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Genetics (遺伝学)

Mount Usu / Sarobetsu post-mined peatland
From left: Crater basin in 1986 and 2006. Cottongrass / Daylily

The study of genes, genetic variation, and heredity in living organisms

Gene system

  1. simple Mendelian systems
  2. serial gene systems
  3. multiple gene systems (同義遺伝子)
  4. opositional gene systems (離反遺伝子)
  5. modifier systems
  6. cytoplasmic systems
  7. systems composed of interacting cytoplasmic and chromosomal genes
    Ex. Aquilegia ecalcarata: no spur (spur = calcar)

    × A. vulgalis, × A. canadensis - no spure
    × A. chrysantha, × A. alpina – spur at the probability of 1/16

    → mediated or determined by multiple genes

Fundamental genetics (基礎遺伝学)

[ Mendel ]

Mendelian rules or laws (メンデルの法則)

Law of segregation of genes (the first law)
Law of independent assortment (the second law)
Law of dominance (the third law)

[ reproduction ]

Cytogenetics (細胞遺伝学)

Chromosome cytology (染色体細胞学)

Keywords: karyotype, telocentric/metacentric, univalents (divalens, multivalents), chiasmata, (stages of miosis) diakinesis (metaphase I (MI) metaphase II (MII))
Chromosome counts (squash technique vs thin sections), stains, pre-treatments, karyotype analysis (giemsa staining, metaphase plate)
Genetics of polyploids
Tetrasomic ratios
Duplicate loci
Hormonal regulation of gonadal functions
dimorphism ┏━>_hypothalamus
____releasing hormones
____anterior pituitary (AP, 下垂体前葉)
___ ┣━━━━━━┓
____interstitial cells_androgen-binding protein
┗━━┛negative feedback
__hypothalamus 視床下部

anterior pituitary 脳下垂体前葉
spermatogenesis 精子生成


mammary gland 乳腺
uterus 子宮
fertilized 着床
placenta 胎盤

when estrogen is excess, it works to hypothalanus that starts to secrete LH
many feedbacks
Releasing hormones
FSH/LH-RH: Glx-His-Trp-Ser-Tyr-Gly-Leu-Arg-Pro-Gly (pig, sheep)

dimorphism 2-pyrrolidore carboxylic acid

TSH (thyroid-stimulating hormone) 甲状腺刺激ホルモン

Differentiation of hormones: differentiating from common base genes, infering from the resembled structures
Prolactin CMGH
___━━┗┳┛ single peptide

GH (growth hormone) 成長ホルモン
MTH (mammotrophic hormone) 乳腺刺激ホルモン, GH means MTH on the above figure

Ex. amino acids of P191 GH 191 in human (pig = P198)
           α-chain  β-chain
    CG        92        139
    LH        89        113
    FSH        -        115

α-chains are roughly common between the hormons but β-chains are different

Dimorphism (二型性)

Sex determination
Differences in the differentiation of genital glands among species

Human egg

Development of gonads (生殖腺発達)
Emergence of PCG (PCGの発生)
Egg: sex

germ plasm: cells gotten germ plasm gather and produce PCG

Development of gonads (nephros: 腎臓の前駆体)
                    ♂                   ♀

Mesonephros      → epididymis (副睾丸)  degenerate
wolffian duct    → seminal veside,      degenerate
                      vas deferens
müllerian duct   → degenerate (退化)    oviduct, uterus, vagina
urogential sinus →                      vaginal vestibule,
    (cloaca)                             clitoris, labia

19th    Primordian germ cells
25-30th Wolffian duct
        appears (形成開始)
37-45th gonadal ridge develops
44-48th Müllerian duct appears
50th    urogenital sinus appears
60th    W.M.V. complete
        ♀                          ♂
                              43-50 testicular cords appear
                              60    sertoli cells appear
                                    degeneration of M. begins
                              65    intestitial cells apper
60-75   formation of vagina   60-75 growth of W
        commences                   fusion labio-scorotal
75      degenation of W       78    M-degeneration completes
                                    germ cells enter to meiosis
105     prepuce formation     105   prepuce formation
                                    ovary development commences
120                                 uterus completes
160-260 formation of vagina         - growth of external
        completes                     genitalia
Universal sex determination mechanism (性決定機構)
consider XY type only
1) Myopus
1966 Frank: mouse

♀ → ♂, ♀
♀ → ♀ only --- Why!

