chapter 3 genetic analysis of l inkage and chromosome mapping

YANGTZE NORMAL UNIVERSITY

Chapter 3 Genetic analysis of linkage and chromosome mapping

Key points: 1. Sex-chromosome and sex determination

2. Linkage versus independent assortment 2. Linkage versus independent assortment 3.3. Incomplete linkage Incomplete linkage4.4. Mapping in Drosophila and maize Mapping in Drosophila and maize 5.5. The accuracy of mapping experiments The accuracy of mapping experiments 6.6.The genetic map of drosophilaThe genetic map of drosophila7.7.Somatic cell hybridization and human gene mappingSomatic cell hybridization and human gene mapping


• 1. The discovery of sex-chromosomes• 2. types of sex determination. Basically, four type of chromosomal sex-deterBasically, four type of chromosomal sex-deter

mining mechanisms exist; the XY, ZW, X0, and compound chromosomal mechanismining mechanisms exist; the XY, ZW, X0, and compound chromosomal mechanism:m:

• (1) The XY system: male(XY), female(XX). Including humans, mammals, some amphibians and fish, as well as many insects and dioecious plants, etc.

• (2) The ZW system: male(ZZ), female(ZW). Including birds, Lepidoptera, some amphibians, reptiles, and Silkworm

• (3) XO system: male(XO), female(XX). Including Orthoptera insects such as grasshoppers and cockroach

• Some animals such as Bniella, their sexes are determined by environment factors

Section 1 Sex-chromosome and sex determination


第一节性染色体与性别决定

• 一、性染色体的发现• 二、性别决定的几种类型 • 1 、 XY 型：雄性： XY 、雌性： XX 。人类、哺乳类、某些两栖类和某些鱼类，

以及很多昆虫和雌雄异株的植物等 )• 2 、 ZW 型：雄性： ZZ 、雌性： ZW 。鸟类、鳞翅目昆虫、某些两栖类、

爬行类动物及家蚕 • 3 、 XO 型：雌体的性染色体为 XX ，雄性只有一条单 X 染色体，为 XO ，如

一些蚱蜢和蟑螂 • 有些动物的性别决定依赖于环境因素，如后嗌


Section 2 Sex-linked inheritance第二节性连锁遗传 --- 果蝇伴性遗传研究


Sex-linked inheritance1. When homozygous dominant genes are passed with homogametic-se

x individuals, dominant characters are expressed in both male and female individuals in the F1 generation. In the F2 generation, the separation proportion of dominance versus recessiveness is 3:1 and that of sex 1:1. The meternal grandfather passes the character to his grandson

2. When homogametic-sex individuals pass homozygous recessive genes to their offspring, the criss-cross inheritance exihited in the F1 generation; that is, the mother passes traits to her son and the father to his daughter. In the F2 generation, the separation ratio of traits and sexes is 1:1

3. The transmission and expression of genes located on sexual chromosomes are dependent on sexes. Results of reciprocal crosses show differences in phenotypic ratios in both F1 and F2 generations


性连锁遗传 --- 伴性遗传的特点

• 1 、当同配性别传递纯合的显性基因时， F1 雌雄个体都为显性性状； F1 性状的分离呈 3 显性： 1 隐性；性别的分离呈 1 ： 1 ，其中隐性个体的性别与祖代隐性体一样，即外祖父的性状传递给外孙

• 2 、当同配性别传递纯合的隐性基因时， F1 表现交叉遗传，即母亲把性状传给儿子，父亲的性状传给女儿， F2

性状与性别的比均为 1 ： 1• 3 、决定性状的基因在性染色体上；性状的遗传与性别有

关；正交与反交 F1 的结果不同；表现特殊的交叉遗传规律。


伴 X 连锁遗传：抗 VD 佝偻病，色盲，血友病伴 Y 连锁遗传：毛耳缘

Figure of sex-linked inheritance in humans性连锁遗传 --- 人类的伴性遗传图示

X-linked inheritance disorders: Anti-VD rickets, Color blindness, hemophiliaWith Y-linked inheritance:Hairy-eared edge


