Molecular and Quantitative Animal Genetics E-Book

Hasan Khatib

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1165

Veröffentlichungsjahr: 2014

Beschreibung

Animal genetics is a foundational discipline in the fields of animal science, animal breeding, and veterinary sciences. While genetics underpins the healthy development and breeding of all living organisms, this is especially true in domestic animals, specifically with respect to breeding for key traits.  

Molecular and Quantitative Animal Genetics is a new textbook that takes an innovative approach, looking at both quantitative and molecular breeding approaches. The bookprovides a comprehensive introduction to genetic principles and their applications in animal breeding. This text provides a useful overview for those new to the field of animal genetics and breeding, covering a diverse array of topics ranging from population and quantitative genetics to epigenetics and biotechnology. Molecular and Quantitative Animal Genetics will be an important and invaluable educational resource for undergraduate and graduate students and animal agriculture professionals.

Divided into six sections pairing fundamental principles with useful applications, the book's comprehensive coverage will make it an ideal fit for students studying animal breeding and genetics at any level.

Leseprobe

Table of Contents

Title page

Copyright page

Contributors

Manuscript Reviewers

Preface

1: Decoding and Encoding the “DNA” of Teaching and Learning in College Classrooms

Introduction

Teaching and Learning: Definitions

Understanding Learning

Understanding Teaching

Implications for Classroom Design in the Twenty-First Century

Final Thoughts

References

Review Questions

Section 1: Quantitative and Population Genetics

2: Mating Systems: Inbreeding and Inbreeding Depression

Introduction

Inbreeding

Cause of Inbreeding Depression

Quantifying Inbreeding

Genomics and Inbreeding

Summary

Further Reading

References

Review Questions

3: Genomic Selection, Inbreeding, and Crossbreeding in Dairy Cattle

Introduction

Genomic Selection

Crossbreeding

Inbreeding and Genetic Defects

Summary

References

Review Questions

4: Basic Genetic Model for Quantitative Traits

Introduction

Quantitative Traits

Expected Value and Variance: The Normal Distribution

Basic Genetic Model for Quantitative Traits

Heritability and Selection

Predicting Rate of Genetic Change from Selection

Further Reading

References

5: Heritability and Repeatability

Introduction

Heritability

Estimation of Heritability and Variance Components

Prediction of Breeding Values and of Response to Selection

Repeatability

References

6: Applications of Statistics in Quantitative Traits

Population and Sample

Descriptive Statistics

Graphically Examining the Distribution of the Data

Normal Distribution

Exploring Relationships between Variables

Summary

Appendix 6.1

Further Reading

References

Review questions

Section 2: Applications of Genetics and Genomics to Livestock and Companion Animal Species

7: Genetic Improvement of Beef Cattle

Introduction

Single Trait Selection

National Cattle Evaluation

Multiple Trait Selection

Summary

Further Reading

References

8: Genetic Improvement in Sheep through Selection

Products from Sheep

Selection Among Breeds

Selection within a Breed or Population and the Key Equation

Adjustment for Environmental Effects

Phenotypic Selection

Estimated Breeding Values (EBV)

Using Multiple Sources of Information

Genetic Correlations

Selection Intensity

Generation Interval (L)

Predicting Progress from Selection

National Genetic Improvement Programs

Summary

Further Reading

References

Review Questions

9: Genetic Improvement Programs for Dairy Cattle

Introduction

Data Collection Infrastructure

Estimation of Breeding Values

Selection for Increased Productivity

Selection for Functional Traits

Sire Selection

Summary

Further Reading

References

Review questions

10: Genetic and Genomic Improvement of Pigs

Introduction

Domestication of Swine and Breed Development

Methods of Selection and Mating Systems

Traits of Economic Importance

Development of Molecular genetic Approaches

QTL, Candidate genes, and Genetic Improvement

Sequencing the Pig Genome

Genomic Selection

Databases

Cloning, Transgenics, and Breeding Pigs as Biological Models

Future Applications to Genetic Improvement

Acknowledgments

Further Reading

References

Review questions

11: Equine Genetics

Color

Genetic Defects

Inbreeding and Relationship

Selection and Improvement

New Technologies

Further Reading

Color

Diseases

Inbreeding and Relationship

Heritability Estimates

Stallion Testing and Genetic Evaluation

Genomics

References

Review Questions

12: Genetics and Genomics of the Domestic Dog

Introduction to Canine Research

The Dog Genome

Uncovering the Genetic Basis of Phenotypes

Future Challenges

Summary

Further Reading

References

Review Questions

13: The Sheep Genome

Investment in Sheep Genome Research

Overview of the Sheep Genome

Genomic Resources in Sheep

Application of Genomic Resources

Summary

References

Review Questions

14: Goat Genetics and Genomic Progress

Introduction

Genetics and Goat Domestication

Taxonomy

Goat Chromosome Number and Structure

Patterns of Inheritance

Quantitative Trail Loci (QTL)

Progress in Goat Genomics

Biotechnologies and Goat Genetics

Summary

Further Reading

Review Questions

Section 3: Molecular Genetics of Production and Economically Important Traits

15: Bioinformatics in Animal Genetics

Introduction

Bioinformatics and Animal Genetics

The Importance of Bioinformatics in Genomics Research

Gene Expression

Gene Regulation

Epigenetics

Genomic Data Manipulation

Bioinformatics Perspectives in Animal Genetics

References

Review Questions

16: Genome-wide Association Studies in Pedigreed Populations

Introduction

Methods and Tools for GWAS in Pedigreed Populations

Things to Remember About Analysis

What Did We Miss?

Acknowledgments

References

17: Molecular Genetics Techniques and High Throughput Technologies

Central Dogma of Molecular Biology

Review of Properties of Nucleic Acids

Purification of Nucleic Acids from Cells

Determining the Quantity and Purity of Nucleic Acids

Polymerase Chain Reaction (PCR)

Determining the Identity of DNA

Concept of Parallelization and High Throughput Assays

Next Generation Sequencing Technology

Summary

Further Reading

Review questions

18: Single Genes in Animal Breeding

Introduction

Mapping and Identifying Single Genes

What Types of DNA Sequence Alterations Create Single Gene Effects?

Examples of Single Genes in Animal Breeding

Summary

References

Review questions

19: Molecular Genetics of Coat Color: It is more than Just Skin Deep

Introduction

Pathways of Melanocyte Migration and Differentiation from the Neural Crest

Melanocyte Signaling and Regulation

Melanin Production and Transport

Conclusions

Summary

Key Terms

References

Review questions

20: Molecular Genetics-Nutrition Interactions in Ruminant Fatty Acid Metabolism and Meat Quality

Introduction

Genetics-nutrition Interactions in Ruminants

Educating Australian Undergraduate Students in Molecular Genetics-nutrition Interactions in Ruminants

Review of Fatty Acids and Their Manipulation, Metabolism, and Effect on Quality in Ruminants

Concluding Remarks

Appendix 20.1: Fats and Beef Quality Laboratory Practicals

Appendix 20.2: Sensory Evaluation of Meat Quality in Grain-fed Versus Grass-fed Beef

Appendix 20.3: Total Lipid Extraction from a Beef Cut for Fatty Acid Analysis

Appendix 20.4: Molecular Genetics Laboratory Practical

References

21: Nutritional Epigenomics

Introduction

Epigenomic Machinery and Gene Regulation

Nutrients and Histone Modification

Nutrients and Epigenetics in Bovine Cells: One Definitive Example of the Nutrient-Epigenetic-Phenotype Relationship

Summary

Note

References

Review Questions

Section 4: Genetics of Embryo Development and Fertility

22: Genomics of Sex Determination and Dosage Compensation

Genotypic Sex Determination (GSD)

Environmental Sex Determination (ESD)

Dosage Compensation in Mammals: X Chromosome Inactivation

Activity Patterns of Sex Chromosomes during Gametogenesis

Escape from X Inactivation

Abnormalities in Chromosomal Sex

Sex Reversal

Summary

Further Reading

Review Questions

23: Functional Genomics of Mammalian Gametes and Preimplantation Embryos

Introduction

Gamete and Embryo Development

Transcriptomics

Proteomics

Systems Biology

Conclusion

Further Reading

References

24: The Genetics of

In

Vitro

Produced Embryos

In

v

itro

Production: from Livestock to Humans

Unlocking Developmentally Important Genes in the Pre-Implantation Embryo

IVP: Potential Source of Genetic Alteration?

