Use of randomly amplified polymorphic DNA markers for the genetic analysis of relatedness and diversity in chickens and turkeys

Diversidade genética entre três linhagens de codorna selecionadas para produção de ovos

A diversidade genética entre três linhagens de codorna (Coturnix japônica) foi avaliada utilizando-se a técnica de random amplified polymorphic DNA (RAPD). As linhagens selecionadas para produção de ovos foram identificadas como amarela, azul e vermelha por meio de anilhas no pé esquerdo. Seis primers de RAPD amplificaram 55 loci, os quais geraram padrão de bandas intensa e reproduzível em gel de agarose. Os resultados indicaram polimorfismos dentro e entre as linhagens. A similaridade de Jaccard média e o índice de diversidade Shannon revelaram alta diversidade dentro das linhagens de codornas. O teste de Mantel por meio do algoritmo unweighted pair-group method using arithmetic average (UPGMA) e a dispersão de coordenadas principais indicaram diferenciação genética significativa, embora em baixo nível. Os resultados sugerem que a diversidade genética dentro e entre as linhagens de codornas da Universidade Estadual de Maringá são promissoras para uso em programas de melhoramento.

Evaluation of genetic variability and distances among five Iranian native chicken populations using RAPD markers

Genetic variability was studied on five Iranian native chicken populations using Random Amplified Polymorphism DNA (RAPD) markers. The purpose of this study was for the analysis of variation within and between Iranian native chicken populations and for the reconstruction of a phylogenetic tree for these populations using the RAPD marker assay. The populations surveyed were from five provinces including Mazandaran (MZD), Isfahan (ISF), Yazd (YZD), Fars (FRS) and West Azerbaijan (WAZ). On the base of results of this study, the FRS and MZD populations had the highest genetic distance (0.182) and the FRS and ISF populations the lowest one (0.066). The YZD and MZD populations had the highest (0.208) and lowest (0.156) within-population genetic diversity. The phylogenetic tree was reconstructed on UPGMA method and showed two main separated groups. The ISF and FRS populations were first clustered into one group and, then, were clustered into a larger group with YZD and WAZ. Another consists MZD population was clustered separately from this group. This study showed that RAPD technique is an useful tool for evaluation of genetic variation among domesticated animals.

Genetic relationships among six Iranian goat populations based on random amplified polymorphic DNA markers

The objectives of this study were to assess the genetic variability among six Iranian goat breeds including: Markhoz (MR), Korki of South Khorasan (KK), Black Lori (BL), Najdi (NJ), Korki of Raeini (KR), Tali (TL) and to evaluate the genetic relationships between populations using RAPD markers. The genetic characterization of these genetic resources is essential to conservation and breeding programs. Blood sample (50 individuals per breeds) were collected from spreading location of these breeds. DNA extraction was carried out by Salting-Out method. Initially, a total of 16 ten and eleven-nucleotide arbitrary primers were used but 10 of 16 primers revealed a pattern with scorable amplified bands. From a total number of 115 scored bands 62 (53.9%) and 53 (46.1%) were described as polymorphic and monomorphic, respectively. The average number of bands per primer 11/5 and with sizes varying from 220 to 2310 bp in length. Nei's genetic distances varied between 0.081 and 0.227 in the populations. The phylogenetic tree was reconstructed on Neighbor-Joining method and showed two main separated groups. One includes KK, TL, KR in a branch and then NJ. Another consists BL and MR. This research was showed that RAPD technique is an useful tool for evaluation of genetic variation among of domesticated animals.

Microsatellite marker-based genetic analysis of relatedness between commercial and heritage turkeys (Meleagris gallopavo)

The turkey is second only to the chicken in importance as an agriculturally important poultry species. Unlike the chicken, however, genetic studies of the turkey continue to be limited. For example, to date, many genomic investigations have been conducted to characterize genetic relationships between commercial (CO) and non-CO chicken breeds, whereas the nature of the genetic relatedness between CO and heritage turkeys remains unknown. The objective of the current research was to use microsatellites to analyze the genetic relatedness between CO and heritage domestic turkeys including Narragansett, Bourbon Red, Blue Slate, Spanish Black, and Royal Palm. Primer pairs specific for 10 previously described turkey microsatellite markers were used. The phylogenetic analysis showed that the Blue Slate, Bourbon Red, and Narragansett were genetically closely related to the CO strain, with a Nei distance of 0.30, and the Royal Palm and Spanish Black were the least related to the CO strain, with Nei distances of 0.41 and 0.40, respectively. The present work provides a foundation for the basis of using heritage turkeys to genetically improve CO populations by introgression.