The pedigree of human color blindness


Figure of X-linkage in Drosophila

果蝇性连锁遗传图


Example of sex-limited inheritance chicken鸡的伴性遗传


Section 3 The direct evidence of chromosome theory of heredity 第三节遗传的染色体学说的直接证明


Section 4 Y chromosome and sex determination in Drosophila

The critical factor in determining sex is the ratio of X chroThe critical factor in determining sex is the ratio of X chromosomes to the number of haploid sets of autosomes (A) pmosomes to the number of haploid sets of autosomes (A) presentresent :1. when X \ A = 0.5, the male2. when X \ A = 1, the female3. when the ratio of X \ A ranges 0.5 from 1, the intersexual


Drosophila


第四节果蝇中的 Y 染色体及其性别决定• 果蝇的性别决定并不取决于 X 和 Y 染色

体，而取决于性染色体和常染色体之间的平衡关系，也就是 X\A 的比率关系：

• 一、当 X\A=0.5 时，为雄性 • 二、当 X\A 的比率 =1 时，为雌性 • 三、当 X\A 的比率介于 0.5 与 1 之间时，

表现为间性


1. Barr body refers to an inactivated X chromosome, which is also called sex chromatin body

2. Dosage compensation effect ： If one of the two X chromosomes is inactive in the cells of females, the dosage of genetic information that can be expressed in males and females is equivalent

3. Lyon hypothesis

4. Molecular mechanism of random X inactivation

Section 5 Dosage compensation effect


第五节剂量补偿效应• 一、 Barr 小体：一种与性别和 X 染色体

数目有关的异染色质化的小体，它存在于雌性细胞间期核

• 二、剂量补偿效应：在 XY 性别决定机制的生物中，使性连锁基因在两种性别中有相等或近乎相等的有效剂量的遗传效应

• 三、 Lyon 假说 • 四、 X 染色体随机失活的分子机制


Barr Bodies in various human karyotypes


The mechanism of inactivation


Section 6 Crossing over and recombination of linkage gene Linkage versus independent assortment


The relationships between the three genetic laws

The law of separation is the basis of the independent assortment law and the law of linkage and crossing over, which lead to a wide variety of genetic variations in the organisms

For the independent assortment law and the law of linkage and crossing over, there existed the difference in the transmission of genetic recombination. The genetic recombinations in the former result from the different chromosomes and that in the latter from the homologue

Their genetic variations are limited by the length and number of chromosomes, respectively


三大定律的关系• 分离律是自由组合律和连锁定律的基础，而

后者是生物体遗传的性状发生变异的主流；自由组合与连锁交换二者的差别在于前者是由不同源的染色体所传递，重组类型是由染色体间重组造成，而后者则是由同一对同源染色体所传递的，是染色体内重组所产生的，自由组合受生物染色体对数的限制，而连锁交换则受到其染色体长度的限制


Linkage inheritanceLinkage inheritance: is the tendency of genes located in the same chromosome to be associated in inheritance. Linked genes have their loci along the same chromosome, do not assort independently, but can be separated by crossing over.Complete linkage produces only parental or non-crossover gametes.Incomplete linkage produces this exchanged gamete, called recombinant or crossover gametes


Cytological evidence of cross-over


Genetic mechanism of linkage and cross-over


Crossovers and recombinationsSingle crosso

vers单交换

Multiple crossovers多交换


Linkage and exchange基因间的连锁与交换

完全连锁


Linkage and exchange基因间的连锁与交换

不完全连锁


Cross experiment of two pairs of contrasting traits of pea香豌豆的杂交试验

Flower color: purple (Flower color: purple (P)P) dominant versus red (p) recessive dominant versus red (p) recessive Pollen grain shape: long (LPollen grain shape: long (L)) dominant versus round (l) recessive dominant versus round (l) recessive


Purple and long (PPLL)×red and round (ppll)

ResultsResults ：：Phenotypes of FPhenotypes of F11 are dominant are dominant ，， four phenotypes of Ffour phenotypes of F22;;

The ratio of four phenotype of FThe ratio of four phenotype of F22is different of classic ratio of 9:3:3:1is different of classic ratio of 9:3:3:1 ，， two parental two parental

phenotypes are higher than theory numberphenotypes are higher than theory number ，， and two combined phenotypes are less tand two combined phenotypes are less than theory numberhan theory number


Purple and round (PPll)×red and long (ppLL)


Purple and round (PPll)×red and long (ppLL)

