Ovčereja na Norveškem

Ovčereja na Norveškem

Packgoats

Pack goats? Look here.

ASD talk - Growth performance of station tested rams in Slovenia

I attended the 17th ASD congress in Abano (Italy). I had a presentation about our model development for genetic evaluation of performance tested rams on test stations in Slovenia.

Growth performance of station tested rams in Slovenia

Fitting lactation curves/functions in R

It is quite some time ago since I wrote a set of lactation curves/functions in R. I put those functions in the animSci package. However, the package is in a mess for quite some time now - I was adding some new functions, but did not have time to finish the job properly. This is also the reason that package was not published. I got several inquries about the lactation functions. Therefore, I compiled the package and checked that lactation curves work as they should. The package is now published here with a warning.

The key fact to fit a particular lactation curve in R is to create a function that will take a numeric variable (days in milk) and create a design matrix that can be fed to model fitting function such as lm() or similar, e.g.,

someFunc <- function(x, ...) ... lm(y ~ someFunc(x)) 

It must be noted that this approach is not the most efficient for large datasets, since design matrix can be large, but this is a well known problem with using lm() in R. I implemented four lactation functions: Wood, Wilmink, Ali-Schaeffer, and Guo-Swalve, but others can be added. Bellow is the R code to run the lactation curves example on a data set of four milk traits in goats and the resulting figure. It would be interesting to compare this functions with Legendre polynomials (see here) and splines.

## Add my repository
tmp <- c("http://gregor.gorjanc.googlepages.com",           
         contrib.url(repos=getOption("repos"),
         type=getOption("pkgType")))

## Install the package
install.packages("animSci", contriburl=tmp, dep=TRUE)

## Load the package
library(package="animSci")

## Run the lactation curve examples
example(topic="lactCurves")

P.S. I got a nice cover up from David Smith.

Some lactation curves for milk traits in goat

EAAP Talk: Inference of genotype probabilities and derived statistics for PrP locus in sheep

I had a talk (see bellow) today at 60th EAAP meeting in Barcelona at the Sheep and Goats free communications session. Details of the talk are in the paper (a shortened version will appear on the EAAP site in the following days, but you might prefer the long version instead). I got some nice responses which is great. I have to mention that EAAP granted me a scholarship to present our results. This is greatly appreciated. I will post more about the trip to Barcelona in few days.

Inference of genotype probabilities and derived statistics for PrP locus in sheep

S kozami nad plevel

Lep primer, kako lahko s kozami uspešno "saniramo" zaraščeno površino s pleveli. Uspeh na slikah je kar preveč dober. Če bi imeli bistveno večjo površino, uspeh najbrž ne bi bil tako dober - pri tem je ključna obtežba - za "čiščenje" mora biti obtežba ZELO velika.

Generation interval calculation example

Here is a nice sheet with example of generation interval calculation in a flock of sheep.

Test for scrapie in goats

See here.

Chip for sheep

There is a lot of work in the area of SNP-chips for sheep. See:

• International Sheep Genomics Consortium (YouTube video)
• Australian Sheep Gene Mapping Web Site
• Sheep Genomics
• ...

However, genomic selection with "standard" chips might not be so successful in all sheep populations since there is a lot of variation in a sense that that the linkage disequilibrium is not so strong as in cattle - though I am saying that without having much experience!

Growth performance of station tested rams in Slovenia

This is our short communication for ASD 2009.

Update 2009-03-13: We had to shorten the manuscript to three pages. This of course lead to the exclusion of some results that will be published elsewhere.

Growth performance of station tested rams in Slovenia

Publish at Scribd or explore others: Draft Research Academic Work growth Sheep

Življenjska prireja ovc bovške in oplemenjene bovške pasme

Pri diplomski nalogi Kendi Perčič (PDF 575 kB) smo analizirali življenjsko prirejo ovc bovške in oplemenjene bovške pasme. Sedaj smo en del tega dela pripravili za objavo v reviji - tokrat hrvaški. Prispevek si lahko ogledate tukaj.

Genetski in selekcijski vidiki plodnosti ovac

Pravkar sem končal z branjem diplomske naloge Jernejke Drolec (1993) "Genetski in selekcijski vidiki plodnosti ovac". Moram priznati, da sem bil presenečen nad širino naloge in pokritostjo literature. Ker me tema zelo zanima, sem nalogo hitro prebral in bom v prihodnje najbrž še velikokrat pokukal vanjo.

Domestication of sheep and goats

GlobalDiv posted a new newsletter, where the interesting information about the domestication of sheep and goats. I can not copy the relevant part here, but you can take a look at page 6. Basically it says that there probably was not a domestication bottleneck in sheep and goats as it probably occured in cattle. This might be also the reason, we have so much variability in sheep and goats today in comparison to cattle.

