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GENETICS |

* Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan; and
Kochi Prefectural Livestock Experimental Station, Sakawa, Kochi 789-1233, Japan
1 Corresponding author: tsudzuki{at}hiroshima-u.ac.jp
| ABSTRACT |
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Key Words: chicken line genetic diversity genetic structure individual assignment microsatellite
| INTRODUCTION |
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To date, several investigations with chickens, using microsatellite markers, have been carried out to assess genetic diversity and genetic relationships in and among various populations of indigenous and commercial chickens including Jungle Fowl (Takahashi et al., 1998; Vanhala et al., 1998; Zhou and Lamont, 1999; Wimmers et al., 2000; Romanov and Weigend, 2001; Zhang et al., 2002; Hillel et al., 2003; Osman et al., 2006; Tadano et al., 2007). Hillel et al. (2003) reported for commercial chicken lines that layer lines generally possessed slightly less variability than broilers. Among layer lines, brown egg layers were the most polymorphic, and White Leghorn lines were the least polymorphic. Furthermore, higher variability in broiler lines was also generally observed in other investigations (Vanhala et al., 1998; Zhang et al., 2002).
The interesting result for clustering and assigning individuals to source population was reported by Rosenberg et al. (2001). They genotyped at 27 microsatellite loci for a total 600 individuals belonging to 20 chicken breeds (30 individuals genotyped in each breed) and discussed relations between clustering success rate and the number of markers used or the number of individuals per breed used. When using all 27 markers, around 98% clustering success rate was obtained. They concluded that at least 12 to 15 highly variable markers should be genotyped in at least 15 to 20 individuals per hypothesized population. Moreover, they mentioned that high expected heterozygosity, number of alleles, and fixation index (FST) are appropriate criteria to select the highly variable markers for obtaining high clustering success rate, but FST value is weaker than expected heterozygosity and number of alleles.
The current study was carried out to estimate genetic diversity of commercial chicken lines and to characterize each line genetically, based on 40 microsatellite markers together with many individuals per line assayed. At the same time, availability of an individual assignment test using a distance-based method (Piry et al., 2004) for chicken populations was demonstrated. The results from the current study would contribute to the appropriate managements avoiding loss of genetic variability in these lines and to future improvements for these lines.
| MATERIALS AND METHODS |
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In total, 536 birds belonging to 12 chicken lines reared in Japan were investigated. These lines were bred based on 5 breeds (Leghorn, Plymouth Rock, Rhode Island Red, Cornish, and New Hampshire Red), respectively. As for a criterion of sample size per breed or population for biodiversity study of domestic animals, FAO guidelines recommend that 25 individuals per breed or population should be assayed (FAO, 1998). Hence, sample size per line in the current study ranged from 34 to 48 individuals. Information about lines sampled is shown in Table 1
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Microsatellite Genotyping
Forty microsatellite markers (Table 2
) distributed on 22 autosomes were chosen, in view of covering the genome widely and obtaining precise results. Details for these markers are available from the ArkDB Database Web site by the Roslin Bioinformatics Group (http://www.theark-db.org/). Of 40 markers, 15 markers were a part of 30 recommended markers by a joint International Society of Animal Genetics-FAO working group for biodiversity study of chicken (http://dad.fao.org/). Additionally, 5 markers (ADL0268, LEI0228, MCW0034, MCW0183, and MCW0295), which show high expected heterozygosity, were reported as more effective markers for cluster analysis and individual assignment in chickens (Rosenberg et al., 2001). Expected heterozygosity of these 5 markers reported by Rosenberg et al. (2001) ranged from 0.718 to 0.924. The PCR and genotyping were carried out by the methods of Tadano et al. (2007).
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Standard within-line diversity was assessed by calculating total number of alleles (TNA) and mean number of alleles per locus (MNA), observed (direct count) heterozygosity (HO), unbiased expected heterozygosity (HE; Nei, 1987), and polymorphic information content (PIC; Botstein et al., 1980), using CERVUS version 2.0 (Marshall et al., 1998). A test of the Hardy-Weinberg equilibrium (HWE) at each locus-line combination was implemented by a test analogous to Fishers exact test based on the Markov chain method (Markov chain length, 100,000; dememorization steps, 10,000) using ARLEQUIN version 2.000 (Schneider et al., 2000).
The inbreeding coefficient (FIS) per line and the pairwise proportion of different alleles between lines (pair-wise FST; Weir and Cockerham, 1984) were calculated using FSTAT version 2.9.3.2 [EC] (Goudet, 2001). The level of significance for pairwise FST was determined from the permutation test using the sequential Bonferroni procedures (Rice, 1989). Additionally, FST per each microsatellite across all lines was also calculated as a measure of highly polymorphic marker, along with expected heterozygosity.
