Coefficient Of Genetic Identity Research Articles

Estimation of Jacquard's genetic identity coefficients with bi-allelic variants by constrained least-squares.

The Jacquard genetic identity coefficients are of fundamental importance in relatedness research. We address the estimation of these coefficients as well as other relationship parameters that derive from them such as kinship and inbreeding coefficients using a concise matrix framework. Estimation of the Jacquard coefficients via likelihood methods and the expectation-maximization algorithm is computationally very demanding for large numbers of polymorphisms. We propose a constrained least squares approach to estimate the Jacquard coefficients. A simulation study shows constrained least squares achieves root-mean-squared errors that are comparable with those of the maximum likelihood approach, in particular when founder allele frequencies are unknown, while obtaining enormous computational savings.

Development of 25 Novel Microsatellite Loci and Genetic Variation Analysis in Breeding Populations of the Pearl Oyster,Pinctada fucata

AbstractIn this study, we screened 103,050 gene sequences ofPinctada fucataand identified 1450 simple sequence repeats (SSRs) distributing in 1355 sequences, in which 97 have sufficient flanking sequences for primer design, and 25 novel microsatellite loci were stable and polymorphic withNawhich varied from 2 to 6. Six microsatellite loci were found in the open reading frame of their corresponding sequences. With the 25SSRloci, five breeding populations and a wild population, a total of 240 individuals from wild population (W), three consecutive selected populations (G1,G2,andG3), and two backcross populations (Do, Dr) (40 individuals per population) were assayed. In these populations, we detected 108 alleles of 111 bp to 362 bp. Each population had meanHoof 0.5718–0.7366 and meanHeof 0.5830–0.6954. Except theFst = 0.0697 (W vs.G3), pairwiseFstvalues ranged from 0.0131 to 0.0473, the genetic identity coefficients varied from 0.8688 to 0.9663, and genetic distance ranged from 0.0343 to 0.1307, all of these suggested that the breeding populations had genetic differentiation but at a low level generally. Besides, all the genetic index values, backcross populations (Do, Dr) were higher than correspondingG3values, indicating that backcross could make the offspring incline to the recurrent parents.

Population genetics of the Chilean frog Batrachyla Leptopus (Leptodactylidae)

Electrophoretic variation of proteins encoded by 14 loci was analyzed in eight (five continental and three insular) populations of the Chilean leptodactylid frog Batrachyla leptopus. The overall proportion of polymorphic loci was estimated to be 18.7% and the average number of alleles per locus, 1.2, while observed and expected heterozygosities were 1.7 and 5.1%, respectively. The estimated coefficient of genetic identity was 0.940; the corresponding figure for genetic distance was 0.063. F-statistics analysis showed a total inbreeding coefficient (Fit) of 0.855 and high levels of genetic subdivision (Fst = 0.596) as well as of inbreeding within populations (Fis = 0.640). However, there was only a moderate level of genetic differentiation (Fst = 0.181) between the insular group of populations and the continental group.

Genetic Analysis of Major Histocompatibility Complex Class I Antigens, Serum Transferrins and Red Blood Cell Antigens in Norwegian Breeds of Cattle

BoLA class I antigens, serum transferrins (Tf) and red blood cell (rbc) antigens were determined in five rare local Norwegian cattle breeds as well as in the main cattle population, Norwegian Cattle (NRF). Highly significant breed differences were found for all these marker systems, except for the Z blood group system, and some of the linked loci within the C-system. The estimated allele frequencies were used to calculate genetic identity coefficients and to construct a dendrogram. The mean identity coefficient was 0.328 for BoLA, 0.923 for Tf, and ranged from 0.561 to 0.997 (mean 0.909) for the rbc systems. The low identity coefficients for BoLA, compared with those of Tf and rbc, may indicate that genetic forces may have had a different impact on BoLA than on the other systems under study.

Maccullochella ikei, an endangered species of freshwater cod (Pisces: Percichthyidae) from the Clarence River system, NSW and M. peelii mariensis, a new subspecies from the Mary River system, Qld

The eastern freshwater cod, Maccullochella ikei, from the Clarence River system, NSW, is described and M. peelii mariensis is described as a new subspecies from the Mary River system, Qld. The Murray cod, M. p. peelii and the trout cod, M. macquariensis, are indigenous to the Murray-Darling River system. Using electrophoretic data for 19 presumed loci, the coefficient of genetic identity between M. p. peelii and M. ikei was 0.72 and the banding-patterns of the muscle general protein, liver esterases and five other enzymes, were species-specific. A high proportion of abnormal and inviable hybrid larvae in a cross-breeding experiment indicate that post-zygotic isolating mechanisms have evolved between M. p. peelii and M. ikei. The coefficient of genetic identity between M. p. peelii and M. p. mariensis was 0.85 and banding patterns of muscle general protein were diagnostic. Canonical variates analysis using 18 morphological and nine meristic characters, clearly separated both spccies and the subspecies. Maccullochella ikei is distinguished from M. p. peelii by having longer pelvic fins, larger orbit length, and larger and morphologically distinct sagittalotoliths. Maccullochella p. mariensis differs from M. p. pee/ii by the combination of a deeper and shorter caudal peduncle, longer pelvic fins, larger sagittal otoliths and lesser extension of the first anal pterygiophore towards the first caudal vertebra, and from M. ikei by the combination of a deeper caudal peduncle, greater postorbital head length, smaller orbit, larger interorbital width, fewer scale rows below the lateral line, shorter fifth-sixth dorsal spine and lesser extension of the first anal pterygiophore. Although each species has distinctive colouration and mottling, there is some intra-specific variation. Maccullochella macquariensis is distinct from the other species by having a straight head profile, jaws of similar length, 14 precaudal vertebrae and distinctive colouration. There was a dramatic reduction in the distribution and abundance of cod in the eastern drainage during the early 1900s and cod were probably extinct in the Richmond and Brisbane River systems by the end of the 1930s. Maccullochella ikei and M. p. mariensis are each represented by one, small population. Possible causes of the decline, and the management strategies taken to conserve the endangered M. ikei are discussed.

