[1]刘粉香,陶申童,吴吉妍,等.林木多元性状数据QTL区间作图统计分析及其在杨树上的应用[J].南京林业大学学报(自然科学版),2018,42(03):067-72.[doi:10.3969/j.issn.1000-2006.201705020]
 LIU Fenxiang,TAO Shentong,WU Jiyan,et al.Statistical analysis of interval mapping with multivariate traitdata in forest trees and its application in poplars[J].Journal of Nanjing Forestry University(Natural Science Edition),2018,42(03):067-72.[doi:10.3969/j.issn.1000-2006.201705020]
点击复制

林木多元性状数据QTL区间作图统计分析及其在杨树上的应用
分享到:

《南京林业大学学报(自然科学版)》[ISSN:1000-2006/CN:32-1161/S]

卷:
42
期数:
2018年03期
页码:
067-72
栏目:
研究论文
出版日期:
2018-05-15

文章信息/Info

Title:
Statistical analysis of interval mapping with multivariate trait data in forest trees and its application in poplars
文章编号:
1000-2006(2018)03-0067-06
作者:
刘粉香12陶申童1吴吉妍1姚 丹1童春发1*
1.南京林业大学林学院,江苏 南京 210037; 2.三江学院计算机科学与工程,江苏 南京 210012
Author(s):
LIU Fenxiang12TAO Shentong1WU Jiyan1YAO Dan1TONG Chunfa1*
1. College of Forestry,Nanjing Forestry University,Nanjing 210037,China; 2. Department of Computer Science and Engineering,Sanjiang University,Nanjing 210012,China
关键词:
多元性状数据 QTL定位 杨树 R语言
Keywords:
Keywords:multivariate trait data QTL mapping poplar R language
分类号:
S722
DOI:
10.3969/j.issn.1000-2006.201705020
文献标志码:
A
摘要:
【目的】传统的数量性状基因座(QTL)定位统计分析方法是针对自交系产生实验群体而建立的,不能直接应用到林木这种杂合度较高生长周期较长的异交物种中。针对林木多元性状数据,将传统的QTL区间作图方法应用到林木杂交F1代作图群体中。【方法】考虑分子标记各种可能的分离比以及连锁相信息,建立林木多元性状数据QTL定位统计分析模型,并用R语言编写了相应的计算软件包mvqtlmap。在美洲黑杨和小叶杨杂交F1代群体中,对2014年5月29日至9月24日期间调查的6个时间点树高数据进行了QTL定位分析。【结果】有4个QTL定位在母本美洲黑杨的遗传连锁图谱上,有6个QTL分布在父本小叶杨的遗传连锁图谱上,这些QTL分别位于第1、5、7、9、11和19号染色体上,平均解释0.8%~6.7%的表型方差。【结论】研究结果可为在林木上利用多个性状或多个时间点性状数据进行QTL定位提供统计分析方法及计算工具。所建立的程序包可在网站http://www.bioseqdata.com/mvqtlmap/mvqtlmap.htm上自由下载。
Abstract:
Abstract: 【Objective】Traditional statistical methods for mapping quantitative trait loci(QTLs)have been well established, especially for experimental populations generated with inbred lines. However, they cannot be directly applied in forest trees because such species have high heterozygosity and long-term generation. In this study, we applied the interval mapping method to an F1 hybrid population of forest trees for multivariate trait data.【Methods】The statistical model incorporated various segregations of molecular markers, including QTLs, and different linkage phases between any adjacent markers. An R package called mvqtlmap was developed to implement the calculation in practice for parameter estimates of the statistical model. Based on the two parent-specific linkage maps of Populus deltoides and P. simonii, we performed QTL mapping for tree heights which were measured at six different time points from May 29 to September 24, 2014 with the developed software package. 【Results】Consequently, four QTLs affecting tree height were located on the female linkage map of P. deltoides, and six QTLs were found on the male linkage map of P. simonii. These QTLs were distributed on chromosomes 1, 5, 7, 9, 11 and 19, explaining an average of 0.8%-6.7% of the phenotypic variance. 【Conclusion】We therefore provided a useful statistical method with a computing tool for mapping QTLs with multivariate data from forest trees and demonstrated its application with a real example using poplar. The package of mvqtlmap is free download on the website of http://www.bioseqdata.com/mvqtlmap/mvqtlmap.htm.

