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LociScan,a tool for screening genetic marker combinations for plant variety discrimination

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To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrim-ination,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 opti-mization 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.

Plant variety discriminationGenetic marker combinationVariety discrimination powerGenetic algorithm

Yang Yang、Hongli Tian、Hongmei Yi、Zi Shi、Lu Wang、Yarning Fan、Fengge Wang、Jiuran Zhao

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Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,Maize Research Institute,Beijing Academy of Agriculture and Forestry Sciences,Beijing 100097,China

Scientific and Technological Innovation Major Project(2030)Science and Technology Innovation Capacity Building Project of BAAFSHainan Province Science and Technology Special Fund北京学者计划

2022ZD04019KJCX20230303ZDYF2023XDNY077BSP041

2024

10.1016/j.cj.2024.01.001

作物学报(英文版)

作物学报(英文版)

CSTPCD
ISSN：
年,卷(期)：2024.12(2)
  • 69