The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0.944 and 0.00322, respectively. We identified a correlation between the lineages distribution and the genetic distance, whereby Valley-type Tibetan sheep had a closer genetic relationship with introduced breeds (Dorper, Poll Dorset and Suffolk) than with other indigenous breeds. Similarly, the Median-joining profile of haplotypes revealed the distribution of clusters according to genetic differences. Moreover, copy number analysis based on the five mitochondrial coding genes was affected by the genetic distance combining with genetic phylogeny; we also identified obvious non-synonymous mutations in ATP6 between the different levels of copy number expressions. These results imply that differences in mitogenomic compositions resulting from geographical separation lead to differences in mitochondrial function.

Core subset selection from collections hosted by seed banks, grow in importance as the number of accessions and genetic marker information rapidly increases. A data set of 20,526 single-nucleotide polymorphism (SNP) markers characterizing 7986 Mexican creole wheat landraces, was used to test 11 methods for core subset selection, through optimization criteria containing average genetic distance and genetic diversity. Allele richness was used as an additional criterion to qualify the generated core subsets. Three replications with random samples of 1500 SNP loci, each comprising a maximum of 3000 alleles, were used to perform the method evaluations through four different objective functions. The LR greedy search (LR) and LR with random first pair (LRSemi) were consistently best across all assays for maximizing the objective functions, and they performed well even for criteria not included in those functions. The Tukey's HSD (honest significant difference) multiple comparisons grouped those methods together with the sequential forward selection (SFS) and SFS with random first pair (SFSSemi) strategies as the top set of approaches. All of them are simple heuristic maximization algorithms, and outperformed two more sophisticated optimization approaches: parallel mixed replica exchange and replica exchange Monte Carlo. For their efficiency to optimize the objective functions and computing speed, the LRSemi and SFSSemi methods demonstrated to be good alternatives for core subset selection from large collections of highly homozygous accessions characterized by many biallelic markers.

Levels of inter- and intrapopulation genetic variation were determined in five North American populations of leafy spurge using chloroplast DNA (cpDNA) RFLPs and RAPD markers. Thirteen plastome types were identified among 123 individuals collected from five geographically separated populations. Number of plastomes within a population ranged from one to seven, with four of the populations having a predominate type plus one or more rarer types. Some plastome types were shared by populations, but plastome distribution among populations was nonrandom. RAPD markers indicated greatest relatedness among individuals within a population. Relatedness among populations as established through RAPDs was greater for geographically closer populations; this relationship was not observed for cpDNA markers. Differences in the range of movement for pollen and seed may account for differences between results of the cpDNA and RAPD analyses. The high degree of genetic variability among North American leafy spurge suggests possible multiple introductions or a high degree of variability within leafy spurge populations in its native range.

Red rice is a major weed in rice production in the southern United States. Red rice and rice intercross because they are the same species. Our objectives were to determine the genetic diversity represented by accessions of red rice and to identify DNA markers that might be useful in identifying hybrids between red and cultivated rice. Red rice accessions were collected from Arkansas and other rice-producing states. Seventy-nine red rice accessions, 10 known or putative hybrid derivatives of red rice and cultivated rice (RC hybrids), and seven rice cultivars were analyzed using microsatellite DNA markers developed for cultivated rice. Microsatellite markers differentiated awned and awnless red rice accessions, six of the seven rice cultivars, and all 10 RC hybrids tested. Thus, these markers were useful in identifying red rice types and RC hybrids.

Heterosis is a main force underlying the hybrid seed industry in maize. Our experimental approach consists of a correlation study between retrotransposon-related genetic distances between parental inbred lines and hybrid performance. The assumption is that, at least for certain traits, heterosis results from genome rearrangements, largely related to retrotransposon insertions and/or removals. Fifteen maize inbred lines and one F1 hybrid, representative of the genetic diversity among sweet corn and field corn lines were screened for polymorphism by retrotransposon microsatellite amplified polymorphism markers. DNA fingerprints served as row data for estimating genetic diversity of maize inbred lines and its correlation with the heterotic effect in their hybrids. A correlation between phenotypic and molecular distances was evident only at the level of individual inbred lines. Weak correlation between genetic distances and heterosis effect was observed for the average of all inbred lines. Phenotypic distances negatively correlated with heterosis for insertion height, diameter of the ear and number of kernel rows per ear. The relative contribution of each inbred line to heterosis in its derived hybrids was also estimated. Accordingly, we identified inbred lines with increased genetic distances that mostly add to the heterosis effect in their hybrids and that we recommend as prospective to be used in maize breeding programmes.

