Unique Genetic Resource Research Articles

Vascular Flora of Bardača Complex

This work gives overview and basic characteristics of vascular flora of Bardaca complex: ecological indicator values, biological spectrum and spectrum of areal types. Total of 316 herbal species are found during floristic research conducted on the area of Bardaca. Out of that number, six species are in the phylum Pteridophyta (two in class Equisetatae and four in class Filicatae ), and 310 species belong to Magnoliophyta (232 in class Magnoliate and 78 in class Liliate ). Based on the ecological analysis of found herbal species, researched area is mesophyll with neutral and low acidly ground, medium rich with mineral substances, with adequate light and warmth regime. Ten life forms have been found through the analysis of the biological spectrum of flora. Among them are hemicryptophyta (33,86%) and cryptophyta (geophyta 21,52% and aquatic helo-hidrophyta 7,91%). By analyzing areal types, 27 flora elements have been found, among which dominate flora elements of wide distribution (Euro-Asian, Circumpolar, Cosmopolitan and Adventive) with 204 herbal species (64,55%). Rational use of Bardaca complex, according to the principles of sustainable development, implies keeping unique genetic resources because of many exponents of relic tertiary flora are present.

Estimates of effective population size and inbreeding in South African indigenous chicken populations: implications for the conservation of unique genetic resources

Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6–78.6) in comparison to the field populations (point estimate range 118.9–580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. Fst estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, Fst estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic diversity ascribed to population differences within groups (FSC = 0.106). The results suggest that significant genetic erosion has occurred within the conservation flocks due to inbreeding, pronounced effects of random drift and selection. It might be necessary to introduce new breeding individuals from the respective field populations in order to increase the effective population sizes of the conservation flocks and counter the effects of genetic erosion.Electronic supplementary materialThe online version of this article (doi:10.1007/s11250-016-1030-9) contains supplementary material, which is available to authorized users.

Unlocking the genetic diversity of Creole wheats.

Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement.

Identification of quantitative trait loci for body temperature, body weight, breast yield, and digestibility in an advanced intercross line of chickens under heat stress

BackgroundLosses in poultry production due to heat stress have considerable negative economic consequences. Previous studies in poultry have elucidated a genetic influence on response to heat. Using a unique chicken genetic resource, we identified genomic regions associated with body temperature (BT), body weight (BW), breast yield, and digestibility measured during heat stress. Identifying genes associated with a favorable response during high ambient temperature can facilitate genetic selection of heat-resilient chickens.MethodsGenerations F18 and F19 of a broiler (heat-susceptible) × Fayoumi (heat-resistant) advanced intercross line (AIL) were used to fine-map quantitative trait loci (QTL). Six hundred and thirty-one birds were exposed to daily heat cycles from 22 to 28 days of age, and phenotypes were measured before heat treatment, on the 1st day and after 1 week of heat treatment. BT was measured at these three phases and BW at pre-heat treatment and after 1 week of heat treatment. Breast muscle yield was calculated as the percentage of BW at day 28. Ileal feed digestibility was assayed from digesta collected from the ileum at day 28. Four hundred and sixty-eight AIL were genotyped using the 600 K Affymetrix chicken SNP (single nucleotide polymorphism) array. Trait heritabilities were estimated using an animal model. A genome-wide association study (GWAS) for these traits and changes in BT and BW was conducted using Bayesian analyses. Candidate genes were identified within 200-kb regions around SNPs with significant association signals.ResultsHeritabilities were low to moderate (0.03 to 0.35). We identified QTL for BT on Gallus gallus chromosome (GGA)14, 15, 26, and 27; BW on GGA1 to 8, 10, 14, and 21; dry matter digestibility on GGA19, 20 and 21; and QTL of very large effect for breast muscle yield on GGA1, 15, and 22 with a single 1-Mb window on GGA1 explaining more than 15 % of the genetic variation.ConclusionsThis is the first study to estimate heritabilities and perform GWAS using this AIL for traits measured during heat stress. Significant QTL as well as low to moderate heritabilities were found for each trait, and these QTL may facilitate selection for improved animal performance in hot climatic conditions.