Genetic diversity in Alpine sheep breeds - emphasis on Slovenian breeds

Dalvit et al. have published a paper "Genetic diversity in Alpine sheep breeds" in Small Ruminant Research. They attempted to study the genetic diversity --> similarity via microsatellite molecular markers in breeds of sheep kept in the region of Alps. Their study involved animals of the following breeds:

• Italy
• Bergamasca (TIHO, SRR paper)
  
• Biellese (TIHO)
  
• Schwarzbraunes Bergschaf = Black-brown mountain sheep (TIHO)
• Tiroler Bergschaf = Tiroler mountain sheep (TIHO)
  
• Schnalserschaf = ??? sheep (???)
  
• Germany
• Brillenschaf = Carinthian (TIHO-DE, TIHO-AT, AT)
  
• Weisses Bergschaf = White mountain sheep (TIHO)
  
• Slovenia
• Bovška = Bovec (Drobnic@, TIHO)
  
• Jezersko-Solčavska = Jezersko-Solčava (Drobnic@, TIHO)

My interest in this article is of course due to the Slovenian breeds of sheep: the Bovec sheep and the Jezersko-Solčava sheep breed. The main result regarding these two breeds are that Bovec, Jezersko-Solčava and Carinthian were in the same cluster according to the Reynolds' genetic distance (e.g. see this lecture). This is partly an expected result, since to my knowledge Jezersko-Solčava and Carinthian are phenotypically very similar and the origin and history of these two breeds are similar. Sometimes a name Seeländerschaf was also used for Brillenschaf, which basically means Jezersko (~ lake land) sheep. The following Fst and mean molecular coancestry (MC) values were obtained:

• Jezersko-Solčava - Carinthian, Fst = 0.053, MC = 0.188
  
• Jezersko-Solčava - Bovec, Fst = 0.056 , MC = 0.201
  
• Bovec - Carinthian, Fst = 0.084, MC = 0.176
  

Surprisingly, the molecular coancestry showed that Jezersko-Solčava breed has a bit more similarities with Bovec than with Carinthian breed, though Fst was lower for Jezersko-Solčava - Carinthian pair. The difference for mean molecular coancestry is not large, but I would say that Jezersko-Solčava and Carinthian are phenotypically much more similar. Bovec sheep is phenotypically quite different to Jezersko-Solčava. There surely have been different ways of selection of Bovec and Jezersko-Solčava breed since the former is today used for milk production, while the later is not milked at all and used as a meat type sheep i.e. only for rearing lambs. In study of Dalvit et al. Carinthian animals were sampled from Germany. I wonder if the same results would be obtained with animals from Austria. Additionally, TIHO site "states" that there has been some introgression of White mountain (Weisses Bergschaf) breed into Carinthian breed in Germany. However, this does not mean that Carinthian breed in Germany today still has any of the "genes" from White mountain. For example, in Slovenia Romanov rams were used in some flocks of Jezersko-Solčava sheep, but those animals were never treated as Jezersko-Solčava, but as a separate breed called improved Jezersko-Solčava or JSR in short. JSR breed is today a breed with the biggest population among sheep in Slovenia. Jezersko-Solčava breeds is maintained in its "original" environment, but also in some other parts of the Slovenia.

It was also interesting that Jezersko-Solčava and Carinthian were not clustered with Bergamasca. Historical records for both breeds say that at some time in the past breeders used Bergamasca and Paduaner rams. It seems that only some introgression of Bergamasca was done. The following Fst and molecular coancestries (MC) were obtained:

• Jezersko-Solčava - Bergamasca, Fst = 0.050, MC = 0.185
• Carinthian - Bergamasca, Fst = 0.077, MC = 0.160
• Jezersko-Solčava - Carinthian, Fst = 0.053, MC = 0.188

The mean molecular coancestry for the Jezersko-Solčava - Bergamasca pair was practically of the same value as for the Jezersko-Solčava - Carinthian pair, while Carinthian - Bergamasca pair had a bit lower value. I again think this is not consistent with the history of Jezersko-Solčava and Carinthian breed. Bergamasca breed was involved in both populations, but that was some time ago. I would expect more similarities between animals of Jezersko-Solčava and Carinthian breed. These peculiarities could be due to the Germans vs Austrian Carinthian population, chosen set of microsatellites, substructures etc.

P.S. Slightly different results were obtained in "another version" as published in "Best Practices Manual for sheep and goat breeding". In that version, Jezersko-Solcava and Carinthian breed has greater similarity than Jezersko-Solcava (or Carinthian) and Bovec breed.

P.S. See also the "Atlas of Alpine sheep breeds" by Feldmann et al.