PGD: Genetic Screening and Human Embryos

Screening the Embryo: to Infinity and Beyond?

Embryogenetics: What's Next?

Summary

Key Terms

References

Review Questions

Supplementary Videos

Section 5: Genetics of Animal Health and Biotechnology

25: Understanding the Major Histocompatibility Complex and Immunoglobulin Genes

Introduction

Overview of the Immune System

The Major Histocompatibility Complex Loci

Immunoglobulin Loci

Summary

Key Terms

Further Reading and References

Review Questions

26: Livestock and Companion Animal Genetics: Genetics of Infectious Disease Susceptibility

Introduction

Why is Studying the Genetics of Disease Susceptibility Important?

Present Applications of Genetic Selection Tools for Predicting Disease Susceptibility

Current Research into Genetic Selection for Livestock Health

Challenges Faced when Studying the Genetics of Disease Resistance in Livestock

Should We Select for Increased Disease Resistance?

Summary

Key Terms

Further Reading

Review Questions

27: Animal Genetics and Welfare

Introduction

A Continued Need for Genetic Improvements and Knowledge

Welfare

Genetic Advancement and Animal Welfare

Genetic Selection that Adversely Affects Farmed Animal Welfare

Summary

References

Review Questions

28: Animal Biotechnology: Scientific, Regulatory and Public Acceptance Issues Associated with Cloned and Genetically Engineered Animals

What is Animal Biotechnology?

Cloning

Genetic Engineering

Ethical, Moral, and Animal Welfare Concerns

Summary

Further Reading

References

Review Questions

29: Intellectual Property Rights and Animal Genetic Resources

Introduction

Old McDonald's Farm Meets Dolly (and Her Lawyer)

What is Intellectual Property?

Forms of Intellectual Property

Here a Patent, There (Not) a Patent

Forms of Payment or Remuneration

Case Studies

E-I-E-I-O: The Alphabet Soup of Domestic and International Issues

Public Sector Research and IP – Domestic and International

Access to Animal Genetic Resources

Summary

Note

Further Reading

References

Review Questions

Index

End User License Agreement

List of Tables

Table 1.1  Definitions

1

of the verb

to teach

and the noun

teaching

.

Table 1.2  Definitions

1

of the verb

to learn

and the noun

learning

.

Table 1.3  Components of “Learning to Learn” in higher education as (a) understanding “learning” and (b) understanding “knowledge” of a discipline (reproduced with permission from Wingate, U., 2007. A framework to transition: supporting “learning to learn” in higher education.

Higher Education Quarterly

61(3):391–405).

Table 1.4  Example of an alignment scheme among instructors' activities, students' activities and tests to assess learning using the revised Bloom's Taxonomy (Krathwohl, 2002) as a frame of reference.

Table 1.5  Examples of learning activities that may be used to substitute for PowerPoint lectures: What to do in a 50 minute lecture to engage students?

Table 2.1  Increase in the proportion of homozygous loci in each generation with selfing – the most intense form of inbreeding.

Table 2.2  The increase in the expected proportion of homozygous loci over 10 generations of intensive inbreeding with different types of close matings.

Table 2.3  Effects of inbreeding in sheep

a

.

Table 2.4  Effects of inbreeding in US Holstein dairy cows

a

.

Table 2.5  Outcross Jersey bulls: High Net Merit $ Jersey bulls with a low relationship with current US Jersey cows, December 2012.

Table 2.6  Theoretical effect of inbreeding on genotypic value (G), breeding value (BV), and gene combination value (GCV).

Table 2.7  Theoretical effect of inbreeding on genotypic value (G), breeding value (BV), and gene combination value (GCV) with different degrees of dominance.

Table 2.8  Possible inbred (homozygous) individuals and their genotypic values with complete dominance.

Table 2.9  For question

2.f

.

Table 2.10  For question

3

.

Table 2.11  For question

4

.

Table 2.12  For question

5

.

Table 2.13  For question

6

.

Table 6.1  The list of some descriptive statistics for qualitative and quantitative variables.

Table 6.2  The body condition score of 487 beef cattle from six different breeding farms.

Table 6.3  Raw value and corresponding

z

scores for 10 animals from Dorset and Targhee breeds.

Table 6.4  Weaning weights (kg) and grease fleece weights (kg) simulated for 10 sheep.

Table 7.1  Relationship between the proportion of animals selected (

p

) and selection intensity (

i

).

Table 7.2  Relationship between a candidate for selection and specific relatives, assuming the absence of any inbreeding.

Table 8.1  Lamb preweaning and weaning weight adjustment factors.

Table 8.2  Characteristics of two lambs and calculation of corrected and adjusted 60-day weaning weights (all in lb).

Table 8.3  Age of ewe adjustment factors for fleece weight and litter size.

a

Table 8.4  Heritability estimates for several sheep traits.

a

Table 8.5  Weighting factors (b) for different sources of information in calculation of EBV for litter size and fleece weight and EBV accuracies.

Table 8.6  Estimates of genetic correlations among important fleece, body weight, and reproduction traits in sheep.

a

Table 8.7  Potential within flock selection intensities (i)

a

in ram lambs and ewe lambs for different flock reproductive rates.

Table 8.8  Example calculation of generation interval in sires and dams in a flock of 100 ewes.

Table 8.9  Estimated breeding values and maternal index value for US Polypay sheep born in 2002 through 2011 and enrolled in the National Sheep Improvement Program.

Table 10.1  Effects of mating systems on traits of economic importance in swine.

Table 10.2  Example of traits and their heritabilities and relative economic values.

Table 10.3  Genetic correlations among several important pork production traits.

Table 10.4  Individual genetic markers and genes considered in marker assisted selection in pigs.

Table 10.5  Single-step genetic evaluation with and without genomic information on 2023 dam line pigs born in and after 2009.

Table 11.1  Summary of coat color genes and their effects.

Table 11.2  Inbreeding coefficients in various breeds of horse.

Table 11.3  Heritability estimates in horses.

Table 13.1  Useful URLs.

Table 14.1  Taxonomic hierarchy of the goat.

Table 14.2  Impact of select gene variants on goat phenotypes.

Table 14.3  Examples of genomic progress from the overview of the domestic goat in the National Center for Biotechnology.

Table 18.1  Selected examples of DNA alterations associated with single gene traits.

Table 21.1  Mechanisms of epigenomic regulations.

Table 21.2  Factors affecting epigenomic regulation.

Table 24.1  Large-scale expression studies profiling mammalian pre-implantation embryo development.

Table 28.1  Typical broiler performance in the USA from (a) Havenstein et al. (2003) and (b) Gordon (1974).

Table 28.2  Some examples of traits targeted for improvement in GE animals for agricultural applications. Modified from Kues and Niemann (2004).

Table 29.1  Forms of intellectual property in the United States most relevant to animal genetics research.

Table 29.2  Summary of international conventions and treaties related to intellectual property and animal genetics.

List of Illustrations

Figure 1.1  Educational stages across the lifespan of a citizen of the United States with an average life expectancy at birth of 78 years.

Figure 1.2  Behaviorist approach to learning defined as a measurable change in behavior (response) contingent upon antecedents (stimuli) arranged in a way that alter the frequency of learner-generated trial-and-error responses in which reinforcements are expected to increase the rate of desirable responses and punishments are expected to decrease the rate of undesirable responses.

