Kontrola uzgoja u srodstvu u populaciji banijske šare svinja pomoću optimizacijskih metoda

The aim of the study was to estimate genetic diversity parameters for Banija spotted pig population and to apply optimisation methods to control the inbreeding in the population in three different scenarios. The first scenario consisted of minimizing inbreeding by minimizing the average kinship without considering breeding values. The second scenario was to minimize inbreeding by minimizing the average kinship accounting for breeding values. The third scenario was to apply traditional optimal contribution selection by maximizing the breeding value of the offspring. A total of 5 boars and 49 sows were selected to create mating plan minimise inbreeding in the next generation. The average inbreeding coefficient in the population was 6.97, while effective population size was 8.47. In the first scenario, different kinship constrains between candidates resulted in a change in the number of selected animals and a change in the average breeding values, such that the number of selected candidates increased when the constraint on kinship was stronger, with a simultaneous decrease in breeding values. The second scenario resulted in increased inbreeding when additional weight was placed on genetic gain. The Maximisation of breeding values resulted with drastically increased average inbreeding coefficient in the next generation. Due the small total and effective population size, the application of optimisation methods demonstrated that genetic improvement is possible at a high cost of loss of the genetic variability and preservation of diversity remains the first objective in the breeding programme for Banija spotted pig.Cilj istraživanja bio je procijeniti parametre genetske raznolikosti za populaciju banijske šare svinje i primijeniti metode optimizacije s ciljem kontrole uzgoja u srodstvu u populaciji u tri različita scenarija. Prvi scenarij bio je minimizirati uzgoj u srodstvu minimiziranjem prosječnog srodstva u populaciji bez uključivanja uzgojnih vrijednosti. Drugi scenarij bio je minimiziranje uzgoja u srodstvu minimiziranjem prosječnog srodstva uzimajući u obzir uzgojne vrijednosti. Treći scenarij bio je primijeniti tradicionalni pristup selekciji s optimiziranim doprinosima doprinosa maksimiziranjem uzgojne vrijednosti u potomstvu. Ukupno je odabrano 5 nerastova i 49 krmača za izradu plana sparivanja koji će omogućiti minimiziranje inbreedinga u sljedećoj generaciji. Prosječni F u populaciji bio je 6,97, a Ne 8,47. U prvom scenariju različita ograničenja srodstva između kandidata rezultirala su promjenom broja odabranih životinja i mijenjanjem prosječnih uzgojnih vrijednosti tako da se broj odabranih kandidata povećavao kada je ograničenje srodstva bilo jače, uz istodobno smanjenje uzgojnih vrijednosti. Drugi scenarij rezultirao je povećanim uzgojem u srodstvu kada je dodana dodatna težina na genetski napredak. Maksimiziranje uzgojnih vrijednosti rezultiralo je dramatičnim povećanjem koeficijenta uzgoja u srodstvu u sljedećoj generaciji. Zbog male ukupne i efektivne veličine populacije, primjena metoda optimizacije pokazala je da je genetski napredak moguć uz veći gubitak genetske varijabilnosti, a očuvanje raznolikosti ostaje prvi cilj u uzgojnom programu analizirane pasmine