ResultsResults ：：Phenotypes of FPhenotypes of F11 are dominant are dominant ，， four phenotypes of Ffour phenotypes of F22;;

The ratio of four phenotype of FThe ratio of four phenotype of F22is different of classic ratio of 9:3:3:1is different of classic ratio of 9:3:3:1 ，， two parental two parental

phenotypes are higher than theory numberphenotypes are higher than theory number ，， and two combined phenotypes are less tand two combined phenotypes are less than theory numberhan theory number


Coupling phase and repulsion phase

Coupling phase: Allelic arrangement in which mutant are on the same chromosoCoupling phase: Allelic arrangement in which mutant are on the same chromosome and wild-type alleles are on the homologueme and wild-type alleles are on the homologueRepulsion phase: allelic arrangement in which each homologous chromosome has Repulsion phase: allelic arrangement in which each homologous chromosome has mutant and wild-type allelesmutant and wild-type alleles coupling phasecoupling phase versus versus repulsion phaserepulsion phase

相引相：两个显性性状（基因）或两个隐性性状（基因）连在一起遗传相斥相：一个显性性状（基因）和一个隐性性状（基因）连在一起遗传


The separation law is fit to the allelic gene in the two experiment

性状 F2表现型 F2个体数 F2分离比例

紫花(显) 4831+390=5221

红花(隐) 1338+393=1731

长花粉粒( )显 4831+393=5224

圆花粉粒( )隐 1338+390=1728

紫花(显) 226+95=321

红花(隐) 97+1=98

长花粉粒( )显 226+97=323

圆花粉粒( )隐 95+1=96

花色

花粉粒形状

相引相

相斥相

花色

花粉粒形状

3:1

3:1

3:1

3:1


Crossing-over Value （交换值）CCross-over valueross-over value ，， called recombined ratiocalled recombined ratio ，， refer to the percent orefer to the percent of recombined gametes. The formula isf recombined gametes. The formula is ：：

％总配子数重组型配子数交换值 100(%)

亲本型配子 + 重组型配子

What are method used to test the number of recombined gametesWhat are method used to test the number of recombined gametes ？？

Test cross and self-crossingTest cross and self-crossing


Linkage and cross-over between C-Sh


Cross over value between P-L(1)

Given the ratio of four gamete produced by FGiven the ratio of four gamete produced by F11 PL, Pl*, pL*, and PL, Pl*, pL*, and

pl is a, b, c, and d respectively; Thenpl is a, b, c, and d respectively; Then ：： a+b+c+d=1a+b+c+d=1 a=d, b=ca=d, b=c


Cross over value between P-L(2)Four phenotypes of nine genotype of FFour phenotypes of nine genotype of F22 are are ：：

P_L_ (PPLL, PPLl, PpLL, PpLl)P_L_ (PPLL, PPLl, PpLL, PpLl) ：： aa22+2ab+2ac+2bc+2ad+2ab+2ac+2bc+2adP_ll (PPll, Ppll) P_ll (PPll, Ppll) ：： bb22+2bd+2bdppL_ (ppLL, ppLl) ppL_ (ppLL, ppLl) ：： cc22+2cd+2cdppll ppll ：： dd22

%1212.006.006.0

06.02

)(1

44.0

44.0192.0

%2.19%1006952

13382

cbLP

dacb

da

dpl

d

间交换值

：两种重组型配子的比例

：两种亲本型配子的比例配子的比例：

The recessive homogenous individuals (ppll) number of FThe recessive homogenous individuals (ppll) number of F22 may gains from observ may gains from observ

ation (1338)ation (1338) ，， its ratio is (1338/6952)its ratio is (1338/6952)


The relationship between cross-over value, distance between genes, linkage strength, and genetic distance


Gene location/localization/mapping基因定位与染色体作图

Gene location/localizationGene location/localization ：： refer to determine location and sequenrefer to determine location and sequence of genes on chromosome.ce of genes on chromosome.Related distance of linked genes may be determined on the basis of cRelated distance of linked genes may be determined on the basis of cross-over value between two gene, and the sequence may not.ross-over value between two gene, and the sequence may not.For exampleFor example ：：

Maize color C/colorless c, and round Sh/wrinkled sh are on chroMaize color C/colorless c, and round Sh/wrinkled sh are on chromosome 9mosome 9 ；； and the cross-over value between C-Sh is 3.6%.and the cross-over value between C-Sh is 3.6%.