Individual assignment test was implemented by GEN-ECLASS2 (Piry et al., 2004); a distance-based method with modified Cavalli-Sforza chord distance (DA; Nei et al., 1983) was used. This method does not require the HWE or absence of linkage disequilibrium among loci, and the DA distance showed higher percentage of individuals assigned to the source population than other distances (Cornuet et al., 1999). The probability that each individual was assigned to or not to candidate lines was estimated using a Monte Carlo resampling method (Paetkau et al., 2004; number of simulated individuals = 10,000; type I error = 0.01, applying rejection threshold of 0.05).
Genetic distance between each line pair based on allele frequencies was evaluated by DA (Nei et al., 1983). A dendrogram was constructed based on the DA distance by the neighbor-joining method (Saitou and Nei, 1987). The DA genetic distance is better suited to obtain correct tree topology than other distances, regardless of a mutation model (Takezaki and Nei, 1996). The robustness of tree topologies was evaluated with a bootstrap test of 1,000 resampling across loci. A series of these processes was carried out using DISPAN (Ota, 1993). The dendrogram was edited using TREEVIEW version 1.6.6 (Page, 1996).
| RESULTS |
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The variations for each microsatellite are summarized in Table 2
. A total of 268 distinct alleles were detected at the 40 microsatellite loci in 536 birds. Across all lines, the average number of alleles per locus was 6.7 (268/40), with the range from 3 (MCW0037, MCW0067, MCW0165, and MCW0248) to 16 (LEI0228). Forty-two of all 268 alleles (15.7%) were unique to only 1 line (unique alleles). The unique alleles were observed in 21 loci of all 40 microsatellite (52.5%). The highest number of unique alleles was detected in ADL0284 and LEI0228, which had 4 unique alleles across all lines, respectively. Most unique alleles distributed with a low frequency, that is, 30 of 42 unique alleles (71.4%) had a frequency of lower than 10%. The frequency of unique alleles ranged from 0.0104 to 0.5729. The HE per locus ranged from 0.377 (MCW0248) to 0.877 (ADL0284). The FST per locus ranged from 0.139 (MCW0078) to 0.453 (MCW0233). In terms of the HE, higher values were observed at ADL0284, MCW0134, and LEI0228. As for number of alleles, LEI0228, LEI0196, and ADL0284 were more highly polymorphic. In regard to the FST value, which indicates component of genetic variation between lines, MCW0233, ADL0169, and MCW0183 had higher values than others. Especially, ADL0284, MCW0134, LEI0228, LEI0196, and ADL0257 showed high expected heterozygosity and many alleles at the same time. These markers would be more effective for this kind of study. On the contrary, a combination of low expected heterozygosity and a small number of alleles were observed at MCW0078 and MCW0248.
Intraline Genetic Diversity
Genetic diversity within each line is summarized in Table 3
. The highest number of alleles per line was observed in the Red Cornish (RCN) line (TNA = 187 and MNA = 4.68) with the highest PIC value of 0.585. The least number of alleles was observed in the New Hampshire Red (NHS) line (TNA = 85 and MNA = 2.12) with the lowest PIC value of 0.241. The number of unique alleles ranged from 1 [White Leghorn (WL)-B line and White Cornish line] to 11 (RCN), and the NHS line had no unique alleles. Relatively high frequencies (exceeding 20% in the line) were observed in 6 cases, half of which were detected in the Rhode Island Red (RIR)-B line.
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In all 480 HWE tests (40 loci in 12 lines), 25 cases (5.2%) could not be tested because they were monomorphic in the line. Of the remaining 455 tests, significant deviations from the HWE at the 5% level were observed in 46 cases (10.1%). In these deviations, 60.9% (28/46) cases had a heterozygosity excess. Conversely, 39.1% (18/46) cases had a heterozygosity deficit. All lines showed statistically significant deviations from the HWE for at least 1 locus; the number of locus deviated from the HWE ranged from 1 (NHS) to 14 (WR-A). A noticeable case of deviations from the HWE was observed in the WR-A line, in which 13 of 14 deviated loci were caused by excess of heterozygosity. Additionally, all deviations in the 3 WL lines also reflected the heterozygosity excess.
Global Genetic Structure
Large genetic difference was observed (overall FST = 0.298, in Table 2
); that is, around 30% of the microsatellite variation among 12 lines was due to line differentiation.
