1) The document lists plant species and their genome sizes. It also provides links to databases for viewing gene annotations, synteny, and functional analyses. 2) Details are given about sequencing and assembling the Norway spruce genome, including its size of 422.9 Mb across 1,446 scaffolds. 3) The use of RAD-seq to generate SNP markers for linkage mapping and QTL analyses in plants is discussed. Examples show its application in mapping populations of spruce.

1. 2016/12/15 @
1

2. 2016/12/15 2

3. 2016/12/15 3
K laxaflora
S polyrhiza
L usitatissimum
Micromonas sp RCC299
A coerulea
C rubella
G max
B stricta
C sinensis
P virgatum
P persica
A lyrata
E grandis
Z mays
M esculenta
O sativa
F vesca
S purpurea
B rapa FPsc
T cacao
V carteri
A thaliana
B distachyon
M guttatus
S tuberosum
P patens
C clementina
R communis
S viridis
S moellendorfii
C subellipsoidea C-169
C reinhardtii
P hallii
G raimondii
S fallax
E salsugineum
A trichopoda
M truncatula
V vinifera
O lucimarinus
M domestica
S lycopersicum
C papaya
M pusilla CCMP1545
C grandiflora
S bicolor
B stacei
C sativus
P vulgaris
P trichocarpa
M acuminata
S italica
SBM
Chlorophyte
Fabidae
Embryophyte
Rosid
Tracheophyte
Eudicot
Angiosperm
Malpighiales
Brassicales-Malvales
Viridiplantae
Citrus
Pentapetalae
Malvidae
Panicoideae
Brassicaceae
Grass
https://phytozome.jgi.doe.gov/pz/portal.html#
Arabidopsis thaliana
52

4. •
2016/12/15 4
Licensed under CC-BY 4.0 ©Togo picture gallery by DBCLS
• GenomeBentoProject
http://wiki.lifesciencedb.jp/mw/GenomeBentoProject

5. 2016/12/15 5
0
2000
4000
6000
8000
10000
12000
14000
16000
(Mb)
https://www.ncbi.nlm.nih.gov/genome
NCBI genome

6. 2016/12/15 6
ü 40
ü 2n = 6x = 42
ü
ü
DNA
Genome A
Genome B
Genome D
1 2 3 4 5 6 7

7. 2016/12/15 7
,
ü
ü
,
, ,
ü
ü

8. •
Licensed under CC-BY 4.0 ©Togo picture gallery by DBCLS
• GenomeBentoProject
http://wiki.lifesciencedb.jp/mw/GenomeBentoProject
2016/12/15 8
→

9. 2016/12/15 9
0
500
1000
1500
2000
2500
(Mb)
https://www.ncbi.nlm.nih.gov/genome
NCBI genome

10. 2016/12/15 10
ü
ü 732.2 Mb
ü 10
ü C4
ü 5
ü

11. DNA
ü Simple Sequence Repeats (SSR) markers
QTL
(codominant maker) multiallelic
ü Single Nucleotide Polymorphism (SNP) markers
SSR
GWAS
ü NGS
RAD-Seq GBS low depth WGS
SNP
2016/12/15
11
RAD-Seq
SNPposition

12. ü
ü
ü
2016/12/15 12
DNA
A
B
ds1
http://link.springer.com/article/10.1007/s00122-011-1572-1

13. 2016/12/15 13
Phytozome
https://phytozome.jgi.doe.gov/pz/portal.html#

14. 2016/12/15 14
Functional annotation
https://phytozome.jgi.doe.gov/pz/portal.html#

15. 2016/12/15 15
Gene Ancestry

16. 2016/12/15 16
Gene variation

17. 2016/12/15 17
genome synteny
Sobic.001G394400 phyB
http://chibba.agtec.uga.edu/duplication/index/locus
PLANT GENOME DUPLICATION DATABASE
LOC_Os03g19590

