茶花鸡群体遗传多样性

茶花鸡是我国具有独特遗传特性的地方家禽品种,为了进一步阐明其群体遗传变异和遗传结构状况,采用了33个家鸡特异性的微卫星标记对该鸡种自然群体中30个个体进行了多态性电泳检测。33个微卫星座位共检测到105个等位基因,所有座位都呈现出多态性,每个座位的等位基因数在2~5个之间,平均每个座位等位基因数3.20个。群体平均杂合度和平均多态信息含量分别为0.612 9和0.527 6。结果表明,茶花鸡自然群体遗传多样性较丰富。     

Isolation and evaluation of 18 microsatellite markers in Siniperca chuatsi (Basilewsky)

Eighteen novel microsatellite markers were isolated in the Chinese perch Siniperca chuatsi (Basilewsky) using the FIASCO method, from (AC/TG)(n) , (AG/TC)(n) , (AT/TA)(n) , (GATA/CTAT)(n) and (GATT/CTAA)(n) repeat genomic libraries. The number of alleles per locus ranged from two to eight in a sample of 30 individuals from a wild population. Observed heterozygosity was between 0.100 and 0.737. Seven loci showed significant deviation from Hardy-Weinberg equilibrium, null alleles were suggested at nine loci but no linkage disequilibrium between loci was detected. These loci could be useful in the population genetic study of S. chuatsi.     

PERMANENT GENETIC RESOURCES: Fifteen polymorphic microsatellite DNA loci from Hawaii's Metrosideros polymorpha (Myrtaceae: Myrtales), a model species for ecology and evolution

We developed 15 polymorphic microsatellite loci from the Hawaiian tree Metrosideros polymorpha. These loci were screened against two varieties from several populations and from 23 individuals from one mid-elevation population on Hawaii Island. Loci were variable with the number of alleles per locus ranging from three to 24. Polymorphic information content ranged from 0.222 to 0.941, and observed heterozygosity ranged from 0.261 to 0.955.     

Isolation and characterization of 12 polymorphic microsatellite markers for the frog Pelophylax hubeiensis

Twelve polymorphic microsatellite loci were isolated from an (AC)n- and (AG)n-enriched DNA library for the endemic Chinese frog Pelophylax hubeiensis (Ranidae). The number of alleles per locus ranged from two to eight, with a mean of 5.17. The observed and expected heterozygosities ranged from 0.226 to 0.839 and from 0.204 to 0.826, with means of 0.568 and 0.656, respectively. No significant linkage disequilibrium was detected among these loci. However, two significant deviations from HWE were discovered at loci Pehu-11 and Pehu-12 (P<0.05). MICRO-CHECKER tests showed that null alleles could be present at locus Pehu-12. These polymorphic microsatellite loci can be employed for exploring mating mechanisms, population genetic structure and other relevant genetic investigations of P. hubeiensis.     

Microsatellite DNA markers in Populus tremuloides.

Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars.     

Development of DNA microsatellite markers in the multiband butterflyfish (Chaetodon multicinctus)

Twelve polymorphic microsatellite loci were developed in the multiband (pebbled) butterflyfish Chaetodon multicinctus. The loci were scored in 45 individuals from Hawaii. There were five to 21 alleles per locus with observed heterozygosity ranging from 0.419 to 0.883. Four of the primer sets also reliably amplified polymorphic loci in Chaetodon quadrimaculatus. We expect these markers to be useful for studies of genetic population structure and kinship, for example to determine whether new recruits settling onto reefs are related.     

Isolation and characterization of 16 polymorphic microsatellite loci in the endemic Hawaiian damselfly Megalagrion xanthomelas (Odonata: Coenagrionidae)

Microsatellite loci have been isolated from two species of endemic Hawaiian damselflies, Megalagrion xanthomelas and M. eudytum, that are of conservation concern. Sixteen polymorphic loci were characterized in 32 M. xanthomelas from one population on Molokai and one on Hawaii Island. The total number of alleles per locus ranged from two to 16 and observed population heterozygosity ranged from 0.0 to 0.963. Eleven of these loci amplified successfully in M. eudytum as well. These loci will be used to further conservation efforts and infer genetic consequences of Pleistocene glaciations.     