Sex chromosome

26 ♂ → XY (somatic reproduction)
181♂ → XY

XX XX YY death
_↘ ↗
_↙ ↘
XY XY --- XX propagating in this manner

        Normal      ♂XY    ♀XX     ♀XY
                      66     224      203
        Abnormal    ♂XXY   ♀XO    ♀XYY   ♀XY/XYY
                       3       4        1          1

♀XX × XXY♂, XXY♂, XX/XXY/XXXY♂: all testes have no sperm (no ability of reproduction)

        ♂XY ×     XO♀   XO♀   XYY♀   XY/XYY♀
        F1 ♂:♀ =   1/3    0/6     0/6       0/10

⇒ present gene that cancels out the effect of Y and develops ♀ of which sex chromosome is XY?

Cattanach translocation

P:__CCXTY (♂) × CCXX (♀) →

Male parent: both somatic and germ cells are normal
Germ cell (XY) - normal testis

____albino____not agouti___ C-var_______agouti_____albino
_____________C-variegated_not CCXXTY_not CCXTY_not CCXX
F1_____2n = 40____ 39/40_____2n = 40
_______no Y_______XTO, XTX
_______XTX - master stream
CCXX or CCXO: close to non-disjunction (CCXO)
F1♂ testis: no germ cells and normal accessory genital glands

⇔ XTO = ♂, XTX = ♂

Single active theory proposed by Russel:
only one chromosome has the activity
⇒ each cell has differently-active X

X-chromosome is also mosaically active
Lyonization (= X-inactivation): one fellow of the pair is active → Barr body

mammal: number of Y choromosomes more or equal to 1 tends to becomes male (male or Y has the priority of sex determinaiton)

Q. What factors determine the sex of individuals if the sex chromosomes do not determine the sex?

CCXY(♂) × XTaXTa(♀)

Ta (tabby): hair with a grey or tawny coat mottled with black like a horse, not like a rabbit

→ XTaY(♂)__XTaX(♂)__XTaXTa(Ta-var♀)
__abnormal_tabby____ Ta-variegated
⇒ a half of males are tabby and the remainders are abnormal → the sex chromosomes do not determine the sex
XTaXTa used for the experiment showed no chromosomal defect → is this derived from ♂?

SXR: sex-reversal
sex ♂:♀ should be 1:1 in nature
Phylogenetically SXR does not exist in ♀

XTaY(♂) AASXr × XX(♀) AA
_______AA:AASXr = 1:1__Sxr: the gene that changes from ♀ to ♂
_____________♀ → ♂
if it is XTaY(♂), all of the ♀ F1 become ♂, it is contradict with the result of experiment
if the gene is on sex chromosome and is not on autosome
_________Xsxr × XX
__♂ ← XXSxr______XSxrY - different from the experimental results
_______ AASxr × AA
AA:AASxr = 1:1 ⇒ Sxr is on the autosome
P____ (♀)XTaX × (♂)XTaY or XY
_____________| 17 pairs
F1____ XTaX(♀)__XX(♀)__XTaY__XY
_________1:______ 1:_____1:____1
therefore, it is normal
XXXY → ♂: Y-chromosome greatly affects the expression of male in general
XO → ♀: XO usually develops female ⇒

Case. what occurs when AASxr is inserted into XO under the assumption that Sxr is on normal chromosomes

AASxrXO → ♀
___AAXTaO(♀) × XYAASxr(♂)
__________________________└ can not form the normal sperm

⇒ Asxr becomes ♂ even when XO. AASxr becomes ♂ even when XX

sex is determined not only by sex chromosome but also by A. SXR is discovered from various species

Self or non-self recognition (自己と非自己の認識)

Chromosomal genetics (染色体遺伝学)

1903, 04, 09 Rosenberg D: irregularity of chromosome distribution during meiosis on hybrids

Drosera obovata (2n = 30): observed the meiosis →
irregularity of the bivalent chromosome formation of the hybrid

1919 Winge Ø or Ö: Polyploidic new species derived from hybridization

P: 2n = 14 × 2n = 14 →
F1: 2n = 14 [self-fertilization n = 14(♂), n = 14(♀)] →
F2: 2n = 28
confrimed by chrysanthemum (Sakamoto), wheat (Kihara), etc.

