Aquatic Species Breeding,Conservation Management Assisted System Based On R Software And Its Application

Best linear unbiased prediction?BLUP?breeding technology has been widely used in aquaculture species breeding and approved successfully in many more species,e.g.atlantic salmon,tilapia new strain exploration.The advantage of this technology is cost-effective and more accuracy in breeding value estimation,while its drawback is complicated calculation process and huge amount of calculation.One key factor of BLUP breeding is breeding value estimation.R is open,free software for statistic coding environment and supply statistical analysis and graphical intuitive display.What is more important is that R is applied in the quantitative genetic breeding.So,this thesis will develop the related scripts during the aquatic species breeding and conservation based R in order to improve the aquatic germplasm breeding work's accuracy and precision and address the complicated calculation problem in breeding program.The results showed that:1.Family based BLUP mating program developed by RUsing R 3.1,14 we develop the related scripts during the BLUP breeding,which contain i2016Tilapia.R and Mating_breeding₂016Carp05.The previous one is used to raw data set collection,checking,integrating and transformation used to calculate in DMU software.The latter one is used to make the mating design after the breeding values calculated by DMU.In order to validate these scripts,the article takes the common carp and tilapia for example,the first script produce the integrated data set which include growth performance,gender,tagging number,pedigree information and so on.Pedigree data set and best mixed model also supplied in this step.The second script can quote the raw data outputted by DMU and can integrate the breeding values with the previous collected data set.Note:the parameters should be setting in the second script:N_Siglem present the number of male in one family plus one?1 male × 2 female in common carp,3 male × 4 female in tilapia?.The final mating table can be produced by running two scripts.2.Overlapping specie conservation and random specie conservation simulation developed by RProduceSimData_output.R and BottSim.R were developed for species conservation based R 3.1.14.In the first scipt which used to conservation simulation,NumLocus present number of locus,PopSize present population size,FamSize stand for the family size,SexRatio present the sex ratio,NumOverlap present the number of generations in overlapping pattern,IterStep present the iterated steps.After setting the above parameters,we can run this script and produce the simulated data set which can be used to do genetic diversity analysis.The parameter directoverlap needed to be paid more attention,where it equals to Incresement present the back overlapping conservation and equals to Decresement present the forward overlapping conservation.BottSim.R was used to bottle neck analysis and output the observed allel number,expected allel number,oberserved heterozygosity,expected heterozygosity and fixed index.For bottle neck analysis,BottleSim2.6.1 was introduced to do some bottle neck analysis and BottSim.R can used to plot the bottle neck analysis result.3.Application of mating program design using R in Huanghe new strain carp80 families?60 selection families and 20 control families?of Huanghe new strain generation 3 were generated according to the quantitative genetic based BLUP method by the scripts in the chapter 2 scripts and the data set collected of Huanghe new strain carp generation 2.Besides these,Cultural test for 8 weeks using randomly selected 48 families?38 selection families and 10 control families?with 240 total number showed the results:compared to the control,selection line had the 20.84%body weight gain.Whatever normal feed or higher carbohydrate feed supplementation can make the selection have better growth performance than the control line.Furthermore,for the long data set?contains the all generation data?analysis process,data integration and checking part can take the less time?half a day?than the previous SAS scripts?one week?.80 families mating program only use 5 minutes while in the past it finish require 3 days.Using the chapter 2 scripts can control and supervise the whole data management process...