Genetic diversity of nine populations of the black goat (Capra hircus) in Sichuan, PR China

Sixteen polymorphic primers screened from 100 random primers were selected to analyze the randomly amplified polymorphic DNA (RAPD) of 540 domesticated black goats (Capra hircas) from 9 different geographical populations in Sichuan Province of China. After the test, 170 entirely repeatable RAPD markers representing goat polymorphisms were obtained from the 16 polymorphic primers, the lengths of the markers ranging from 0.1 to 2.5 kb. The genetic distance among the black goat populations ranges from 0.1051 to 0.2978. The similarity coefficient (0.9002) between Jintang and Lezhi black goats was the highest in the 9 populations, followed by the coefficient (0.8953) between Jialing and Yinshan goats, while that between Jiangan and Huili goats was found to be the lowest (0.7424). The coefficient of differentiation among population genes (Gst) was 0.2766, indicating a comparatively low degree of differentiation among the black goat populations. A UPGMA dendrogram constructed from similarity coefficients showed that the two populations from Huili and Baiyu, which are found mostly on the Western Sichuan plateau and in mountainous areas, clustered together, and the other seven populations formed another group. It can also be clearly seen that the Huili and Baiyu populations are very special, and must have been closely related in the past, even though their link with the other populations is quite weak as a result of genetic communication. The results of the experiment offer some crucial scientific data useful for the breeding of black goats.

Molecular analysis of the relatedness of five domesticated turkey strains

Our knowledge of the genetic relatedness among the eight existing domesticated turkey strains is limited. To begin to address this paucity, genetic relatedness among five turkey strains (Blue Slate, Bourbon Red, Narragansett, Royal Palm, and Spanish Black) was investigated using three molecular marker systems: randomly amplified polymorphic DNA (RAPD), microsatellite, and SNPs derived from a sequence tagged site and a cloned RAPD fragment. The RAPD analyses were based on five primers that revealed a total of 14 informative DNA fragments in all five populations. The microsatellite analyses involved two informative alleles from three primer-pairs. A total of nine SNPs were detected, one of which appeared to be strain specific. This SNP formed the basis of a PCR-RFLP genotyping procedure developed to distinguish one of the strains from the other four. Evidence from these analyses including the SNP-based RFLP-PCR suggests that Royal Palm is distinct from the other four strains, though more closely related to Narragansett. These data provide, for the first time, molecular evidence of the potential relationships among noncommercial domesticated turkey strains.

Use of RAPD-PCR for genetic analysis of Nicobari fowl of Andamans

1. The present study was conducted to estimate genetic relatedness among Nicobari fowls (Brown, Black and White) and an exotic bird (White Leghorn) using random amplified polymorphic DNA (RAPD) polymorphism. 2. A total of 25 decamer primers were screened among all the breeds of which 24 primers amplified the genomic DNA, generating 2000 to 200 bp bands. Ten primers generated reproducible and distinct RAPD profiles and were used for further analysis. 3. A total of 94 bands were amplified and 30 polymorphic bands (32%) were produced. The number of polymorphic loci ranged from 1 to 5 with an average of 3.0. 4. Among the native breeds Brown Nicobari showed higher genetic similarity (0.85) than Black Nicobari (0.80) and White Nicobari fowl (0.82). 5. Brown Nicobari showed high genetic similarity with Black Nicobari (0.87 +/- 0.029); least similarity was between White Nicobari and White Leghorn (0.77 +/- 0.028). 6. The RAPD profile of all Nicobari fowls on amplification with the primers PBG5 and PBA12 showed specific bands of molecular size 1050 and 785 bp, respectively. 7. The native breeds showed the least genetic distance with each other while White Leghorn appeared to be most distant from the native breeds.