Law: when F1 is sterile, polyploid F2 is born by occurring in regression phenomena

P: AA × BB n = 7 = A, n = 7 = B (different strains)

→ F1: AB [AB(♂) × AB(♀)] → F2: AABB

1919-24 Kihara (木原 均): chromosome complement and genome

genome: a minimum set of genes that are required for life

→ genome analysis (Triticumx = 7 is the standard)

chromosome hypothesis on the mechanisms of heredity

to demonstrate this, a few complemental discoveries are obtained

Sex-controlled inheritance and mechanisms on sex determinants

→ discovered sex chromosome

1902 Maclung: Conocephalus melaenus

heteromorphic pair of chromosomes (不等対染色体) = affecting sex determination

Def. of sex chromosomes by Wilson: X-and Y-chromosomes
1905 Wilson: stink bug, X-chromosome ♂ = 1X, ♀ = 2X
The discovery of sex chromosomes were later in plants than in animals
1923 Kihara & Ono

Rumex acetosa ♂ 2n = 12 + XX, ♀ 2n = 12 + XY1Y2
– also confirmed on diplont
specific pairing type - e.g., Humulus lupulus and H. scandens
sex chromosome

Ex. spinach - dioecism: 2n = 12, x = 6 → no sex chromosomes

aploid (anorthoploid): formed n = 13 (12 + 1) → x = 6 → forming 6 series of aploids
observed aneuploid chromosomes →
dectecting that the dysplasia of sexual organ is induced by the specific chromosome becoming aneuploid the location(s) that determine sex is surveyed
sex chromosome
___X-ray cut →

sex abnormality induced by cutting chromosome with different lengths
determining the location that is related to sex abnormlity by the length

→ applying to gene maps on chromosoems

1924 Allen CF: Sphaerocarpos acetosa (moss)

haplont (半数体) during the gametophyte generation
n = 7 + X (large), ♀ n = 7 + Y (small)

Structural changes in chromosomes (染色体の構造変化)
Unsplit chromosomes

Chromosome break
Symmetrical intrachanges

inter-arm inversion
intra-arm inversion

asymmetrical intrachanges

inter-arm deletion
intra-arm deletion

symmetrical interchange
asymmetrical interchange


metaphase configuration
anaphase configuration

Split chromosomes

chromatid break
isochromatid break
symmetrical intrachange
asymmetrical intrachange
symmetrical interchange
asymmetrical interchange


anaphase configuraiton

Genome (ゲノム)

A complete set of DNA in the individual, including all of its genes
Each genome contains all of the information needed to build and maintain that individual

= coding DNA + noncoding DNA + mitochondrial DNA + chloroplast DNA

Polyploid (倍数体)

1916 Winkler H 1916
Neopolyploid (新倍数体)
any newly-formed polyploid →
neopolyploidy: the condition of being a neopolyploid
Euploidy (真数性)
The condition of a cell, tissue, or organism that has one or more multiples of a chromosome set, diploid (2n), triploid (3n), tetraloid (4n), pentaloid (5n), hexaloid (6n)… Euploids with more than two sets of chromosomes are POLYPLOIDS.

Minimum: 2n = 4 (we have known)

Heteroploidy (異型倍数性) Ex. Chromosome numbers in Artemisia
Haploidy (倍数性):

diploid (2倍体): having twice the basic (haploid) number of chromosomes
triploid (3倍体), tetraploid (4倍体), pentaploid (5倍体), hexaploid (6倍体), octoploid (8倍体)

Aneuploidy (inclucing monosomics and trisomics, s.l.) (異数性)
A condition in which more or less than a complete set of chromosomes is found in each cell of individual. Typically, aneuploids have one extra or one missing chromosome → Trisomic, Tetrasomic
Autopolyploid (autoploidy, 同質倍数体)
Ex. AA × BB → AB → AABB (autoploidy, 倍化)

