060310391
0560565
0
2015/9/26 13:00-14:45
@1 - 4
(Biometrics)
• Bio-
• -metrics
• Biometrics
Morphometrics =
Chemometrics =
Econometrics =
Pscychometrics =
Bibliometrics =
Biometrics, Biometry
• “Biometry, the ac.ve pursuit of biological
knowledge by quan.ta.ve methods.”
– R.A. Fisher, 1948
hLp://digital.library.adelaide.edu.au/coll/special//fisher/
Tester M, Langridge P(2010) Breeding technologies to increase crop
producTon in a changing world. Science 327: 818
GenBank
PDB 3
Medline
hLp://www.ncbi.nlm.nih.gov/genbank/staTsTcs
Jensen et al. (2006) Nat Rev Genet 7: 119
0 2E+11 4E+11 6E+11 8E+11 1E+12 1.2E+12 1.4E+12
Date May-86 Sep-88 Dec-90 Apr-93 Dec-94 Aug-96 Apr-98 Feb-00 Oct-01 Jun-03 Feb-05 Oct-06 Jun-08 Feb-10 Oct-11 Jun-13 Feb-15 GenBank (NIH
geneTc seq. DB)
WGS (whole Genome Shotgun)
Bases
0 20000 40000 60000 80000 100000 120000
1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 Yearly
Total
hLp://www.rcsb.org/pdb/staTc.do?p=general_informaTon/pdb_staTsTcs/index.html
1
1 1500Gb (50 )
30
500
4
3750
Informa.on
≠ Knowledge
Informa.on
↓
Knowledge
Q.
• e
• e:
y = G + e
cm
•
E
y = G + E + e
Frankham et al. (2002) IntroducTon to conservaTon geneTcs. Cambridge University Press
G E
• G
E GEI
y = G + E + GEI + e
Watanabe et al. (2005) Ann Bot. 95:1131
…
• G
QTL g i
y = ∑ g i + E + e
Informa.on Knowledge !
•
•
•
0 9/26
1
1.1) 9/26
1.2) 10/17
1.3) 10/24
2
2.1) 10/31
2.2) QTL 11/7
2.3) GWAS 11/14
2.4) 11/21
2.5) × 12/5
3
3.1) 12/12
3.2) 12/19
3.3) : 12/26
1/5
4 1/16
1.1)
「丸、三角、四角、ハート、星」と記述できます。
これらの形は、
では、これらはどのように記述すればよいでしょう？
x y
t
t
y
y (t)
T 2T
輪郭上を等速度で周回する点の座標を、
時間軸に対してグラフを描くと、輪郭の形を
「波の形」として数学的に記述できます
1 2 3 4 5 6 7 8 9 10 11 12
1
2 3
4 5
染色体地図
1
2
3
4
5
「日本晴」型
「カサラス」型
QTLの効果の視覚化
•
1.2)
2
3
4
1
•
1.3)
• 5000
…
Kindly provided by Mr. Arturo Garcia (USDA-ARS)
•
Montes et al. (2011) Field Crops Research 121:268–273
F2
2.1)
•
•
F1
×
100 100! / 2 = 4.67 x 10
157•
経路に蓄積されたフェロモン (灰色の濃さは蓄積量を表す）
障害物
a
t k i j
c
都市i
都市k
都市h 都市j 都市i、j間に蓄積されたフェロモン量
都市i、j間の距離 都市A
都市C 都市B
都市D
都市E
b
(遺伝子座A)
(遺伝子座B)
(遺伝子座D)
(遺伝子座E) (遺伝子座C)
都市A-B間の距離
（遺伝子座A-B間の組換え価 または対数尤度の絶対値）
2009 11: 177
2.2) QTL
Ashikari et al. (2005)
• QuanTtaTve Trait Loci:
QTL
2.3)
品種の特徴
（例えば、玄米形） DNAマーカーデータ
B A A A B B B A B A B A A B B B A A A A A A B B A A A B A A A A B B A A A B A A B B A B A B A A B B A B A B B A B A A A B B A A B A B A A B B A B B B B A A A A B B A A A B A B B A A A B A B A B B A B B B A B A B A A B A B A A B A B B A A A A A B A B A A A B B A A A A B B B A B B A A B A B B B B A B B A B A A B A B A A B B A A B B B B A A B A A B A A B A A A B A A A B A B B A A B B A A A A B B B B A B A B B A B B B B A A B B B B A A A A A B A A B B A A A A A A A A B A B B B A
両者間の関連を 解析する
<- - - - 品種A - - - ->
<- - - - 品種B - - - ->
<- - - - 品種C - - - ->
<- - - - 品種H - - - ->
•
Atwell et al. (2010) Nature 465: 627
2.4)
•
1975
/ 292
1982
1984
→
•
2.5) ×
• ×
Hammer et al. TRENDS in Plant Science 11:1360
3.1)
Fig. 4. Convergent evolu0on of feeding morphology and color among East African cichlid fishes. Species from Lake Tanganyika are in the leA column; those from Lake Malawi are to the right. Each of the illustrated fishes from Lake Malawi are more closely related to one another than to any species in Lake Tanganyika.
hLp://www.pnas.org/ Albertson et al. (2003)
1996
•
Saitou and Nei (1987)
3.2)
•
Thomson et al. (2007)
•
-0.6 -0.4
-0.2 0
0.2 0.4
0.6
PCO1 (33.8%) -0.4
-0.2 0 0.2 0.4 0.6 0.8
PCO2 (25.7%)
-0.6 -0.4 -0.2 0
0.2 0.4 0.6
PCO3 (16.1%)
-0.6 -0.4 -0.2 0 0.2 0.4 0.6
PCO3 (16.1%)
Izu Pen. Oshima Is.
Niijima Is.
Kozu Is.
Miyake Is. Mikura Is. Hachijo Is.
1.0
0.0 0.5
Fig. The ancestries of 332 accessions inferred from genotype data of 179 RFLP markers.
3.3)
•
•
Medline
Jensen et al. (2006) Nat Rev Genet 7: 119
Jensen et al. (2006) Nat Rev Genet 7: 119
•
•
–
–
•
– k-means
– SOM
•
– SVM
•
– LASSO
– SVM
–
•
–
–
•
– EM
–
MCMC
•
–
–
1.1)
1.3)
1.2)
2.1)
2.2)
QTL
2.3)
2.4)
2.5)
×
3.1) 3.2)
3.3)
42
Wheat&field&in&Faryab&province&From&‘Review&of&the&Wheat&Seed&Sector&in&Afghanistan’&(FAO)
Landrace Inquilab&91
Watanabe et al. (2005) Ann Bot. 95:1131
DNA
y i = f (x i1 , x i 2 ,..., x iN )
DNA
NGS DNA
DNA
JST CREST
0 10 20 30
0 5 10 15 20 25
Brix
co u n t
lt15FALSE TRUE
hLp://www.shokulife.com/arTcles/archives/63
GS
y
x
y = f (x) \\\
Los Mochis,
Mexico
2 /
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2016 vol.12