Genetic diversity and relationship of Indonesian indigenous chickens inferred from microsatellite DNA markers

A total of 1178 individuals of nearly complete sampling of 49 populations belong to 14 most popular Indonesian indigenous chicken breeds, geographically localized in different islands, were genotyped using 20 microsatellite DNA markers to investigate their molecular diversity and genetic relationship. In total, 259 alleles were observed among 49 populations of Indonesian indigenous chickens across 20 loci. The mean number of alleles (MNA) per locus ranged from 4.20 to 7.60. The observed (HO) and expected heterozygosity (HE) values averaged over loci varied from 0.50 to 0.67 and from 0.55 to 0.72, respectively, and they displayed a similar distribution pattern to that observed for MNA across the populations. The results indicated that there was rich and unique genetic diversity among most of the populations. The presence of significantly positive FIS values (P < 0.05), suggested the occurrence of inbreeding within most of these populations, leading to partition genetic diversity among the major islands. Some localized chicken populations have developed a distinct genetic background due to historical trading and long term geographic isolation. On the other hand, a few populations kept in urban areas may have been genetically introgressed with commercial chicken breeds/lines to some extent, forming different genetic structure. These findings will serve as scientific basis for the development of rational policies to sustainably conserve and utilize these unique Indonesian indigenous chicken genetic resources.

Genetic Relationship in Cicer Sp. Expose Evidence for Geneflow between the Cultigen and Its Wild Progenitor.

There is a debate concerning mono- or poly-phyletic origins of the Near Eastern crops. In parallel, some authors claim that domestication was not possible within the natural range of the wild progenitors due to wild alleles flow into the nascent crops. Here we address both, the mono- or poly-phyletic origins and the domestications within or without the natural range of the progenitor, debates in order to understand the relationship between domesticated chickpea (Cicer arietinum L.) and its wild progenitor (C. reticulatum Ladizinsky) with special emphasis on its domestication centre in southeastern Turkey. A set of 103 chickpea cultivars and landraces from the major growing regions alongside wild accessions (C. reticulatum, C. echinospermum P.H Davis and C. bijugum K.H. Rech) sampled across the natural distribution range in eastern Turkey were genotyped with 194 SNPs markers. The genetic affinities between and within the studied taxa were assessed. The analysis suggests a mono-phyletic origin of the cultigen, with several wild accession as likely members of the wild stock of the cultigen. Clear separation between the wild and domesticated germplasm was apparent, with negligible level of admixture. A single C. reticulatum accession shows morphological and allelic signatures of admixture, a likely result of introgression. No evidence of geneflow from the wild into domesticated germplasm was found. The traditional farming systems of southeaster Turkey are characterized by occurrence of sympatric wild progenitor—domesticated forms of chickpea (and likewise cereals and other grain legumes). Therefore, both the authentic crop landraces and the wild populations native to the area are a unique genetic resource. Our results grant support to the notion of domestication within the natural distribution range of the wild progenitor, suggesting that the Neolithic domesticators were fully capable of selecting the desired phenotypes even when facing rare wild-domesticated introgression events.

Fine mapping of bone structure and strength QTLs in heterogeneous stock rat

We previously demonstrated that skeletal structure and strength phenotypes vary considerably in heterogeneous stock (HS) rats. These phenotypes were found to be strongly heritable, suggesting that the HS rat model represents a unique genetic resource for dissecting the complex genetic etiology underlying bone fragility. The purpose of this study was to identify and localize genes associated with bone structure and strength phenotypes using 1524 adult male and female HS rats between 17 to 20weeks of age. Structure measures included femur length, neck width, head width; femur and lumbar spine (L3–5) areas obtained by DXA; and cross-sectional areas (CSA) at the midshaft, distal femur and femoral neck, and the 5th lumbar vertebra measured by CT. In addition, measures of strength of the whole femur and femoral neck were obtained. Approximately 70,000 polymorphic SNPs distributed throughout the rat genome were selected for genotyping, with a mean linkage disequilibrium coefficient between neighboring SNPs of 0.95. Haplotypes were estimated across the entire genome for each rat using a multipoint haplotype reconstruction method, which calculates the probability of descent at each locus from each of the 8 HS founder strains. The haplotypes were then tested for association with each structure and strength phenotype via a mixed model with covariate adjustment. We identified quantitative trait loci (QTLs) for structure phenotypes on chromosomes 3, 8, 10, 12, 17 and 20, and QTLs for strength phenotypes on chromosomes 5, 10 and 11 that met a conservative genome-wide empiric significance threshold (FDR=5%; P<3×10−6). Importantly, most QTLs were localized to very narrow genomic regions (as small as 0.3Mb and up to 3Mb), each harboring a small set of candidate genes, both novel and previously shown to have roles in skeletal development and homeostasis.

