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Chromosome Structure and Implications for Inheritance: Segregation, Independent Assortment, and Linkage

This article explores the structure and function of chromosomes in relation to inheritance. It discusses topics such as chromosome numbering, landmarks, heterochromatin and euchromatin, mitosis and meiosis, and the cell cycle. It also explores telomere shortening, development of gametophytes, and key differences between mitosis and meiosis.

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Chromosome Structure and Implications for Inheritance: Segregation, Independent Assortment, and Linkage

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  1. Chromosome structure, function and implications for inheritance: segregation, independent assortment and linkage ATGGGCACTGCCACT R r Source: plant-genetics.kais.kyoto-u.ac.jp

  2. A chromosome is a single DNA molecule complexed with histone proteins • DNA is highly compacted: DNA + histone proteins = chromatin • Nucleosome structure • Source: abcam.com

  3. Chromosome numbering/naming • Numbering starts with the “largest” chromosome Source: ucl.ac.uk

  4. Chromosome landmarks • Centromere(s) Source: nature.com

  5. Chromosome landmarks • Telomere(s) Source: conciergemedicinela.com Source: jyi.org

  6. Heterochromatin and euchromatin • The degree of compactness of DNA - implications for degree of gene expression Duggan, N. M. & Tang, Z. I. (2010) The Formation of Heterochromatin.  Nature Education 3(9):5

  7. Heterochromatin and euchromatin • Heterochromatin: highly compact, inaccessible for transcription, and less likely to contain highly expressed genes • Constitutive: • ~ Always compact • Facultative: • varying degrees of compactness depending on individual, developmental stage • Implications for epigenetics • Euchromatin: relaxed, accessible, and more likely to contain expressed genes

  8. Mitosis and Meiosis • Mitosis: 2n 2n • Meiosis 2n n • Mitosis: 2 identical daughter cells • Meiosis: 4 daughter cells, which may be genetically different • Mitosis: zygote until death • Meiosis: specialized cells V v V V V v V v v v V v Mitosis Meiosis

  9. The cell cycle • G1: RNA and protein synthesis, but no DNA replication • S: DNA synthesis. The total DNA content goes from 2n to 4n • G2: After DNA synthesis and before mitosis. At this point a diploid cell contains two complete diploid sets of chromosomes • M: Mitosis 

  10. Mitosis

  11. Mitosis: Example: Maize; 2n=2x=20Prophase: Chromatin contracts. Each chromosome consists of two sister chromatids. One is "original" chromosome, other is copy made during S phase. Chromatids held together at centromere. At late Prophase, attachment of spindle fibers to centromeric region and dissolution of nuclear membrane. Continued contraction of paired chromatids. 20 sets of 2 sister chromatids = 40 chromatids. • Metaphase:Orientation of paired chromatids on Metaphase "plate". 20 sets of sister chromatids aligned on plate = 40 chromatids.

  12. Mitosis: Example: Maize; 2n=2x=20Anaphase: Sister chromatids migrate to opposite poles. Separation of sister chromatids accomplishes the equal distribution of chromosomal material. 20chromatids migrate to each pole.  • Telophase: Single chromatids, or at this point, chromosomes, return to the relaxed Interphase state. Cytokinesis divides original cell into two daughter cells. Two cells, each with 10 pairs of chromosomes = 20 chromosomes per cell.  Maize :  2n=2x=20

  13. Telomere shortening during mitosis • Telomeres: Repetitive DNA sequences at ends of chromosomes. Each time the cell divides, the telomere shortens.  Eventually, the chromosomes become "so frayed that the cell senesces". In some cells- eggs, sperm, and cancer cells - an enzyme known as telomerase allows for "reconstruction" of the telomere, thus prolonging cell life.   

  14. Development of the male gametophyte • Pollen mother cell (PMC)  • PMC undergoes meiosis • Meiosis gives a tetrad of microspores Note, this is different than ♀

  15. Development of the female gametophyte • Megaspore mother cell (MMC)  • MMC undergoes meiosis • Of 4 megaspores produced 1 survives (most species) • Three post-meiotic mitoses 1 2 3

  16. Meiosis 1 Prophase (5 stages) Leptonema: Longitudinal duality of chromosomes not discernible. Zygonema: Pairing of homologous chromosomes. Formation of synaptonemal complex and zygotene DNA synthesis. Pachynema: Pairing persists: synaptonemal complex + crossovers. Bivalent = 2 homologous chromosomes = 2 sets of 2 chromatids. Crossing over occurs (chiasma; chiasmata). Diplonema: Synaptonemal complex dissolves; visualize longitudinal duality. Diakinesis: Continued bivalent contraction. 

