Genome-wide association study to identify the genetic background of resistance to mastitis in dairy cattle : doctoral dissertation

Ashja, Ali (author), Dovč, Peter (mentor), Zorc, Minja (comentor)

Mastitis is a serious problem for the dairy industry, leading to economic losses and affecting milk quality. This study aimed to identify genetic factors associated with mastitis resistance by conducting a genome-wide association study (GWAS) for the somatic cell score (SCS). Phenotypic records of 350 Holstein Friesian cows were obtained from the Slovenian Cattle Recording Scheme Database and consisted of around 1500 milk control data from 2012 to 2023 collected on a single farm in Slovenia. Corresponding genotypic data were also retrieved from the same database and genotyped using the Illumina BovineSNP50 BeadChip (Illumina, Inc., San Diego, CA, USA). For the association study, three SCS parameters were considered, including lactation mean somatic cell score (LM_SCS), maximum SCS value (SCSMAX), and top three mean value of SCS (TOP3). After performing a GWAS using FarmCPU and BLINK models, five significant SNPs associated with the TOP3 trait in the first lactation were found on BTA 14, 15, 22, and 29. The identified SNP markers were associated with 7 known candidate genes (DNASE1L3, SLC36A4, ARMC1, PDE7A, MMP13, CD44, and IL-17RD). In addition, the identified genes were significantly enriched in the IL-17 signalling pathway. These results indicated potential genetic markers and genes associated with SCS and mastitis resistance in the Holstein Friesian cows from Slovenia.

• Language: English
• Keywords: dairy cattle, mastitis, genetics, genome-wide association study, GWAS, somatic cell count
• Work type: Doctoral dissertation
• Typology: 2.08 - Doctoral Dissertation
• Organization: BF - Biotechnical Faculty
• Place of publishing: Ljubljana
• Publisher: A. Ashja
• Year: 2025
• Number of pages: 1 spletni vir (1 datoteka PDF (IX, [96] str.)
• PID: 20.500.12556/RUL-170569
• UDC: 636.2:575(043.3)=111
• COBISS.SI-ID: 243660547
• Publication date in RUL: 10.07.2025

Secondary language

• Language: Slovenian
• Title: Genomska asociacijska študija za identifikacijo genetskega ozadja odpornosti na mastitis pri mlečnem govedu : doktorska disertacija

Abstract

Mastitis je resen problem v prireji mleka, saj povzroča ekonomske izgube in vpliva na kakovost mleka. V naši študiji smo želeli z izvedbo genomske asociacijske študije (GWAS) za oceno števila somatskih celic (OŠSC) identificirati genetske dejavnike, povezane z odpornostjo proti mastitisu. Fenotipske podatke za 350 krav črno-bele pasme (ČB) smo pridobili iz Centralne baze Govedo in so obsegali približno 1500 podatkov o mlečnih kontrolah v obdobju od leta 2012 do 2023 na eni večjih farm krav molznic v Sloveniji. Genotipske podatke za te živali, ki so bili pridobljeni z genotipizacijo z Illumina BovineSNP50 BeadChip (Illumina, Inc., San Diego, CA, ZDA), smo dobili iz iste podatkovne zbirke. Za asociacijsko študijo smo obravnavali tri parametre OŠSC, povprečno število somatskih celic v laktaciji (LM_SCS), najvišjo vrednost OŠSC za vsako kravo (SCSMAX) in povprečje treh najvišjih vrednosti OŠSC za vsako kravo (TOP3). Po izvedbi GWAS z uporabo modelov FarmCPU in BLINK smo identificirali pet pomembnih SNP-jev, povezanih z lastnostjo TOP3 v prvi laktaciji na BTA 14, 15, 22 in 29. Identificirani SNP označevalci so bili povezani s sedmimi znanimi kandidatnimi geni (DNASE1L3, SLC36A4, ARMC1, PDE7A, MMP13, CD44 in IL17RD). Poleg tega smo ugotovili, da so bili identificirani geni pomembno obogateni v signalni poti IL-17. Ti rezultati nakazujejo pomembne nove potencialne genetske označevalce in vzročne gene, povezane z OŠSC in odpornostjo na mastitis pri kravah črno-bele pasme v Sloveniji.

• Keywords: mlečno govedo, mastitis, genetika, genomska asociacijska študija, GWAS, število somatskih celic, doktorske disertacije