African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World.

At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers.

The biodiversity and genetic structure of Balearic sheep breeds.

The Balearic sheep breeds, Mallorquina, Menorquina, Roja Mallorquina, Ibicenca and one possible new genetic group, Formentera, constitute a unique genetic resource in the Mediterranean farming landscape, displaying high genetic diversity levels and being well differentiated among themselves and with respect to the continental sheep breeds. We used a microsatellite panel of markers to study genetic diversity and relationships with other Spanish breeds. The results reported in this study have important implications for the use, conservation and breeding of Balearic sheep stocks. A mean number of 7.59 alleles was found among the Balearic sheep breeds for the microsatellites scored. The whole mean value of observed heterozygosity amounted to 0.62, whereas the expected heterozygosity value was 0.69, suggesting the presence of a great degree of genetic variability, although a significant deficit of heterozygotes was detected for some markers. Genetic distance estimates showed that Balearic sheep are differentiated from the other Spanish breeds and in particular, from the Merino type. The Ibicenca breed showed the highest distance value from other breeds. The neighbour-net method of analysis clustered the Roja Mallorquina, Menorquina and Mallorquina breeds. The Structure results clearly demonstrated the genetic differentiation among the four Balearic sheep breeds, with the Ibicenca and Formentera races joined, with slight migration among them. Few external genetic influences from the Spanish mainland breeds were detected.

Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation.

BackgroundThe animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host and the diet adopted by the host. Although the importance of gut microbiota of humans has been well demonstrated, there is a paucity of research regarding non-human primates (NHPs), especially herbivorous NHPs.ResultsIn this study, an analysis of 97,942 pyrosequencing reads generated from Rhinopithecus bieti fecal DNA extracts was performed to help better understanding of the microbial diversity and functional capacity of the R. bieti gut microbiome. The taxonomic analysis of the metagenomic reads indicated that R. bieti fecal microbiomes were dominated by Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria phyla. The comparative analysis of taxonomic classification revealed that the metagenome of R. bieti was characterized by an overrepresentation of bacteria of phylum Fibrobacteres and Spirochaetes as compared with other animals. Primary functional categories were associated mainly with protein, carbohydrates, amino acids, DNA and RNA metabolism, cofactors, cell wall and capsule and membrane transport. Comparing glycoside hydrolase profiles of R. bieti with those of other animal revealed that the R. bieti microbiome was most closely related to cow rumen.ConclusionsMetagenomic and functional analysis demonstrated that R. bieti possesses a broad diversity of bacteria and numerous glycoside hydrolases responsible for lignocellulosic biomass degradation which might reflect the adaptations associated with a diet rich in fibrous matter. These results would contribute to the limited body of NHPs metagenome studies and provide a unique genetic resource of plant cell wall degrading microbial enzymes. However, future studies on the metagenome sequencing of R. bieti regarding the effects of age, genetics, diet and environment on the composition and activity of the metagenomes are required.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1378-7) contains supplementary material, which is available to authorized users.

CONSERVATION AND IP PROTECTION OF UNIQUE CROP GENETIC RESOURCES AND PRODUCTS OF CASHEW

Protection and management of intellectual property rights over unique crop genetic resources, biodiversity, new cultivars in crops and unique products from crops attains significance in the back drops of globalisation and trade liberalisation. Members of WTO, including India are taking earnest efforts to protect the sovereign rights over crop genetic resources and biodiversity by enacting specific Acts. A deep knowledge about these Acts and their implications is essential for achieving their specific goals. India has implemented Protection of Plant Varieties & Farmers Rights Act, 2001 to protect IP rights over unique farmer cultivars, traditional cultivars, extant cultivars and new cultivars in crops. The Biodiversity Act provides protection of germplasm available in the country by regularizing access to biodiversity, its sustainable use, conservation and benefit sharing arising from use of biodiversity. The Geographical Indications (Registration and Protection) Act-1999 provides for the protection and management of IP rights of communities over unique cashew products. Fenny is a unique product of cashew from Goa and this has been accepted as a Geographical Indication (GIs) from our country. Similarly, there are other cashew products in different parts of our country that can be protected and marketed as GIs in national and international markets. The paper highlights the provisions, prospects and problems of protection and management of intellectual property rights over unique cultivars, germplasm, genetic resources and products of cashew in India.

