改进型遗传算法在种子园无性系配置设计中的应用

doi:10.11707/j.1001-7488.20180404

摘要/Abstract

摘要： [目的]使用优化算法优化种子园无性系配置的设计方案，以保证种子园子代在具有较高的遗传增益的前提下维持丰富的遗传多样性，为高世代种子园的无性系配置设计提供参考。[方法]基于已有的内蒙古红花尔基樟子松国家良种基地的樟子松亲本为材料，采用SSR分子标记技术及其分析软件确定樟子松亲本之间的遗传距离，使用优化算法开展基于遗传距离的樟子松种子园无性系配置优化设计，并基于研究目标改进原有的优化方法，最后与传统的种子园无性系配置方案、其他优化方法得到的方案进行对比分析。[结果]使用本文改进的优化算法获得的种子园无性系配置方案优于传统的顺序错位以及其他方法的种子园配置方案，该方法能够使遗传距离较近的无性系在配置上保持最大距离，减少近亲交配机会，在一定程度上扩大了子代的遗传基础。[结论]当已知种子园无性系亲本间遗传距离时，可利用本文提出的基于传统遗传算法进行改进的多种群并行自适应的方法，即改进型自适应并行遗传算法，来实现基于遗传距离的种子园无性系优化配置。

关键词: 种子园, 无性系配置, 遗传距离, 遗传算法

Abstract: [Objective]The optimization algorithm was used to optimize the design of clonal distribution of the seed orchard, so as to ensure rich genetic diversity in the next generation while maintaining high genetic gain, and provide advice on the clonal distribution of the high generation seed orchard.[Method]The genetic distance between the parents of Pinus sylvestris var. mongolica was determined using SSR markers and relevant analysis software, the parent trees were selected from the existing P. sylvestris var. mongolica in the National Production Base of Improved Seeds in Honghuaerji of Inner Mongolia. Based on this genetic relationship, the optimization algorithm was used to optimize the clonal deployment by computer simulations, and the original optimization method was improved by accommodating the objectives of the current study. Finally, the optimized clonal deployment was compared with the traditional clonal deployment and other options in a seed orchard.[Result]The seed orchard clonal deployment plan created by optimization algorithm is better than the traditional sequential dislocation method and other methods. This method can keep the maximum distance between the clones which have closer genetic relationship and reduce the chance of inbreeding, therefore enlarging the genetic basis of the offspring to a certain extent.[Conclusion] When the genetic distances between parents were given, the Improved Adaptive Parallel Genetic Algorithm, which was improved by changing the adaptive method based on the traditional Genetic Algorithm, can be used to optimize clonal deployment in seed orchard based on genetic distance.

Key words: seed orchard, clonal deployment, genetic distance, genetic algorithm

中图分类号:

S722.8⁺3

王晴, 齐建东, 崔晓晖, 李伟. 改进型遗传算法在种子园无性系配置设计中的应用[J]. 林业科学, 2018, 54(4): 30-37.

Wang Qing, Qi Jiandong, Cui Xiaohui, Li Wei. Application of Improved Genetic Algorithm in Clonal Deployment for Seed Orchard[J]. Scientia Silvae Sinicae, 2018, 54(4): 30-37.

