Title Molecular dissection of inbreeding depression for semen quality traits in cattle Title (croatian) Molekularna disekcija inbriding depresije za svojstva kvalitete sperme kod goveda Author Maja Ferenčaković Mentor Ino Čurik (mentor)Mentor Johann Soelkner (mentor) Committee member Miroslav Kapš (član povjerenstva)Committee member Johannes Arjen Lenstra Committee member Vlatka Čubrić Čurik (član povjerenstva)Granter University of Zagreb Defense date and country 2015-03-25, Croatia Scientific / art field, BIOTECHNICAL SCIENCES Universal decimal classificationUDC ) 636/637 - Animal husbandry and breeding. Produce of domestic animals and game Abstract Runs Of Homozygosity (ROH) are a newly introduced approach for identifying inbreeding in
diploid individuals. This approach is more reliable and available than pedigree data, but the
lack of universal standards about ROH definition and identification introduces serious bias in
ROH studies. In this thesis, ROH were analyzed in five cattle breeds (Brown Swiss,
Fleckvieh, Norwegian Red, Pinzgauer and Tyrol Grey). The effects of SNP chip density and
genotyping errors were tested on Brown Swiss, Pinzgauer and Tyrol Grey in order to establish
the most optimal settings for precise estimation of levels of autozygosity. Data from the 50 k
chip led to an overestimation of the number of ROH shorter than 4 Mb, since the analysis
could not identify heterozygous SNPs present on the denser chip. Conversely, data from the
denser chip underestimated the number of ROH longer than 8 Mb, unless the presence of a
small number of heterozygous SNP genotypes was allowed within a ROH. Using this options
ROH were identified in Brown Swiss, Fleckvieh, Norwegian Red and Tyrol Grey. Levels of
autozygosity were calculated and compared with pedigree inbreeding coefficients. For all four
breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8
Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. In contrast, inbreeding
estimates based on FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived
estimates. Pearson correlations between FROH and FPED ranged from 0.50 to 0.72, as
dependent on pedigree depth. In the analysis of inbreeding depression a significant influence
of FPED, FROH2 - 4 Mb and FROH > 2 Mb on total number of spermatozoa in 554 Fleckvieh bulls was
found. Exact autozygous regions that influence this trait were detected on chromosomes 7, 10,
17, 20, 22 and 27 containing 41 genes. Five obvious candidate genes were found which are
known to be directly associated with spermatogenesis, energy levels in spermatozoa and
osmotic balance of the sperm. In conclusion, genotyping errors and SNP chip density do
affect estimates of autozygosity from ROH, ROH distributions (number and size) enables
precise estimation of autozygosity at individual and population levels in cattle and genomic
autozygosity does have influence on bull semen quality.
Abstract (croatian) “Runs Of Homozygosity” (ROH) nov su pristup utvrđivanja inbridinga kod diploidnih
organizama i smatraju se pouzdanijim i više dostupnim od rodovnika, no nedostaju
jedinstveni standardi za njihovu uporabu. U ovoj disertaciji ROH su analizirani kod pet
pasmina goveda (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer i Tyrol Grey). Utjecaj
gustoće genomske informacije (SNP chipa) i utjecaj genotipskih pogrešaka na detekciju
ROH-ova istražen je na pasminama Brown Swiss, Pinzgauer i Tyrol Grey. SNP chip manje
gustoće sustavno je precjenjivao broj ROH-ova <4 Mb, što je uzrokovalo i precjenjivanje
inbridinga. Gušći SNP chip podcjenjivao je velike segmente osim u slučaju kada se
dozvoljavao određen broj heterozigotnih genotipova. Koristeći ova saznanja procijenjen je
ROH inbriding (FROH) za populacije Brown Swiss, Fleckvieh, Norwegian Red i Tyrol Grey, te
je uspoređen s koeficijentima inbridinga iz rodovnika (FPED). Za sve četiri populacije
vrijednosti FROH > 8 Mb i FROH > 16 Mb bile su slične vrijednosti FPED dok su FROH > 1 Mb i FROH > 2
Mb vrijednosti inbridinga bile mnogo veće od FPED. Pearsonovi korelacijski koeficijenti
između FROH i FPED bili su rasponu od 0.50 do 0.72, a vrijednost je ovisila o dubini rodovnika.
Kod analize inbriding depresije uočen je značajan utjecaj FPED, FROH2 - 4 Mb i FROH > 2 Mb na
ukupan broj spermatozoida kod bikova Fleckvieh pasmine. Detekcija autozigotnih regija koje
utječu na ovo svojstvo otkrila je regije na kromosomima 7, 10, 17, 20, 22 i 27 u kojima je
pronađen 41 gen od kojih je pet izglednih kandidata, jer su povezani sa spermatogenezom,
razinom energije spermatozoida i osmotskom ravnotežom spermatozoida i sjemene tekućine.
Sve navedeno dovodi sljedećih zaključaka; greške genotipizacije i gustoća SNP chipa imaju
utjecaj na identifikaciju ROH-ova; ROH metodom procijenjena autozigotnost predstavlja
dobar pokazatelj stupnja inbridinga; autozigotnost genoma je povezana s plodnošću bikova.
Keywords
inbreeding
inbreeding depression
SNP chip data
cattle
bull semen quality
Keywords (croatian)
inbriding
inbriding depresija
SNP chip
goveda
kvaliteta sjemena bikova
Language english URN:NBN urn:nbn:hr:204:490168 Study programme Title: Agricultural Sciences Catalog URL http://161.53.95.232/cgi-bin/wero.cgi?q=550429003117 Type of resource Text File origin Born digital Access conditions Open access Terms of use Created on 2018-04-27 07:32:36
