Analiza genetske strukture krškopoljskega prašiča na osnovi rodovnika

Pečnik, Žan (author), Malovrh, Špela (mentor)

V populaciji krškopoljskega prašiča smo želeli ugotoviti stanje genetske raznolikosti in postaviti temelje smernicam ohranjanja populacije za sedaj ter v bodoče. Raziskavo smo opravili na osnovi podatkov o poreklu. Genetsko strukturo populacije smo ocenili tako z dolgo uveljavljenimi (Wright, Malecot) kot tudi z novejšimi pristopi (MacCluer, Boichard, Ballou, Kalinowski, Baumung). Uporabili smo različno programsko opremo (SAS/STAT, PEDIG, CFC, Mendel). Celotna populacija je obsegala 2.940 živali, ki so bile rojene med letoma 1992 in 2017. Standardni odklon za velikost družin po merjascih je znašal 6,72 potomcev, kar kaže na izrazito neenakomerno rabo merjascev. Povprečni generacijski interval je bil 2,56 let. Delež znanih prednikov, ekvivalent popolnih generacij prednikov in indeks popolnosti porekla se s časom povečujejo ter omogočajo vse zanesljivejši izračun koeficienta inbridinga in efektivne velikosti populacije. Povprečno sorodstvo v referenčni populaciji je znašalo 13,95 %. Povprečni koeficient inbridinga celotne populacije je bil 4 %. Efektivna velikost populacije je znašala 51, kar pomeni, da je populacija ogrožena. Izguba genetske raznolikosti zaradi neenakih prispevkov osnovalcev in naključnega genetskega toka je bila 6,7 %. Korelacija med koeficientom inbridinga in koeficientom bližnjega inbridinga je znašala 0,99, kar pomeni, da je večina inbridinga v referenčni populaciji nastala na novo. Z izračunom koeficienta parcialnega inbridinga in koeficienta parcialnega ancestralnega inbridinga smo ugotovili, da je po enajstih linijah osnovalcev nastalo največ inbridinga. S simulacijo dedovanja smo razkrili bolj ali manj verjetno izgubljene in ogrožene alele osnovalcev. Za populacijo je izgubljenih vsaj 25 osnovalcev. Posebno pozornost je potrebno nameniti ohranjanju potomcev tistih osnovalcev, katerih aleli so najbolj verjetno ogroženi. Pridobljeni rezultati so pomembni, saj omogočajo enostavno upravljanje s skladom genov v populaciji in s posledičnim ohranjanjem genetske raznolikosti naše edine avtohtone pasme prašičev.

• Language: Slovenian
• Keywords: prašiči, pasme, avtohtone pasme, krškopoljski prašič, genetska struktura, genetska raznolikost, inbriding
• Work type: Master's thesis/paper
• Organization: BF - Biotechnical Faculty
• Year: 2019
• PID: 20.500.12556/RUL-112672
• COBISS.SI-ID: 4318600
• Publication date in RUL: 01.11.2019

Secondary language

• Language: English
• Title: Analysis of genetic structure in krskopolje pig using pedigree data

Abstract

Genetic variability in the Krškopolje pig population was estimated with the objective to set directions for effective conservation program. Pedigree data was used for this study. To evaluate genetic structure, we used long established (Wright, Malecot) as well as recent approaches (MacCluer, Boichard, Ballou, Kalinowski, Baumung). Software packages SAS/STAT, PEDIG, CFC and Mendel were applied for pedigree analyses. Pedigree file included 2,940 animals born in years 1992 to 2017. Standard deviation of family size in sires was 6.72 offspring, showing very unequal number of mattings per boar. Average generation interval was 2.56 years. Because the proportion of known ancestors, average complete generation equivalent and pedigree completeness index have increased over time, the estimates of inbreeding coefficient and effective population size are more reliable. The average coancestry in the reference population was 13.95% and the average inbreeding coefficient was 4.0%. The effective population size was estimated to 51, indicating that the population is endangered. Estimated genetic diversity reduction due to the random genetic drift and unequal founder contributions was 6.7%. Estimated correlation between Wright's (i.e. standard) inbreeding coefficient and Kalinowski’s coefficient of recent inbreeding was 0.99, suggesting that the majority of inbreeding in the reference population occurred in recent years. The estimates of partial coefficient of inbreeding and partial coefficient of ancestral inbreeding have shown that eleven founder lineages contributed the majority of inbreeding. Results from gene dropping analysis are probabilities of extinction, high risk of extinction and future extinction of founder alleles; at least alleles from 25 founders are entirely lost for today's population of Krškopolje pig. Special attention should be paid to the preservation of descendants of those founders whose alleles are the most likely at risk. Results obtained in this study allow managing the genetic pool of population and contribute to conservation of the genetic diversity of the only indigenous pig breed in Slovenia.

• Keywords: pigs, breeds, indigenous breeds, Krskopolje pig, genetic structure, genetic diversity, inbreeding