18. 2016/12/15 18
genome synteny
PLANT GENOME
DUPLICATION DATABASE
http://chibba.agtec.uga.edu/duplication/index/dotplot

19. 2016/12/15 19
DNA
C
A
SNP
Togo picture gallery by DBCLS is
Licensed under a Creative Commons 2.1 (c)
A
B
DNA -

20. 2016/12/15 20
Sorghum bicolor
( )
(y)
(x)
Togo picture gallery by DBCLS is licensed under a
Creative Commons Attribution 2.1
y = f (x)
(y)
(x)
(x’)
y’ = f (x’)
NGS SNP

21. 2016/12/15 21
0
10 1
(10 9 )
10

22. 2016/12/15 22
DNA
DNA

23. 2016/12/15 23
ü RAD-Seq SNP SNP
-> QTL GWAS
ü
By katorisi (Own work) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY 3.0
By Ellen Levy Finch (Elf) (Own work) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0

24. 2016/12/15 24
By Inti-sol (Own work) [GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0
(http://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 2.5-2.0-1.0
(http://creativecommons.org/licenses/by-sa/2.5-2.0-1.0)], via Wikimedia Commons

25. 2016/12/15 25
ü
ü 422.9 Mb , 1,446 scaffolds
ü
ü
ü 19
ü 2006
By Beeblebrox (Own work) [CC BY-SA 3.0
(http://creativecommons.org/licenses/by-sa/3.0)], via
Wikimedia Commons

26. 2016/12/15 26
By Franz Eugen Köhler, Köhler's Medizinal-Pflanzen
(List of Koehler Images) [Public domain], via Wikimedia
Commons
ü
ü The Norway spruce genome sequence
and conifer genome evolution.
Nature. (2013)497:579-84.
ü
ü 20G
By Michael Vadon CC BY-SA 4.0
https://commons.wikimedia.org/wiki/File%3ARockefeller_Ce
nter_Christmas_Tree_05.jpg
2016 Rockefeller Center Christmas Tree

27. Nystedt et al. Nature 000, 1-6 (2013) doi:10.1038/nature12211
The gene-space and transcribed fraction of the P.abies 1.0 assembly.
ü
ü
ü

28. 2016/12/15 28

29. ü ConGenIE: Conifer Genome Integrative Explorer
http://congenie.org
ü PopGenIE: Populus Genome Integrative Explorer
http://popgenie.org
2016/12/15 29

30. 2016/12/15 30
RAD-Seq
1 1 2 3 3 1
4 4 1
1 2 3 4

31. 2016/12/15 31
Abies sachalinensis ( )
ü
ü
(Pinus)
(Abies)
ü
ü
ü
http://www.fpri.hro.or.jp/gijutsujoho/doumoku-db/doumoku/N2 /todomatu.htm
http://www.jawic.or.jp/woods/sch.php?nam0=todomatsu
http://bvi.rusf.ru/taksa/i0057/0057886.jpg

32. 2016/12/15 32
!?
ü
ü
ü →
ü QTL →
ü 20Gb
ü
ü SSR 4 , SSR 3
ü
RAD-seq → SNP

33. 2016/12/15 33
→
2011 5 P1 P2
(530m)
(1200m)
P1 P2
(230m)

34. 2016/12/15 34
→
ü 2011 5 P1 P2
ü 2012 5 DNA
ü 2013 SSR →
ü 2011 2014 →QTL
ü 2 376 RAD-Seq
ü Stacks
http://catchenlab.life.illinois.edu/stacks/

35. 2016/12/15 35
ü JoinMap
ü RAD-Seq 500 SNP
ü 12

36. 2016/12/15 36
ü RAD-Seq SNP SNP
-> QTL GWAS
Fumihiko Ueno [CC BY 3.0
(http://creativecommons.org/licenses/by/3.0)], via Wikimedia
Commons
https://www.ffpri.affrc.go.jp/labs/cjgenome/indexj.html