Scientia Silvae Sinicae ›› 2020, Vol. 56 ›› Issue (11): 176-186.doi: 10.11707/j.1001-7488.20201119
• Review • Previous Articles Next Articles
Sheng Zhu1,2,3,Minren Huang1,3,*
Received:
2020-07-23
Online:
2020-11-25
Published:
2020-12-30
Contact:
Minren Huang
CLC Number:
Sheng Zhu,Minren Huang. Recent Advances and Prospect of the Genomic Selection in Forest Genetics and Tree Breeding[J]. Scientia Silvae Sinicae, 2020, 56(11): 176-186.
Table 1
List of genomic selection tools"
工具 Tools | 年份 Year | 计算机语言 Language | 统计学模型 Statistical model | PubMed |
BLR | 2010 | R | Bayesian ridge regression | https://cran.r-project.org/web/packages/BLR/ |
rrBLUP | 2011 | R | GBLUP | https://doi.org/10.3835/plantgenome2011.08.0024( |
synbreed | 2012 | R | GBLUP, Bayesian LASSO, Bayesian ridge regression | PMID: 22689388 ( |
BGLR | 2014 | R | BayesA, BayesB, BayesCπ, Bayesian LASSO | PMID: 25009151 ( |
GVCBLUP | 2014 | C++ | GBLUP | PMID: 25107495 ( |
GS3 | 2014 | Fortran | GBLUP, Bayesian LASSO, BayesCπ | https://github.com/alegarra/gs3 |
VIGoR | 2015 | R | Bayesian ridge regression | https://cran.r-project.org/web/packages/VIGoR/ |
GAPIT | 2016 | R | sBLUP (SUPER BLUP), cBLUP (compressed BLUP) | PMID: 22796960 ( |
sommer | 2016 | R | GBLUP | PMID: 27271781 ( |
breedR | 2016 | R | GBLUP | http://famuvie.github.io/breedR/ |
BGGE | 2017 | R | Bayesian ridge regression | https://cran.r-project.org/web/packages/BGGE/ |
BLUPGA | 2018 | R | BLUP|GA | PMID: 29891736 ( |
GenSel | 2018 | Julia | BayesCπ | https://github.com/austin-putz/GenSel |
Table 2
Study reports of genomic selection on forestry trees"
属Genus | 种Species | PubMed |
油棕属Elaeis | 油棕E. guineensis | PMID: 25488416 ( |
油棕E. guineensis | PMID: 28588233 ( | |
桉属Eucalyptus | 巨桉×尾叶桉E. grandis × E. urophylla | PMID: 22309312 ( |
巨桉×尾叶桉E. grandis × E. urophylla | PMID: 28662679 ( | |
巨桉×尾叶桉E. grandis × E. urophylla | PMID: 31084883 ( | |
尾叶桉×巨桉E. urophylla × E. grandis | PMID: 31084883 ( | |
尾叶桉×巨桉E. urophylla × E. grandis | PMID: 29362102 ( | |
多苞桉E. polybractea | PMID: 29891736 ( | |
橡胶树属Hevea | 橡胶树H. brasiliensis | PMID: 31708955 ( |
橡胶树H. brasiliensis | https://doi.org/10.1016/j.bindcrop2019.111464 ( | |
云杉属Picea | 欧洲云杉P. abies | PMID: 30563448 ( |
白云杉P. glauca | PMID: 25442968 ( | |
白云杉P. glauca | PMID: 24781808 ( | |
西加云杉P. sitchensis | https://doi.org/10.1007/s11295-017-1118-z ( | |
黑云杉P. mariana | PMID: 28454519 ( | |
松属Pinus | 海岸松P. pinaster | PMID: 26566829 ( |
海岸松P. pinaster | PMID: 27515254 ( | |
火炬松P. taeda | PMID: 22271763 ( | |
火炬松P. taeda | PMID: 21973055 ( | |
火炬松P. taeda | PMID: 23585458 ( | |
杨属Populus | 美洲黑杨×欧美杨P. deltoides× P. euramericana | 朱嵊等, 待发表Zhu et al., unpublished |
Fig.1
Wordcloud of the genomic selection cases in forestry trees The keywords for breeding population, the amount of markers, the target trait and the statistical methods are denoted in purple, red, black and yellow, respectively. The font size represents the frequency of those keywords in the studies on the tree genomic selection. This wordcloud chart is drawn by the Python package wordcloud (https://pypi.org/project/wordcloud/)."
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