Genetic diversity and relationships of korean chicken breeds based on 30 microsatellite markers.

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (FIT) in native chicken was 0.234±0.025. Over 30.7% of FIT was contributed by within-population deficiency (FIS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds

Genetic relationships between wild progenitor pear (Pyrus L.) species and local cultivars native to Georgia, South Caucasus

The genetic diversity of 108 individuals of wild pear species (Pyrus communis subsp. caucasica, P. balansae, P. salicifolia, P. syriaca, P. demetrii, P. bulgarica, P. ketzkhovelii, P. sachokiana) and 35 samples of local and introduced cultivated pears from the country of Georgia were compared to 73 individuals of wild P. communis subsp. caucasica and P. communis subsp. pyraster in the collection of USDA-ARS National Plant Germplasm System (NPGS). Pyrus communis subsp. caucasica from both Georgia and the NPGS, P. communis subsp. pyraster from the NPGS, and P. salicifolia from Georgia were differentiated, based on analysis of eleven microsatellite markers. In addition, accessions of P. communis subsp. caucasica from Georgia were genetically distinct from accessions of the same subspecies in the NPGS collection that originated from other European and Middle Eastern Asian countries. Local pear cultivars in Georgia were genetically similar to P. communis subsp. caucasica and P. balansae growing wild in Georgia suggesting that they may have originated from native pear trees that could serve as unique genetic resources for pear breeding programmes.

Genetic diversity and gene flow in Clarias gariepinus from Lakes Victoria and Kanyaboli, Kenya

The African catfish Clarias gariepinus is an important species in the rapidly expanding aquaculture industry in East Africa. Most Kenyan catfish farmers use stocks with unknown genetic characteristics, with uncertified seeds and inter-basin exchange of brood stocks threatening the genetic distinctness of wild populations. Using 346 base pairs of D-loop sequence variation, genetic diversity and gene flow between C. gariepinus populations from Lake Victoria and its satellite, Lake Kanyaboli, were explored. A total of 17 haplotypes were identified in 52 individuals sampled, with the two populations sharing four haplotypes, and one haplotype being the most frequent (50%) in both populations. Catfish from Lake Victoria showed marginally higher genetic variation compared to those from Lake Kanyaboli, reflected in the higher number of haplotypes, singletons, polymorphic sites and haplotype and nucleotide diversities. Yet neither population showed signs of significant loss of diversity compared to other wild populations of the species. Clarias gariepinus from Lakes Victoria and Kanyaboli clustered into one clade, showing low population structuring and with a between-population FST value of 0.026, which was not indicative of significant (p ≥ 0.05) differentiation between the two lakes. Nevertheless, each population contained 60–64% of unique haplotypes. Inter-basin transfer of Clarias populations and human impact on Lake Kanyaboli should be controlled to conserve the unique Clarias genetic resources in the lake basin of Kenya.

High-throughput transcriptome sequencing identifies candidate genetic modifiers of vulnerability to fetal alcohol spectrum disorders.