Autotetraploid (同質4倍体)

             Normal meiosis  Abnormal meiosis
    Parents  AA × AA        AA × AA      AA × AA
    Gametes  A--+-A          AA--+-A       AA--+-AA
    Progeny  AA              AAA           AAAA
             Normal diploid  Autotriploid  Autotetraploid
             (fertile)       (sterile)     (fertile)
Allopolyploid (alloploidy, 異質倍数体)
(aka, allopolyploidy, amphidiploidy, amaphiploidy)

Allotetraploid (異質4倍体)

              AA   BB                        Delayed
    Step 1    AB   + (unreduced gamete)      AA       BB
           AA ABB    (triploidy)             AAAA     BBBB
                     = restoration nuculei
           A  ABB                            AA       BB
    Step 2 +  AABB   cf. Segmented           AABB     +

Segmental vs genomic alloploidy

Paring: auto – frequent, allo – rare

β-chromosomes (= accessory chromosome or supernumery chromosome)

not belonging to neither autosome (A) or sex chromosome (X, Y)
β = chromosome of heterochromatin?

Polyploids in plants

Plant species: 30-35% (percentages of polyploidy)
Perennials: polyploidy
Trees: not much polyploidy
Annuals: diploidy
Pteridophytes: > 70%

Pattern of doubling moment

somatic – often
gametic - rare (need 2 steps)

Haploid (半数体)
with a single basic set of chromosomes characterizing the species

→ formation of haploid by pollen culture - effective to breed improvement and gene development

Terms: adelophycean (adj.): referring to the inconspicuous phase in the life history of an alga, alternating with the macroscopic (delophycean) phase

Superiority of polyploid (倍数体の優位性)
Caryotype analysis of Trillium chromosomes - non-homologous

→ autosome X = 5 (A + B + C + D + E)

Haplotype (ハプロタイプ)

Haplotype network
Fig. 1. Distribution of ndhF-rpl32 haplotypes and haplotype network. The sizes of the circles and pie charts are proportional to the number of individuals sampled (N) for both distribution maps and haplotype network. In the haplotype network, numbered and colored circles represent shared haplotypes and squares denote unique haplotypes. Thicker lined circles and squares (cp-1 to cp-19) are haplotypes found in Taiwan. The distributions of haplotypes in Taiwan (and its offshore islands) and the Hawaii islands are shown in enlarged maps. The map of Taiwan is demarcated by the seven major climatic regions of the island (36), with areas above 2,000 m shown in gray. (Chang et al. 2015)

[ evolution ]

Population genetics (集団遺伝学)

Three researchers contributed population genetics greatly

Fisher, Halane and Wright

Fisher, Ronald Aylmer (1890-1962)
mathematics, statistics, biology, genetics and academic

used mathematics to combine Mendelian genetics and Darwinian natural selection

1915 the evolution of sexual preference

sexual selection and mate choice

1930 the genetical theory of natural selection

a core work of the neo-Darwinian modern evolutionary synthesis

1930 (Fisher's) Foundamental theorem of natural selection (in the book)

The rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time

increase in fitness = genetic variance

Haldane, John Burdon Sanderson (1892-1964)
physiology, genetics, evolutionary biology and mathematics
1924 in Russian (1936 in English) Oparin, Alexander

the primordial soup theory (= Oparin–Haldane hypothesis)

1924-1934: a series of "A mathematical theory of natural and artificial selection"

quantitative analysis, e.g., selection coefficient (淘汰係数), k
industrial melanism, k = 0.33-0.50

1932 "the causes of evolution"
Wright, Sewall (1889-1988)
geneticist and evolutionary biology

evolutionary theory and path analysis (path coefficient) -
significance of random genetic drift
1931 "Evolution in Mendelian populations"

shifting balance theory (平衡推移理論) (Wright 1932)

1. Genetic drift (in a sub-divided population)
2. Natural selection (within the population)
3. New adaptations by the competition among the sub-populations

1950s' controversy on the significance of genetic drift

discussed by Wright vs Fisher

Muller, Hermann Joseph (1890-1967)
1950 "Our load of mutations"

emphasized the significance of mutation for various genetic diseases