This paper documents a positive correlation between the genetic distance to the world technological frontier (United Kingdom, United States) and the year of the onset of the fertility transition across countries. This result is robust to controlling for a large set of geographical, climatic, historical, and institutional variables. Two main mechanisms could explain this reduced-form relationship. First, genetic distance to the world technological frontier can affect the onset of the fertility transition through its impact on the timing and intensity of technology adoption. Second, genetic distance to the technological frontier can capture other cultural differences and the process of diffusion of cultural norms that are related to fertility but not through technology adoption. We find suggestive evidence supporting both mechanisms.

Hybrid breeding relies on selection of genetically unrelated and complementary parents for key traits. The objective of this study was to examine genetic variation and identify unique sorghum genotypes using phenotypic and simple sequence repeat (SSR) markers and to determine their relationships with combining ability and heterosis for grain yield. A total of 32 landraces and four cytoplasmic male sterile (CMS) lines were phenotyped using 25 agro-morphological traits and genotyped with 30 polymorphic SSR markers. The landraces were crossed with four CMS lines using a line × tester mating design. The 128 hybrids, 36 parentals and four check varieties were field-evaluated using a 12 × 14 alpha lattice design with three replications. General combining ability (GCA), specific combining ability (SCA) and heterosis for grain yield were determined. Genetic distance estimates ranged from 0.39 to 0.60 and 0.50 to 0.79, based on phenotypic and SSR markers, respectively. Landraces 72572, 75454, 200654, 239175, 239208, 244735A and 242039B and CMS lines ICSA 743 and ICSA 756 displayed positive and significant GCA effects for grain yield. Based on the SCA effects of yield, lines were classified into three heterotic groups aligned to the different cytoplasmic systems of testers. Lines with high GCA effects rendered hybrids with highly significant SCA effects with high mid-parent heterosis (MPH) for grain yield. Both marker systems were effective in demarcating sorghum genotypes that provided desirable cross-combinations with high combining ability effects and MPH for grain yield. The selected genotypes are recommended as potential parents for sorghum hybrid breeding in moisture stress environments.

Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple sequence repeat markers. A total of 539 alleles were detected. The allele number per locus ranged from 2 to 21, with a mean allele number of 9.2. The average genetic diversity index was 0.66, with values ranging from 0.01 to 0.89. Comparing the three genomes of wheat, the B genome had the highest genetic diversity (0.66) and the D genome the lowest diversity (0.61). A STRUCTURE analysis based on the Bayesian model-based cluster analysis followed by a graphical representation of the distances by non-parametric multidimensional scaling revealed a distinct partition of the Eritrean wheat accessions into two major groups. This is the first report of the genetic diversity and structure of Eritrean bread wheat.

In the 1970s a large proportion of the people of Western Sahara went into exile, settling as refugees in camps in Tindouf, Algeria. They took with them their traditional pastoralist way of life and their breeds of small ruminants, which formed the main part of their diet. Almost three decades later, these breeds, having endured the war and the exodus, are in danger of extinction, firstly because of their situation, and secondly because of scientific ignorance about them. In the present paper, we develop a genetic characterization of the Sidaun and Kerrian breeds of sheep and the Buzguender breed of goats in the Saharawi refugee camps. The results indicate that all the breeds studied still have a high level of genetic differentiation and are not showing signs of recent exotic gene migrations. This is encouraging, for it indicates that we are in time to conserve these genotypes of high ecological value for their capacity to survive in the desert.

