Microsatellite-Based Genetic Diversity Among Three Duck Populations in Sumatera Island

This study aimed to determine the genetic diversity among three duck populations (Bayang, Pegagan, and Pitalah) reared in Sumatera island, Indonesia, using microsatellite markers. Genetic diversity among populations (n = 90) was determined using 22 microsatellite markers, based on several indices: number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), polymorphism information content (PIC), and Wright’s F-statistics ( ). The total number of alleles detected across loci was 121. The Na per locus ranged from 2 (APH24, CAUD128, and CAUD009) to 18 (CAUD048 and CAUD040). The mean Ho (0.429) dan He (0.509) indicated that the level of genetic diversity among populations was moderate, while the mean PIC (0.46) suggested that the tested loci were informative for assessing genetic diversity. The mean F-statistics ( ) were 0.148, 0.198, and 0.060, respectively. The  value indicated that the level of genetic differentiation among populations was moderate. The results confirms a moderate genetic diversity among populations, which could be beneficial for designing conservation and utilization of the local ducks in Sumatera island

POU class 1 homeobox 1 gene polymorphisms associated with growth traits in Korean native chicken

Objective POU class 1 homeobox 1 (POU1F1) mediates growth hormone expression and activity by altering transcription, eventually resulting in growth rate variations. Therefore, we aimed to identify chicken POU1F1 polymorphisms and evaluate the association between single nucleotide polymorphisms (SNPs) and growth-related traits, and logistic growth curve parameter traits (α, β, and γ). Methods Three SNPs (M_1 to M_3) were used to genotype 585 F1 and 88 F0 birds from five Korean native chicken lines using a polymerase chain reaction–restriction fragment length polymorphism method. Results Single marker analyses and traits association analyses showed that M_2 was significantly associated with body weight at two weeks, weight gain from hatch to 2 weeks, and weight gain from 16 to 18 weeks (p<0.05). M_3 was significantly associated with weight gain from 14 to 16 weeks and from 16 to 18 weeks, and asymptotic body weight (α) (p<0.05). No traits were associated with M_1. The POU1F1 haplogroups were significantly associated with weight gain from 14 to 16 weeks (p = 0.020). Linkage disequilibrium test and Haploview analysis shown one main haploblock between M_2 and M_3 SNP. Conclusion Thus, POU1F1 significantly affects the growth of Korean native chickens and their growth curve traits

High Levels of Genetic Variation in MHC-Linked Microsatellite Markers from Native Chicken Breeds

The major histocompatibility complex (MHC) is a highly polymorphic gene region that regulates cellular communication in all specific immune responses. In this study, we investigated 11 microsatellite (MS) markers in the MHC-B region of chicken populations from four countries: Sri Lanka, Bangladesh, South Korea, and Nigeria. The MS markers were divided into two sets. Set 1 included five novel MS markers, which we assessed using 192 samples from 21 populations. Set 2 included six previously reported markers, which we assessed using 881 samples from 29 populations. The Set 1 MS markers had lower polymorphism (polymorphic information content (PIC) &lt; 0.5) than the Set 2 markers (PIC = 0.4–0.9). In all populations, the LEI0258 marker was the most polymorphic, with a total of 38 alleles (PIC = 0.912, expected heterozygosity (He) = 0.918). Local populations from Sri Lanka, Bangladesh, and Nigeria had higher allele diversity and more haplotypes for Set 2 MS markers than Korean and commercial populations. The Sri Lankan Karuwalagaswewa village population had the highest MHC diversity (mean allele number = 8.17, He = 0.657), whereas the white leghorn population had the lowest (mean allele number = 2.33, He = 0.342). A total of 409 haplotypes (89 shared and 320 unique), with a range of 4 (Rhode Island red) to 46 (Karuwalagaswewa village (TA)), were identified. Among the shared haplotypes, the B21-like haplotype was identified in 15 populations. The genetic relationship observed in a neighbour-joining tree based on the DA distance agreed with the breeding histories and geographic separations. The results indicated high MHC diversity in the local chicken populations. The difference in the allelic pattern among populations presumably reflects the effects of different genotypes, environments, geographic variation, and breeding policies in each country. The selection of MHC allele in domestic poultry can vary due to intensification of poultry production. Preserved MHC diversity in local chicken provides a great opportunity for future studies that address the relationships between MHC polymorphisms and differential immune responses

Analysis of Genetic Diversity Indonesian Ducks Using Microsatellite Marker

Conservation of genetic diversity plays an important role in sustaining local breeds. A number of Indonesian local duck breeds, namely Bayang, Pegagan, Pitalah (Sumatran Ducks), Magelang, Mojosari, Rambon, and Turi (Javanase Ducks) are included as local assets and play an important role in socio-economic. A total of 206 ducks corresponding to Sumatran (SM) and Javanese (JW) duck populations was estimated using 22 duck microsatellite markers. Within the twenty-two polymorphic loci, number of alleles per locus (Na), polymorphism information content (PIC), observed heterozygosity (Ho), expected heterozygosity (He), Hardy-Weinberg equilibrium (HWE) test and Wright’s F-statistics were determined by Cervus and GenAlEx software. As a results, three to 22 alleles per locus were found across all the populations. The PIC, Ho and He across all populations ranged from 0.087 (APH24) to 0.907 (CAUD040), from 0.029 (APH24) to 0.863 (CAUD048) and from 0.090 (APH24) to 0.916 (CAUD0448), respectively. Nine loci were detected under Hardy-weinberg equilibrium (P<0.01). The JW duck population were indicated to have higher genetic variation (Na=6.32; Ne=3.15; Ho=0.465; He=0.578) compared to SM duck. The mean fixation coefficient of subpopulation within the total population which indicated approximately 39% of the genetic variation was due to population differences, and 61% was caused by differences of among individuals. The moderate magnitude of genetic diversity observed within the investigated duck populations suggests that these populations are quite rich reservoirs of genetic diversity that should be preserved