参考文献/References:

[1] LANDER E S, GREEN P. Construction of multilocus genetic linkage maps in humans [J]. Proceedings of the National Academy of Sciences, 1987, 84(8): 2363-2367.
[2] LANDER E S, BOTSTEIN D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps [J]. Genetics, 1989, 121(1): 185-199.
[3] HALEY C S, KNOTT S A. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers [J]. Heredity, 1992, 69(4): 315-324.
[4] MARTINEZ O, CUMOW R. Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers [J]. TAG Theoretical and Applied Genetics, 1992, 85(4): 480-488.
[5] JIANG C, ZENG Z B. Multiple trait analysis of genetic mapping for quantitative trait loci [J]. Genetics, 1995, 140(3): 1111-1127.
[6] KAO C H, ZENG Z B, TEASDALE R D. Multiple interval mapping for quantitative trait loci [J]. Genetics, 1999, 152(3): 1203-1216.
[7] MACGREGOR S, KNOTT S A, WHITE I, et al. Quantitative trait locus analysis of longitudinal quantitative trait data in complex pedigrees [J]. Genetics, 2005, 171(3): 1365-1376.
[8] TONG C F, LI H G, WANG Y, et al. Construction of high-density linkage maps of Populus deltoides×P. simonii using restriction-site associated DNA sequencing [J]. Plos One, 2016, 11(3): e0150692.
[9] TONG C, BO Z, LI H, et al. Model selection for quantitative trait loci mapping in a full-sib family [J]. Genetics & Molecular Biology, 2012, 35(3): 622-631.
[10] DEMPSTER A P, LAIRD N M, RUBIN D B. Maximum likelihood from incomplete data via the EM algorithm [J]. Journal of the Royal Statistical Society: Series B(Methodological), 1977, 39: 1-38.
[11] 施季森, 童春发. 林木遗传图谱构建和QTL定位统计分析 [M]. 北京: 科学出版社, 2006.
[12] CHURCHILL G A, DOERGE R W. Empirical threshold values for quantitative trait mapping [J]. Genetics, 1994, 138: 963-971.
[13] DOERGE R W, CHURCHILL G A. Permutation tests for multiple loci affecting a quantitative character [J]. Genetics, 1996, 142(1): 285-294.
[14] AKAIKE H. A new look at the statistical model identification [J]. IEEE Transactions on Automatic Control, 1974, 19(6): 716-723.
[15] SCHARZ G. Estimating the dimension of a model [J]. Annals of Statistics, 1978, 6: 461-464.
[16] WU R L, MA C X, PAINTER I, et al. Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species [J]. Theoretical Population Biology, 2002, 61(3): 349-363.
[17] WU R L, LIN M. Functional mapping-how to map and study the genetic architecture of complex dynamic traits [J]. Nat Rev Genet, 2006, 7: 229-237.
[18] LI Y, WU R. Functional mapping of growth and development [J]. Biological Reviews of the Cambridge Philosophical Society, 2010, 85(2): 207-216.
[19] WU R L. Genetic mapping of QTLs affecting tree growth and architecture in Populus: implication for ideotype breeding [J]. Theor Appl Genet, 1998, 96: 447-457.
[20] DU Q, GONG C, WANG Q, et al. Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus(QTL)analysis and association studies [J]. The New Phytologist, 2016, 209(3): 1067-1082.
[21] SU C, WANG W, GONG S, et al. High density linkage map construction and mapping of yield trait QTLs in maize(Zea mays)using the genotyping-by-sequencing(GBS)technology [J]. Frontiers in Plant Science, 2017, 8: 706.

相似文献/References:

[1]李婕,王忠*,李永慈*,等.异速生长的QTL定位模型及一因多效性扩展[J].南京林业大学学报(自然科学版),2014,38(03):035.[doi:10.3969/j.issn.1000-2006.2014.03.007]
 LI Jie,WANG Zhong*,LI Yongci*,et al.A novel QTL mapping model for allometric growth and pleiotropic extension[J].Journal of Nanjing Forestry University(Natural Science Edition),2014,38(03):035.[doi:10.3969/j.issn.1000-2006.2014.03.007]

备注/Memo

备注/Memo:
基金项目:国家自然科学基金面上项目(31270706); 江苏高校优势学科建设工程资助项目(PAPD) 第一作者:刘粉香(445212034@qq.com),博士生。*通信作者:童春发(tongchf@njfu.edu.cn),教授。
更新日期/Last Update: 2018-06-06