Indigenous livestock resources are strategic in the socio-economics of rural agricultural systems to ensure food security in resource-poor countries. Therefore, better understanding of genetic variation holds the key to future utilization through conservation. We report the first analysis of genetic diversity of Nigerian sheep based on the D-loop region of the Ovis aries mitochondrial genome using 1 179 bases between sites 15 437 and 16 616 base pairs. A sample of 290 animals made up of Balami, West African Dwarf (WAD), Uda and Yankasa breeds were randomly collected from across Nigeria. Ninety-six haplotypes were observed with a high mean haplotype diversity of 0.899 ± 0.148. Gene diversity was highest in Uda (0.921 ± 0.021) and lowest in WAD (0.852 ± 0.061). Population specific FST indices varied from 0.00133 in Uda to 0.00335 in WAD. Yankasa had the highest number of polymorphic sites (201), while the least was in Uda (96). Analysis of molecular variance revealed that 0.23 percent of the variation is found among populations compared with 99.77 percent variation found within populations. The phylogenetic tree indicates that the mitochondrial lineages of these sheep breeds originated from a common source consistent with first divergence of Yankasa followed by WAD, while Balami and Uda remain more closely related. These results suggest that evolutionary divergence of Nigerian sheep breeds based on mitochondrial DNA D-loop sequence may be coincident with geographical distribution in Nigeria and suggest significant interbreeding. This could have implications for managing improvement and conservation strategies and long-term conservation of Nigerian indigenous sheep.

The objective of this study was the morphological characterization of the sheep population in the southwest of Tunisia. A joint analysis of quantitative and qualitative characters was carried out on 987 animals of three breeds: two local breeds (Barbarine (BAR) and Queue Fine de l'Ouest (QFG and QFT)) and an exotic breed introduced from Morocco, the D'man (DMN) breed.

Results on quantitative characters (height at withers (HG), body length (LC), thorax perimeter (PT), body weight of males (P♂) and body weight of females (P♀)) showed a significant superiority of the Queue Fine de l'Ouest breed compared to the other two breeds. On the other hand, results on qualitative characters (fleece color, horn and wattles) showed white to be the dominant color of the fleece in the Barbarine and Queue Fine breeds, while for the D'man breed there were various colors. Generally, females of the three breeds were polled while males were horned for the Queue Fine and polled for the Barbarine and D'man breeds. The Barbarine distinguishes itself from the other breeds by the total absence of wattles which are predominantly missing in the other two breeds.

Genetic distances estimated on the basis of quantitative characters showed that distances found between the Barbarine-D'man and Fine Tail of Ouest-D'man breeds were higher than those found between the Barbarine-Queue Fine breeds.

Introduction. Turkey potentially has a very rich source of sweet (Prunus avium) and sour (P. cerasus) cherries. P. avium is apparently native to some parts of Northern Turkey, where Giresun is located. Identification of the sweet cherry cultivars produced in Turkey will help in choosing appropriate cultivars and aid in the preservation of natural resources required for breeding studies. The most conventional method of cultivar identification is based on the assessment of morphological characteristics. However, this method is insufficient to distinguish closely related cultivars. The aims of our study were to determine the molecular profile of sweet cherry accessions grown in Giresun, Turkey, and to determine their genetic relationships. Materials and methods. In our study, we identified 44 sweet cherry accessions grown in Giresun by using genetic markers (SSR, Simple Sequence Repeat), and we determined the genetic relationships among the sweet cherry genotypes. For DNA isolation, we collected young leaves sampled on a single plant per accession, then amplification of microsatellite loci was performed. In total, ten SSR primer pairs, previously isolated from peach and sweet cherry, were used. Genetic similarity values were calculated. A cluster analysis was performed to generate a dendrogram. Results and discussion. Of the ten primers tested, six primer pairs did not result in suitable amplification products with the 44 accessions studied. The remaining four polymorphic SSR primer pairs produced 33 alleles with an average of 8.25 putative alleles per locus, ranging from 7 to 11. Depending on the accessions, similarity ratios ranged from 0.32 to 0.98, with a mean value of 0.64. In conclusion, the results obtained demonstrate a high level of polymorphism among sweet cherry genotypes from a single province in Turkey.