Figure 1.3  Constructivist approach to learning defined as an increasing level of ability in solving complex problem. The zone of proximal development (ZPD) is the area beyond what a student can do alone (blue core circle), but possible with the assistance of a more competent peer or adult with proper temporary scaffolding that helps the learner expand their abilities after internalizing new knowledge and skills (dots), connecting them (lines) into increasingly complex patterns of recognition or abilities.

Figure 1.4  Main instructional design features of (a) a traditional lecture-based course and (b) a course designed as an interactive learning environment, highlighting what the teacher and the students do before, during, and after a period of classroom instruction and how grades are assigned.

Figure 2.1  Inbreeding coefficients for US Jersey dairy cattle born between 1960 and 2012. From: USDA Animal Improvement Program Laboratory website (www.cdcb.us/eval/summary/inbrd.cfm?), Bovine Inbreeding Trends Menu/Jersey/Inbreeding Trend, Accessed April 28, 2014).

Figure 2.2  Pedigree (

left

) and path diagram (

right

) for individual X resulting from the mating of a half-brother (S) with his half-sister (D), with the alleles present at a single locus in the three grandparents.

Figure 2.3  Ronald Hogg with one of his Hampshire rams. The Hampshire flock was in the Hogg family for over 50 years and virtually closed to outside breeding for the last 30 years of its existence. In the last two years of the flock's ownership by the Hogg family (1980 and 1981), the median inbreeding coefficient of lambs was 10.7% and ranged from 1.4 to 29.6%, and the median inbreeding coefficient of ewes was 4.3% and ranged from 0.0 to 28.1%. During these two years, lamb mortality was very high and positively related to level of inbreeding (1.3 lamb deaths per 100 lambs born/0.01 increase in lamb inbreeding coefficient) (Lamberson et al., 1982).

Figure 2.4  Four generation pedigree of Hampshire ewe 18420 from the R.W. Hogg and Sons flock of Salem, Oregon (numbers in parentheses are the registration numbers recorded with the American Hampshire Sheep Association: the letters are arbitrary and used to simplify the identification of each animal).

Figure 2.5  Path diagram for individual X (Hampshire ewe 18420).

Figure 3.1  Manhattan graph of the absolute value of estimated allele substitution effects for milk yield in US Holstein cattle based on SNP genotypes from the BovineSNP50 BeadChip (source: USDA-ARS Animal Improvement Programs Laboratory).

Figure 3.2  Average inbreeding coefficients for US Holstein and Jersey cattle, according to year of birth (source: www.cdcb.us/eval/summary/trend.cfm?).

Figure 4.1  Frequency distribution of a group of beef cattle according to their body condition score (BCS). BCS is defined in five categories, varying from BCS = 1 for “very thin” to BCS = 5 for “very fat.”

Figure 4.2  Frequency (counting) of beef cattle calves according to their weaning weight, in kg.

Figure 4.3  Probability density of weaning weight in beef cattle calves, in kg.

Figure 6.1  Random sampling of a sub-group from a population.

Figure 6.2  Measurement categories of data.

Figure 6.3  Graphical presentations of data given in Table 6.2 by a pie chart (a), line (b) and bar chart.

Figure 6.4  Histograms of REA data for across breeds (top) and within breeds (bottom).

Figure 6.5  Box and whisker plot drawn for ribeye area.

Figure 6.6  Some common probability distributions for discrete and continuous variables.

Figure 6.7  Empirical rule to estimate the area under normal curve.

Figure 6.8  Some different normally distributed curves from simulated data for 1000 sheep for 60 weaning weight (top) and grease fleece weights (bottom).

Figure 6.9  Nine different scatterplots with various associations and distributions.

Figure 6.10  Linear regression between average daily gain (

ADG

) and daily feed intake (

DFI

) for 17 cows. Dots represent real observations (

X

i

,

Y

i

). The straight regression line shows the expected, or fitted, values of the dependent variable (ADG). The errors

e

i

are the deviation of the observations from their expected values.

Figure 7.1  Normal distribution truncated at 0.5 SD above the mean of 0. In this example, the proportion selected (shaded region) would be approximately 30% and the selection intensity

i

 ≈ 1.14 (standard deviation: SD).

Figure 8.1  Representative breeds of sheep in the US of the five general classes. From

left

to riIght,

top row

: maternal – Polypay, range/wool – Targhee, hair – Katahdin. From

left

to

right

,

bottom row

: dairy – East Friesian, Terminal/sire – Hampshire. (Photos courtesy of David L. Thomas. All photographs from Department of Animal Sciences, University of Wisconsin–Madison.)

Figure 8.2  A list of the top active Polypay sires for the USA Maternal Index (from www.nsip.org).

Figure 9.1  Average breeding value for milk yield (milk BV) for US Holstein and Jersey cattle, according to year of birth (source: http://aipl.arsusda.gov/eval/summary/trend.cfm).

Figure 9.2  Relationship between Australian breeding value for milk yield and actual phenotypic level of milk yield per lactation, for three levels of supplemental concentrate feeding (source: Fulkerson, W. J., T. M. Davison, S. C. Garcia, G. Hough, M. E. Goddard, R. Dobbs, and M. Blockey 2008. Holstein-Friesian dairy cows under a predominantly grazing system: Interaction between genotype and environment.

J. Dairy Sci.

91:826–839. Copyright (c) Elsevier, 2008).

Figure 9.3  Average breeding value for daughter pregnancy rate and somatic cell score in US Holstein cattle, according to year of birth (source: http://aipl.arsusda.gov/eval/summary/trend.cfm).

Figure 10.1  Selection and breeding pyramid in modern pig breeding (adapted in part from Dekkers, J., Mather, P.K. and Knoll, E.F. 2011. Genetic improvement of the pig. In Rothschild, M.F. and A. Ruvinsky (eds),

The Genetics of the Pig

. 2nd edn. Ch. 16. CAB International, Wallingford, 507 pp).

Figure 10.2  Use of SNP chip to do GWAS and genomic selection.

Figure 12.1  

There's a breed for that.

Each dog breed was created to possess certain physical and behavioral attributes that enhance their ability to learn and perform a task.

Figure 12.2  

Population bottleneck in the Leonberger.

The Leonberger is a large breed from Germany that was developed in the mid-1800s to be a companion and a protector. During World War I, the Leonberger population was nearly wiped out by violence and starvation. In 1922, a group dedicated to re-establishing the breed identified 25 dogs that possessed the Leonberger phenotype. Only seven of these dogs (five females, two males) were deemed suitable for breeding. Within four years, 350 Leonbergers had been selectively bred, enough to provide foundation stock to new kennels. Today, the Leonberger is an intelligent and loyal family pet that ranks 103rd among registration statistics published by the American Kennel Club.

Figure 12.3  

Genetic testing identifies phenotypically normal carriers.

A family of English Cocker Spaniels segregates a recessively-inherited, fatal renal disease. Prior to development of the genetic test, only obligate carriers (those who had produced affected progeny) could be identified. Development of a genetic test allowed for identification of carriers and enabled continuation of this line with careful breeding.

Figure 12.4  

The dog behind the genome.

A publically available, high-resolution draft sequence of the dog genome was generated using Tasha, a female Boxer. Tasha was selected for her high degree of homozygosity. Previously, the private company Celera Genomics generated a low-resolution draft sequence, using a black Standard Poodle named Shadow. Shadow was selected because he was the personal pet of J. Craig Venter, founder of Celera Genomics.

Figure 12.5  

SINEC_Cf elements create phenotypic diversity.

The merle coat pattern is caused by an insertion at the intron 10/exon 11 boundary of

SILV

(left). Extreme piebald is associated with an insertion upstream of

MITF

(center). The saddle tan phenotype is the result of an insertion in intron 1 of

ASIP

(right).

