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2 results on '"HiSeq"'

1. Conversion of Land Use from Upland to Paddy Field Changes Soil Bacterial Community Structure in Mollisols of Northeast China.

Author

Sun, Minglong, Li, Tie, Li, Dongmei, Zhao, Yuanling, Gao, Fengmei, Sun, Lianfa, and Li, Xin

Subjects
*BACTERIAL communities, *MOLLISOLS, *PADDY fields, *LAND use, *SOIL composition, *LAND management, *UPLANDS
Abstract

Mollisols are extremely important soil resource for crop and forage production. In northeast China, it is a major land use management practice from dry land crops to irrigated rice. However, there is few data regarding soil quality and microbial composition in Mollisols during land use transition. Here, we analyzed the upper 30 cm of soil from land with more than 30 years of paddy use and from adjacent areas with upland crops. Our results showed that land use and soil depth had a significant effect on soil properties and enzyme activities. Soil moisture (SM) and soil organic carbon (SOC) contents were substantially higher in paddy fields than in upland crop lands, while nitrogen-related enzyme activities were lower. Following the land use change, bacterial diversity was increased and bacterial community composition changed. Taxonomic analyses showed that Proteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes were the dominant phyla present. At family level, Gemmatimonadaceae decreased with land use change, while Syntrophorhabdaceae and Syntrophacea that play a part in methane cycling and nitrifying bacteria such as Nitrospiraceae increased, indicating that the structure and composition of the bacterial community might be a promising indicator of Mollisol health. Redundancy analysis indicated that land use type had a stronger effect on the soil bacterial community composition than soil depth. Additionally, bacterial community composition was closely associated with soil parameters such as soil moisture, pH, SOC, NO3−-N, and NH4+-N. Overall, land use change affects the physical and chemical properties of the soil, resulting in changes in the composition of the soil bacterial community and flora. These changes could provide a view of the bacterial community assembly and functional shifts following land use change. [ABSTRACT FROM AUTHOR]

Published
2021
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2. Construction of a high-density mutant library in soybean and development of a mutant retrieval method using amplicon sequencing

Author

Mai Tsuda, Kyoko Takagi, Takehiko Shimizu, Takashi Sayama, Naohiro Yamada, Satoshi Watanabe, Kayo Machita, Harumi Sasaki, Minoru Nishimura, Yuichi Katayose, Toyoaki Anai, Satomi Mori, Hiroyuki Kanamori, Akito Kaga, and Masao Ishimoto

Subjects
HiSeq, Ethyl methanesulfonate, Nonsense mutation, Mutant, MiSeq, Mutagenesis (molecular biology technique), Biology, DNA sequencing, High Resolution Melt, symbols.namesake, chemistry.chemical_compound, Nextera technology, Next generation sequencing, Genetics, High resolution melting, Amplicon sequencing, Sanger sequencing, EMS mutagenesis, High-Throughput Nucleotide Sequencing, food and beverages, Mutant library, chemistry, Mutagenesis, Mutation (genetic algorithm), Mutation, symbols, Soybeans, Mutation density, DNA pooling, Research Article, Biotechnology
Abstract

Background Functions of most genes predicted in the soybean genome have not been clarified. A mutant library with a high mutation density would be helpful for functional studies and for identification of novel alleles useful for breeding. Development of cost-effective and high-throughput protocols using next generation sequencing (NGS) technologies is expected to simplify the retrieval of mutants with mutations in genes of interest. Results To increase the mutation density, seeds of the Japanese elite soybean cultivar Enrei were treated with the chemical mutagen ethyl methanesulfonate (EMS); M2 seeds produced by M1 plants were treated with EMS once again. The resultant library, which consisted of DNA and seeds from 1536 plants, revealed large morphological and physiological variations. Based on whole-genome re-sequencing analysis of 12 mutant lines, the average number of base changes was 12,796 per line. On average, 691 and 35 per line were missense and nonsense mutations, respectively. Two screening strategies for high resolution melting (HRM) analysis and indexed amplicon sequencing were designed to retrieve the mutants; the mutations were confirmed by Sanger sequencing as the final step. In comparison with HRM screening of several genes, indexed amplicon sequencing allows one to scan a longer sequence range and skip screening steps and to know the sequence information of mutation because it uses systematic DNA pooling and the index of NGS reads, which simplifies the discovery of mutants with amino acid substitutions. Conclusions A soybean mutant library with a high mutation density was developed. A high mutation density (1 mutation/74 kb) was achieved by repeating the EMS treatment. The mutation density of our library is sufficiently high to obtain a plant in which a gene is nonsense mutated. Thus, our mutant library and the indexed amplicon sequencing will be useful for functional studies of soybean genes and have a potential to yield useful mutant alleles for soybean breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2079-y) contains supplementary material, which is available to authorized users.

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