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- Title
PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping.
- Authors
Xia, Lei; Shi, Mijuan; Li, Heng; Zhang, Wanting; Cheng, Yingyin; Xia, Xiao-Qin
- Abstract
Simple Summary: The challenges and expenses associated with accessing pedigree information pose a clear technical weakness that impedes the widespread adoption of selective breeding schemes in aquaculture. In large offspring populations, such as fish, using a small number of markers can substantially reduce the cost of parentage assignment. Theoretically, it is feasible to calculate the smallest parentage marker set from a given marker pool by exhaustively enumerating all possible marker combinations when full parental genotypes are known. However, the sheer number of markers can render the exhaustive method impractical. To address this, we have developed an online software that utilizes exhaustive and greedy algorithms to identify the smallest possible parentage marker set for closed populations. The tool was tested and proven to be effective in narrowing down the number of markers, thus providing technical support for large-scale parentage assignment applications. Parentage assignment is a genetic test that utilizes genetic characteristics, such as molecular markers, to identify the parental relationships within populations, which, in commercial fish farming, are almost always large and where full information on potential parents is known. To accurately find the true parents, the genotypes of all loci in the parentage marker set (PMS) are required for each individual being tested. With the same accuracy, a PMS containing a smaller number of markers will undoubtedly save experimental costs. Thus, this study established a scheme to screen low-redundancy PMSs using the exhaustive algorithm and greedy algorithm. When screening PMSs, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms the probability of exclusion (PE). With the conjunctive use of the two algorithms, non-redundant PMSs were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. Then, a low-redundancy PMS can be composed using two or more of these non-redundant PMSs. This scheme effectively reduces the number of markers in PMSs, thus conserving human and experimental resources and laying the groundwork for the widespread implementation of parentage assignment technology in economic species breeding.
- Subjects
GREEDY algorithms; FISH farming; ALGORITHMS; FISHERIES; GENETIC testing; SHORT tandem repeat analysis
- Publication
Biology (2079-7737), 2024, Vol 13, Issue 2, p100
- ISSN
2079-7737
- Publication type
Article
- DOI
10.3390/biology13020100