Figure 12.6  

Wisdom Panel® Insights™ Mixed Breed Identification Test

. A SNP-based test to determine ancestry in a mixed breed dog reveals purebred ancestors. A computer algorithm is used to predict the most likely breeds within three generations. An asterisk (*) denotes a breed detected at a lower confidence.

Figure 12.7  

Classical linkage analysis of osteosarcoma in a Scottish Deerhound family

. Individuals shaded in black are affected. Haplotypes, combinations of alleles that are co-inherited, are depicted below individuals as vertical bars with allele designations to the side. Paternal chromosomes are shown on the left; maternal chromosomes on the right. The haplotype denoted in red segregates with the phenotype. Recombination events delimit the critical interval harboring the causative locus to a 4.5 Mb region between FH3836 and REN44K21. Reprinted with permission from Phillips et al., 2010

Genomics

96:220–227.

Figure 12.8  

GWAS for a neurological disorder in Cavalier King Charles Spaniels

. A Manhattan plot (so named because it resembles a skyline) shows the canine chromosomes on the

x

-axis, and the −log

10

of the

p

-value on the

y

-axis. Each dot represents the

p

-value obtained for a single SNP, with the highest points indicating the greatest observed associations. These results show a strong association with the phenotype on chromosome 7. Reprinted with permission from Gill et al., 2012

Neurobiology of Disease

; 45:130–136.

Figure 12.9  

Dalmatian/Pointer backcross pedigree

. Solid black shading indicates individuals homozygous for the urinary defect; half shading indicates phenotypically normal carriers. In the first generation, a single Pointer (□) possessing the wild type urinary metabolism alleles was crossed with a Dalmatian. In subsequent generations, carriers were backcrossed to Dalmatians in order to maintain breed standards and diversity. Modified and reprinted with permission from

Mammalian Genome

2006; 17:340–345.

Figure 13.1  Assignments on the sheep linkage map over time. (Courtesy J. Maddox, 2011)

Figure 14.1  Phenotypic manifestations of genetic variation in goats.

Figure 15.1  DNA Sequencing. Automatic process based on chain termination method using dideoxynucleotides.

Figure 15.2  Shotgun sequencing. Method usually employed in sequencing long DNA, normally more than 1000 base pairs in length.

Figure 15.3  Sequence alignment. Comparison of two sequences in order to find common properties between them.

Figure 15.4  Genome assembly. Original DNA sequence is reconstructed from ordering large number of short DNA fragments.

Figure 15.5  Gene annotation. A process where biological or relevant information is linked to a gene or a specific genomic location.

Figure 15.6  Gene expression. Gene products are synthetized based on the information deciphered from the DNA sequence.

Figure 15.7  RNA-Seq analysis. Frequent steps during a gene expression analysis aimed at quantification of messenger RNAs.

Figure 15.8  Gene regulation. Schematic representation of factors that influence genes activity, making them “active” or “inactive.”

Figure 15.9  Graphical representation of methylation status in a fragment of DNA.

Figure 16.1  Illustration of genotype calls for three human SNPs. Figure 16.1(a) shows a tight clustering of the three genotypes and no ambiguous calls. Figure 16.1(b) assigns only two of the three possible genotypes and misses out an entire cluster of what could be the heterozygous individuals. Figure 16.1(c) shows less tight clustering with some partial overlap between the clusters resulting in some missing genotypes. These figures illustrate why it is important to visually inspect the genotypes for the “winning SNPs.”

Figure 16.2  Box plots of uric acid levels for the three genotypes of the most significant SNP in a GWAS of two Italian cohorts (Li et al., 2007). Reproduced from Li et al. (2007) under the creative commons license (http://creativecommons.org/licenses/by/2.5/).

Figure 16.3  Manhattan plot for the GWAS on uric acid levels in two Italian Cohorts (Li et al., 2007). Reproduced from Li et al. (2007) under the creative commons license (http://creativecommons.org/licenses/by/2.5/).

Figure 16.4  Illustrative examples of QQ plots from McCarthy et al. (8). Plot (a) shows a QQ plot where there is no overall inflation of P values. Plot (b) shows an overall inflation of P values. Plot (c) suggests overall inflation as well as some real significant results. Plot (d) shows no evidence for inflation but strong evidence for real effects. Reprinted by permission from Macmillan Publishers Ltd:

Nature Reviews Genetics

. May; 9(5):356–369, copyright (2008) www.nature.com/nrg/.

Figure 1  QQ plots of the p values from the simulated association analyses with or without correction for population stratification using a simulated Case-Control study on the basis of Han Chinese individuals (Chen et al., 2009). The columns correspond to the Q-Q plots of the uncorrected, GC-corrected, and PCA-corrected

p

values. The rows correspond to 20%, 40%, 80%, and 100% stratification of the simulated case and control samples.(A–C) 20% stratification: 500N cases, 400N and 100S controls.(D–F) 40% stratification: 500N cases, 300N and 200S controls.(G–I) 80% stratification: 500N cases, 100N and 400S controls.(J–L) 100% stratification: 500N cases and 500S controls.Originally published as Figure 4 in Chen et al. (2009). Reprinted from

The American Journal of Human Genetics

, Vol. 85, Chen et al., Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation, pp. 775–785 Copyright (2009), with permission from The American Society of Human Genetics.

Figure 17.1  

Central dogma of molecular biology.

The central dogma of molecular biology is a synthesis made by Francis Crick based on previous discoveries of the steps taken to make protein from DNA. It elegantly describes the direction of information flow in biology. DNA is replicated so information is copied to itself, as depicted by the arrow pointing to itself. RNA is made from DNA through a process called transcription. Eventually, functional proteins are synthesized by translating information in the RNA. There are exceptions to this route of information flow. For example, many viruses including HIV use a type of enzyme called reverse transcriptase that can make DNA molecules using their RNA as a template. Animal genomes also contain elements known as retrotransposons that are only capable of moving themselves in the genome by using the reverse transcription of an intermediate RNA product. However, many retrotransposons lose their mobility due to mutations and are often found as dormant remnants within the genome.

Figure 17.2  

Structure of DNA.

A DNA strand is made of a stretch of deoxyribonucleotides. Each deoxyribonucleotide is composed of a deoxyribose in the center, a phosphate group attached to the 5th carbon of the deoxyribose ring, a hydroxyl group to the thirrd carbon of the sugar ring, and a nitrogenous base to the first carbon. DNA strands pair up to form a double stranded structure when condition permits hydrogen bond formation. Two hydrogen bonds are formed between the pairing of an adenosine and a thymine while three hydrogen bonds are formed between a cytosine and a guanine. Because there are more hydrogen bonds between a C-G pair, the pairing is chemically stronger than an A-T pair.

Figure 17.3  

Extraction and purification of nucleic acids.

Cells are lysed to release a mixture of DNA, RNA, proteins, and lipids. The mixture can then be separated and purified into different classes of biomolecules. Note that lipids are structural components of membranes in cells and that monomer lipids are only shown after membranes are broken.

Figure 17.4  

UV spectrophotometry of nucleic acids.

The UV absorption spectrum of pure nucleic acid solution has a peak at 260 nm and low absorption at 230 and 280 nm. The concentrations of DNA and RNA can be calculated using the formula: [DNA] = A

260

 × 50 ng/μL, and [RNA] = A

260

 × 40 ng/μL.

Figure 17.5  

Gel electrophoresis of nucleic acids.

