Plant breeding and genetics club videos

Plant breeding and genetics club at K-state have a nice website, which hosts videos from the symposia they organised (there was one in 2013 and one is planned for 2015).

Potential of genotyping-by-sequencing for genomic selection in livestock populations

Our new paper titled "Potential of genotyping-by-sequencing for genomic selection in livestock populations" has been published in Genetics Selection Evolution. This work shows that genotypes called from low-coverage sequencing data can be equally or even more powerful for genomic prediction than high-quality SNP genotypes. In particular manipulation of coverage allows us to increase number of genotyped individuals at the expense of genotype quality and this can bring us a long way before accuracy of genomic predictions falls significantly. Another useful application is in increasing selection intensity by genotyping more/all selection candidates.

Simulation of different strategies to implement genomic selection in plant breeding

Our submitted abstract for the VIPCA conference.

Gorjanc G, Crossa J, Dreisigacker S, Autrique E, Hickey J

Genomic information provides a rich resource for plant improvement. The greatest advantage of genomic information is achived when used early in a programme. The aim of this contribution was to present different ways of utilizing genomic information in cross and self pollinated species early in the bi-parental population (BP) cycle in the F2 generation by simulation. Simulation mimicked a real breeding programme with BP of different degree of relationship. Simulated trait heritability was 0.5. Predictions were always within a focal BP (BPX) avoiding the effect of inflated accuracy due to population structure. Measure of interest was the correlation between true and predicted additive genetic value (accuracy). Predictions were based on training on collected data within BPX, from BP having one parent in common with BPX (BPPC), from BP having one grand-parent in common with BPX (BPGC), and from unrelated BP (BPUR). Results show that genomic predictions can be accurate early in the cycle. Accurate predictions within the BPX can be obtained with a small number of markers and moderate phenotyping of F2 derived lines. With 200 markers and 50 phenotypes accuracy was around 0.60 and increased to 0.80 with 100 phenotypes. Use of information from relatives requires denser marker panels and more phenotypes to properly model the expanding number of linkage blocks in progressively distantly related BP. However, these requirements can be spread over many related BP reducing the cost per BP. For example accuracy of 0.6 can be achieved by using 1,000 markers and 50 phenotypes from 4 BPPC and 40 BPUR or by using 10,000 markers and 50 phenotypes from 8 BPGC and 50 BPUR. Requirement for denser marker panels increases needed investment, which can be offset by proper use of imputation method making the whole procedure cost effective for real applications.

InterBull and ICAR papers

Reliability of breeding values in selected populations Partitioning International Genetic Trends by Origin in Holstein bulls

Polyploidy in sugarcane

While reading UseR conference abstracts I came across this sentence: "Sugarcane is polypoid, i.e., has 8 to 14 copies of every chromosome, with individual alleles in varying numbers." Vau! This generates really complex genotype system. Say we have biallelic gene with alleles being A and B. In diploids the possible genotypes are AA, AB, and BB. Given the above sentence in sugarcane possible genotypes are any permutation of A's and B's in a series of 8 to 14 alleles. I am not sure if 9, 11, and 13 are also allowed, that is having even number of chromosomes. In any case such permutations result in really large numbers!

Thinking about this a bit further it appears that the whole system is not that complex once we realize that genotyping does not tell as about the order of alleles (we can not distinguish between AB and BA), which simplifies from all possible permutations to all possible combinations, e.g., for biallelic gene in tetraploids this would correspond to 5 combinations and 16 permutations.

Bellow is an R snippet that shows how to enumerate all possible combinations or permutations

## Load package having nice combinatorial functions
library(package="gtools")
 
## Specify alleles - just two for simplicity
alleles <- c("A", "B")
 
## Possible genotypes for diploids
combinations(n=length(alleles), r=2, v=alleles, repeats.allowed=TRUE)
##      [,1] [,2]
## [1,] "A"  "A" 
## [2,] "A"  "B" 
## [3,] "B"  "B" 
 