GENETIC DIVERSITY OF CROATIAN AUTOCHTHONOUS PIG BREEDS

Cilj rada bio je opisati genetsku strukture te parametre genetske raznolikosti autohtonih pasmina svinja Hrvatske temeljem dosadašnjih podataka u dostupnoj literaturi. Očuvanju genetske raznolikosti autohtonih pasmina se posljednjih desetljeća pridaje sve veća pozornost jer predstavljaju kulturno i genetsko nasljeđe te zbog svoje otpornosti na bolesti i prilagodljivosti različitim uvjetima mogu imati važnu ulogu u popravljanju konstitucijskih svojstava hibrida i plemenitih pasmina. Povećana uporaba hibridnih linija i plemenitih pasmina u uzgoju i proizvodnji rezultirala je smanjenjem populacija izvornih pasmina te promjenom njihove genetske strukture. Kao posljedica navedenog, populacije izvornih pasmina imaju vrlo visoku stopu uzgoja u srodstvu, nisku genetsku raznolikost te vrlo često u ovakvim populacijama dolazi do procesa „uskog grla“. U cilju održavanja genetske raznolikosti hrvatskih autohtonih pasmina svinja potrebno je provoditi plansko sparivanje uz kontrolu podrijetla, praćenje održive stope uzgoja u srodstvu te provoditi selekciju s optimiziranim doprinosom u uzgojnim programima.The purpose of the study was to show the genetic structure and diversity parameters of Croatian autochthonous pig breeds based on available literature data. The preservation of genetic diversity of autochthonous breeds has recently been increasingly emphasized due to their cultural and genetic importance. Their resistance to disease and their adaptability to different conditions can play an important role in the improvement of constitutive characteristics of hybrid and noble pig breeds. The increased use of hybrids and modern breeds in breeding and production resulted in a decrease in the populations of autochthonous breeds and a change in their genetic structure. As a consequence, the population of autochthonous breeds has a very high rate of inbreeding, low genetic diversity and very often in these populations there is a bottleneck process. In order to maintain genetic diversity of Croatian autochthonous pig breeds, it is necessary to carry out planned breeding with control of origin, monitor sustainable inbreeding rate and carry out optimum contribution selection in breeding programmes

Genomic Characterization of Local Croatian Sheep Breeds-Effective Population Size, Inbreeding & Signatures of Selection

The Istrian (IS) and the Pag sheep (PS) are local Croatian breeds which provide significant income for the regional economy and have a cultural and traditional importance for the inhabitants. The aim of this study was to estimate some important population specific genetic parameters in IS (N = 1293) and PS (N = 2637) based on genome wide SNPs. Estimates of linkage disequilibrium effective population size (Ne) evidenced more genetic variability in PS (Ne = 838) compared to IS (Ne = 197), regardless of historical time (both recent and ancient genetic variability). The discrepancy in the recent genetic variability between these breeds was additionally confirmed by the estimates of genomic inbreeding (FROH), which was estimated to be notably higher in IS (FROH>2 = 0.062) than in PS (FROH>2 = 0.029). The average FROH2–4, FROH4–8, FROH8–16, and FROH>16 were 0.26, 1.65, 2.14, and 3.72 for IS and 0.22, 0.61, 0.75, and 1.58 for PS, thus evidencing a high contribution of recent inbreeding in the overall inbreeding. One ROH island with > 30% of SNP incidence in ROHs was detected in IS (OAR6; 34,253,440–38,238,124 bp) while there was no ROH islands detected in PS. Seven genes (CCSER1, HERC3, LCORL, NAP1L5, PKD2, PYURF, and SPP1) involved in growth, feed intake, milk production, immune responses, and resistance were associated with the found autozygosity. The results of this study represent the first comprehensive insight into genomic variability of these two Croatian local sheep breeds and will serve as a baseline for setting up the most promising strategy of genomic Optimum Contribution Selection

Control of inbreeding in Banija spotted pig using optimisation methods

Cilj rada bio je procijeniti i opisati specifične parametre populacije banijske šare svinje, te primijeniti metodu selekcije s optimalnim doprinosima u svrhu postizanja istovremenog genetskog napretka i kontrole uzgoja u srodstvu u tri različita scenarija. Scenariji su se sastojali od minimiziranja srodstva bez uzimanja u obzir uzgojnih vrijednosti, minimiziranje srodstva uzimajući u obzir i uzgojne vrijednosti jedinki, te maksimiziranje uzgojnih vrijednosti. Ukupno je odabrano 5 nerasta i 49 krmača za izradu sheme parenja. Specifični populacijski parametri banijske šare svinje pokazali su nisku razinu genetske raznolikosti uz visoke prosječne koeficijente uzgoja u srodstvu i nisku efektivnu veličinu populacije. Zbog male ukupne i efektivne veličine populacije, primjena optimizacijskih metoda pokazala je da je genetsko poboljšanje moguće na račun gubitka genetske raznolikosti u populaciji. No, primjena optimizacijskih metoda rezultirala je nižom prosječnom srodnošću odabranih jedinki.The purpose of this paper was to evaluate and describe specific parameters for Banija spotted pig population, and to apply optimal contribution selection to achieve simultaneous genetic progress and inbreeding control in three different scenarios. These scenarios consisted of minimizing kinship without taking breeding values into account, minimizing kinship with considering breeding values of individuals, and maximizing breeding values. A total of 5 boars and 49 sows were selected to create a breeding scheme. The specific population parameters for Banija spotted pig showed a low level of genetic diversity with high average inbreeding coefficients and a low effective population size. Due to the small total and effective population size, the use of optimization methods has shown that genetic improvement is possible at the expense of loss of genetic diversity in the population. However, the application of optimization methods resulted in lower average kinship between selected individuals