In a gel electrophoresis, nucleic solutions are added to one end of an agarose gel. An electric field is applied such that negatively charged nucleic acid molecules move from the negatively charged cathode to the negatively charged anode. A size marker is usually included by the side of the nucleic acid samples as a reference for interring sizes of nucleic acids. The gel is typically stained with ethidium bromide, which is a fluorescent dye that binds to double stranded nucleic acids. In a laboratory, the stained gel is visualized in a dark room under a UV light so that only nucleic acids are visible. The bright bands and smears on the dark background represent nucleic acids in the gel. A tight band is many nucleic acids molecules of the same size packed at the same position of the gel. A smear along the path of nucleic acid movement is simply many bands that cannot be easily distinguished. For example, sizes of molecules in genomic DNA or degraded RNA vary extensively so they are manifested as smears. Although RNA are single stranded molecules, there are extensive internal base-pairing, which makes them detectable by ethidium bromide.

Figure 17.6  

Polymerase chain reaction.

(a)

One cycle of a PCR reaction. Double stranded DNA is denatured to become single stranded and allowed to bind with primers. DNA polymerase extends the DNA strands by adding free nucleotides to the ends of primers.

(b)

Amplification occurs in cycles where newly synthesized DNA from the previous cycle also serves as templates for the next cycle. Therefore the amount of DNA flanked by the two primers grows exponentially.

Figure 17.7  

Real-time PCR.

In a real time PCR experiment, the abundance of DNA is monitored through fluorescence detection. The threshold cycle (C

t

) is determined by setting a threshold line right above the baseline fluorescent signal and finding the number of the cycle that intersected with the threshold.

Figure 17.8  

Chain terminator sequencing of DNA.

Chain terminator (Sanger) sequencing takes place in a mixture of (1) DNA template to be sequenced; (2) DNA primer from where the sequence begins; (3) free deoxynucleotides and fluorescently labeled dideoxynucleotides; (4) DNA polymerase; and (5) necessary pH buffering agents and ion strength. Shown is a DNA fragment with the sequence ACGAT following the primer. The sequencing reaction results in five unique DNA fragments, each representing one of the bases in the sequence and is labeled at the end by fluorescent dideoxynucleotides. The fluorescently labeled fragments are resolved by gel electrophoresis. The fluorescent signals can then be read and processed into a sequence read.

Figure 17.9  

RFLP genotyping of DNA.

Using PCR, DNA flanking a polymorphism, in this case a SNP, is amplified for three individuals. Each individual has two DNA fragments amplified, each coming from either the paternal or maternal chromosome. The DNA have identical sequence among the individuals except at the SNP site, where the first individuals have a genotype AA, that is, A for both the paternal and maternal chromosomes, individual 2 AG and individual 3 GG. The DNA molecules are digested by EcoRI, which recognizes a six-base motif GAATTC. The digestion products are resolved by electrophoresis. When the SNP genotype is AA, both the paternal and maternal alleles are digested, giving rise to two digested fragments. When the SNP genotype is AG, only one of the alleles is digested therefore both cut and uncut DNA are present. When the SNP genotype is GG, neither of the alleles is digested so the DNA stays intact.

Figure 17.10  

Northern blot of RNA.

RNA is extracted and size fractionated by gel electrophoresis followed by transfer to a membrane. RNA is immobilized on the membrane and subject to hybridization with radio-labeled DNA probes. The radioactivity can then be visualized by exposing a film or by a phosphor imager.

Figure 17.11  

Gene expression profiling by microarrays.

Specific oligonucletoide probes are synthesized and attached to each of the thousands of spots on the surface of microarrays. RNA samples are labeled and hybridized with the microarray surface. The signal intensity of each spot is then determined and used to estimate the amount of RNA hybridization (thus gene expression). The simultaneous hybridization and detection of many spots on the microarray allow quantification of expression of many genes.

Figure 17.12  

Cost to sequence a genome.

This graph is generated from data downloaded from www.genome.gov/sequencingcosts/. The cost is plotted at log scale over time. The time marks for the critical events are approximate. The initial human genome sequences were announced in 2000 and published in 2001. At the time, the cost to sequence a human genome was 100 million dollars. Note that the total cost for the Human Genome Project, which started many years before 2001, was much higher than the price in 2001. The first next-generation sequencer (454) was introduced in 2004 and data from that technology was published in 2005. However, next generation sequencing did not become popular until after 2007, when the cost for sequencing a genome began to plunge.

Figure 17.13  

Illustration of a next-generation sequencing technology.

The Illumina sequencing platform (Genome Analyzer or HiSeq system) is illustrated. Sequencing is operated on a glass slide called flow cell. Each flow cell contains several distinct units called lanes to accommodate multiple samples. There are billions of oligonucleotides attached to the surface of the flow cell. These oligonucleotides are complementary to adaptor sequences that are added to the ends of fragmented DNA samples. DNA fragments are amplified by PCR using primers complementary to adapters and extensively diluted to make a sequencing library, a large collection of fragmented unique DNA molecules. The sequencing library can then be loaded onto the flow cell to be sequenced. Sequencing begins with a process called cluster generation, in which clusters of identical sequences are generated using single molecules as template. This results in scattered spots on the flow cell, where each spot contains many molecules with identical sequence and spots are distant from each other. Illumina sequencing is achieved by sequentially adding fluorescence labeled nucleotides. The nucleotides are chemically modified such that only one nucleotide can be added to the end of a DNA chain at a time. Once the fluorescence labeled nucleotides are added, the flow cell is digitally scanned. The color of the fluorescence determines what nucleotide has just been added. Subsequently, the terminator at the end of the newly added nucleotide is removed to allow extension of additional nucleotide. This process is repeated by a certain number of cycles, thus the sequential arrangements of bases on the template can determined.

Figure 17.14  

Two approaches using next-generation sequencing to determine genome sequences.

Genome sequence of an animal can be determined by two approaches. Both approaches begin with fragmenting DNA randomly to generate a library of sequences (“shotgun” sequences). For

de novo

assembly, sequences are merged together in a specific order based on their overlaps. These merged sequences produce an assembly of the unknown genome sequence. Alternatively, when a high quality reference genome is available (such as cattle), shotgun sequences can be aligned to the reference. This takes advantage of the fact that genome sequences of additional individuals are highly similar to the reference genome. The aligned sequences can then be used to identify variations in the genomes of individuals.

Figure 18.1  Planned mating designs used to map single genes. Different parent breeds are denoted by black and light gray shading and by homozygous genotypes in the top row. Expected frequency of the various single gene genotypes in the F2 and backcross progeny are shown at the bottom.

Figure 18.2  Example of a gene mapping analysis (linkage analysis) to identify the chromosomal location of a major gene. The

y

-axis in the figure corresponds to p-value from a statistical test of marker-trait association and the

x

-axis corresponds to marker location. Each vertical panel corresponds to a different chromosome, such that the whole figure represents the entire genome (excepting the X chromosome). A large bovine half-sib family (136 daughters of the same sire) were evaluated for the trait (ovulation rate) and genotyped with a SNP (single nucleotide polymorphism) panel that included 2701 autosomal SNP markers. In simple terms, the analysis groups daughters by alternative SNP alleles inherited from their sire at a given SNP and asks the question, do the two groups of daughters differ in ovulation rate? For SNPs closest to the gene of interest, groups of daughters inheriting alternative SNP alleles from the sire will differ most greatly in ovulation rate. The highest peak (on Chromosome 10) corresponds to the location of the gene being mapped. Source: B.W. Kirkpatrick.

Figure 18.3  Backcross design used in mapping the gene responsible for double muscling in cattle (Charlier et al., 1995). The F

1

parent in the second generation of the pedigree passes either the muscular hypertrophy allele (mh) or normal, wild-type allele (+) on to offspring who are distinguishable by degree of muscularity (double muscled vs. normal). Genotyping genetic markers throughout the genome and subsequent analysis of association between marker genotype and muscling phenotype led to the identification of a region on bovine chromosome 2 containing the gene for muscular hypertrophy.