参考文献

程祥, 张梅, 毛建丰,等. 2016.有限种群油松种子园的遗传多样性与交配系统. 北京林业大学学报, 38(9):8-15.
(Cheng X, Zhang M, Mao J F, et al. 2016. Gene diversity and mating system of Pinus tabuliformis in finite population seed orchard. Journal of Beijing Forestry University, 38(9):8-15.[in Chinese])
方攀, 张运城, 袁虎威,等. 2013.樟子松SSR反应体系优化. 基因组学与应用生物学, 32(3):413-419.
(Fang P, Zhang Y C, Yuan H W, et al. 2013. Optimization of SSR reaction system of Pinus sylvestris var. mongolica. Genomics and Applied Biology, 32(3):413-419.[in Chinese])
贾乃光. 1985. 种子园无性系配置设计程序. 北京林学院学报, (3):24-27.
(Jia N G. 1985. A computer program for clone arrangements in seed orchard. Journal of Beijing Forestry University, (3):24-27.[in Chinese])
蒋建林, 程坤, 王璨璨,等. 2012. 基于改进遗传算法的集合覆盖问题. 数学的实践与认识, 42 (5):120-126.
(Jiang J L, Cheng K, Wang C C, et al. 2015. Improved genetic algorithm for set covering problem. Mathematics in Practice and Theory, 42(5):120-126.[in Chinese])
梁一池. 1995. 种子园配置设计的计算机处理系统. 福建林学院学报, (2):156-159.
(Liang Y C. 1995. The computer processing system on the arrangement designs for seed orchard. Journal of Fujian College of Forestry, (2):156-159.[in Chinese])
梁一池. 1991.计算机辅助种子园配置设计. 福建林学院学报, (2):136-141.
(Liang Y C. 1991. Computer-aided design for arrangement in seed orchard. Journal of Fujian College of Forestry, (2):136-141.[in Chinese])
林晗, 洪滔, 陈辉,等. 2010. 应用遗传算法的工业原料林多树种造林设计. 林业科学, 46(5):92-101.
(Lin H, Hong T, Chen H, et al. 2010. Multi-species design in planting industrial forests by genetic algorithm. Scientia Silvae Sinicae, 46(5):92-101.[in Chinese])
王章荣. 2012. 高世代种子园营建的一些技术问题. 南京林业大学学报:自然科学版, 36(1):8-10.
(Wang Z R. 2012. Techniques on establishment and management of advanced-generation seed orchard. Journal of Nanjing Forestry University:Natural Science Edition, 36(1):8-10.[in Chinese])
吴承祯, 洪伟. 1997. 用遗传算法改进约束条件下造林规划设计的研究. 林业科学, 33 (2):38-46.
(Wu C Z, Hong W. 1997. An improved method of afforestation planning and design under restricted conditions using the genetic algorithm. Scientia Silvae Sinicae, 33(2):38-46.[in Chinese])
吴承祯, 洪伟. 2000. 模拟退火法优化约束条件下造林规划设计的研究. 自然资源学报, 15 (1):86-90.
(Wu C Z, Hong W. 2000. An optimized method of afforestation planning and design under restricted conditions using the simulated annealing algorithm. Journal of Natural Resources, 15(1):86-90.[in Chinese])
吴浩扬, 朱长纯, 常炳国,等. 1999. 基于种群过早收敛程度定量分析的改进自适应遗传算法. 西安交通大学学报, 33 (11):29-32.
(Wu H Y, Zhu C C, Chang B G, et al. 1999. Adaptive genetic algorithm to improve group premature convergence. Journal of Xi'an Jiaotong University, 33(11):29-32.[in Chinese])
许鲁平. 2002. 杉木第一代生产性改良种子园高产配置设计及产量预测的研究. 林业勘察设计, (1):26-30.
(Xu L P. 2002. Study on high yield configuration design and yield prediction of first generation improved seed orchard of Chinese fir. Forestry Prospect and Design, (1):26-30.[in Chinese])
杨培华, 樊军锋, 刘永红,等. 2005.油松高世代种子园营建技术. 中南林学院学报, 25(6):65-69.
(Yang P H, Fan J F, Liu Y H, et al. 2005. Studies on establishing techniques for the advanced generation seed orchards of Pinus tabulaeformis Carr. Journal of Central South Forestry University, 25(6):65-69.[in Chinese])
袁虎威, 梁胜发, 符学军,等. 2016. 山西油松第二代种子园亲本选择与配置设计. 北京林业大学学报, 38(3):47-54.
(Yuan H W, Liang S F, Fu X J, et al. 2016. Parental selection and deployment design in the second-generation seed orchard of Chinese pine in Shanxi Province.Journal of Beijing Forestry University, 38(3):47-54.[in Chinese])
Chaloupková K, Stejskal J, El-Kassaby Y A, et al. 2016. Optimum neighborhood seed orchard design. Tree Genetics & Genomes, 12(6):105.
El-Kassaby Y A, Fayed M, Klápště J, et al. 2014. Randomized, replicated, staggered clonal-row (R 2 SCR) seed orchard design. Tree Genetics & Genomes, 10(3):555-563.
Hodge G R, White T L. 1993. Advanced-generation wind-pollinated seed orchard design. New Forests, 7(3):213-236.
Holland J H. 1975. Adaptation in natural and artificial systems. MIT Press, 6(2):126-137.
LstibuůRek M, Elkassaby Y A. 2010. Minimum-inbreeding seed orchard design. Forest Science, 56(6):603-608.
LstibuůRek M, Stejskal J, Misevicius A, et al. 2015. Expansion of the minimum-inbreeding seed orchard design to operational scale. Tree Genetics & Genomes, 11(1):1-8.
Morgante M, Olivieri A M.1993. PCR-amplified microsatellites as markers in plant genetics. Plant Journal for Cell & Molecular Biology, 3(1):175-182.
Nei M, Chesser R K. 1983. Estimation of fixation indices and gene diversities. Gauthier-Villars, 47 (3):253-259.
Srinivas M, Patnaik L M. 1994. Adaptive probabilities of crossover and mutation in genetic algorithms. IEEE Transactions on Systems Man & Cybernetics, 24(4):656-667.
White T L, Adams W T, Neale D B. 2007. Forest genetics-concepts, scope, history and importance. Wallingford, UK:CABI Publisher, 1-14

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