1. PRINCIPLES OF CROP PRODUCTION (3 CREDIT HOURS)
LECTURE 11
CONTIG
SEQUENCE CONTIG
LINKAGE GROUP
LINKAGE ANALYSIS
GENETIC DRIFT
INTERFERENCE
LATERAL GENE TRANSFERS

2. CONTIG
A contig (from contiguous) is a set of overlapping DNA segments that together represent a consensus region of DNA.
In bottom-up sequencing projects, a contig refers to overlapping sequence data (reads).

3. SEQUENCE CONTIGS
A sequence contig is a contiguous, overlapping sequence read resulting from the reassembly of the small DNA fragments generated by bottom-up sequencing strategies.
The bottom-up DNA sequencing strategy involves shearing genomic DNA into many small fragments (bottom), sequencing these fragments, reassembling them back into contigs and eventually the entire genome (up).
In bottom-up sequencing projects, amplified DNA is sheared randomly into fragments appropriately sized for sequencing.
The subsequent sequence reads, which are the data that contains the sequence of each fragment, are assembled into contigs, which are finally connected by sequencing the gaps between them resulting in a sequenced genome.

4. SEQUENCE CONTIGS
The ability to assemble contigs depends on the overlap of reads.
Because shearing is random and performed on multiple copies of DNA, each portion of the genome should be represented multiple times in different fragment frames.
In other words, the sequences of the fragments (and thus the reads) should overlap.
After sequencing, the overlapping reads are assembled into contigs by assembly software.

5. LINKAGE GROUP All the genes on a single chromosome.
They are inherited as a group; that is, during cell division, they act and move as a unit rather than independently.
The existence of linkage groups is the reason some traits do not comply with Mendel’s law of independent assortment, i.e., the principle applies only if the genes are located on different chromosomes.
A linkage group is a collection of genes that are close enough in a genome to be inherited together.
The transcription and translation of genes in the group may or may not be linked together.
In simple cells lacking a nucleus called prokaryotes, the genes that make up operons units can be considered linkage groups.

6. LINKAGE GROUP
Eukaryotes, more complex cells, do not have an equivalent structural grouping in their genomes but despite a lack of operons, they can contain many linkage groups
Both prokaryotes and eukaryotes pass on linkage groups largely through recombination.
When a linkage group is involved in recombination, all the genes within the group tend to stay together, so all of the genes’ activities are relocated at the same time.
This movement can be to a different place on the same chromosome or to a different chromosome altogether.
Usually, nucleic acid movement by recombination does not disrupt a linkage group’s function.
Linkage groups can be broken apart during recombination, but the probability of that happening is fairly low.

7. LINKAGE ANALYSIS
In this approach, the aim is to find out the rough location of the gene relative to another DNA sequence called a genetic marker, which has its position already known.
All our chromosomes come in pairs, one inherited from our mother and one from our father. Each pair of chromosomes contains the same genes in the same order, but the sequences are not identical. This means it should be easy to find out whether a particular sequence comes from our mother or father. These sequence variants are called maternal and parental alleles.

8. LINKAGE ANALYSIS
In the case of the disease gene, the alternative alleles will be the normal allele and the disease allele, and they can be distinguished by looking for occurrences of the disease in a family tree or pedigree.
Genetic markers are DNA sequences that show polymorphism (variation in size or sequence) in the population.
They are present in everyone and they can be typed (the allele can be identified) using techniques such as the PCR.
This ability to determine the parental origin of a DNA sequence allows us to show whether recombination has taken place.
Recombination occurs in germ cells-the cells that make eggs and sperms.
In these cells, the maternal and paternal chromosomes pair up and exchange parts.
After recombination, the chromosomes contain a mixture of maternal and paternal alleles.

9. LINKAGE ANALYSIS
Diseased genes are mapped by measuring recombination against a panel of different markers spread over the entire genome.
In most cases, recombination will occur frequently, indicating that the disease gene and marker are far apart.
Some markers, however, due to their proximity, will tend not to recombine with the disease gene and these are said to be linked to it.
Ideally, close markers are identified that flank the disease gene and define a candidate region of the genome between 1 and 5 million bp in length.
The gene responsible for the disease lies somewhere in this region.
A B C If A is the disease gene and B and C are genetic markers,
a b c recombination is likely to occur much more frequently
A B c between A & C than it is
A B C a b C between A & B. This allows
a b c the disease gene to be mapped
relative to the markers B & C.

10. GENETIC DRIFT
When the population is large, the impact of genetic drift is much milder. When the reproductive population is small, however, the effects of sampling error can alter the allele frequencies significantly.
Genetic drift is therefore considered to be a consequential mechanism of evolutionary change primarily within small, isolated populations.
Although both processes affect evolution, genetic drift operates randomly while natural selection functions non-randomly.
While natural selection has a direction, guiding evolution towards heritable adaptations to the current environment, genetic drift has no direction and is guided only by the mathematics of chance.
As a result, drift acts upon the genotypic frequencies within a population without regard to their phenotypic effects.
In contrast, selection favors the spread of alleles whose phenotypic effects increase survival and/or reproduction of their carriers, lowers the frequencies of alleles that cause unfavorable traits, and ignores those that are neutral.

11. GENETIC DRIFT
In natural populations, genetic drift and natural selection do not act in isolation; both forces are always at play, together with mutation and migration.
However, the magnitude of drift on allele frequencies is larger when the absolute number of copies of the allele is small, e.g., in small populations.
Genetic drift or allelic drift is the change in the frequency of a gene variant (allele) in a population due to random sampling.
The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces.
A population’s allele frequency is the fraction of the copies of one gene that share a particular form.
Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation.

12. INTERFERENCE
The effect of one crossing over event in altering the probability of another crossing over event occurring at a nearby location.
This probability can be either increased (positive interference) or decreased (negative interference) but the latter is more usual.
Positive Interference: one crossover event inhibits the chances of another crossover event.
Negative Interference: It increases the chance of a second crossover.

13. INTERFERENCE
Recombination is initiated by programmed double-strand breaks (DSBs) of chromosomes.
During the repair of some DSBs, chromosome arms are exchanged generating crossovers (COs).
In most organisms, COs are not distributed randomly.
Closely spaced COs are observed less frequently than would be expected from a random distribution. This phenomenon is also known as crossover interference.
Each chromosome typically receives at least one crossover, which is known as “CO assurance”.

14. LATERAL GENE TRANSFERS
Also called horizontal gene transfers.
The transmission of genes between individual cells.
These mechanisms not only generate new gene assortments, they also help move genes throughout populations and from species to species.
The methods include transformation, transduction and conjugation.

15. EPIGENETICS
Relating to or arising from nongenetic influences on gene expression.
As an organism grows and develops, carefully orchestrated chemical reactions activate and deactivate parts of the genome at strategic times and in specific locations.
Epigenetics is the study of these chemical reactions and the factors that influence them.

16. THE END