Morphometric studies of five allopatric parasitoid populations (genus Psyttalia Walker) from coffee plantations in Cameroon (Nkolbisson), Ghana (Tafo) and Kenya (Rurima, Ruiru and Shimba Hills) and one non-coffee population (from Muhaka, Kenya) were compared with individuals of Psyttalia concolor (Szépligeti), a species released in several biological control programmes in the Mediterranean Region since the 20th Century. Analyses of wing vein measurements showed the second submarginal cell of the fore wing and its adjoining veins had the heaviest principal component weights and served as the main contributing variables in the diagnostic differentiation of the populations. Two populations (Rurima and Ruiru) were found to be the closest to each other and with the strongest phenetic affinity toward P. concolor (and forming one cluster). Populations from Shimba Hills (of unknown identity), Nkolbisson (P. perproximus (Silvestri)) and Tafo formed a second cluster and were separated from P. concolor. Comparison using amplified fragment length polymorphism (AFLP) also showed the Shimba, Nkolbisson and Tafo populations forming a cluster in a dendrogram generated from their genetic distances, with the Shimba and Tafo populations placed as the most closely related species. Based on consistent morphological similarities, morphometric and ecological data coupled with the genetic evidence from AFLP data, the Shimba population is suggested as belonging to the P. perproximus group and, thus, represents a new occurrence record in Kenya. Our results also support earlier conclusion from cross mating data that populations from Rurima and Ruiru belong to the Psyttalia concolor species-group.

China has an abundant and a wide variety of goose resources. The systemic estimation of genetic diversity of Chinese indigenous geese will provide an important scientific basis for the conservation and utilization of the resource. Twenty-six Chinese native goose populations were studied to estimate genetic diversity and genetic structure using 31-microsatellite markers. The genetic relationships between populations were analyzed in combination with their geographic distribution and origin of these breeds. According to the allele frequencies of 31-microsatellite loci, polymorphic information content (PIC), average heterozygosity (H) and DA genetic distances were calculated. Twenty-nine of the 31 microsatellite loci were medium or high polymorphism, so the 29 microsatellite markers were effective markers for analysis of genetic relationship among goose breeds. The average expected heterozygosity (HE) was between 0.501 and 0.705, the numeric order of which was consistent with that of PIC, and which reflected the strong genetic potential and strong adaptability. The topology of phylogenetic tree constructed from a Neighbour- Joining method based on DA genetic distances, showed general patterns of relationship and genetic structure among the populations studied. Topology analysis revealed that the twenty-six Chinese populations were divided into five groups and that the genetic relationships among the populations had obvious association with their historical relations and geographical distribution.

Fruit flies (Diptera: Tephritidae) are a species-rich and economically important group. The phylogenetic relationships among the many taxa are still to be fully resolved and the monophyly of several groups is still to be confirmed. This paper reports a study of the phylogenetic relationships among 23 economically important tephritid species (representing several major lineages of the family) which examines the sequence of a region of mitochondrial DNA encompassing the cytb, tRNASer and ND1 genes. Substitutions characteristic of particular taxa were found that could help classify members of the family at any developmental stage. The trees obtained by the maximum parsimony, neighbour joining and maximum likelihood methods were generally compatible with present morphological classification patterns. However, the data reveal some characteristics of the phylogenetic relationships of this family that do not agree with present classifications. The results support the probable non-monophyletic nature of the subfamily Trypetinae and suggest that Bactrocera cucurbitae (Coquillet) is more closely related to the genus Dacus than to other species of Bactrocera.

Twenty four Chinese native duck breeds were studied to estimate genetic diversity and genetic structure using microsatellite markers. The genetic relationships between breeds were analyzed in combination with their geographic distribution. A total of 28 microsatellite markers were amplified. All the breeds exhibited genetic diversity, through the estimation of polymorphic information content (PIC) and mean heterozygosity (H) index. The mean genetic diversity of the populations was 0.569, while the PIC values for Chinese native duck breeds was relatively high. Neighbour-joining was used to calculate genetic distances. Cluster analysis divided the twenty-four populations into five groups, and the genetic relationships among the populations had obvious association with their phylogenetic relationship with historical relations and geographical distribution. The developmental history of native duck breeds in China appears to have had an effect on their genetic structure.