Hence, there are three or more than three pairs of gene involved in gHence, there are three or more than three pairs of gene involved in gene locatingene locating

Linkage groups is a group of gene that have their loci on the same chromosome. ILinkage groups is a group of gene that have their loci on the same chromosome. In a species, there are as many linkage groups as there are homologous pairs of chrn a species, there are as many linkage groups as there are homologous pairs of chromosome or as the haploid number of chromosomesomosome or as the haploid number of chromosomes


Mapping （染色体图）

Sturtevan and mapping


Sequence of two pair of genes

The cross-over value between C-Sh is 3.6 unitsThe cross-over value between C-Sh is 3.6 units ；；Then, there are two possible sequences of themThen, there are two possible sequences of them


Two-point test (1)两点测验

Three crosses between three pairs of geneThree crosses between three pairs of gene

For example: there are three pairs of linked genes on chromosome 9.For example: there are three pairs of linked genes on chromosome 9.

Grain colorGrain color ：： color (C) dominant versus colorless c recessivecolor (C) dominant versus colorless c recessive ；；

shapeshape ：： round Sh dominant versus wrinkled sh recessiveround Sh dominant versus wrinkled sh recessive ；；

StarchStarch ：： non-sticky Wx dominant versus sticky wx recessive.non-sticky Wx dominant versus sticky wx recessive.

(1) (CCShSh×ccshsh) F(1) (CCShSh×ccshsh) F11 ×× ccshshccshsh

(2) (wxwxShSh×WxWxshsh) F(2) (wxwxShSh×WxWxshsh) F11 ×× wxwxshshwxwxshsh

(3) (WxWxCC×wxwxcc) F(3) (WxWxCC×wxwxcc) F11 × × wxwxcc wxwxcc


Results of two points test


Two points test (2)

Estimate three cross-over valuesEstimate three cross-over values


Two points test (3)

Determine distance and related location of between genes.Determine distance and related location of between genes.C-Sh: 3.6C-Sh: 3.6 Wx-Sh: 20Wx-Sh: 20 Wx-C: 22Wx-C: 22


Three points test (1/7-2/7)

1. Cross1. Cross ：：P:P: wrinkled, non-sticky, color × round, sticky, colorless wrinkled, non-sticky, color × round, sticky, colorless

shsh ++ ++ ++ wxwx ccshsh ++ ++ ++ wxwx cc ↓ ↓FF11and test cross: round, non-sticky, color × wrinkled, sticky, colorlessand test cross: round, non-sticky, color × wrinkled, sticky, colorless

+sh +wx +c shsh wxwx cc +sh +wx +c shsh wxwx cc ↓ ↓2. Observe traits and class2. Observe traits and class

How many phenotypes of F2 , if incomplete linkage ？


Three points test(3/7-4/7)

3. Group and count3. Group and count ；；4. Determine parental and two-cross over gamete4. Determine parental and two-cross over gamete ；；

测交后代的表现型 F1配子种类粒数交换类别饱满、糯性、无色 + wx c 2708凹陷、非糯、有色 sh + + 2538饱满、非糯、无色 + + c 626凹陷、糯性、有色 sh wx + 601凹陷、非糯、无色 sh + c 113饱满、糯性、有色 + wx + 116饱满、非糯、有色 + + + 4凹陷、糯性、无色 sh wx c 2

总数 6708

亲本型

单交换

单交换

双交换


Three points test(5/7)

5. Determine the related location5. Determine the related location

Compare parental gametes with two-cross over gametesCompare parental gametes with two-cross over gametes ：：

The different allele located between two same genesThe different allele located between two same genes

For exampleFor example ：： to compare + wx c and sh wx c show only sh is distinto compare + wx c and sh wx c show only sh is distin

ctct ，， hence, sh locate between wx and chence, sh locate between wx and c ；；

LikewiseLikewise ，， comparsion sh + + and + + + show that only sh locus is dcomparsion sh + + and + + + show that only sh locus is d

istinctistinct ，， this also suggest sh locate between wx and cthis also suggest sh locate between wx and c