Fetal alcohol spectrum disorders (FASD) is a leading cause of neurodevelopmental disability. Genetic factors can modify vulnerability to FASD, but these elements are poorly characterized. We performed high-throughput transcriptional profiling to identify gene candidates that could potentially modify vulnerability to ethanol's (EtOH's) neurotoxicity. We interrogated a unique genetic resource, neuroprogenitor cells from 2 closely related Gallus gallus lines having well-characterized robust or attenuated EtOH responses with respect to intracellular calcium mobilization and CaMKII/β-catenin-dependent apoptosis. Samples were not exposed to EtOH prior to analysis. We identified 363 differentially expressed genes in neuroprogenitors from these 2 lines. Kyoto Encyclopedia of Genes and Genomes analysis revealed several gene clusters having significantly differential enrichment in gene expression. The largest and most significant cluster comprised ribosomal proteins (38 genes, p = 1.85 × 10(-47) ). Other significantly enriched gene clusters included metabolism (25 genes, p = 0.0098), oxidative phosphorylation (18 genes, p = 1.10 × 10(-11) ), spliceosome (13 genes, p = 7.02 × 10(-8) ), and protein processing in the endoplasmic reticulum (9 genes, p = 0.0011). Inspection of gene ontogeny (GO) terms identified 24 genes involved in the calcium/β-catenin signals that mediate EtOH's neurotoxicity in this model, including β-catenin itself and both calmodulin isoforms. Four of the identified pathways with altered transcript abundance mediate the flow of cellular information from RNA to protein. Importantly, ribosome biogenesis also senses nucleolar stress and regulates p53-mediated apoptosis in neural crest. Human ribosomopathies produce craniofacial malformations and 11 known ribosomopathy genes were differentially expressed in this model of neural crest apoptosis. Rapid changes in ribosome expression are consistently observed in EtOH-treated mouse embryo neural folds, a model that is developmentally similar to ours. The recurring identification of ribosome biogenesis suggests it is a candidate modifier of EtOH vulnerability. These results highlight this approach's efficacy to formulate new, mechanistic hypotheses regarding EtOH's developmental damage.

Genome-wide sequencing and an open reading frame analysis of dichlorodiphenyltrichloroethane (DDT) susceptible (91-C) and resistant (91-R) Drosophila melanogaster laboratory populations.

The Drosophila melanogaster 91-R and 91-C strains are of common origin, however, 91-R has been intensely selected for dichlorodiphenyltrichloroethane (DDT) resistance over six decades while 91-C has been maintained as the non-selected control strain. These fly strains represent a unique genetic resource to understand the accumulation and fixation of mutations under laboratory conditions over decades of pesticide selection. Considerable research has been done to investigate the differential expression of genes associated with the highly DDT resistant strain 91-R, however, with the advent of whole genome sequencing we can now begin to develop an in depth understanding of the genomic changes associated with this intense decades-long xenobiotic selection pressure. Here we present the first whole genome sequencing analysis of the 91-R and 91-C fly strains to identify genome-wide structural changes within the open reading frames. Between-strain changes in allele frequencies revealed a higher percent of new alleles going to fixation for the 91-R strain, as compared to 91-C (P<0.0001). These results suggest that resistance to DDT in the 91-R laboratory strain could potentially be due primarily to new mutations, as well as being polygenic rather than the result of a few major mutations, two hypotheses that remain to be tested.

Population genetic diversity of the northern snakehead (Channa argus) in China based on the mitochondrial DNA control region and adjacent regions sequences

Genetic variation and population structure of northern snakehead (Channa argus) from eight locations in China were investigated using mitochondrial DNA control region and adjacent regions sequences. Sequence analysis showed that there were 105 haplotypes in 260 individuals, 48 unique haplotypes and 57 shared haplotypes, but no common haplotype shared by all populations. As a whole, the haplotype diversity was high (h = 0.989), while the nucleotide diversity was low (π = 0.00482). AMOVA analysis detected significant genetic differentiation among all eight populations (FST = 0.328, p < 0.01) and 66.17% of the total variance was resulted from intra-population differentiation. UPGMA analysis indicated that the eight populations could be divided into four major clusters, which was consistent with that the eight sampled locations were belonged to four isolated river systems. The neutrality and mismatch distribution tests suggested that the eight populations of C. argus in the sampling locations underwent recent population expansion. Among the eight populations, the Erhai Lake population may represent a unique genetic resource and therefore needs to be conserved.

High-resolution genome screen for bone mineral density in heterogeneous stock rat.