The camel population in India is facing a severe decline which demands that immediate steps are taken to ensure its conservation. Characterisation is an integral part of the conservation program. The Polymerase Chain Reaction-Randomly Amplified Polymorphic DNA profile of unrelated camels of the Bikaneri (29), Jaisalmeri (30) and Kachchhi (18) breeds were analyzed. Reproducible polymorphic bands with varying frequencies among the three breeds of camel were obtained with five oligonucleotide primers. A total of 75 bands were amplified, of which 27 (36%) were polymorphic. The probability of obtaining identical fingerprints was observed to be the lowest in primer GC-10 (5.7%) followed by OP-08 (8.7%), GT-10 (11.3%), G-2 (15.5%) and G-1 (80%). Breed informative bands were amplified. The maximum genetic variability was observed in the Bikaneri (0.80±0.05) followed by the Kachchhi (0.84±0.06) and the Jaisalmeri (0.87±0.05) breeds. The inter-breed genetic distance estimates indicated a closer relationship in the Bikaneri-Kachchhi camels, (0.075), followed by the Jaisalmeri-Kachchhi (0.106) and Bikaneri-Jaisalmeri (0.132) breeds. A similar genetic relationship was observed when the degree of population subdivision was measured between the Bikaneri-Kachchhi (0.529), Jaisalmeri-Kachchhi (0.558) and Bikaneri-Jaisalmeri (0.566) breeds.

Allozyme electrophoresis was used to assess genetic variability and differentiation in 22 populations of Gressittacantha terranova Wise (Hexapoda, Collembola) from a coastal area of Victoria Land between the Mariner Glacier and the Nansen Ice Sheet. Allelic frequencies were determined at five enzyme loci: Phi, Pgm, Hk, Mpi and Mdh. Levels of variability, estimated as rates of heterozygosity, were higher than those calculated for the same loci in taxonomically related and non-related species of non-Antarctic Collembola. Thus, in spite of the ecological simplicity of Antarctic terrestrial ecosystems, G. terranova is characterized by high levels of genetic variability, and the 22 populations could be divided into three geogaphic groups, separated by the Aviator and Campbell glaciers. Genetic differentaton reflects the geographic arrangement of the populations, suggesting that the glaciers are effective barriers to gene flow, and that the patchy distribution of collembolan species in Antarctica has the potential to induce, in the long term, microspeciation processes. Interestingly, detectable genetic differentiation was observed between six populations collected at Edmonson Point, even though these are very close to each other, indicating the impact of geographic isolation even within short distances. The only exception to the congruence between genetic and geographic structuring was provided by the population of Apostrophe Island, for which a recent introduction with individuals coming from southern populations is suggested.

The genetic relationship among Nigeria's breeds of sheep and their crosses was studied using microsatellite DNA polymorphisms. DNA samples extracted from four Nigeria's breeds of sheep (West African Dwarf, the Balami, Uda and Yankassa) and their crosses were analysed using 30 Bovine microsatellite markers for diversity studies. Twenty of the markers were amplified by the sheep genome. Nineteen of the loci were polymorphic and were used to calculate genetic distances (Ds) between the breeds based on allele frequencies of the microsatellite. The phylogenetic relationships between the breeds were similarly estimated.

With the total number of loci studied, 285 alleles were generated and a high degree of heterozygosity was recorded (0.57 to 0.72). A relatively high degree of reliability could be placed on the tree topology with the relationship between breeds displaying a closer relationship between the Yankassa and Uda (Ds 0.356). The genetic distance was 0.432, 0.534 and 0.665 between the West African Dwarf (WAD) and the Yankassa, Uda and Balami respectively which also indicated a closer relationship between the Yankassa and the WAD compared to the essentially Northern breeds (Uda and Balami). This further confirms the evolutionary divergence of the breeds which makes them distinct entities.

The data suggests that microsatellite DNA markers are very useful tools for studying the genetic relationships among these sheep breeds. The highly polymorphic alleles could similarly be exploited in breed improvement and development.

The second internal transcribed spacer (ITS2) of the ribosomal RNA gene array of 6 species of diplozoids; Eudiplozoon nipponicum, Paradiplozoon bliccae, P. homoion, P. megan, P. pavlovskii and P. sapae, was amplified by PCR and sequenced. These sequences clearly demonstrate discrimination at the species level and confirm the validity of species determined by morphological identification. No intraspecific variation was found in the ITS2 sequences. There were no differences in the ITS2 sequences of P. homoion from populations parasitizing different host species. The length of the PCR product allowed discrimination of E. nipponicum from the Paradiplozoon species. Digestion of the amplified ITS2 fragment with enzymes AluI, HaeIII and HinfI provided useful genetic markers for species identification. The genetic relationships between diplozoids again demonstrated that E. nipponicum was the most genetically distinct species, whereas P. bliccae and P. sapae were the species most closely related. This represents the first molecular taxonomic study of these interesting parasites and demonstrates the utility of these methods for addressing questions of systematics.