LociScan, a tool for screening genetic marker combinations for plant variety discrimination
文献类型： 外文期刊
作者： Yang, Yang 1 ; Tian, Hongli 1 ; Yi, Hongmei 1 ; Shi, Zi 1 ; Wang, Lu 1 ; Fan, Yaming 1 ; Wang, Fengge 1 ; Zhao, Jiuran 1 ;
作者机构： 1.Beijing Acad Agr & Forestry Sci, Maize Res Inst, Beijing Key Lab Maize DNA Fingerprinting & Mol Bre, Beijing 100097, Peoples R China
关键词： Plant variety discrimination; Genetic marker combination; Variety discrimination power; Genetic algorithm
期刊名称：CROP JOURNAL （ 影响因子：6.6； 五年影响因子：6.5 ）
ISSN： 2095-5421
年卷期： 2024 年 12 卷 2 期
页码：
收录情况： SCI
摘要： To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrimination, it is desirable to identify the optimal marker combinations. We describe a marker combination screening model based on the genetic algorithm (GA) and implemented in a software tool, LociScan. Ratio -based variety discrimination power provided the largest optimization space among multiple fitness functions. Among GA parameters, an increase in population size and generation number enlarged optimization depth but also calculation workload. Exhaustive algorithm afforded the same optimization depth as GA but vastly increased calculation time. In comparison with two other software tools, LociScan accommodated missing data, reduced calculation time, and offered more fitness functions. In large datasets, the sample size of training data exerted the strongest influence on calculation time, whereas the marker size of training data showed no effect, and target marker number had limited effect on analysis speed. (c) 2024 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY -NCND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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