We previously demonstrated that skeletal mass, structure, and biomechanical properties vary considerably in heterogeneous stock (HS) rat strains. In addition, we observed strong heritability for several of these skeletal phenotypes in the HS rat model, suggesting that it represents a unique genetic resource for dissecting the complex genetics underlying bone fragility. The purpose of this study was to identify and localize genes associated with bone mineral density in HS rats. We measured bone phenotypes from 1524 adult male and female HS rats between 17 and 20 weeks of age. Phenotypes included dual-energy X-ray absorptiometry (DXA) measurements for bone mineral content and areal bone mineral density (aBMD) for femur and lumbar spine (L3-L5), and volumetric BMD measurements by CT for the midshaft and distal femur, femur neck, and fifth lumbar vertebra (L5). A total of 70,000 polymorphic single-nucleotide polymorphisms (SNPs) distributed throughout the genome were selected from genotypes obtained from the Affymetrix rat custom SNPs array for the HS rat population. These SNPs spanned the HS rat genome with a mean linkage disequilibrium coefficient between neighboring SNPs of 0.95. Haplotypes were estimated across the entire genome for each rat using a multipoint haplotype reconstruction method, which calculates the probability of descent for each genotyped locus from each of the eight founder HS strains. The haplotypes were tested for association with each bone density phenotype via a mixed model with covariate adjustment. We identified quantitative trait loci (QTLs) for BMD phenotypes on chromosomes 2, 9, 10, and 13 meeting a conservative genomewide empiric significance threshold (false discovery rate [FDR] = 5%; p < 3 × 10(-6)). Importantly, most QTLs were localized to very small genomic regions (1-3 megabases [Mb]), allowing us to identify a narrow set of potential candidate genes including both novel genes and genes previously shown to have roles in skeletal development and homeostasis.

Chakhao(delicious) rice landraces (Oryza sativaL.) of North-east India: collection, conservation and characterization of genetic diversity

Rice landraces have been developed through artificial selection imposed by farmers during the long-term domestication process. Although the global rice diversity is well characterized, few studies have conducted an in-depth analysis of genetic diversity on a local scale. In India, there are many locally adapted non-Basmati aromatic rice landraces in which the pace of improvement is slow, despite their high economic values. The aromatic and quality rice landraces of Manipur, locally calledChakhao(delicious), are important, considering their high economic and cultural values. To conserve and encourage improvement of these landraces, we collectedChakhaoaccessions from eight districts of Manipur. The aim of the current study was to investigate the level of genetic diversity and structure of 37Chakhaolandraces based on genotyping with 47 microsatellite markers. The genetic diversity analysis revealed high gene diversity (0.673) within theChakhaopopulation, with values ranging from 0.303 (Poireiton) to 0.471 (mixedChakhao). TheChakhaorice accessions could be divided into six subgroups based on genetic structure analyses. The population structure derived from the STRUCTURE analysis largely correlated with the farmers' classification ofChakhaolandraces. The results of genetic diversity analyses and the indigenous knowledge of the names and use ofChakhaolandraces would facilitate the conservation and utilization of this unique genetic resource.

Chicken Production Systems, Performance and Associated Constraints in North Gondar Zone, Ethiopia

Survey was conducted in three districts (Quara, Alefa and Tach Armachiho) of Amhara region northwestern Ethiopia. Semi structured questionnaire, participatory rural appraisal and ranking trials were used. Extensive production systems is the dominant management practices of chicken with small feed supplementation. Three peasant associations from each districts and a total of 180 households were selected using multistage simple random sampling technique based on chicken potential. Farmers were interviewed using semi-structured questionnaire and additional data was obtained from key-informants through group discussion. This investigation revealed that average flock size/ household was 16.11 for Quara, 16.33 for Alefa and 16.73 chickens for Tach Armachiho district. About 90% both in Quara, and Tach Armachiho and about 2.4% in Alefa districts of chicken owners are constructed separate shelter for chickens. The average eggs laid/clutch/hens is 16.88, 14.23and 11.9 eggs for Quara, Alefa and Tach Armachiho districts, respectively. Annual egg production of local hens is 60.20, 55.87 and 36.94 eggs/hen for Quara, Alefa and Tach Armachiho districts, respectively. Seasonal outbreaks of diseases and predation were the two major causes for loss of chickens. Women are responsible in managing chickens in all the study sites. Therefore, emphasis should be given in availing production technologies including breeding systems, organizing input supply system for chicks, feed, vaccines and veterinary drugs for chicken and eggs. The influential bodies should consider the importance of indigenous genetic resources and struggle to develop appropriate technologies at conserving the unique genetic resources and improving village flock production and productivity.