  17. Meiosis 1 • Metaphase I: • Bivalents  appear on the Metaphase plate.The random alignment of non-homologous chromosomes is the basis of independent assortment. • Anaphase I: • The physical separation of homologous chromosomes is the basis of segregation. • Telophase I. • Each pole receives one-half of the original chromosome number of the meiocyte, i.e. one set of chromosomes in the case of diploidy.

  18. Meiosis 2 • Prophase II. Chromatin condensation • Metaphase II. Chromosomes align on Metaphase plate • Anaphase II. Sister chromatids go to opposite poles • Telophase II. Cytokinesis: Tetrad

  19. Key differences between mitosis and meiosis • Meiosis: Homologous chromosomes pair and separate at Anaphase I; sister chromatids separate at Anaphase II • Mitosis: No pairing of homologous chromosomes • Meiosis: Crossing over may generate new configurations at alleles at linked loci • Mitosis: A special case • Meiosis: 4 daughter cells, which may be genetically different • Mitosis: 2 identical daughter cells • Meiosis 2n to n • Mitosis is 2n to 2n 

  20. Key differences between mitosis and meiosis • Meiosis: occurs in specialized cells (megaspore mother cell (MMC); pollen mother cell (PMC) • Mitosis: occurs from the zygote stage onward through the life of the organism V v V V V v V v v v V v

  21. Linkage • The association of two or more phenotypic characters in inheritance because the genes controlling these characters are located in the same chromosome • The closer the gene locations, the stronger the association • Genes carried by the same chromosome are members of the same linkage group • The number of possible linkage groups (assuming sufficient marker loci and no major blocks of monomorphism) corresponds, therefore, to the “n” number of chromosomes in the organism in question

  22. Linkage Complete: Pairs of loci are so close together that crossing over rarely occurs and recombinant types are generally not recovered Partial: Pairs of loci are sufficiently far apart that some recombinant types are recovered

  23. Linkage • Crossing over refers to the physical exchange between homologous chromosomes • Recombination is the genetic result of crossing over and is detected by new combinations of alleles at two or more loci • Genetic variability • New combinations of alleles at linked loci • Intra-genic recombination

  24. Meiosis Prophase I Leptonema: Zygonema: Pairing of homologous chromosomes. Formation of synaptonemal complex and zygotene DNA synthesisPachynema: Pairing persists: synaptonemal complex + crossovers. Bivalent = 2 homologous chromosomes = 2 sets of 2 chromatids. Crossing over occurs (chiasma; chiasmata) Diplonema: Diakinesis:

  25. Linkage Terms describing the allelic condition at linked loci cisaka coupling trans aka repulsion A……..B a……..b A……..b a……..B

  26. Linkage • Keys points in non-sister chromatid exchange: • Crossing over does not involve loss or addition of chromatin • Only two chromatids are involved in any single crossover event • There may be multiple crossovers between non-sister chromatids • Any combination of crossover configurations can occur, and the outcome of such configurations can be radically different

  27. Linkage Types of Crossovers Single crossover 2-strand double crossover 3-strand double crossover 4-strand double crossover

  28. Linkage Factors affecting meiotic crossing over Sex chromosomes Position on chromosome

  29. Linkage OWB Dominant 2-row; normal starch; hulled grain; long awns VV WW NNLL Locus abbreviations and alleles Vrs1 = V: V, v GBSS = W: W,w Nud = N: N,n LKs2 = L: L,l OWB Recessive 6-row; waxy starch; naked grain; short awns vvwwnnlll W w V v N n L l W w V v N n L l

  30. Linkage Alleles at all loci: segregation V on a different chromosome than W, N, and L: therefore alleles at V show independent assortment with those at W, N, and L W, N, L on same chromosome: Therefore potential for linkage W “far enough” from N and L to show no linkage (independent assortment) N and L close enough to show linkage OWB Dominant 2-row; normal starch; hulled grain; long awns VV WW NNLL OWB Recessive 6-row; waxy starch; naked grain; short awns vvwwnnlll W w V v N n L l W w V v N n L l

  31. Independent assortment and recombination could lead to an entirely new combination of traits: 2-row; waxy starch; hulled grain; short awn OWB Dominant 2-row; normal starch; hulled grain; long awns VVWWNNLL x OWB Recessive 6-row; waxy starch; naked grain; short awns vvwwnnll W W w V V v N N n L L l W w w V v v N n n L l l F1

  32. Meiosis 1 & Crossing Over – Cell 1 v V v V V v V v v V v V V v After DNA replication Pairing and crossing over Pre-meiotic Heterozygous parent Anaphase I w W w W W w W w w W w W W w n n n n N N N N n n N N n N l l l l L L L L l L l L L l

  33. Meiosis 2 & Crossing Over – Cell 1 Anaphase II v w N L N V W L n V W l v w n l N V W L 2row, non-waxy, hulled, long awn Non-Recombinant v w N L 6row, waxy, hulled, long awn Recombinant 2row, non-waxy, naked, short awn Recombinant n V W l 6row, waxy, naked, short awn Non-Recombinant v w n l