Figure 18.4  Myostatin expression and gene knockout in a mouse model. Myostatin expression (a, b; blue stain) during fetal development on day 9.5 and day 10.5 is specific to the cell types that will become muscle in the adult mouse. Mice missing the myostatin gene (d,f) exhibit dramatic increase in muscularity compared to normal mice (c,e) with a functional myostatin gene. All images from McPherron et al. (1997). Reprinted by permission from Macmillan Publishers Ltd:

Nature

Alexandra C. McPherron, Ann M. Lawler, Se-Jin Lee. Regulation of skeletal muscle mass in mice by a new TGF-beta superfamily member.

Nature

, 387, 83–90. Copyright 1997.

Figure 18.5  Pedigree with inbreeding loop and affected individual (B) useful in homozygosity mapping. The ancestor (A) to which B traces through both paternal and maternal sides of the pedigree is a carrier (blue chromosome) of a detrimental recessive allele. The gene causing the detrimental phenotype associated with the recessive allele in individual B must be located in the narrow region, which is blue in both chromosomes.

Figure 18.6  By 2008 it became apparent to Angus breeders in the USA that a genetic defect was becoming more prevalent in the breed. The defect manifested as stillborn calves with gross skeletal deformities (

A

: photo courtesy of Laurence Denholm, NSW Dept. of Primary Industries) leading to the common name of Curly Calf syndrome, more properly arthrogryposis multiplex. The disease manifested itself because of the heavy use of a sire, GAR Precision 1680 (B), popular as a trait leader for $Beef value (highlighted in green in C). By using a recently developed genetic marker chip incorporating >50,000 single nucleotide polymorphism (SNP) markers and homozygosity mapping, Dr. Jonathon Beever at the University of Illinois was able to map the genetic defect and identify its basis (a deletion spanning two genes) in less than four months. The defect did not originate in GAR Precision 1680, but could be traced back to his maternal grandsire (carrier ancestors highlighted in yellow). Rapid development of a genetic marker test permitted identification of non-carrier offspring of this elite sire and related animals for subsequent use in breeding.

Figure 18.7  Schematic diagram of a stereotypical eukaryotic gene showing some of the typical features. Enhancer sequences can be located at variable distances relative to the gene and are variable in sequence motif. CAT and TATA boxes are conserved sequences important for promotion of gene transcriptions (promoter region). Exons denote the regions of the gene that carry the code that will be translated into a protein and are separated by non-coding, intron sequences. The entirety of the gene is initially transcribed into an RNA sequence, which is then processed (spliced) to remove the intronic regions; consensus donor and acceptor splice sites are indicated with M corresponding to either an A or C base and Y corresponding to either a C or T at that position.

Figure 18.8  Use of a sex-linked gene for feathering to aid in determining sex of chicks. A male line fixed for the slow feathering allele (k) is bred to a female line hemizygous for the fast feathering allele (K). Among resulting offspring, those exhibiting fast feathering are males and those exhibiting slow feathering are females.

Figure 18.9  Use of a sex-linked gene for dwarfism to enhance efficiency of broiler production in chickens. Z and W denote sex chromosomes; dw and + denote alleles at a gene for dwarfism on the Z chromosome. Two lines (A, B) are crossed to produce a paternal line that is crossed with a maternal line derived from two other lines (C, D), one of which is fixed for a sex-linked allele for dwarfism (dw). In the second generation AB hybrids are crossed with CD hybrids to produce broiler chicks with nearly normal growth rate. The CD broiler hens are smaller in size due to the dwarf allele and thus have lower maintenance cost, greater heat tolerance and higher stocking rate in housing.

Figure 18.10  For question

2

and

3

.

Figure 19.1  Melanoblasts (stained in blue) begin as precursors from the neural crest and migrate across the body of the embryo.Reproduced with permission from MacKenzie, M. A., Jordan, S. A., Budd, P. S. and Jackson, I. J. Activation of the receptor tyrosine kinase

Kit

is required for the proliferation of melanoblasts in the mouse embryo.

Developmental Biology

, 192, 99–107. Copyright © 1997, Elsevier.

Figure 19.2  Color-sided in cattle is a unique spotting pattern resulting from a structural variation that encompasses the KIT gene. Color-sided can be found in the Belgain Blue (a) and Brown Swiss breeds (b and c) and is semi-dominant, as can be observed in these heterozygous (c) and homozygous (b) individuals.Reprinted by permission from Macmillan Publishers Ltd:

Nature

. Keith Durkin, Wouter Coppleters, Cord Drogemuller, Nadine Cambisano, Tom Druet. Serial translocation by means of circular intermediates underlies colour sidedness in cattle.

Nature

, vol. 482, issue 7383. Copyright 2012.

Figure 19.3  Disruption of the MC1R receptor leads to loss of eumelanin production, as can be seen in these chestnut (on the left, homozygous recessive e/e) and bay (E/-)mares.(photo credit S. Brooks)

Figure 19.4  Insertion of a retrotransposon element results in the merle color in dogs, as well as ocular and auditory health issues. The insertion is readily apparent in the product size produced by PCR amplification of this region (wild-type: a, heterozygous: b, homozygous: c).Reproduced with permission from Clark, L. A., Wahl, J. M., Rees, C. A. and Murphy, K. E. 2006. Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog.

Proceedings of the National Academy of Sciences of the United States of America

, 103, 1376–1381. Copyright (2006) National Academy of Sciences, U.S.A.

Figure 19.5  In the cat, two TYR alleles result in temperature-sensitive dilution of the coat color, cs (homozygote on left) and the milder cb (homozygote on the right). Compound heterozygotes (cs/cb) exhibit a moderate degree of coat dilution. Reproduced with permission from Lyons, L. A., Imes, D. L., Rah, H. C. and Grahn, R. A. 2005b. Tyrosinase mutations associated with Siamese and Burmese patterns in the domestic cat (

Felis catus

).

Anim Genet

, 36, 119–126. Copyright © 2005, John Wiley & Sons, Inc.

Figure 19.6  Lavender (B), a recessive dilution of the underlying plumage color (A) is the result of a single base change in the MLPH gene sequence in the chicken. Reproduced with permission from Vaez, M., Follett, S. A., Bed'hom, B., Gourichon, D., Tixier-Boichard, M. and Burke, T. 2008. A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken.

BMC Genetics

, 9, 7.

Figure 20.1  DNA transcription and translation process diagram.

Figure 20.2  Teaching and research sheep yard: University of Tasmania, Cambridge TAS, Australia.

Figure 20.3  Teaching undergraduate students body condition scoring in genetically divergent lambs: University of Tasmania, Cambridge TAS, Australia.

Figure 20.4  Animal science students working in groups with experimental sheep flock during a field practical: University of Tasmania, Cambridge TAS, Australia.

Figure 20.5  Sheep nutrition-genetics interactions feeding trial with students: University of Tasmania, Cambridge TAS, Australia.

Figure 20.6  Meat quality student field trip: Longford Meatworks TAS, Australia.

Figure 20.7  Animal science student visit to Nichols Poultry hatchery TAS, Australia.

Figure 20.8  Explaining Robotic Milking with owner John Van Adrichem at Togari TAS, Australia.

Figure 20.9  DNA quantification using Nanodrop by UTAS animal science students during a molecular genetics laboratory practical on sequence homology between sheep blood, wool, and human cheek cells.

Figure 20.10  Sample gel electrophoresis of PCR products from UTAS animal science students during a molecular genetics laboratory practical on sequence homology between sheep blood, wool, and human cheek cells.

Figure 20.11  Comparative unit “Student Evaluation of Teaching and Learning” (SETL) scores between Animal Production Systems and Faculty means (2004–2010) involving 125 students with an 83% response rate.

Figure 20.12  Comparative unit “Student Evaluation of Teaching and Learning” (SETL) evaluation between Animal Production Systems and Faculty means (2004–2010) involving 125 students with an 83% response rate.

