage is a key parameter for evaluating the adaptability of a rice cultivar to a specific rice-growing region. Given the above facts, it is of high importance to study the associated genes and sites controlling days to heading (DH) and plant height (PH) of rice in Heilongjiang Province. Bulked segregant analysis (BSA) combined with high-throughput sequencing can effectively exclude interferences from background genomic differences, making it suitable for analyzing the associated sites of complex agronomic traits in early generations.Methods: In this study, an F3 segregating population was obtained by crossing two main cultivars that are grown under different temperatures and day-light conditions in Heilongjiang. Two pools of extreme phenotypes were built for the DH and PH of the population. For SNP and InDel variants obtained from whole-genome resequencing in the pools, an association analysis was performed using the Euclidean distance (ED) algorithm and the SNP/InDel index algorithm.Results: The intersection of SNP and InDel regions associated with the phenotypes was considered to obtain the final associated sites. After excluding interferences from the cloned genes on chromosomes 2 and 7, a total length of 6.34 Mb on chromosomes 1, 3, and 10 and 3.16 Mb on chromosomes 1 and 10 were left associated with PH and DH, respectively. Then, we performed a gene annotation analysis for candidate genes in the remaining regions using multiple genome annotation databases. Our research provides basic data for subsequent gene mapping and cloning.Discussion: By mining more genetic loci associated with the days to heading and plant height of rice, we may provide abundant genetic resources for refined molecular breeding in Heilongjiang Province.

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“…Genomic DNA extraction from leaf samples collected at the joining stage adopted the CTAB protocol [36], and DNA quality was assessed using a NanoDrop One C (Thermo Fisher Scientific, Assembled in the USA). The 198 lines and parents of the MC population were genotyped using the Wheat 16K SNP array from Mol Breeding Company (Shijiazhuang in Hebei province; http://www.molbreeding.com).…”

Section: Methodsmentioning

confidence: 99%

Section: Genotypingmentioning

confidence: 99%

A promising QTLQSns.sau-MC-3D.1likely superior toWAPO1for wheat spikelet number per spike shows no adverse effects on yield-related traits

Zhou

Yang

et al. 2023

Preprint

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Spikelet number per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop higher-yielding wheat varieties. A genetic linkage map constructed using the GenoBaits Wheat 16K Panel and the 660K SNP array contained 5991 polymorphic SNP markers spanning 2813.26 cM. A total of twelve QTL for SNS were detected in the recombinant inbred line (RIL) populationmsf× Chuannong 16 (MC), and two of them, i.e.,QSns.sau-MC-3D.1andQSns.sau-MC-7A, were stably expressed.QSns.sau-MC-3D.1had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison ofQSns.sau-MC-3D.1with previously reported SNS QTL suggested that it is likely a novel one. A kompetitive allele-specific PCR (KASP) marker, KASP-10, tightly linked toQSns.sau-MC-3D.1was developed to successfully validate its effect in three segregated populations and a natural population. Genetic analysis indicated thatWHEAT ORTHOLOG OFAPO1(WAPO1) was a candidate gene forQSns.sau-MC-7A. The combined additive effect ofQSns.sau-MC-3D.1andWAP01had a great additive effect increasing SNS by 7.10%. In addition, our results suggested that SNS is not affected by 1BL/1RS translocations in the MC RIL population. Correlation analysis between two major QTL and other agronomic traits showed thatQSns.sau-MC-3D.1was likely independent of these agronomic traits. However, the H2 haplotype ofWAPO1may affect effective tiller number and plant height. This indicated that the breeding potential ofQSns.sau-MC-3D.1is better than that ofWAPO1. The geographical distribution ofQSns.nsau-MC-3D.1showed thatQSns.sau-MC-3D.1positive allele frequency was dominant in most wheat-producing regions of China and it has been positively selected among modern cultivars released in China since the 1940s. Two genes,TraesCS3D03G0222600andTraesCS3D03G0216800, associated with SNS development were predicted in the physical interval ofQSns.sau-MC-3D.1. qRT-PCR results of the two genes showed that only the expression level ofTraesCS3D03G0216800was significantly different between msf and CN16. These results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of genes underlyingQSns.sau-MC-3D.1, and provide a basis for marker-assisted selection breeding.Author summaryIn this study, we identified two major QTL (QSns.sau-MC-3D.1andQSns.sau-MC-7A) in a RIL population.WAPO1was demonstrated to be the candidate gene forQSns.sau-MC-7A. QSns.sau-MC-3D.1was a novel and stably expressed QTL, and further confirmed in different genetic backgrounds. Our results further demonstrate thatQSns.sau-MC-3D.1has better breeding potential because of its no adverse effect on other agronomic traits thanWAPO1, and it has been positively selected during Chinese breeding programs since the 1940s. Taken together, the identification ofQSns.sau-MC-3D.1offers a promising resource to further increase wheat yields.

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Genomic DNA extraction from the plant leaves using the CTAB method

Cited by 13 publications

References 2 publications

Metagenomic Analysis of Bacterial Communities and Antibiotic Resistance Genes in Penaeus monodon Biofloc-Based Aquaculture Environments

Metagenomic Analysis of Bacterial Communities and Antibiotic Resistance Genes in Penaeus monodon Biofloc-Based Aquaculture Environments

QTL-seq analysis identified the genomic regions of plant height and days to heading in high-latitude rice

A promising QTLQSns.sau-MC-3D.1likely superior toWAPO1for wheat spikelet number per spike shows no adverse effects on yield-related traits

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