| 1. |
- Fouilloux, Anne, et al.
(author)
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Building on Communities to Further Software Sustainability
- 2023
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In: Computing in science & engineering (Print). - : IEEE COMPUTER SOC. - 1521-9615 .- 1558-366X. ; 25:3, s. 84-88
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Journal article (peer-reviewed)abstract
- The Nordic e-Infrastructure Collaboration on Earth System Modeling Tools is a small community comprising members with diverse backgrounds, skills, and interests. Largely dependent on temporary staff to develop, operate, and maintain large scientific codes, this community devised strategies to enhance software reusability and sustainability. These strategies include collaborating with other communities for support, adopting Open Science as well as findable, accessible, interoperable, and reusable principles to optimize resource usage, growing essential knowledge within the community, and setting up a community of practice to facilitate onboarding and offboarding. The strategies also promote inclusiveness, foster external collaboration, and recognize technical contributions.
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| 2. |
- Peng, Yanchun, et al.
(author)
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Genome-Wide Association Studies of Free Amino Acid Levels by Six Multi-Locus Models in Bread Wheat
- 2018
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In: Frontiers in Plant Science. - : FRONTIERS MEDIA SA. - 1664-462X. ; 9
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Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have been widely used to dissect the complex biosynthetic processes of plant metabolome. Most studies have used single-locus GWAS approaches, such as mixed linear model (MLM), and little is known about more efficient algorithms to implement multi-locus GWAS. Here, we report a comprehensive GWAS of 20 free amino acid (FAA) levels in kernels of bread wheat (Triticum aestivum L.) based on 14,646 SNPs by six multi-locus models (FASTmrEMMA, FASTmrMLM, ISISEM-BLASSO, mrMLM, pKWmEB, and pLARmEB). Our results showed that 328 significant quantitative trait nucleotides (QTNs) were identified in total (38, 8, 92, 45, 117, and 28, respectively, for the above six models). Among them, 66 were repeatedly detected by more than two models, and 155 QTNs appeared only in one model, indicating the reliability and complementarity of these models. We also found that the number of significant QTNs for different FAAs varied from 8 to 41, which revealed the complexity of the genetic regulation of metabolism, and further demonstrated the necessity of the multi-locus GWAS. Around these significant QTNs, 15 candidate genes were found to be involved in FAA biosynthesis, and one candidate gene (TraesCS1D01G052500, annotated as tryptophan decarboxylase) was functionally identified to influence the content of tryptamine in vitro. Our study demonstrated the power and efficiency of multi-locus GWAS models in crop metabolome research and provided new insights into understanding FAA biosynthesis in wheat.
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