Date of Publication:
August 10, 2019

Publication:
The Better Breeding Blog

Excerpt:
The aim of selection is to increase the frequency of desired alleles and decrease the frequency of undesired genes in a population, ideally producing animals that breed true for the genotypes and phenotypes selected for.

One influence on the effectiveness of selection on gene frequency changes is the initial gene frequency in a population. Consider two alleles at locus A: A₁ is wanted and A₂ is not. This graph plots the frequency of A₂ in each successive generation, showing the effect of selection against that unwanted allele A₂ over many generations:

Read the rest of the article: https://betterbreeding.solutions/index.php/blog/effectiveness-of-selection-initial-gene-frequency-and-fitness-differences

Date of Publication:
August 02, 2019

Publication:
The Better Breeding Blog

Excerpt:
Below are some tables that summarise the levels of confidence and numbers of matings required to detect a completely recessive allele.
These assume that all the mates are of one group, such as all are known carriers, or all are daughters, or all are randomly picked from a population.

Read the rest of the article: https://betterbreeding.solutions/index.php/blog/summaries-of-levels-of-confidence-and-numbers-of-matings

Date of Publication:
June 21, 2019

Publication:
Frontiers in Genetics, June 2019, Volume 10, Article 586

Abstract:
The development of high-quality chromosomally assigned reference genomes constitutes a key feature for understanding genome architecture of a species and is critical for the discovery of the genetic blueprints of traits of biological significance. South American camelids serve people in extreme environments and are important fiber and companion animals worldwide. Despite this, the alpaca reference genome lags far behind those available for other domestic species. Here we produced a chromosome-level improved reference assembly for the alpaca genome using the DNA of the same female Huacaya alpaca as in previous assemblies. We generated 190X Illumina short-read, 8X Pacific Biosciences long-read and 60X Dovetail Chicago® chromatin interaction scaffolding data for the assembly, used testis and skin RNAseq data for annotation, and cytogenetic map data for chromosomal assignments. The new assembly VicPac3.1 contains 90% of the alpaca genome in just 103 scaffolds and 76% of all scaffolds are mapped to the 36 pairs of the alpaca autosomes and the X chromosome. Preliminary annotation of the assembly predicted 22,462 coding genes and 29,337 isoforms. Comparative analysis of selected regions of the alpaca genome, such as the major histocompatibility complex (MHC), the region involved in the Minute Chromosome Syndrome (MCS) and candidate genes for high-altitude adaptations, reveal unique features of the alpaca genome. The alpaca reference genome VicPac3.1 presents a significant improvement in completeness, contiguity and accuracy over VicPac2 and is an important tool for the advancement of genomics research in all New World camelids.

Read the rest of the article: https://www.frontiersin.org/articles/10.3389/fgene.2019.00586/full

Date of Publication:
July 27, 2019

Publication:
The Better Breeding Blog

Excerpt:
To recap from last week:

1. The formulae for one offspring per mating and with mates from the same group
(eg all are known carriers, or all are daughters of the tested sire, or all are randomly selected from a population) are:

Read the rest of the article: https://betterbreeding.solutions/index.php/blog/the-maths-of-matings-part-2

Date of Publication:
unknown

Publication:
Molecular Cytogenetics and Genomics Laboratory, Texas A&M University

Excerpt:
In 2005, the alpaca became the first camelid species to have its genome sequenced, in an effort led by Dr. Warren Johnson at the National Cancer Institute. The Alpaca Genome Project, which also includes the generation of a medium-density Radiation Hybrid (RH) map for the alpaca, set the foundation for genomic studies in camelids.

Read the rest of the article: https://betterbreeding.solutions/index.php/blog/the-maths-of-matings-supplementary

Date of Publication:
unknown

Publication:
unknown

Excerpt:
Australia as a leader in the sheep industry has the experience, infrastructure, institutions, and assisted reproductive technologies required for genetic improvement of alpaca herds. With the development of artificial insemination, embryo transfer techniques, in vitro production of embryos (IVP) and the inauguration of a genetic improvement program for alpacas, it will be possible to develop a breed of extra fine Australian alpaca comparable to the alpaca kept by the Incas before the conquest in relatively few years.

Read the rest of the article: https://pdfs.semanticscholar.org/171f/a1d370c674b4e10ae9d03c1a1c71c326fdfa.pdf

Date of Publication:
July 21, 2019

Publication:
The Better Breeding Blog

Excerpt:
In The Maths of Matings, Part 1 I promised to write a supplementary post explaining mathematical logs, and here it is!

Read the rest of the article: https://betterbreeding.solutions/index.php/blog/the-maths-of-matings-supplementary

Date of Publication:
July 19, 2019

Publication:
The Better Breeding Blog

Excerpt:
Having gone over confidence levels, it’s time to apply that and step through some maths!

Let’s now calculate confidence levels and the required number of test matings to be statistically confident that a tested animal is not a carrier of a recessive allele.

Everything below assumes that the tested animal is a sire, that there is one offspring from one mating, and that all mates (dams) are of the same type for the allele of interest. That is, they are either all known carriers, or are all daughters of the tested sire, or are all randomly selected from the same population.

Read the rest of the article: https://betterbreeding.solutions/index.php/blog/the-maths-of-matings-part-1