Genetic structure and admixture in sheep from terminal breeds in the United States

Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright’s F_ST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright’s F_ST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using admixture , and based on cross-validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness.     

Whole-genome resequencing analyses of five pig breeds,including Korean wild and native,and three European origin breeds

Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds. 1,673.1 Gb of sequence reads were mapped to the Swine reference assembly, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage. We detected 20,123,573 single-nucleotide polymorphisms (SNPs), of which 25.5% were novel. We extracted 35,458 of non-synonymous SNPs in 9,904 genes, which may contribute to traits of interest. The whole SNP sets were further used to access the population structures of the breeds, using multiple methodologies, including phylogenetic, similarity matrix, and population structure analysis. They showed clear population clusters with respect to each breed. Furthermore, we scanned the whole genomes to identify signatures of selection throughout the genome. The result revealed several promising loci that might underlie economically important traits in pigs, such as the CLDN1 and TWIST1 genes. These discoveries provide useful genomic information for further study of the discrete genetic mechanisms associated with economically important traits in pigs.     

Genetic variation and relationships of eighteen Chinese indigenous pig breeds

Chinese indigenous pig breeds are recognized as an invaluable component of the world''s pig genetic resources and are divided traditionally into six types. Twenty-six microsatellite markers recommended by the FAO (Food and Agriculture Organization) and ISAG (International Society of Animal Genetics) were employed to analyze the genetic diversity of 18 Chinese indigenous pig breeds with 1001 individuals representing five types, and three commercial breeds with 184 individuals. The observed heterozygosity, unbiased expected heterozygosity and the observed and effective number of alleles were used to estimate the genetic variation of each indigenous breed. The unbiased expected heterozygosity ranged between 0.700 (Mashen) and 0.876 (Guanling), which implies that there is an abundant genetic variation stored in Chinese indigenous pig breeds. Breed differentiation was shown by fixation indices (F_IT, F_IS, and F_ST). The F_ST per locus varied from 0.019 (S0090) to 0.170 (SW951), and the average F_ST of all loci was 0.077, which means that most of the genetic variation was kept within breeds and only a little of the genetic variation exists between populations. The Neighbor-Joining tree was constructed based on the Nei D_A (1978) distances and one large cluster with all local breeds but the Mashen breed, was obtained. Four smaller sub-clusters were also found, which included two to four breeds each. These results, however, did not completely agree with the traditional type of classification. A Neighbor-Joining dendrogram of individuals was established from the distance of – ln(proportions of shared alleles); 92.14% of the individuals were clustered with their own breeds, which implies that this method is useful for breed demarcation. This extensive research on pig genetic diversity in China indicates that these 18 Chinese indigenous breeds may have one common ancestor, helps us to better understand the relative distinctiveness of pig genetic resources, and will assist in developing a national plan for the conservation and utilization of Chinese indigenous pig breeds.     

Genetic diversity,population structure and phylogenetic relationships of three indigenous pig breeds from Jiangxi Province,China, in a worldwide panel of pigs

Dongxiang Spotted, Pingxiang Two‐End‐Black and Yushan Black pigs are three indigenous breeds in Jiangxi Province, China, that have been listed in the national conservation program for Chinese indigenous livestock germplasm. Here, we investigated the genetic diversity and population structure of the nucleus populations of these three breeds in a worldwide context of European and Chinese pigs using Illumina Porcine 60K chips. Our data indicate that Dongxiang Spotted and Yushan Black pigs have recently experienced severe inbreeding. The two breeds show large runs‐of‐homozygosity values, long‐range extents of linkage disequilibrium and reduced observed heterozygosity. In contrast, Pingxiang Two‐End‐Black pigs are rich in genetic diversity and have few inbred individuals. Both phylogenetic and admixture analyses illustrate that Dongxiang Spotted and Yushan Black pigs are genetically close to their geographical neighbors in East China and that Pingxiang Two‐End‐Black pigs have a close relationship with three other Two‐End‐Black breeds in central China. Finally, we reconstructed the family structures of the three breeds and propose a reliable breeding strategy to better conserve these breeds.     