Within- and between-strain genetic variability in White Leghorn population detected through RAPD markers

1. Five White Leghorn (WLH) strains, namely G, H, I, J and C, differing in selection history, were screened for randomly amplified polymorphic DNA (RAPD) polymorphism using 50 random decamer primers. 2. Only 12 primers detected polymorphism between the strains. Out of 96 bands scored using these primers, only 21 (21.9%) were found to be polymorphic. 3. Strains differed considerably for within-population genetic similarity, estimated either by band sharing (WS=0.836 to 0.968) or band frequency (WF=0.820 to 0.969). 4. Between-strain genetic similarity estimates, based on band sharing (BS) as well as on band frequency (BF) ranged from 0.756 to 0.958 and from 0.830 to 0.996, respectively. Strains C and H were most closely related to each other, while J appeared to be more distant from other strains. 5. The between-strain genetic distance estimates also revealed similar trends. 6. A phylogenetic tree, derived using Nei's coefficient of similarity revealed similar relationships between the WLH strains.

Genetic diversity among chicken breeds estimated through randomly amplified polymorphic DNA

The randomly amplified polymorphic DNA (RAPD) markers were used to detect polymorphism among five breeds of chicken i.e. White Leghorn and Rhodes Island Red (selected for part period egg production and egg mass respectively), Red Cornish and White Plymouth Rock (selected for early body weights) and Kadaknath (native breed). Twelve of the fifty random primers screened yielded distinct polymorphic RAPD profiles. Of the total 96 fragments amplified, about 25% showed polymorphism. Using the RAPD data matrix, the within population and between population genetic similarity was estimated. The selected improved breeds showed higher within population genetic similarity in comparison to the native breed. The two meat type breeds showed a high level of genetic similarity between themselves. The White Leghorn breed showed a low genetic similarity with other breeds. The native breed showed highest similarity with Rhodes Island Red. The dendogram was constructed to show phylogenetic relationship among these breeds. As expected, the genetic distances were lowest within similar type breeds and were highest between dissimilar type breeds. The results indicated the effectiveness of RAPD in detecting polymorphism between chicken populations and their applicability in population studies and establishing genetic relationships among the chicken populations.

Genomic polymorphism in Uruguayan Creole cattle using RAPD and microsatellite markers

Uruguayan Creole cattle inhabit areas that cannot sustain conventional farming. They have adapted to fragile environments and are influenced only by natural selection. In this study, random amplified polymorphic DNA (RAPD) and microsatellite (MS) markers were used to analyse Creole cattle genome polymorphism. A comparative analysis using the RAPD technique was performed in pooled DNA of three cattle breeds (Holstein Friesian, Creole and Hereford) in order to evaluate their amplification patterns. A primary screening of RAPD primers allowed us to select and use those with higher percentage of GC base composition. A total of 215 loci ranging between 300 and 2500 bp were amplified. Bandsharing frequency (BSF) among breeds showed that less related fingerprints were observed between Creole and Hereford cattle (0.77), while the highest similarity frequency corresponded to Holstein Friesian compared to Hereford (0.81). Specific RAPD bands were identified in the three DNA pools and they were tested in every individual of each breed. It may be possible to isolate and sequence these bands to create breed-specific molecular markers. The identification of multiple alleles of the MSCYP 21 in Creole cattle with an heterozygosity of He = 0.846 supported the variability of this genetic resource. The use of molecular markers such as RAPD s and microsatellites is proposed to establish genetic distance among American Creole cattle and possibly related ancestral Iberian breeds.

Genetic distinctness of African, Asian and South American local chickens

The genetic variability of various local chicken populations derived from Bolivia, India, Nigeria and Tanzania was evaluated with 22 microsatellites. Between two and 11 alleles per locus were detected. All populations showed high levels of heterozygosity with the lowest value of 45% for the population named Aseel from India and the highest value of 67% for Arusha from Tanzania. A dendrogram was constructed based on CHORD distance by upgMa analysis. Within this tree the populations were assorted according to their geographical origin. Bootstrapping values within the dendrogram were between 37 and 99%. The contribution of the determination of genetic variability with genetic markers to the decision on conservation and/or further use of the populations in crossbreeding programs designed to create genetic stocks with improved adaptability and productivity in tropical countries is discussed.

Measurement of within and between population genetic variability in quails

1. To detect polymorphism in various quail lines, Randomly Amplified Polymorphic DNA (RAPD) markers were tested and were found to be effective. 2. Twenty decamer primers were selected at random and tested, and 6 of these generated distinct polymorphic patterns between the quail lines. 3. Out of a total of 60 bands amplified using 6 selected primers, 19 (31.7%) were found to be polymorphic. 4. Genetic similarity within the lines ranged from 0.726 in HBW to 0.836 in KLQ. 5. Genetic similarity estimates between the populations ranged from 0.709 to 0.808.

