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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(PDF)

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

Issue:
2018年03期
Page:
67-72
Column:
研究论文
publishdate:
2018-05-15

Article Info:/Info

Title:
Statistical analysis of interval mapping with multivariate trait data in forest trees and its application in poplars
Article ID:
1000-2006(2018)03-0067-06
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
Keywords:
Keywords:multivariate trait data QTL mapping poplar R language
Classification number :
S722
DOI:
10.3969/j.issn.1000-2006.201705020
Document Code:
A
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.

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.

Last Update: 2018-06-06