西南地区地方品种猪血液蛋白遗传多样性研究

本实验采用水平板淀粉凝胶电泳技术,研究滇南小耳猪、迪庆藏猪、明光小耳猪、福贡猪、越南野猪和贵州从江香猪共20个个体共计42个基因座位的蛋白质多态性,发现其基因型和基因频率大部分相似,只有Tf、Hp、EsD、Amy－1、CEs和6PGD等六个座位具有多态性;多态座位百分比和平均杂合度分别为P=0．0714,H=0．051。用UPGMA法分别对由基因频率所计算的标准遗传距离和欧氏几何距离 进行聚类分析,结果表明贵州从江香猪和其他几个云南猪品种（系）的距离最远。     

AFLP analysis of genetic relationships among papaya and its wild relatives (Caricaceae) from Ecuador

The AFLP technique was used to assess the genetic relationships among the cultivated papaya ( Carica papaya L.) and related species native to Ecuador. Genetic distances based on AFLP data were estimated for 95 accessions belonging to three genera including C. papaya, at least eight Vasconcella species and two Jacaratia species. Cluster analysis using different methods and principal co-ordinate analysis (PCO), based on the AFLP data from 496 polymorphic bands generated with five primer combinations, was performed. The resulted grouping of accessions of each species corresponds largely with their taxonomic classifications and were found to be consistent with other studies based on RAPD, isozyme and cpDNA data. The AFLP analysis supports the recent rehabilitation of the Vasconcella group as a genus; until recently Vasconcella was considered as a section within the genus Carica. Both cluster and PCO analysis clearly separated the species of the three genera and illustrated the large genetic distance between C. papaya accessions and the Vasconcella group. The specific clustering of the highly diverse group of Vasconcella x heilbornii accessions also suggests that these genotypes may be the result of bi-directional introgression events between Vasconcella stipulata and Vasconcella cundinamarcensis.     

Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds

The origin of cattle on Chirikof Island, off the coast of Alaska, is not well documented. We assessed genetic differentiation of cattle isolated on Chirikof Island from several breeds commonly used for commercial production in North America including breeds popularly believed to have contributed to the Chirikof Island population. A set of 34 microsatellite loci was used to genotype Angus, Charolais, Hereford, Highland, Limousin, Red Angus, Salers, Shorthorn, Simmental, Tarentaise and Texas Longhorn cattle sampled from North America and the Chirikof Island population. Resulting F(ST) statistics for these loci ranged from 0.06 to 0.22 and on average, 14% of total genetic variation was between breeds. Whether population structure was modelled as a bifurcating tree or genetic network, Chirikof Island cattle appeared to be unique and strongly differentiated relative to the other breeds that were sampled. Bayesian clustering for multiple-locus assignment to genetic groups indicated low levels of admixture in the Chirikof Island population. Thus, the Chirikof Island population may be a novel genetic resource of some importance for conservation and industry.     

Genetic relationships between Spanish Assaf (Assaf.E) and Spanish native dairy sheep breeds

At present, the Assaf is the main dairy sheep in Spain. The Spanish Assaf (Assaf.E) was formed by male-mediated absorption of native Spanish sheep. Here we assess the genetic relationships among the Assaf.E and major native Spanish dairy breeds using microsatellites to contribute to the knowledge of the formation and within-population genetic variability of the breed. Blood samples from 44 unrelated Assaf.E individuals from 23 different Assaf.E flocks spread throughout 6 different Spanish provinces were obtained and genotyped using 14 microsatellites. Up to 312 additional samples belonging to the Awassi and Milchschaf sheep breeds and to six native Spanish dairy sheep breeds (Castellana, Churra, Latxa, Manchega, and Rubia de El Molar) as well as samples from Merino individuals to be used as the outgroup were also analysed observed (H_o) and expected (H_e) heterozygosity, rarefacted number of alleles per locus and distances based on molecular coancestry information were computed. Probabilities of assignment of the Assaf.E individuals to native Spanish dairy sheep breeds and cryptic genetic structure in the whole dataset were also assessed. It can be concluded that the Assaf.E breed has low genetic variability and high genetic distance with respect native Spanish dairy sheep breeds. From our results, the formation of the Assaf.E breed basically occurred via the absorption of individuals belonging to the Entrefino type, particularly to the Castellana and Manchega populations. Furthermore, Churra individuals may have participated in the formation of the Assaf.E breed at an early moment of the introduction of the breed into Spain.     

Genetic relationships between Spanish Assaf (Assaf.E) and Spanish native dairy sheep breeds

At present, the Assaf is the main dairy sheep in Spain. The Spanish Assaf (Assaf.E) was formed by male-mediated absorption of native Spanish sheep. Here we assess the genetic relationships among the Assaf.E and major native Spanish dairy breeds using microsatellites to contribute to the knowledge of the formation and within-population genetic variability of the breed. Blood samples from 44 unrelated Assaf.E individuals from 23 different Assaf.E flocks spread throughout 6 different Spanish provinces were obtained and genotyped using 14 microsatellites. Up to 312 additional samples belonging to the Awassi and Milchschaf sheep breeds and to six native Spanish dairy sheep breeds (Castellana, Churra, Latxa, Manchega, and Rubia de El Molar) as well as samples from Merino individuals to be used as the outgroup were also analysed observed (H_o) and expected (H_e) heterozygosity, rarefacted number of alleles per locus and distances based on molecular coancestry information were computed. Probabilities of assignment of the Assaf.E individuals to native Spanish dairy sheep breeds and cryptic genetic structure in the whole dataset were also assessed. It can be concluded that the Assaf.E breed has low genetic variability and high genetic distance with respect native Spanish dairy sheep breeds. From our results, the formation of the Assaf.E breed basically occurred via the absorption of individuals belonging to the Entrefino type, particularly to the Castellana and Manchega populations. Furthermore, Churra individuals may have participated in the formation of the Assaf.E breed at an early moment of the introduction of the breed into Spain.     