Figure 20.13  Hydrolysis of triacylglycerides in ruminants.

Figure 20.14  Gel electrophoresis diagram.

Figure 20.15  Double-stranded DNA is dissociated and a radioactive or fluorescent primer is annealed to the DNA (A); four separate reactions are performed to synthesize new DNA, each reaction contains all four deoxynucleotides and a small portion of one of the dideoxynucleotide bases (B); DNA is synthesized, terminating each time a ddNTP is incorporated (C); DNA from all four reactions is separated on a gel in side-by-side lanes to produce a sequence ladder (D); the sequence is read from the bottom up, and is the compliment (opposite) of the base identified in the gel.

Figure 20.16  Sequence ladder by radioactive sequencing compared to fluorescent peaks.

Figure 21.1  A 3D illustration of the basic structure of a nucleosome. (from http://en.wikipedia.org/wiki/File:Nucleosome.jpg).

Figure 21.2  DNA methylation and histone modification.

Figure 21.3  

S

-Adenosyl methionine (ademetionine, AdoMet, SAM, SAMe, SAM-e) (Modified from http://en.wikipedia.org/wiki/File:S-adenosylmethionine.jpg).

Figure 21.4  Dynamic state of histone acetylation.

Figure 21.5  Dietary HDAC inhibitors (from Dashwood RH and Ho E, Dietary histone deacetylase inhibitors: from cells to mice to man,

Seminars in Cancer Biology

7(5): 363–369, 2007. Reprinted with permission from Roderick H. Dashwood, Emily Ho. Dietary histone deacetylase inhibitors: From cells to mice to man.

Seminars in Cancer Biology

, vol. 17, issue 5. Copyright © Elseiver, 2007.

Figure 21.6  Diagram of cell cycle and cell cycle checkpoints.

Figure 21.7  Regulation of the cell cycle: The G1/S checkpoint control and effects of butyrate treatment. The color indicates the expression level of the genes (red indicating up-regulated genes and green indicating down-regulated genes). Reproduced with permission from Wu S, Li RW, Li W, Li CJ. Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells.

PLoS One

. 2012;7(5):e36940.

Figure 22.1  Overview of genes involved in sex determination in mammals, specifically the mouse. Reprint of Figure 1 from Kashimada and Koopman 2010,

Development

, 137:3921–3930.

Figure 22.2  A gynandormorph chicken. The left half of this bird displays male characteristics, while its right half displays female characteristics. This “split” phenotype provides evidence that sexual identity is cell autonomous, instead of being controlled entirely by sex hormones circulating throughout the bird's entire body. Reprint of Figure 1 from Zhao et al. 2010,

Nature

, 464:237–242. Reprinted by permission from Macmillan Publishers Ltd:

Nature

: Zhao et al. 2010,

Nature

, 464:237–242, copyright 2010.

Figure 22.3  A tortoiseshell cat showing orange and black patches of fur indicative of heterozygosity at the X-linked O gene. (Photo courtesy of Emily Thompson, SUNY Oswego.)

Figure 22.4  X chromosomes identified by fluorescent labeling of the

Xist

gene. Flourescently labeled

Xist

RNA is visible in the vicinity of the inactive X chromosome (Xi), while the acive X chromosome (Xa) has no

Xist

RNA near it. Image by B Reinius and C Shi from Wikimedia Commons (http://en.wikipedia.org/wiki/File:XistRNADNAFISH.jpg), modified from Reinius et al.

BMC Genomics

2010, 11:614.

Figure 22.5  X chromosome silencing mechanisms. Reproduced from Figure 3B from Brockdorff 2011

Development

138, 5057–5065.

Figure 22.6  X inactivation and reactivation in embryonic and gametic development. Reproduced from Figure 4 in Céline Morey, Philip Avner. Genetics and epigenetics of the X chromosome.

Annals of the New York Academy of Sciences

, pp. E18–E33. © John Wiley & Sons, 2011.

Figure 22.7  Horned, PIS

+/+

goat (

left

) and polled, PIS

−/−

goat (

right

). Reproduced with by permission from Macmillan Publishers Ltd:

Nature Genetics

. Photo Courtesy of Eric Pailhoux.

Figure 23.1a and b  Gametogenesis (A) Brief description of oocyte and sperm production in ovary and testis, respectively. Formation of haploid germ cells from the diploid precursory cells is illustrated in this figure. Embryogenesis (B) following fertilization, zygote formation and beyond in bovine are demonstrated in this figure, including the gene expression profile (adapted from Memili and First, 2000 and Kues et al., 2008).

Figure 23.2  

Microarray workflow.

The RNAs are extracted from a variety of biological samples in which bovine spermatozoa and embryos are represented as an example here. Following RNA isolation, these transcripts are labeled using fluorescent dyes such as Cy5and Cy3, and then they are hybridized with specific probes in the array such as cDNA probes or oligonucleotides. Following washes, single stranded, fluorescently labeled DNA targets are bound by oligonucleotide probes of the array surface. Each probe features are made up millions of copies of a specific probes, leading up to 200.000 different probes for the genes of interest. After hybridization, these microarray chips are processed using specific imaging systems that are precisely analyzed using software such as Significance Analysis of Microarrays (SAM). Based on these results, differentially expressed genes are determined in biological samples among the individuals or treatments. Briefly, on the SAM plot, a non-zero fold change parameter is selected to display the upregulated and the downregulated significant genes with red and green, respectively. Then, a heat map from all processed data using hierarchical clustering may be generated by taking advantage of such software, GeneTraffic UNO (Iobion Informatics LLC, www.iobion.com). Besides, for multiple comparisons of the data, one-way analysis of variance (ANOVA) may be used as well. The chip picture is obtained from www.affymetrix.com.

Figure 23.3  

MicroRNA biogenesis and function.

Initially miRNA is transcribed as longer Pri-miRNA, which is processed by a RNase III enzyme, Drosha to form Pre-miRNA. Pre-miRNA is exported to cytoplasm by a protein called exportin. Inside cytoplasm, as a result of Dicer processing, mature miRNA forms. One of the strands of miRNA gets incorporated into RNA-induced silencing complex (RISC) to form the final unit for mRNA translational repression.

Figure 23.4  

Protein methods.

Proteins are macromolecules with vital functions in cells during development. Meaningful data can be generated only through a well-designed study with appropriate proteomics approaches-which may include high-throughput methods such as MS and 2D-DIGE or reductionist methods such as western blotting and immunocytochemistry. Often, two approaches are used to validate the results. Quantifying proteins and analyzing the data are essential for developing models to illuminate molecular and cellular underpinnings of developmental mechanisms.

Figure 23.5  

Systems Biology.

A network and a canonical pathways chart are displayed here as two examples of how system biology works using Ingenuity pathway analysis software (IPA). Note that these two interactomes are obtained from two different data set followed by sperm proteomics and embryo RNA-seq. experiments. The network on the left side of the figure is generated from the sperm microarray data whereas the canonical pathways are created from bovine embryo RNA-seq data using IPA software (unpublished results). Up- and down-regulated genes are represented as red and green marks, respectively in the network revealing the interactions between the proteins of interest. On the right side, canonical pathways are represented as blue bar charts containing the genes of interest with the ratio of their log values (yellow plot). In addition to experimental data, public sources can also be used to obtain the gene annotations and their expression data etc. such as NCBI including other research articles. In the figure, “RNA sequencing” is searched at NCBI –PubMed to obtain the research articles containing the data previously published by others. Note that all RNA-seq data might not be obtained from NCBI if the researchers are not published them in the research articles. In that case, these data might be separately requested from the researchers if applicable (see the related equipment in the following links: www.illumina.com, www.affymetrix.com www.eppendorf.com, and www.ingenuity.com).

Figure 24.1  

Embryonic genome activation.