## Possible genotypes for tetraploids
combinations(n=length(alleles), r=4, v=alleles, repeats.allowed=TRUE)ž
##      [,1] [,2] [,3] [,4]
## [1,] "A"  "A"  "A"  "A" 
## [2,] "A"  "A"  "A"  "B" 
## [3,] "A"  "A"  "B"  "B" 
## [4,] "A"  "B"  "B"  "B" 
## [5,] "B"  "B"  "B"  "B" 
 
permutations(n=length(alleles), r=4, v=alleles, repeats.allowed=TRUE)
##       [,1] [,2] [,3] [,4]
##  [1,] "A"  "A"  "A"  "A" 
##  [2,] "A"  "A"  "A"  "B" 
##  [3,] "A"  "A"  "B"  "A" 
##  [4,] "A"  "A"  "B"  "B" 
##  [5,] "A"  "B"  "A"  "A" 
##  [6,] "A"  "B"  "A"  "B" 
##  [7,] "A"  "B"  "B"  "A" 
##  [8,] "A"  "B"  "B"  "B" 
##  [9,] "B"  "A"  "A"  "A" 
## [10,] "B"  "A"  "A"  "B" 
## [11,] "B"  "A"  "B"  "A" 
## [12,] "B"  "A"  "B"  "B" 
## [13,] "B"  "B"  "A"  "A" 
## [14,] "B"  "B"  "A"  "B" 
## [15,] "B"  "B"  "B"  "A" 
## [16,] "B"  "B"  "B"  "B" 
 
## Possible genotypes for 8-14 ploids
spectrum <- seq(from=8, to=14, by=2)
nS <- length(spectrum)
retC <- vector(mode="list", length=nS)
retP <- vector(mode="list", length=nS)
for(i in 1:nS) {
  retC[[i]] <- combinations(n=length(alleles), r=spectrum[i], v=alleles, repeats.allowed=TRUE)
  retP[[i]] <- permutations(n=length(alleles), r=spectrum[i], v=alleles, repeats.allowed=TRUE)
}
combC <- sapply(retC, nrow)
combP <- sapply(retP, nrow)
cbind(spectrum, combC, combP)
##      spectrum combC combP
## [1,]        8     9   256
## [2,]       10    11  1024
## [3,]       12    13  4096
## [4,]       14    15 16384

Created by Pretty R at inside-R.org

19th Animal Science Days (ASD) registration and call for papers

See here.

Kako ravnajo s poginulimi živalmi čez lužo

Glej "Dealing With Deadstock". Pri nas pa v določenih pogledih pretiravamo do skrajne mere. Se povsem strinjam, da mora biti ta segment živinoreje primerno urejen, a za to izvajati "vesoljske" procese ni razumno.

EU petition: STOP Long Animal Transports

If you live in EU, please got to http://www.8hours.eu and add Your vote against long animal transports. Thank you!

AIPL writings and presentations

I noticed that researchers at AIPL (USA) are very active with the current hot topic in animal breeding - genomic (genomewide) selection (Meuwissen et al., 2001). I asked Paul VanRaden for a reprint and he has kindly pointed me to the website of AIPL with conference proceedings and presentations. These two sites are very valubale resource for study - not only forthe topic of genomic selection, but also for dairy cattle breeding!

"Giant" bull and ram

Full story ...

Full story ...

Program and videos from the Lush Visions Symposium - Animal Breeding Plans

Lush Visions Symposium - Animal Breeding Plans was held on April 25, 2008 at the Iowa State University, Ames, IA. Here are links to the programme and videos. Putting videos on the web is really a great thing as we can now watch conferences from home. Of course it is better to be there, but that involves costs, time, etc. I think that traking the videos and publishing them is also a great was to disseminate the work and finally, you at least know which person is behind the name.

Quantitative genetics in maize

Crow wrote a paper "90 Years Ago: The Beginning of Hybrid Maize" in 1998. It is a nice overview of development of hybrid lines of maize - the theory as well as practice (using genetics and agricultural techniques).

On related topic, Edwards and Lamkey analysed effect of inbreeding from quantitative genetics perspective i.e. they estimated all components of variance due to dominant effect of alleles in noninbred and inbred individuals.

Two new chicken breeds for welfare friendly market

UK market will get two breeds that target welfare friendly market. Everything for the buyer! Original news.

Opening farm subsidies to public scrutiny

Mariann Fischer Boel has blogged about opening farm subsisides to public in detail on the internet by the end of April next year. More ...