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A Secure High-Order Gene Interaction Detecting Method for Infectious Diseases. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:4471736. [PMID: 35495886 PMCID: PMC9050263 DOI: 10.1155/2022/4471736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/01/2022] [Indexed: 12/04/2022]
Abstract
Infectious diseases pose a serious threat to human life, the Genome Wide Association Studies (GWAS) can analyze susceptibility genes of infectious diseases from the genetic level and carry out targeted prevention and treatment. The susceptibility genes for infectious diseases often act in combination with multiple susceptibility sites; therefore, high-order epistasis detection has become an important means. However, due to intensive computational burden and diversity of disease models, existing methods have drawbacks on low detection power, high computation cost, and preference for some types of disease models. Furthermore, these methods are exposed to repeated query and model inversion attacks in the process of iterative optimization, which may disclose Single Nucleotide Polymorphism (SNP) information associated with individual privacy. Therefore, in order to solve these problems, this paper proposed a safe harmony search algorithm for high-order gene interaction detection, termed as HS-DP. Firstly, the linear weighting method was used to integrate 5 objective functions to screen out high-order SNP sets with high correlation, including K2-Score, JS divergence, logistic regression, mutual information, and Gini. Then, based on the Differential Privacy (DP) theory, the function disturbance mechanism was introduced to protect the security of individual privacy information associated with the objective function, and we proved the rationality of the disturbance mechanism theoretically. Finally, the practicability and superiority of the algorithm were verified by experiments. Experimental results showed that the algorithm proposed in this paper could improve the detection accuracy to the greatest extent while guaranteeing privacy.
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Lee YR, Kim CW, Han J, Choi HJ, Han K, Lee ES, Kim DS, Lee J, Siddique MI, Lee HE. Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion ( Allium cepa L.). PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112267. [PMID: 34834630 PMCID: PMC8625195 DOI: 10.3390/plants10112267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 05/02/2023]
Abstract
Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F2 segregating population derived from a cross between the doubled haploid line '16P118' and inbred line 'Sweet Green' through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (qSC4.1), glucose (qGC5.1), fructose (qFC5.1), and total sugar content (qTSC5.1) explaining the phenotypic variation (R2%) ranging from 6.07-11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.
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Affiliation(s)
- Ye-Rin Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Cheol Woo Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - JiWon Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Hyun Jin Choi
- Postharvest Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea;
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Eun Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Jundae Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea;
| | - Muhammad Irfan Siddique
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (Y.-R.L.); (C.W.K.); (J.H.); (K.H.); (E.S.L.); (D.-S.K.); (M.I.S.)
- Correspondence: ; Tel.: +82-63-238-6674
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