Allozyme Variation In Spineless Pejibaye (bactris Gasipaes Palmae)

Allozyme variation was examined in three pejibaye (Bactris gasipaes) populations introduced into Hawaii for use in heart-of-palm improvement: Benjamin Constant (Putumayo landrace), San Carlos (Guatuso landrace) and Yurimaguas (Pampa Hermosa landrace). Nine enzymes encoded by 16 putative loci with a total of 38 alleles were resolved from meristem extract. Five loci were fixed in all populations, four additional loci were fixed in SC and one additional locus in BC. Six of the 38 alleles were rare, with three unique to BC and one to Y; two moderately high frequency alleles were unique to SC. Mean number of alleles per locus was lowest (1.6) in SC, with BC and Y having 2.1 alleles. Percentage of polymorphic loci was lowest in SC (44) and highest in Y (69). Observed heterozygosity was lowest in SC (0.051) and BC (0.066) and highest in Y (0.141). Nei’s genetic identity was 0.985 between BC and Y and averaged 0.952 between SC and BC-Y. The low heterozygosities are probably due to a long history of selection and inbreeding (sib-mating) during the domestication process, followed by intensive recent selection for spinelessness and more inbreeding. All populations are very closely related, suggesting a single domestication event in Amazonia.     

Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars

The simple sequence repeat (SSR) or microsatellite marker is currently the preferred molecular marker due to its highly desirable properties. The aim of this study was to develop and characterize more SSR markers because the number of SSR markers currently available in tomato is very limited. Five hundred DNA sequences of tomato were searched for SSRs and analyzed for the design of PCR primers. Of the 158 pairs of SSR primers screened against a set of 19 diverse tomato cultivars, 129 pairs produced the expected DNA fragments in their PCR products, and 65 of them were polymorphic with the polymorphism information content (PIC) ranging from 0.09 to 0.67. Among the polymorphic loci, 2-6 SSR alleles were detected for each locus with an average of 2.7 alleles per locus; 49.2% of these loci had two alleles and 33.8% had three alleles. The vast majority (93.8%) of the microsatellite loci contained di- or tri-nucleotide repeats and only 6.2% had tetra- and penta-nucleotide repeats. It was also found that TA/AT was the most frequent type of repeat, and the polymorphism information content (PIC) was positively correlated with the number of repeats. The set of 19 tomato cultivars were clustered based on the banding patterns generated by the 65 polymorphic SSR loci. Since the markers developed in this study are primarily from expressed sequences, they can be used not only for molecular mapping, cultivar identification and marker-assisted selection, but for identifying gene-trait relations in tomato.     

Isolation and characterization of 23 microsatellite loci in the yellow tang, Zebrasoma flavescens (Pisces: Acanthuridae)

Twenty‐three microsatellites were isolated from the yellow tang (Zebrasoma flavescens), an ecologically and commercially important reef fish. Genetic diversity was assessed in 90 adults collected from Honokohau, Hawaii. The number of alleles per locus varied from four to 29 (mean = 13.8) and observed and expected heterozygosities ranged from 0.15 to 0.94 (mean = 0.70) and from 0.29 to 0.93 (mean = 0.81), respectively. Eight loci exhibited significant departure from Hardy–Weinberg equilibrium due to the presence of null alleles. Exact tests showed no evidence of genotypic disequilibrium between loci. Overall, loci were well resolved, easy to score and highly polymorphic.     

Isolation and characterization of 12 polymorphic microsatellite markers in the tropical house gecko (Hemidactylus mabouia)

We present 12 variable microsatellite loci isolated from the invasive tropical house gecko, Hemidactylus mabouia. Polymerase chain reaction (PCR) primers were tested on 39 individuals from two locations in Miami, Florida. Heterozygote deficiency was detected for four loci, and we attribute this to possible null alleles or population substructure. Some loci successfully amplified PCR products in several congeners, indicating their potential for use in other geckos.     