Determine


Three points test(6/7)

6. Estimate cross over value6. Estimate cross over valueBecause two-cross over occur both two regionBecause two-cross over occur both two region ，， we should add two-cross ovewe should add two-cross over when we estimate the cross over value between genesr when we estimate the cross over value between genes


Three points test (7/7)

7. Mapping 7. Mapping Sh locate between wx and cSh locate between wx and c ；；

wx-sh: 18.4wx-sh: 18.4 sh-c: 3.5sh-c: 3.5 wx-c:21.9wx-c:21.9


Three points mapping in Drosophiloa


Determining the gene sequence


Interference and the coefficient of coincidenceInterference: is the phenomenon that a crossovers event in one region of Interference: is the phenomenon that a crossovers event in one region of the chromosome inhibits a second event in nearby regionsthe chromosome inhibits a second event in nearby regionsCoefficient of coincidence (C): is a ratio of the observed number of doubCoefficient of coincidence (C): is a ratio of the observed number of double-crossovers divided by the expected number of such crossoverle-crossovers divided by the expected number of such crossover

I=1-CI=1-CIf interference is complete and not double crossovers occur, then I=1.0;If interference is complete and not double crossovers occur, then I=1.0;If fewer DCOs than expected occur, I is a positive number and positive If fewer DCOs than expected occur, I is a positive number and positive interference has occurred;interference has occurred;If more DCOs than expected occur, I is a negative number and negative If more DCOs than expected occur, I is a negative number and negative interference has occurred;interference has occurred;Positive interference is most often observed in eukaryotic systemsPositive interference is most often observed in eukaryotic systems


遗传干涉和并发

• 一、干涉（ I ）：每发生一次单交换影响它邻近发生另一次单交换的这种现象

• 二、并发系数（ C ）：观察到的双交换率与预期的双交换率的比值

• 三、 I=1-C


The accuracy of mappingAccording to Poisson distribution of the mapping function: Rf = 1 / 2 (1-e-2x)Rf: Recombination frequencyM = 2X: The genetic distance between genes


大图距的准确计算 -- 作图函数的推导与应用

• 据泊松分布的作图函数： Rf=1/2 （ 1-e-2x ）

• Rf ：基因间的重组值

• M=2X ：基因间的遗传图距


Section 7 Mapping of the human genome on chromosome

Methods of the human gene mapping1. The pedigree method2. Somatic cell hybridization localization method(1) Clone panel(2) Chromosomal aberration3. Gene localization method by DNA molecular technologies(1) Gene localization by clone technologies(2) In situ hybridization


第七节人类基因组的染色体作图• 一人类基因定位方法 • （一）家系分析法： • （二）体细胞杂交定位法： • 1 、克隆分布板法 • 2 、利用染色体异常将基因定位在染色体 • （三） DNA 介导的基因定位法：• 1 、克隆基因定位法 • 2 、原位杂交法


Grandfather method外祖父分析法


Mapping the human genome

Genetic marks: A landmark to identify a gene or DNA sequence such as sites of restriction endonucleases, specific DNA sequences, RFLP, STS, and ESTRestriction fragment length polymorphism (RFLP): a useful genetic marker.Variable number of tandem repeats (VNTR): A different number of 33bp tandem repetitive DNA sequences.DNA fingerprinting: A series of bands produced by restriction endonucleases to cut DNA in Southern Blotting, which are the representative of different DNA fragments located on chromosomes


人类基因组的染色体作图

• 遗传界标：界定一个基因或 DNA 序列的可辩认的标识。如限制性内切酶酶切位点、特定的 DNA 序列、 RFLP 、 STS 、 EST

• 限制性片段长度多态性（ RFLP ）：一种有用的遗传标记

• 数目可变的串联重复序列（ VNTR ）：包含有不同数目的 33bp 的串联重复 DNA 序列

• DNA 指纹：限制性酶消化产物在 southern 杂交中的一系列带纹，不同的带纹代表在染色体不同位置上的不同长度的 DNA 序列。


DNA fingerprinting and molecular markers DNA 指纹带与分子标记


Genetic Markers--Microarray technology遗传标记 -- 微阵列技术


Restriction endonucleases限制性内切酶

chapter 3 genetic analysis of l inkage and chromosome mapping

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