211 KB20 KB2008Dovč, PeterKunej, TanjaOgorevc, JernejStr. 85-91ISSN:1581-9175ISSN:1854-4800COBISSID_HOST:2363272URN:URN:NBN:SI:doc-XZCYBMK3enBiotehniška fakultetaActa agriculturae slovenica. Suplementcandidate genescattlegovedokandidatni genikvantitativni lokusimastitismolecular geneticsmolekularna genetikaQTLquantitative trait lociAn integrated map of cattle candidate genes for mastitis| a step foward to new genetic markers| Integrirana karta kandidatnih genov za mastitis pri govedu| korak naprej pri razvoju novih genetskih označevalcev|To facilitate the development of new genetic markers for mastitis resistance or susceptibility we used genome-wide comparative approach to review all known mastitis-associated loci. We assembled into a map 233 loci that were identified by six different studz approaches (QTLs, association studies, expression experiments, AFLP-, miRNA- and epigenetic- studies). To integrate data from different sources and to identify overlapping regions we presented the results in the form of genetic map. The collected data represent genetic background for mastitis-related traits in cattle. Thirty most promising candidate genes (associated with mastitis in different study approaches or at least in two independent studies, or/and overlapping with QTL regions) were selected from database and in silico searched for genetic variability and putative miRNA target sites in 3'UTR. Thirty-one SNPs in the putative promoter/5' UTR (up to 2 kb upstream) of eight candidate genes were found. Bioinformatic analysis revealed that some promoter SNPs might potentially cause gain/loss of the putative transcription factors. Promoter SNPs were alsopresent in CG dinucleotides and therefore possibly involved in gain/loss of CpG sites. In ten mastitis candidate genes we found 56 SNPs in exons of which 21 were non-synonymous substitutions. Additionally, 23 SNPs in intronic regions and 21 SNPs in 3'UTR were found. MiRNA target analysis revealed 89 putative target sites in 18 candidate genes; however, current SNPs were not identified in the miRNA target binding sites or miRNAs expressed in mammary gland. For SNPs with a putative regulatory role found in candidate genes, functional analyses and association studies are needed to facilitate identification of mastitis resistance or susceptibility alleles possibly involved in mastitis regulatory pathwaysPri iskanju kandidatnih genov ya mastitis smo s pomočjo petih različnih študijskih pristopov (QTL-i, asociacijske študije, ekspresijski eksperimenti, miRNA, AFLP študije in epigenetski faktorji) pregledali 233 lokusov. Da bi sestavili podatke iz različnih virov v smiselno celoto in razkrili prekrivajoče se regije, smo rezultate predstavili v obliki genske karte. Zbrani podatki predstavljajo genetsko ozadje za lastnosti povezane z mastitisom pri govedu. Trideset najbolj obetavnih kandidatov (povezanih z mastitisom v različnih študijskih pristopih ali z vsaj dvema neodvisnima študijama ali/in ležeče v regijah prekrivajočih se s QTL-i) smo izbrali iz podatkovne zbirke in uporabili za in silico iskanje potencialnih, z mastitisom povezanih, molekularnih markerjev in domnevnih tarčnih mest za miRNAv 3' neprevedenih regijah. (3'UTR). V domnevni promotorski/5'UTR (2kb navzgor od začetka prevajanja) smo našli 31 SNP-jev v osmih kandidatnih genih. Analiza z Matinspectorjem je pokazala, da bi nekateri SNP-ji v promotorskih regijah lahko povzročili izgubo/pridobitev vezavnih mest za transkripcijske faktorje. Nekateri SNP-ji v domnevni promotorski regiji povzročajo tudi izgubo/pridobitev CpG mest. V desetih kandidatnih genih smo našli 56 SNP-jev v eksonih, med katerimi je bilo 21 zamenjav ne-sinonimnih. Poleg tega smo našli 23 SNP-jev v intronskih regijah in 21 SNP-jev v 3'UTR. Analiza tarč za miRNA je razkrila 89 domnevnih vezavnih mest za miRNA v 18 kandidatnih genih. V tarčnih zaporedjih za miRNA nismo našli SNP-jev. Za SNP-je z domnevno regulatorno vlogo v kandidatnih genih predlagamo funkcionalne analize in asociacijske študije, ki bi omogočile odkrivanje alel za odpornost oz. dovzetnost za mastitis in prispevale k razumevanju regulatornih poti pri mastitisuTEXTznanstveno časopisjejournalsSlovenian National E-content AggregatorNational and University Library of SloveniaUniverza v Ljubljani, Biotehniška fakulteta