Genetic characterization of biodiversity in highly inbred chicken lines by microsatellite markers

Forty-two microsatellite loci were analysed in 23 highly inbred chicken lines derived from Leghorn, Jungle Fowl, Fayoumi and Spanish breeds. Line-specific alleles among breeds and lines were detected. The band-sharing (BS) values were calculated and the proportion of shared alleles distances (Dps) were estimated. The BS values and Dps between sets of MHC-congenic lines ranged from 0.74 to 0.96, and 0.05-0.35, respectively. The BS values between each pair of noncongenic Leghorn lines were 0.32-0.97, and between Leghorn and exotic (Jungle Fowl, Fayoumi and Spanish) breeds were 0.03-0.55. The Dps between Fayoumi lines and other lines were much larger (0.66-1.34) than within Leghorns, and the Jungle Fowl breed had the largest distances with other lines (1.12-5.38). The phylogenetic consensus tree that was constructed grouped these 23 inbred chicken lines into four different clusters. These results are in accordance with the origin and breeding history of these inbred lines, which indicates that the use of microsatellites for the study of genetic biodiversity is accurate and reliable. In addition, the significance and value of inbred chicken lines in molecular genetic research is discussed.

Randomly amplified polymorphic DNA (RAPD) for evaluating genetic relationships among varieties of guinea fowl

The present study investigated the use of randomly amplified polymorphic DNA (RAPD) in estimating the intra and inter varietal genetic variation in three varieties of guinea fowl (Lavender, Pearl and White). The estimates, measured as band sharing were high for within population (0.946-0.971) and between population (0.990-0.999) genetic similarity. The respective estimates were 0.898-0.929 and 0.923-0.928 when estimated as frequency of occurrence of bands. The results indicated a very low level of intra and inter varietal genetic variation in these guinea fowl varieties, which in turn suggested the low level of genetic variation in these populations. The possible reasons for this high genetic similarity has been discussed.

Evaluation of genetic variability and genetic distances between eight chicken lines using microsatellite markers

The genetic variability and divergence of eight chicken lines were evaluated using nine microsatellite markers. The chicken lines included three White Leghorn hybrids, three Finnish Landrace lines, a Rhode Island Red line, and a broiler hybrid line. All the microsatellite loci were found to be polymorphic, the number of alleles varying from 4 to 13 per locus and 1 to 10 per line, respectively. Observed heterozygosities ranged from 0.00 to 0.91. The highest (0.67) and lowest (0.29) mean heterozygosity per line was observed in the broiler and in White Leghorn of Mäkelä, respectively. Three of the microsatellite loci deviated from the Hardy-Weinberg equilibrium in some populations. F statistics indicated clearly the subdivision of the total population into different lines. The genetic distances confirmed the classification of Finnish Landraces into different lines. A phylogenetic consensus tree was constructed from resampled data (1,000 times) using the neighbor-joining method. According to the phylogenetic tree, the lines were grouped into three clusters, in which the White Leghorns formed one group, two Landraces a second group, and a Landrace, the Rhode Island Red, and the broiler lines a third group. Allele distribution at the loci does not support either the stepwise or the infinite alleles mutation model, but the distribution pattern was quite irregular at different loci.

Map-based quantitative trait locus identification

Poultry gene mappers chose microsatellites as the main source of genetic markers for poultry genome mapping, similar to the marker type used for other farm animals, laboratory animals, and humans. Optimal strategies for applying DNA markers in poultry populations are discussed, including the number of markers to be used, genome representation, population structure, choice of markers, population size, statistical stringency for association between markers and quantitative trait loci (QTL), and biological verification of a linkage. It is shown that an efficient strategy should be based on a combination of a low stringent statistical test for the existence of linkage between a marker and QTL and an appropriate genetic test for the discrimination between true and false linkage. The source of the genetic variation to be used is discussed and, as an illustration, three types of resource populations are presented. The informativeness of different matings using various genotypes of the parents are considered and it appears that selection of markers based on the heterozygosity of the sire is the most efficient marker screening approach.