Calculation of PrP genotype and NSP type probabilities in Slovenian sheep

Paper "Calculation of PrP genotype and NSP type probabilities in Slovenian sheep" is finnaly finnished. I will send it to the journal today. This is a sort of a companion paper to the previous one where the methods were derived and tested, while in this paper we used those methods on all sheep breed in the Slovenian breeding programme for sheep. Here is the abstract:

PrP genotype probabilities in ungenotyped Slovenian sheep were calculated. Altogether 36,083 ewes and rams of various breeds were included into the analysis. PrP genotype was known for 10,504 animals. Five different PrP alleles were present in the data. Pedigree and genotype data structure differed between breeds. Iterative allelic peeling with incomplete penetrance model was used for the calculation of genotype probabilities for each animal given the genotype data of relatives. Analyses were performed for each breed separately. Additionally, NSP (National Scrapie Plan) type probabilities and the average NSP type were calculated from the genotype probabilities. Results were presented for live animals only. There were no animals with additionally identified PrP genotype or NSP type with certainty. With 95 % probability PrP genotype was additionally identified for 0.0 to 5.7 % animals of different breeds. NSP type was additionally identified with the same probability for 0.0 to 34.9 % animals of different breeds. We maintain that the low number of additional identifications was due to: a large number of alleles, intermediate allele frequencies, data structure, a uniform prior, and the use of incomplete penetrance model. Additional identifications provided some cost savings, but did not prove useful in the selection for scrapie resistance of the entire populations. The average NSP type should be used instead, since it can be calculated for all animals and encompasses all information from genotype probabilities.

Use of genotype probabilities in selection on PrP genotype in sheep

I have finished paper on use of genotype probabilities in selection on PrP genotype in sheep. PrP genotype is one of the main factors for susceptibility to scrapie in sheep. Here is the link to the last version of the paper. And the abstract:

PrP genotype probabilities for ungenotyped animals of Jezersko-Solcava sheep breed were calculated. Data consisted of 10,429 animals among which 3,669 had PrP genotype data. There were 2,673 live ungenotyped animals. Five PrP haplotypes were present with the following frequencies: ARR 0.174, AHQ 0.074, ARH 0.083, ARQ 0.632, and VRQ 0.037. All 15 PrP genotypes were found. Iterative allelic peeling with incomplete penetrance model as implemented in GenoProb program was used for calculation of PrP genotype probabilities. There were only some additional PrP genotype and NSP type identifications with high probability. Main reasons for a low number of additional identifications can be attributed to large number of haplotypes with moderate frequencies, incomplete penetrance model, uniform prior, and inherently pedigree and genotype data structure. Incomplete penetrance model caused inflation of small probabilities but has proved to be very useful for field data where conflicting data rise due to pedigree of genotype errors. Novel parameters (maximal NSP type, average NSP type and its variance and accuracy) are proposed that make use of PrP genotype probabilities and can facilitate selection for scrapie resistance. Parameters were derived with emphasis on practical implementation of selection schemes based on NSP types. Maximal NSP type can be used to infer maximal potential scrapie susceptibility of individual ungenotyped animals as well as for whole flocks. Average NSP type makes full use of all PrP genotype probabilities and is the most useful and practical parameter for selection on NSP type and therefore PrP genotype. In addition, accuracy of average NSP type should also be used as selection criteria in order to assess the variability of average NSP type.

PrP allele (haplotype) and genotye frequencies in sheep II

I wrote about better display of PrP haplotype and genotype frequencies in last post. I have proposed a set of histograms instead of a table. However, parallel plot (R example 1, R example 2, random web article) is even better. Here is my attempt to use it on data compiled by Lühken et al. (2008):

• parallel plot of allele (haplotype) frequencies
• parallel plot of genotype frequencies

There is still room for improvement of the plot i.e. axis, ticks, ... For example, I would prefer to have 0-100 % scale on y axis. Anyway, the idea of parallel plot for haplotype/genotype frequencies in case of many haplotypes/genotypes should be clear. Here is also the data and R code to produce the plots.

PrP allele (haplotype) and genotye frequencies in sheep

Lühken et al. (2008) published estimates of PrP allele (haplotype) and genotye frequencies in for 56 sheep breeds in Europe and Middle East. They made a huge one-page table with all the numbers. Gosh, it is hard to read that table! There is to much info. It would be much better if they would plot this data. Well, I did and I think it is much more informative. I just copied their table into a spreadsheet and used R to do the plotting

• plot of allele (haplotype) frequencies
• plot of genotype frequencies

Progress in mapping sheep genome

http://www.engormix.com/e_news_view.asp?news=12256&AREA=OVI

Število živine, podrobni podatki, Slovenija, 1.12. 2007

SURS je objavil stalež živine na dan 1.12.2007. Zame je bistveno tole: "Število drobnice se v letu 2007 ni bistveno spremenilo". Nekaj je sicer večjih sprememb pri številu plemenskih ovc, ki so bile prvič pripuščene in sicer za "ne mlečne" pasme. Sicer pa je število ovc skupaj ocenjeno na 131.180 (~86.500 "ne mlečnih" plemenskih ovc in ~4.000 mlečnih plemenskih ovc), za koze pa na 28.228 (~14.000 "ne mlečnih" plemenskih koz in ~5.000 mlečnih plemenskih koz).

Tukaj pa so povezave do preglednic - pišem tukaj, da ne bom spet polnil svoje zaznamke:

• Število živine
• Prireja mesa ...
• Zakol živine v klavnicah
• Mleko in mlečni izdelki

Pa še povezava do celotnega seznama.