Identification of quantitative trait loci for the fatty acid composition in Korean native chicken

Objective Fatty acid composition is one of the most important meat quality traits because it can contribute to functional, sensorial, and nutritional factors. In this study, quantitative trait locus (QTL) analyses for fatty acid composition traits were investigated in thigh and breast meat of Korean native chicken (KNC). Methods In total, 18 fatty acid composition traits were investigated from each meat sample using 83 parents, and 595 F1 chicks of 20 week old. Genotype assessment was performed using 171 informative DNA markers on 26 autosomes. The KNC linkage map was constructed by CRI-MAP software, which calculated genetic distances, with map orders between markers. The half-sib and full-sib QTL analyses were performed using GridQTL and SOLAR programs, respectively. Results In total, 30 QTLs (12 in the thigh and 18 in the breast meat) were detected by the half-sib analysis and 7 QTLs (3 in the thigh and 4 in the breast meat) were identified by the full-sib analysis. Conclusion With further verification of the QTL regions using additional markers and positional candidate gene studies, these results can provide valuable information for determining causative mutations affecting the fatty acid composition of KNC meat. Moreover, these findings may aid in the selection of birds with favorable fatty acid composition traits

Genetic diversity and phylogenetic relationship analyzed by microsatellite markers in eight Indonesian local duck populations

Objective At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic diversity and phylogenetic relationship of eight local duck populations of Indonesia using microsatellite markers. Methods In total, 240 individuals (30 individuals each population) from Alabio (AL), Bayang (BY), Magelang (MG), Mojosari (MJ), Pegagan (PG), Pitalah (PT), Rambon (RM), and Turi (TR) duck populations were genotyped using 22 microsatellite markers. Results The results showed a moderate level of genetic diversity among populations, with a total of 153 alleles detected over all loci and populations, ranging from 3 to 22 alleles per locus. Observed (Ho) and expected heterozygosity (He), as well as polymorphism information content over all loci and populations were 0.440, 0.566, and 0.513, respectively. Heterozygote deficiency in the overall populations (FIT = 0.237), was partly due to the heterozygote deficiency within populations (FIS = 0.114) and moderate level of genetic differentiation among populations (FST = 0.137). The most diverse population was MG (He = 0.545) and the least diverse population was AL (He = 0.368). The majority of populations were relatively in heterozygote deficiency (except AL), due to inbreeding. The genetic distances, phylogenetic trees, and principal coordinates analysis concluded that the populations can be grouped into two major clusters, resulting AL, MG, and MJ in one cluster separated from the remaining populations. Conclusion The present study revealed a considerable genetic diversity of studied populations and thus, proper management strategies should be applied to preserve genetic diversity and prevent loss of alleles

Estimation of heritability and genetic correlation of body weight gain and growth curve parameters in Korean native chicken

Objective This study estimated the genetic parameters for body weight gain and growth curve parameter traits in Korean native chicken (KNC). Methods A total of 585 F1 chickens were used along with 88 of their F0 birds. Body weights were measured every 2 weeks from hatching to 20 weeks of age to measure weight gain at 2-week intervals. For each individual, a logistic growth curve model was fitted to the longitudinal growth dataset to obtain three growth curve parameters (α, asymptotic final body weight; β, inflection point; and γ, constant scale that was proportional to the overall growth rate). Genetic parameters were estimated based on the linear-mixed model using a restricted maximum likelihood method. Results Heritability estimates of body weight gain traits were low to high (0.057 to 0.458). Heritability estimates for α, β, and γ were 0.211±0.08, 0.249±0.09, and 0.095±0.06, respectively. Both genetic and phenotypic correlations between weight gain traits ranged from −0.527 to 0.993. Genetic and phenotypic correlation between the growth curve parameters and weight gain traits ranged from −0.968 to 0.987. Conclusion Based on the results of this study population, we suggest that the KNC could be used for selective breeding between 6 and 8 weeks of age to enhance the overall genetic improvement of growth traits. After validation of these results in independent studies, these findings will be useful for further optimization of breeding programs for KNC

Association of HSPB1 and CRYAB SNPs with Chicken Meat Quality and Robustness in Five Lines of Korean Native Chicken

The clinical–chemical traits of blood serum are important biomarkers that can be used to investigate health and metabolic status, both of which can affect meat quality traits. In this study, the SNPs in the genes HSPB1 (g. 526A > G; 5\u27UTR) and CRYAB (g. 2471T > C; exon 2) were investigated via an association analysis with meat quality and clinical–chemical traits. In total, 597 native Korean chickens were included in the study. There were no significant associations between the SNP in CRYAB and either meat quality or serum traits. On the other hand, the SNP in HSPB1 was significantly associated (P<0.05) with water–holding capacity (WHC), lightness (L*), and yellowness (b*) of the thigh muscle. In addition, two clinical–chemical traits, high–density lipoprotein (HDL–c) and amylase (Amy), were significantly associated with this SNP. Of these, the WHC, L*, and b* values of the thigh muscle have the dominant effects only, while Amy trait exhibits both additive and dominant effects. These results can provide useful information that can facilitate the improvement of chicken meat quality, and the understanding of the relationship between blood metabolism and meat quality