Calculation of genetic identity coefficients.

Genetic identity coefficients define the kind and amount of gene sharing between two relatives at a single locus. Non-recursive computation of these probabilities depends on cumbersome graph-tracing algorithms. Closely related to the identity coefficients are certain generalized kinship coefficients which can be computed recursively. The present paper clarifies some ideas of Karigl about how to relate identity coefficients to generalized kinship coefficients.

Inter- and Intrapopulation Isozyme Variation in Collections from Sexually Reproducing Populations of the Bean Rust Fungus, Uromyces appendiculatus

Previous studies of isozyme banding patterns in Uromyces appendiculatus compared one isolate per population or location. In this study, five or more isolates were surveyed from each of 12 field collections to estimate genetic variation within and between the source populations. Five enzymes stained in Polyacrylamide slab gels produced 10–21 bands grouped as 10 markers (putative loci); 14 of these bands were present in > 72% of the isolates. Six markers indicated heterozygous loci. Marker I of phosphoglucomutase was the most diverse across the collections; three markers were fixed. One marker pattern was predominant for each enzyme, and one multi-isozyme phenotype occurred in 11 of the 12 collections and 21 of the 66 isolates. A 1986 collection from west-central Minnesota, denoted P24, had the lowest Shannon Diversity Index, the highest proportion of simple (homozygote-like) band patterns, the highest mean number of marker differences from isolates of the other collections, and no phenotypes in common with any other collection. Nei's Coefficient of Genetic Identity averaged 0.952 among 11 of the collections but only 0.791 between P24 and the other collections. Collection P24 may represent a late-season epidemic population of asexually produced spores.

Inter- and Intrapopulation Isozyme Variation in Collections from Sexually Reproducing Populations of the Bean Rust Fungus,Uromyces Appendiculatus

Previous studies of isozyme banding patterns in Uromyces appendiculatus compared one isolate per population or location. In this study, five or more isolates were surveyed from each of 12 field collections to estimate genetic variation within and between the source populations. Five enzymes stained in polyacrylamide slab gels produced 10-21 bands grouped as 10 markers (putative loci); 14 of these bands were present in >72% of the isolates. Six markers indicated heterozygous loci. Marker I of phosphoglucomutase was the most diverse across the collections; three markers were fixed. One marker pattern was predominant for each enzyme, and one multi-isozyme phenotype occurred in 11 of the 12 collections and 21 of the 66 isolates. A 1986 collection from west-central Minnesota, denoted P24, had the lowest Shannon Diversity Index, the highest proportion of simple (homozygote-like) band patterns, the highest mean number of marker differences from isolates of the other collections, and no phenotypes in common with any other collection. Nei's Coefficient of Genetic Identity averaged 0.952 among 11 of the collections but only 0.791 between P24 and the other collections. Collection P24 may represent a late-season epidemic population of asexually produced spores.

Allozyme variation among biotypes of the brown planthopperNilaparvata lugens in the Philippines

Allozyme variation was studied in three Nilaparvata lugens biotypes infesting specific rice varieties and a biotype infesting a weed grass, Leersia hexandra. Of the 20 enzymes in N. lugens for which activity was noted, 9 were polymorphic. Eleven enzyme loci were monomorphic for the same allele in all biotype populations; the rest were polymorphic for two or more alleles. The mean number of alleles per polymorphic locus was 2.3, while the mean number of alleles per locus was 1.5; heterozygosity ranged from 0.02 to 0.06 (biotype 1 greater than biotype 3 greater than Leersia-infesting biotype greater than biotype 2). Allelic frequency differences were observed in five loci among the four biotypes. However, the coefficient of genetic identity (I) of 0.99+ showed that the four biotype populations were genetically close relatives or merely populations of N. lugens undergoing genetic differentiation.