Cassava, Manihot esculenta Crantz, genetic resources: origin of the crop, its evolution and relationships with wild relatives

About 98 species of Manihot are known. All of them are native to the New World and are concentrated in four regions in Brazil and Central America. All the Manihot species so far examined have 2n = 36 chromosomes. Interspecific hybrids between cassava and its wild relatives show relatively normal meiosis, and further generations can be obtained. Electrophoresis shows affinity among wild species of different sections, and between some of them and cassava. Both polyploidy and apomixis may have contributed to speciation in this genus. Polyploidy produced genetic variability, while apomixis is responsible for perpetuating new hybrid types adapted to different environments. Cassava may have originated by hybridization between two wild Manihot species, followed by vegetative reproduction of the hybrid.     

Drosophila virilis and its cosmopolitan relatives in urban islands

Populations of brewery Drosophila have been studied for 2 years. Species distributions diner between breweries, and are very different from those found in woodland and fruitmarkets. It is suggested that breweries form 'urban islands'. One of the commonest species found in breweries appears to be Drosophila virilis , which has not previously been found in Britain. Tests on various characteristics, including courtship song, have shown conclusively that this species is a strain of D. virilis.     

Characterization of the genetic diversity, structure and admixture of British chicken breeds

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average F(ST) of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy-Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average F(IS) of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual-based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.     

金华猪遗传结构及其与太湖猪遗传分化的研究

本研究利用65个微卫星标记结合荧光标记检测技术, 对金华猪I系、II系、III系共271个个体以及嘉兴黑猪、中梅山猪、小梅山猪和二花脸猪等4个太湖猪品种和嵊县花猪各30头的基因型进行了检测, 统计分析了金华猪各品系的遗传结构及各猪种群间的遗传分化。结果显示: 金华猪品系间具有丰富的遗传变异, 平均有效等位基因数以金华猪I系最高, 为3.5; 其次是II系和III系, 分别是2.8和2.5, 金华猪3个品系的平均多态信息含量均高于0.5; I、II、III系的平均观察杂合度分别是0.381、0.399和0.442。金华猪3个品系偏离Hardy-Weinberg平衡的程度不一:I系偏离较大, III系次之, II系相对较小。分析认为金华猪各品系存在一定程度的近交, 品系间存在不同的等位基因。遗传分化结果显示: 金华猪II系和III系间遗传分化相对较小(F_ST＝0.1883), 但它们与I系间的遗传分化较大, F_ST值分别是0.3663和0.3619。同时, 金华猪各品系与太湖猪的遗传关系较近, 其中与中梅山猪群体遗传分化相对较小, F_ST值分别为0.3581、0.3560和0.3572。而金华猪各品系与嵊县花猪的遗传分化最大, F_ST值分别为0.4499, 0.4654和0.4801, 由此可见, 金华猪不同于其他浙江省地方品种, 有着独立的起源和驯化进程。     

The structure of two CONSTANS-LIKE1 genes in potato and its wild relatives

Day length controls development in many plants. In Arabidopsis thaliana, the CONSTANS (CO) gene has been firmly established as a key component in the photoperiodic pathway of floral transition; less is known about CONSTANS-LIKE1 (COL1) orthologues of this gene in Arabidopsis and several other species. The CONSTANS protein comprises two B-box-type zinc fingers, CCT domain, and a variable middle region (MR) which corresponds to exon 2 in the COL1 genes of Solanum species. Solanum COL1 proteins are over 85% identical within the genus and about 50% similar to Arabidopsis CO. Comparative COL1 analysis in several cultivated and wild Solanum species discerned two gene variants, which differed in the structures of exon 2 and introns 1 and 2. In exon 2, two variants were primarily discerned by the numbers of AAC/AAT and CAA/CAG repeats coding for polyasparagine and polyglutamine tracts in MR; therefore two variants were dubbed short and long COL1 genes (sCOL1 and lCOL1). However, intron 1 in lCOL1 was shorter than in sCOL1 due to three indels, whereas intron 2 in available COL1 sequences was represented by three different variants. The temporal profiles of sCOL1 and lCOL1 expression in tuberosum potato dramatically differed under short and long day, and the level of sCOL1 expression exceeded that of lSOL1 by an order of magnitude. Both sCOL1 and lCOL1 were found in each Solanum genome under study and in each individual plant, and the ratio of their copy numbers was not related to plant ploidy and photoperiodic response. Evidently the evolution of two COL1 genes preceded Solanum speciation, and the day-length response of diverse Solanum genotypes does not stem from the primary COL1 structure.     