中国维吾尔族人群MSY1(DYF155S1)基因座多态性及其结构特点

应用荧光标记MVR-PCR、Amp-FLP与DNA序列分析技术等检测106例中国维吾尔族人群无关男性个体血纱样品,揭示了中国维吾尔族人群Y特异的小卫星MSY1 (DYF155S1)基因座5′和3′端多态性及其基因结构特点。DYF155S1基因座的多态性表现为3个方面：（1）长度多态性;（2）5′端多态性;（3）3′端多态性。106例无关个体共检出37个不同长度的片段,5′端检出68个类型,3′端检出23个类型。综合这3方面多态性,106例个体间没有相同,其基因多样性（h）超过0.9999。DNA序列分析发现该基因座5′端表现有7种模块结构,3′端有2种模块结构。DYF155S2片段缺失率约为4.7%。MVR-PCR、Amp-FLP与DNA序列分析技术结合起来可以更充分地揭示人群Y染色体特异的小卫星MSY1（DYF155S1）基因座多态性,并提出命名方式,从而为人类遗传学及法医学研究提供了有用的方法和基础资料。 Abstract:The study is to reveal the diversity and gene structure of 5′ and 3′ end of DYF155S1 locus in Y-chromosome minisatellite among Chinese Uygur population.Fluorescent MVR-PCR（minisatellite variant repeat by PCR）,Amp-FLP(Amplified fragment length polymorphism) and DNA sequencing methods were used repectively to detect 106 unrelated males among Chinese Uygur population.The polymorphisms of DYF155S1 locus could be revealed in three aspects:(1) polymorphic length:the sizes of amplified fragments ranged from 1405 to 2505bp.There are 37 types found among the 106 unrelated males.(2) polymorphism at 5′ end of DYF155S1 locus,68 types found among the 106 unrelated males.(3) polymorphism at 3′ end of DYF155S1 locus,23 types found among the 106 unrelated males.In combination of these three aspects of polymorphism,none of the 106 unrelated males tested had the same allele,and the gene diversity(h) was over 0.9999.Seven and two types of modular structure were founded in the 5′ and 3′ end of DYF155S1 locus,respectively,by DNA sequencing.The alleles at DYF155S2 locus showed yes/no dimorphism and the rate of deletion was 4.7%.The polymorphisms of DYF155S1 locus were fully revealed by using combination of MVR-PCR, Amp-FLP and DNA sequencing methods, and we suggested the nomenclature for alleles of MVR loci.These methods are useful tools and provide basic data for the study of human genetics and forensic medicine.     

Eleven new microsatellite markers for the tropical sea urchin Tripneustes gratilla and cross‐amplification in Tripneustes ventricosa

We describe the isolation, characterization, and application of 11 polymorphic microsatellite loci from the tropical sea urchin Tripneustes gratilla. We genotyped a total of 73 individuals in three subpopulations (two in Hawaii, and one in the Philippines) and found between eight and 33 alleles per locus. We found significant heterozygote deficits within at least one subpopulation at seven out of 11 loci. We were successful at cross‐amplifying four loci in the congeneric Tripneustes ventricosus. When used appropriately, this set of loci will be useful for quantifying population structure in Tripneustes urchins across broad geographical ranges.     