Isoenzyme polymorphisms in Gymnaedenia conopsea and its inferences for systematics within this species

The genetic variability of seven enzymes for a total of eleven loci has been studied by means of starch gel electrophoresis in 16 populations of Gymnaedenia conopsea (Orchidaceae), some coming from humid habitats and some from dry habitats. The calculation of Nei genetic identity coefficients pointed to a heterogeneity in this taxon, which is explained when populations are subdivided in two subgroups according to whether they belong to the “humid” or the “dry” ecotype. It has thus been shown that while the genetic identity among local intraecotypic populations is on the average 0.970, it is 0.654 between the two ecotypes. The data obtained on the allozyme differences and the presence, in the populations examined, of at least one reproductive isolating mechanism, suggest that the two taxa are not simple ecological forms without systematic value, but can be regarded as distinct species, and precisely as “sibling species”, owing to the close resemblance in morphological characters.

Genetic variability in arrhenotokous and thelytokous forms ofMesochorus nigripes [Hym.: Ichneumonidae

Electrophoresis of isozymes was carried out to determine the degree of genetic variability in arrhenotokous and thelytokous forms ofMesochorus nigripes. Although the over-all heterozygosity (Ha) for 12 loci in 10 enzyme systems was 0.187 for the arrhenotokous form and 0.103 for the thelytokous form, a paired comparison t-test showed no significant difference. Nei's coefficient of genetic identity between these 2 forms I=0.982.

Allozyme differentiation in theCucurbita pepo complex:C. pepo var.medullosa vs.C. texana

Two interfertile species ofCucurbita, the wildC. texana and the domesticatedC. pepo (var.medullosa), were hybridized to elucidate the genetic basis of inter-specific differences in isozyme phenotypes. Presented here are descriptions of phenotypes associated with 6 enzyme systems (GOT, IDH, MDH, PER, PGI, PGM). Genetic interpretation for 6 gene loci and 12 alleles is based on F2 segregation data while 10 additional loci and 15 alleles are presumed on the basis of phenotypic variation found throughout theC. pepo complex. A coefficient of genetic identity calculated for single populations of each taxon was within the range that traditionally separates species. However, observations on phenotypes in both taxa leave the taxonomic delimitation of C. texana unresolved. The complexity of banding patterns in some enzyme systems suggests a polyploid origin for the genus Cucurbita.

Genetic differentiation in the molluscan species Littorina rudis and Littorina arcana (Prosobranchia: Littorinidae)

Six populations of Littorina rudis and ihree of L. arcana were screened for elcctrophorctically dctci table variation at 21 enzyme loci. These species reproduce by ovoviviparity and oviparily respectively, and both are members of the L. saxatilis species complex. The mean coefficient of genetic identity between the two species was high (0.957) and no diagnostic loci were observed. Allele frequency differences are maintained in sympatric populations of the two species. Intraspecific values of/ ranged from 0.944 to 0.995 and both species showed marked inter-population genetic heterogeneity, a feature consistent with their limited powers of dispersal. Heterozygosity is high in all populations of both species. Populations of I. rudis have higher mean heterozygosities (= 0.153) then L. arcane (H= 0.132).

A comparison of gene-enzyme variation between Drosophila melanogaster and Drosophila simulans

Genetic variation at eleven gene loci coding for enzymes has been studied in sympatric Greek island populations of Drosophila melanogaster and D. simulans. Only two enzyme loci indicate an absolute interspecific difference. In D. melanogaster, the average number of alleles per locus was 2.37, the mean proportion of polymorphic loci 0.818, and the mean heterozygosity 0.156. The corresponding values in D. simulans were 2.09, 0.455, and 0.173 respectively. The average heterozygosity was found to be higher in the Greek island population of D. simulans than in the Hawaiian population studied by others; allelic differences were observed as well. The coefficient of genetic identity (Nei's I) between the two sibling species was found to be 0.566. A comparison of genetic similarity among Greek, American (U.S.A.) and Japanese D. melanogaster populations, estimated on the basis of allelie frequencies for nine enzymic loci, showed little difference between the populations, giving an average genetic similarity of 0.965.

Genetic redundancy among durum wheat accessions as assessed by SSRs and endosperm proteins

Reducing duplication in ex-situ collections is complicated and requires good quality genetic markers. This study was conducted to assess the value of endosperm proteins and SSRs for validation of potential duplicates and monitoring intra-accession variability. Fifty durum wheat (Triticum turgidum ssp. durum) accessions grouped in 23 potential duplicates, and previously characterised for 30 agro-morphological traits, were analysed for gliadin and high molecular weight glutenin (HMWG) subunit alleles, total protein, and 24 SSRs, covering a wide genome area. Similarity and dissimilarity matrices were generated based on protein and SSRs alleles. For heterogeneous accessions at gliadins the percent pattern homology (PH) between gliadin patterns and the Nei’s coefficient of genetic identity (I) were computed. Eighteen duplicates identical for proteins showed none or less than 3 unshared SSRs alleles. For heterogeneous accessions PH and I values lower than 80 identified clearly off-types with more than 3 SSRs unshared. Only those biotypes differing in no more than one protein-coding locus were confirmed with SSRs. A good concordance among proteins, morphological traits, and SSR were detected. However, the discrepancy in similarity detected in some cases showed that it is advisable to evaluate redundancy through distinct approaches. The analysis in proteins together with SSRs data are very useful to identify duplicates, biotypes, close related genotypes, and contaminations.