During mammalian preimplantation development maternal RNA transcripts (upper line) drive initial development. By the 8–16 cell stage these transcripts are degraded and embryo specific transcripts (lower curve) are activated.

Figure 24.2  

Patterns of methylation during bovine pre-implantation embryo development.

When oocyte and sperm fuse at fertilization there is a rapid de-methylation of the parental genomes as the cells of the embryo divides. When the cells undergo compaction there is a transition to differentiation. It's at this time that the two differing cell types in the developing blastocyst undergo differential levels of remethylation. After the blastocyst stage is obtained, the embryo can implant into the uterus. ICM = inner cell mass and TE = trophectoderm of the blastocyst embryo.

Figure 24.3  

Morphological assessment of embryos.

Compacted morula (A) that were cultured until day 8 of development and either showed signs of blastocoele formation (B) or degeneration (C).

Figure 25.1  

Overview of immune response in mammals.

Animals first attempt to prevent entry of pathogens into the body by anatomical barriers. If pathogens enter the body, the innate (“non-specific”) immune system reacts to the pathogen within hours. The adaptive (“specific”) immune response takes about two weeks to develop, but creates memory cells that can “remember” the pathogen in the future and respond faster if the animal encounters the pathogen a second time. Some pathogens elicit a stronger humoral immune response than a cell-mediated response, and other pathogens elicit a stronger cell-mediated immune response. However, both adaptive immune responses are elicited by pathogens.

Figure 25.2  

The importance of heterozygote advantage at the Major Histocompatibility Loci.

(

A

) This individual is heterozygous at these two MHC loci (Aa and Bb). As a consequence, each MHC allele can present on its surface a wider range of peptides derived from foreign bodies. The lines extending from the surface of the cell are the MHC receptors. The colored shapes (circle, square, triangle, and trapezoid) are different peptides derived from a foreign body. (

B

) This individual is homozygous at these two MHC loci (AA and BB). The individual is not able to present on its cell surface all of the peptides that the individual in diagram

A

can. As a result, a pathogen is more likely to escape detection in this individual than in the individual in diagram

A

. In this diagram, the peptides derived from foreign bodies that remain inside the cell cannot bind to MHC receptors and thus cannot be presented on the surface of the cell.

Figure 25.3  

Interaction between an antigen and an antibody molecule

. The variable regions (red) of the light and heavy antibody chains interact with the antigen (purple oval). The constant (D, J, and C) regions of the light (green) and heavy (blue) antibody chains do not bind to antigen. Hence, the variable domains have evolved to be more polymorphic than the other antibody domains.

Figure 25.4  

Gene rearrangement of light chain immunoglobulin molecules.

The V and J loci that are combined are chosen randomly. Adapted from Fig. 5.4

Kuby Immunology

, 4th edn by R.A. Goldsby, T.J. Kindt, and B.A. Osborne, W.H. Freeman & Co., New York, NY.

Figure 25.5  

Gene rearrangement of heavy chain immunoglobulins.

During class switching, the C

M

or C

D

constant domains are replaced with the new constant domain (either C

G

, C

E

, or C

A

). If, for example, the class switches to C

A

, then all of the 5′ proximal constant domains are deleted along with the rest of the intron during RNA processing. Adapted from Fig. 5.5,

Kuby Immunology

, 4th edn by R.A. Goldsby, T.J. Kindt, and B.A. Osborne, W.H. Freeman & Co., New York, NY.

Figure 25.6  

Gene conversion.

This figure shows gene conversion in the heavy chain after V-D-J joining, but gene conversion also occurs in the light chains. Adapted from Fig. 17.10,

Veterinary Immunology

, 9th edn by I.R. Tizard, “How Antigen-Binding Receptors Are Made,” p. 183, Copyright Elsevier, 2013.

Figure 28.1  Contemporary comparison of 1957 control and 2001 selected broiler carcasses fed the same diet and slaughtered at different ages (from left; 43, 57, 71, and 85 days). Modified from Hill and Kirkpatrick (2010), original photo by G.A. Havenstein. Reprinted with permission from the

Annual Reviews of Animal Biosciences

, Volume 1 © 2013 by Annual Reviews, www.annualreviews.org.

Figure 28.2  The Holstein breeding bull, Elevation, lived in Plain City in the 1970s. Roughly half of the Holstein dairy cows in the United States today are believed to descend from Elevation.

Figure 28.3  Methods for transgenesis in large mammals. Modified from Garrels et al. (2012). (

A

) Pronuclear injection (PNI): With a fine glass capillary linearized DNA molecules are injected into one pronucleus of a zygote. Requires highly skilled experimentalist. Random integration into the genome. High rates of transgene mosaic animals and unwanted concatemeric integrations. Approximately, 1–5% of treated zygotes develop to transgenic offspring. (

B

) Somatic cell nuclear transfer (SCNT): Requires highly skilled experimentalist for enucleation of oocytes and transfer of transgenic somatic cell. Integration into the genome of somatic cells is random in most cases, but can be targeted by homologous recombination. Genetic modification of donor cells with viruses, zinc finger nucleases and transposons, and subsequent use in SCNT has been shown. All offspring should be transgenic, but due to low developmental capacity only 1–5% of reconstructed embryos develop to vital offspring. (

C

) Lentivirus transfection: Requires advanced virus production facility and S2 safety laboratories. Replication-deficient lentiviruses are injected into the perivitelline space. Typically 50–90% of the offspring are transgenic, however, a high mosaicism rate and animals carrying multiple integrations are found. (

D

) Cytoplasmic plasmid injection (CPI): Circular expression plasmids are injected into the cytoplasm by employing transposon systems, active enzyme-catalyzed transgene integration of monomeric units can be achieved. Monomeric insertions into transcriptionally accessible regions are favored. Typically 40–60% of the offspring are transgenic, correlating to 6–10% of treated zygotes. (

E

) Sperm-mediated gene transfer (SMGT) and intracytoplasmic sperm injection (ICSI): For SMGT sperm cells are incubated with DNA, and are subsequently used for artificial insemination, thus avoiding any micromanipulation. However, the transgenesis rates are unpredictable and highly variable between laboratories. A more reliable extension of SMGT is the combination with intracytoplasmic sperm injection (ICSI). In this method sperm cell membranes are damaged (freezing, NaOH or drying) before incubation with DNA, then immobile (dead) spermatozoa are used for ICSI, followed by embryo transfer. However, the ICSI procedure is laborious and requires a highly skillful experimentalist, smoothing out the simplicity of SMGT. Reproduced with permission from Laible, G. Enhancing livestock through genetic engineering – Recent advances and future prospects.

Comparative Immunology, Microbiology and Infectious Diseases

32, 123–137 (2009).

Figure 28.4  Main objectives of agricultural applications for transgenic livestock technology. Image from Laible (2009).

Guide

Cover

Table of Contents

Start Reading

Preface

CHAPTER 1

Index

Pages

iv

ix

x

xi

xii

xiii

xiv

1

2

3

4

5

6

7

8

9

10

11

12

15

16

17

18

19

20

21

22

24

25

26

27

28

29

30

31

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

55

53

54

56

58

60

59

61

62

63

64

67

68

69

70

71

72

73

74

75

76

77

79

80

81

83

84

85

86

87

88

89

90

91

92

93

94

95

96

97

99

100

101

102

103

104

105

106

107

108

109

110

112

113

114

115

116

117

118

119

120

121

123

122

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

145

146

147

148

149

150

151

152

153

154

155

156

157

158

160

161

159

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

179

178

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

199

198

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

229

230

231

232

233

234

235

236

237

238

240

239

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257

258

259

260

261

262

265

266

267

268

269

270

271

272

273

274

275

276

277

278

279

280

281

282

283

284

285

286

287

288

289

290

291

292

293

294

295

296

297

298

299

300

301

302

303

304

305

306

307

308

309

310

311

312

313

314