  34. Meiosis 1 & Crossing Over – Cell 2 v V v V V v V v v V v V V v After DNA replication Pairing and crossing over Pre-meiotic Heterozygous parent Anaphase I w W w W W w W w w W w W W w n n n n N N N N n n N N n N l l l l L L L L l L l L L l

  35. Doubled Haploid Phenotypes 2row, non-waxy, hulled, long awn Non-Recombinant n W l v V w n l 6row, waxy, hulled, long awn n W l v V w n l Recombinant 2row, non-waxy, naked, short awn Recombinant v V N W L N L w v N W L V N L w 6row, waxy, naked, short awn Non-Recombinant N V W L 2row, waxy, naked, short awn Non-Recombinant N V W L v w N L 6row, non-waxy, naked, short awn Recombinant v w N L 2row, waxy, hulled, short awn n V W l Recombinant n V W l 6row, non-waxy, hulled, long awn v w n Non-Recombinant v w n l l

  36. Dihybrid Ratio for Doubled Haploids(2/4 loci) Note: The “recombinant “ types in this case (between the V and W loci) are not due to crossovers. They are due to random alignment of paired homologous chromosomes at Metaphase I

  37. Linkage Test – V and W 2[3] = 2.586; P=0.460; Null hypothesis of no linkage accepted Independent Assortment : Loci are on different chromosomes Random alignment of chromosomes at Metaphase 1

  38. Linkage Test – W and N 2[3] = 5.707; P=0.128; Null hypothesis of no linkage accepted Independent Assortment: Sufficient crossovers between loci far enough apart on same chromosome

  39. Linkage Test – W and L 2[3] = 2.195; P=0.533; Null hypothesis of no linkage accepted Independent Assortment: Sufficient crossovers between loci far enough apart on same chromosome

  40. Linkage - Test N and L 2[3] = 42.293; P=<0.001; Null hypothesis of no linkage rejected Not Independent Assortment = linkage Few crossovers between loci close together on same chromosome

  41. Recombination percentage Parentals (Non-recombinants) >> Recombinants = linkage Linkage is calculated as the total recombinant types/ total population size (9+3)/(37+3+9+33) = 12/82 = 0.146 = 14.6% “The association of two or more phenotypic characters in inheritance because the genes controlling these characters are located in the same chromosome” N L 14.6

  42. N L 14.6

  43. Recombination, double crossovers and map distances • % recombination values are biased due to double crossovers • Double crossovers can give parental combinations of alleles and therefore underestimate the % recombination at values of ~ 10% recombination and higher • At values of ~ 10% recombination and lower double crossovers occur less often than expected • % recombination values are not additive: the maximum of recombination is 50% • Therefore the centiMorgan (cM) – a computed value derived from the observed % recombination

  44. CentiMorgans (cM) The centiMorgan is a unit of distance without a physical basis: the ratio of cM to base pairs can vary enormously across the genome

  45. CentiMorgans (cM)

  46. Three Point Linkage Test rNL=0.14 rWN=0.39 L N W rWL=0.48 The recombination frequency over the interval W – L (rWL) is greater than either rWN or rNL therefore W and L are the two loci furthest apart and N is likely to lie between them. N is likely to be closer to L as rWN > rNL.

  47. Making Linkage Maps • Linkage analysis is now an "automated" procedure: data on thousands, tens of thousands of loci • Key issues in linkage map construction are locus order and distance • The likelihood odds (LOD) score is a test statistic that is used to test the hypothesis that there is no linkage • LOD of 3.00 is approximately equal to P ~ .001 • LOD > 3 then one concludes that two loci are indeed linked.

  48. Value of Genetic Linkage Mapswithin-species • Determine order of loci in the chromosome • Determine how likely it is that non-parental combinations of alleles at linked loci will be obtained • Determine if trait relationships are due to linkage or pleiotropy • Create complete linkage maps (average ~ 100 cM/chromosome) where # chromosomes (n level) = number of linkage groups • Build platforms for • Cloning genes • Anchoring whole genome sequences • Identifying genes controlling quantitative traits

  49. Value of linkage maps within-species Graphical Genotypes • Key points • Alleles at all loci coded as to parental origin • No heterozygotes in this data set; if there were, they would be coded AB • Crossovers are only detected in regions where that individual is polymorphic; crossovers in monomorphic regions not detectable • Double crossovers between loci closer than 10cM may be due to errors in allele calling – therefore may be replace by “-” indicting missing data

  50. Value of linkage maps Anchoring the genome sequence to the genetic map • 94% of scaffolds anchored to the diploid Fragariareference linkage map using 390 genetic markers • Pseudochromosomes ~ linkage groups

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