Genome-wide genetic diversity,population structure and admixture analysis in African and Asian cattle breeds

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.     

Genetic diversity,population structure and subdivision of local Balkan pig breeds in Austria,Croatia, Serbia and Bosnia-Herzegovina and its practical value in conservation programs

Background

At present the Croatian Turopolje pig population comprises about 157 breeding animals. In Austria, 324 Turopolje pigs originating from six Croatian founder animals are registered. Multiple bottlenecks have occurred in this population, one major one rather recently and several more older and moderate ones. In addition, it has been subdivided into three subpopulations, one in Austria and two in Croatia, with restricted gene flow. These specificities explain the delicate situation of this endangered Croatian lard-type pig breed.

Methods

In order to identify candidate breeding animals or gene pools for future conservation breeding programs, we studied the genetic diversity and population structure of this breed using microsatellite data from 197 individuals belonging to five different breeds.

Results

The genetic diversity of the Turopolje pig is dramatically low with observed heterozygosities values ranging from 0.38 to 0.57. Split into three populations since 1994, two genetic clusters could be identified: one highly conserved Croatian gene pool in Turopoljski Lug and the"Posavina" gene pool mainly present in the Austrian population. The second Croatian subpopulation in Lonjsko Polje in the Posavina region shows a constant gene flow from the Turopoljski Lug animals.

Conclusions

One practical conclusion is that it is necessary to develop a "Posavina" boar line to preserve the "Posavina" gene pool and constitute a corresponding population in Croatia. Animals of the highly inbred herd in Turopoljski Lug should not be crossed with animals of other populations since they represent a specific phenotype-genotype combination. However to increase the genetic diversity of this herd, a program to optimize its sex ratio should be carried out, as was done in the Austrian population where the level of heterozygosity has remained moderate despite its heavy bottleneck in 1994.     

Chromosome R-banding patterns and NOR homologies in the European wild pig and four breeds of domestic pig

Four European wild pigs and 27 domestic pigs were studied; three Landrace, 12 village pigs from Papua New Guinea, two Chinese pigs Meishan and 10 Creole pigs from the French Antilles. The R-banding patterns were identical for all domestic breeds despite their different history and geographical divergence. The European wild pigs showed a similar R-banding pattern and a centric fusion between pairs 15 and 17 (2n = 36). The nucleolar organizers (NORs) in the European wild pig and the four domestic breeds were localized on the secondary constriction of chromosomes 8 and 10. All animals exhibited in the majority of metaphases two NORs on both chromosomes 10. In some animals. the NORs were expressed only in one of the homologs of chromosome 8. The Chinese pigs had a high amount of silver precipitates on two homologs of chromosome 8. This study confirms several previous reports on the polymorphism of NOR patterns in different domestic pig breeds.     

Research progress in BYDV resistance genes derived from wheat and its wild relatives

Barley yellow dwarf virus （BYDV） may cause a serious disease affecting wheat worldwide. True resistance to BYDV is not naturally found in wheat. BYDV resistance genes are found in more than 10 wild relative species belonging to the genera of Thinopyrum, Agropyron, Elymus, Leymus, Roegneria, and Psathyrostachy. Through wide crosses combining with cell culture, use ofph mutants, or irradiation, 3 BYDV resistance genes in Th. intermedium, including Bdv2, Bdv3 and Bdv4, were introgressed into common wheat background. Various wheat-Th, intermedium addition and substitution, translocation lines with BYDV-resistance were developed and characterized, such as 7D-TAi#1 （bearing Bdv2）, 7B-7Ai#1, 7D-7E （beating Bdv3）, and 2D-2Ai-2 （bearing Bdv4） translocations. Three wheat varieties with BYDV resistance from Th. intermedium were developed and released in Australia and China, respectively. In addition, wheat-Agropyron cristatum translocation lines, wheat-Ag, pulcherrimum addition and substitution lines, and a wheat-Leymus multicaulis addition line （line24） with different resistance genes were developed. Cytological analysis, morphological markers, biochemical markers, and molecular markers associated with the alien chromatin carrying BYDV resistance genes were identified and applied to determine the presence of alien, chromosomes or segments, size of alien chromosome segments, and compositions of the alien chromosomes. Furthermore, some resistance-related genes, such as RGA, P450, HSP70, protein kinases, centrin, and transducin, were identified, which expressed specifically in the resistance translocation lines with Bdv2. These studies lay the foundations for developing resistant wheat cultivars and unraveling the resistance mechanism against BYDV.