Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run

Background In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006–2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts. Results Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000–2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents. Conclusions The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.

GENETIC DIVERSITY OF EGYPTIAN ARABIAN HORSES FROM EL-ZAHRAA STUD BASED ON 14 TKY MICROSATELLITE MARKERS

The objectives of this study were, firstly, to conduct genetic characterization of Egyptian Arabian horses based on 14 TKY microsatellite markers, secondly, to investigate the powerfulness of these 14 TKY markers for parentage assignment of Arabian horses. A total of 101 horse samples including (Arabian = 71, Thoroughbred = 19 and Nooitgedacht = 11) were analysed by 14 TKY microsatellite markers. The PCR products were electrophoresed on Genetic analyzer 3500 with the aid of Liz standard. The basic measures of the allele’s size and genetic diversity were computed using bioinformatics software. The polymorphism of the TKY markers across the Arabian population showed moderate values for genetic diversity parameters; number of allele (NA) =8.143, effective number of allele (Ne) = 3.694, observed heterozygosity (HO) = 0.599, expected heterozygosity (HE) = 0.691, polymorphic Information Content (PIC) = 0.636 and Inbreeding coefficient (FIS)= 0.128. The combined probability of exclusion (CPE) value of the 14 TKY microsatellite loci of our Arabian horses was 0.9999. The results from current study confirm the applicability and efficiency of TKY microsatellite panel for evaluating the genetic diversity and parentage assignment of Egyptian Arabian horses.Key words: Arabian horses; genetic diversity; microsatellite; TKY markers GENSKA RAZNOVRSTNOST EGIPČANSKIH KONJ ARABSKE PASME IZ KOBILARNE EL-ZAHRAA NA PODLAGI 14 MIKROSATELITSKIH OZNAK TKY Izvleček: Nameni raziskave so bili genetska karakterizacija egipčanskih konj arabske pasme na podlagi 14 mikrosatelitskih označevalecv TKY ter raziskava moči 14 označevalcev TKY za dodelitev staršev arabskih konj. S pomočjo 14 mikrosatelitskih označevalcev TKY je bilo analiziranih 101 vzorcev konj (arabski = 71, čistokrvni = 19 in konji Nooitgedacht = 11). Produkte PCR so analizirali s pomočjo elektroforeze na genskem analizatorju 3500 s pomočjo Liz standarda. Osnovne mere velikosti alela in genske raznovrstnosti so bile izračunane s pomočjo programske opreme za bioinformatiko. Polimorfizem označevalcev TKY v arabski populaciji je pokazal zmerne vrednosti za parametre genske raznolikosti; število alelov (NA) = 8,143, efektivno število alelov (Ne) = 3,694, opazovana heterozigotnost (HO) = 0,599, pričakovana heterozigotnost (HE) = 0,691, polimorfna informacijska vsebina (PIC) = 0,636 in Inbriding koeficient (FIS) = 0,128. Skupna vrednost verjetnosti izključitve (CPE) 14 mikrosatelitskih lokusov TKY njihovih arabskih konj je bila 0,9999. Rezultati te raziskave potrjujejo uporabnost in učinkovitost mikrosatelitske plošče TKY za oceno genetske raznovrstnosti in starševske pripadnosti egipčanskih arabskih konj.Ključne besede: arabski konji; genska raznolikost; mikrosatelit; markerji TKY

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

Background Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows. Methods Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny. Results For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2. Conclusions The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.