The results of an individual assignment test are shown in Table 4
. Of all 536 birds, 518 (96.6%) were properly assigned to the source line at the 5% level. The percentage of correct assignment per line ranged from 91.7% (RIR-B) to 100% [RIR-A and Barred Plymouth Rock (BPR)]. A bird that was not assigned to the source line but to another line was not observed. However, some birds were assigned to the source line together with at least another line. Such cases were mostly observed in the WL-A, WL-B, and WL-C (20.6, 21.6, and 12.5%, respectively). Seven WL-A and 8 WL-B individuals were assigned to the WL-C line along with the source line, respectively. A WL-C individual was assigned to the WL-B, 4 individuals to the WL-A, and the remaining 1 individual was assigned to both WL-A and WL-B and the source line. On the contrary, all RIR-A and BPR individuals were assigned only to the source line, respectively.
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| DISCUSSION |
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Of all 40 microsatellites used, few markers (ADL0257, ADL0284, LEI0196, and LEI0228) were more variable. These markers possessed relatively lower FST values with high HE and many alleles. These findings indicate that more common alleles did not greatly differ in terms of frequency across lines, and these markers are greatly effective for clustering and individual assignment (Rosenberg et al., 2001). These would be more useful to distinguish populations and lead to a reduction of cost for typing.
The highest heterozygosity was observed in the WR-A line, with the HWE deviations due to extreme heterozygosity excess. This line had its origin from a broiler dam line bred by a multinational company. High variability for broiler lines was previously reported in some studies (Vanhala et al., 1998; Zhang et al., 2002; Hillel et al., 2003). Three white egg layer lines in the current study generally showed lower allelic diversity (average TNA and MNA = 112 and 2.81, respectively) and heterozygosity (average HO and HE = 0.468 and 0.454, respectively) than the other lines. As compared with a broiler (WR-A) line, these layer lines showed clearly low genetic variability. However, broiler and layer lines possessed sufficient heterozygosity in the population (FIS = –0.020 to –0.141). The commercial lines are mostly created from linebreeding based on genetically different grandparental lines. These breeding practices among highly selected lines may cause deviations from the HWE due to a large excess of heterozygosity. Fixed alleles were observed in some lines; the NHS showed the most number of monomorphic loci with the lowest diversity. This result indicates that the NHS line has been maintained as a closed flock without introgressions of birds from other lines since creation. Conversely, a high level of allelic diversity was observed in the RIR-A and RCN lines, respectively. Higher allelic diversity of them is thought to be after effects of the introgressions of birds from other lines in the past 10 yr. The NHS line needs to be crossed with other lines in the near future to maintain or improve its productive performances. Other lines, except for WL lines and the NHS, did not show especially low heterozygosity than previously reported (Hillel et al., 2003).
Overall FST value of 0.298 across all lines showed that 29.8% of the genetic variation was explained by the line differences. The result was approximately equivalent to the previous report by Vanhala et al. (1998). They reported overall FST of 0.303 in 8 chicken lines including commercial Leghorn and broiler hybrids. These FST values are higher than those of other livestock species. For instance, MacHugh et al. (1998) reported a FST value of 0.112 from European cattle breeds, and SanCristobal et al. (2006) reported a FST value of 0.21 from European pig breeds.
In the dendrogram based on DA genetic distance, WL lines showed the greatest difference from other lines. Among 3 WL lines, genetic similarities were observed with shallow divergence despite their different breeding histories. Individual assignment tests also showed that the WL lines were genetically close to each other, because 12.5 to 21.6% of individuals of WL lines were simultaneously assigned to other WL lines together with their respected source lines. At the present time, Leghorn lines constitute a large percentage of white egg layers in the poultry industry; however, their genetic foundations may be narrow, because white egg layer lines mostly have their roots in Single Comb White Leghorn (Hillel et al., 2003). On the contrary, genetic relationships among other lines (Plymouth Rock, Rhode Island Red, and Cornish) were not consistent with an original breed of line (their genetic bases) in the dendrogram and showed large divergences on average. For instance, the RIR-A and RIR-B could have the same genetic base, however, the 2 were not genetically close (DA = 0.3517 and pairwise FST = 0.3008). The large genetic difference may attribute to pre-existing genetic variations originating in the dual-purpose breed, along with artificial selection based on economic traits, which largely changes the primary genetic structure. Otherwise, it is thought to be associated with introgressions of birds from other lines into the RIR-A line in the past.
In the poultry industry, commercial layers and broilers, which match present economic demands, occupy a large percentage of commercial birds. Many breeds that are not used in intensive commercial productions have a tendency to be reduced in population size with some exceptions. The current status of the poultry industry leads to the loss of genetic diversity in domestic chickens. The conservation of chicken genetic resources will be more important to fill unanticipated breeding demands for production and research in the future.
In the current study, most individuals were correctly assigned to their source lines in an individual assignment test using the distance-based method (Piry et al., 2004). Genetic characterization at an individual level demonstrated here would be a useful process to conserve chicken genetic resources.
| ACKNOWLEDGMENTS |
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Received for publication June 7, 2007. Accepted for publication August 4, 2007.
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