Control of inbreeding in Banija spotted pig using optimisation methods

Cilj rada bio je procijeniti i opisati specifične parametre populacije banijske šare svinje, te primijeniti metodu selekcije s optimalnim doprinosima u svrhu postizanja istovremenog genetskog napretka i kontrole uzgoja u srodstvu u tri različita scenarija. Scenariji su se sastojali od minimiziranja srodstva bez uzimanja u obzir uzgojnih vrijednosti, minimiziranje srodstva uzimajući u obzir i uzgojne vrijednosti jedinki, te maksimiziranje uzgojnih vrijednosti. Ukupno je odabrano 5 nerasta i 49 krmača za izradu sheme parenja. Specifični populacijski parametri banijske šare svinje pokazali su nisku razinu genetske raznolikosti uz visoke prosječne koeficijente uzgoja u srodstvu i nisku efektivnu veličinu populacije. Zbog male ukupne i efektivne veličine populacije, primjena optimizacijskih metoda pokazala je da je genetsko poboljšanje moguće na račun gubitka genetske raznolikosti u populaciji. No, primjena optimizacijskih metoda rezultirala je nižom prosječnom srodnošću odabranih jedinki.The purpose of this paper was to evaluate and describe specific parameters for Banija spotted pig population, and to apply optimal contribution selection to achieve simultaneous genetic progress and inbreeding control in three different scenarios. These scenarios consisted of minimizing kinship without taking breeding values into account, minimizing kinship with considering breeding values of individuals, and maximizing breeding values. A total of 5 boars and 49 sows were selected to create a breeding scheme. The specific population parameters for Banija spotted pig showed a low level of genetic diversity with high average inbreeding coefficients and a low effective population size. Due to the small total and effective population size, the use of optimization methods has shown that genetic improvement is possible at the expense of loss of genetic diversity in the population. However, the application of optimization methods resulted in lower average kinship between selected individuals

Control of inbreeding in Banija spotted pig using optimisation methods

Cilj rada bio je procijeniti i opisati specifične parametre populacije banijske šare svinje, te primijeniti metodu selekcije s optimalnim doprinosima u svrhu postizanja istovremenog genetskog napretka i kontrole uzgoja u srodstvu u tri različita scenarija. Scenariji su se sastojali od minimiziranja srodstva bez uzimanja u obzir uzgojnih vrijednosti, minimiziranje srodstva uzimajući u obzir i uzgojne vrijednosti jedinki, te maksimiziranje uzgojnih vrijednosti. Ukupno je odabrano 5 nerasta i 49 krmača za izradu sheme parenja. Specifični populacijski parametri banijske šare svinje pokazali su nisku razinu genetske raznolikosti uz visoke prosječne koeficijente uzgoja u srodstvu i nisku efektivnu veličinu populacije. Zbog male ukupne i efektivne veličine populacije, primjena optimizacijskih metoda pokazala je da je genetsko poboljšanje moguće na račun gubitka genetske raznolikosti u populaciji. No, primjena optimizacijskih metoda rezultirala je nižom prosječnom srodnošću odabranih jedinki.The purpose of this paper was to evaluate and describe specific parameters for Banija spotted pig population, and to apply optimal contribution selection to achieve simultaneous genetic progress and inbreeding control in three different scenarios. These scenarios consisted of minimizing kinship without taking breeding values into account, minimizing kinship with considering breeding values of individuals, and maximizing breeding values. A total of 5 boars and 49 sows were selected to create a breeding scheme. The specific population parameters for Banija spotted pig showed a low level of genetic diversity with high average inbreeding coefficients and a low effective population size. Due to the small total and effective population size, the use of optimization methods has shown that genetic improvement is possible at the expense of loss of genetic diversity in the population. However, the application of optimization methods resulted in lower average kinship between selected individuals