Population genetic structure of Nantucket pine tip moth

Summary Variation at polymorphic isozyme loci was analyzed in Nantucket pine tip moth (NPTM) populations from 5 geographic locations. At the North Carolina location, populations representing 3 generations at 3 local sites were also studied. Four of the loci investigated (LAP, MDH, -GPDH and AK), although variable, had few alleles per locus (3–5) and few differences among populations in allele frequencies. At each locus, all populations had the same allele at a high frequency.At the PGM locus, fifteen alleles were identified and allelic frequencies varied among populations. At least eight alleles were present within a population and, in most populations, two or more alleles had high frequencies that differed among populations. An excess of homozygotes over Hardy-Weinberg expectations was found for 7 out of the 10 populations studied, indicating the probable existence of some form of inbreeding structure or populational subdivision within sampled stands.Joint consideration of the results observed for PGM and the other four loci is counterindicative of neutrality at all loci and strongly indicative of genetic differentiation among locally disjunct populations.Published as Paper No. 6751 of the Journal Series of the North Carolina Agricultural Research Service     

Isolation and characterization of 13 microsatellite loci for Percichthys trucha (Percichthyidae)

Thirteen polymorphic microsatellite loci are described for the South American freshwater fish Percichthys trucha. Number of alleles per locus ranged from two to 21 and observed heterozygosities ranged from 0.304 to 0.915 in a sample of 47 individuals from four different sampling locations.     

Statistical genetic considerations for maintaining germ plasm collections

One objective of the regeneration of genetic populations is to maintain at least one copy of each allele present in the original population. Genetic diversity within populations depends on the number and frequency of alleles across all loci. The objectives of this study on outbreeding crops are: (1) to use probability models to determine optimal sample sizes for the regeneration for a number of alleles at independent loci; and (2) to examine theoretical considerations in choosing core subsets of a collection. If we assume that k-1 alleles occur at an identical low frequency of p₀ and that the k^th allele occurs at a frequency of 1-[(k-1)p₀], for loci with two, three, or four alleles, each with a p₀ of 0.05, 89–110 additional individuals are required if at least one allele at each of 10 loci is to be retained with a 90% probability; if 100 loci are involved, 134–155 individuals are required. For two, three, or four alleles, when p₀ is 0.03 at each of 10 loci, the sample size required to include at least one of the alleles from each class in each locus is 150–186 individuals; if 100 loci are involved, 75 additional individuals are required. Sample sizes of 160–210 plants are required to capture alleles at frequencies of 0.05 or higher in each of 150 loci, with a 90–95% probability. For rare alleles widespread throughout the collection, most alleles with frequencies of 0.03 and 0.05 per locus will be included in a core subset of 25–100 accessions.     

Isolation and characterization of 31 polymorphic microsatellite markers in barfin flounder (Verasper moseri) and the cross-species amplification in spotted halibut (Verasper variegatus)

The construction of a genetic linkage map and evaluation of population genetic diversity both require large numbers of polymorphic molecular markers. In the present study, we report 31 polymorphic microsatellite markers, of which 28 were isolated from two repeat-enriched libraries constructed from genomic DNA, and three were detected in two genes (MCH-R1 and MCH-R2) of barfin flounder (Verasper moseri). A total of 94 alleles were detected with an average of 3.0 alleles per locus. The number of alleles, observed and expected heterozygosity per locus ranged from two to six, from 0.30 to 1.00 and from 0.33 to 0.78, respectively. Three loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0016) and no significant linkage disequilibrum between pairs of loci was found. Cross-species amplification of these markers was evaluated using the closely related species spotted halibut (Verasper variegatus). This study will potentially be useful for stock management, constructing of a genetic linkage map, mapping economically important quantitative trait loci (QTL), and studying the population genetic diversity of barfin flounder (Verasper moseri).     

Polymorphic dinucleotide microsatellite loci in the clonal ascidian Diplosoma listerianum: predominance of compound and highly interrupted imperfect repeats

We report the isolation of the first dinucleotide microsatellite loci from the clonal ascidian, Diplosoma listerianum. Most repeats were compound and highly interrupted, with flanking sequences containing many small interspersed repetitive regions. Consequently, most primers detected polymerase chain reaction products outside the expected size range, and only five out of 15 primers detected polymorphic single‐locus markers. Characterization of five variable loci from two UK populations revealed three to seven alleles per locus, with observed heterozygosity of 0.00–0.86 and expected heterozygosity of 0.10–0.66. Three loci showed significant heterozygote deficits either because of inbreeding, population substructure or the presence of null alleles.