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.     

Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

Background

China exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and population structure of Chinese indigenous cattle, a population genetic analysis at both the individual and population levels was conducted and the admixture analysis was performed. We genotyped 572 samples from 20 Chinese indigenous cattle breeds using GeneSeek Genomic Profiler Bovine LD (GGP-LD, 30?K) and downloaded the published data of 77 samples from 4 worldwide commercial breeds genotyped with Illumina BovineSNP50 Beadchip (SNP50, 50?K).

Results

In principal component analysis (PCA) and neighbour-joining (NJ) tree analysis, samples of the same breeds were grouped together, leading to clear separation from other breeds. And Chinese indigenous cattle were clustered into two groups of southern and northern breeds, originated from Asian Bos indicus lineage and Eurasian Bos taurus lineage, respectively. In STRUCTURE K?=?2, a clear transition occurred from the northern breeds to the southern breeds. Additionally, the northern breeds contained a smaller Eurasian taurine (62.5%) descent proportion than that reported previously (more than 90%). In STRUCTURE K?=?3, a distinct descent was detected in the southern Chinese breeds, which could reflect a long-term selection history of Chinese indigenous cattle. The results from TreeMix and f3 statistic provided the evidence of an admixture history between southern breeds and northern breeds.

Conclusions

Consistent with the observed geographical distributions, Chinese indigenous cattle were divided into two genetic clusters, northern indigenous cattle and southern indigenous cattle. Three improved breeds in the northern area also exhibited northern indigenous ancestry. We found that the breeds distributed in the northern China showed more southern lineage introgression than previously reported. Central-located populations appeared to the admixture between southern and northern lineages, and introgression events from European cattle were observed in Luxi Cattle, Qinchuan Cattle and Jinnan Cattle. The study revealed the population structures and levels of admixture pattern among Chinese indigenous cattle, shedding light on the origin and evolutionary history of these breeds.

     

Nucleotide diversity in lignification genes and QTNs for lignin quality in a multi-parental population of Eucalyptus urophylla

Lignin is a major chemical compound of wood and one of the most abundant organic biopolymers on earth. It accumulates in the secondary cell wall of xylem cells and is a major target for tree breeders because of its foreseen role in the emerging bioeconomy. In this study, we paved the way toward an accelerated domestication of a widely grown tree species, Eucalyptus urophylla, by molecular breeding. To this end, we first described the pattern of nucleotide variation occurring at seven structural and regulatory genes of the lignin biosynthesis pathway and found high levels of average nucleotide and haplotype diversity per gene (π?=?0.0065 and Hd?=?0.853). Then, taking advantage of a pre-existing factorial mating design, a candidate-gene-based quantitative trait locus (QTL) detection strategy was used to compare the variation of lignin quality (syringyl by guaiacyl ratio (S/G)) with the nucleotidic variability in these seven genes in 304 genotypes belonging to 33 connected full-sib families. Two genes, encoding cinnamoyl-CoA reductase (CCR) and a Rho-like GTPase (ROP1), were shown to be linked to the variation of S/G through different single and multi-locus single-nucleotide polymorphism (SNP)- and haplotype-based association methods. Providing that relevant candidate genes are selected and their patterns of nucleotide diversity is accurately described, we showed that quantitative trait nucleotides (QTNs) can be detected taking advantage of pre-existing field experiments and trait measurements gathered in the framework of a forest tree breeding program.     

Genome-wide linkage analysis for alcohol dependence: a comparison between single-nucleotide polymorphism and microsatellite marker assays

Both theoretical and applied studies have proven that the utility of single nucleotide polymorphism (SNP) markers in linkage analysis is more powerful and cost-effective than current microsatellite marker assays. Here we performed a whole-genome scan on 115 White, non-Hispanic families segregating for alcohol dependence, using one 10.3-cM microsatellite marker set and two SNP data sets (0.33-cM, 0.78-cM spacing). Two definitions of alcohol dependence (ALDX1 and ALDX2) were used. Our multipoint nonparametric linkage analysis found alcoholism was nominal linked to 12 genomic regions. The linkage peaks obtained by using the microsatellite marker set and the two SNP sets had a high degree of correspondence in general, but the microsatellite marker set was insufficient to detect some nominal linkage peaks. The presence of linkage disequilibrium between markers did not significantly affect the results. Across the entire genome, SNP datasets had a much higher average linkage information content (0.33 cM: 0.93, 0.78 cM: 0.91) than did microsatellite marker set (0.57). The linkage peaks obtained through two SNP datasets were very similar with some minor differences. We conclude that genome-wide linkage analysis by using approximately 5,000 SNP markers evenly distributed across the human genome is sufficient and might be more powerful than current 10-cM microsatellite marker assays.     

基于线粒体DNA的中国亚洲象种群遗传多样性及种群遗传结构

亚洲象是我国国家一级保护动物.本文利用非损伤性取样法,以亚洲象粪便中脱落的肠道上皮细胞为DNA来源,选用线粒体DNA作为分子标记,对分布于我国境内的亚洲象种群的遗传结构和种群遗传多样性进行研究.本研究得到mtDNA序列片段长度为556 bp,经对178个个体进行扩增结果分析,共得到24个单倍型.在5个地理种群中,除南滚河种群外,其他4个种群中的114个个体共享同一单倍型,南滚河种群与其他种群间未观察到共享单倍型.系统发生分析,观察到中国境内现有亚洲象种群在进化上分为两大分支,α和β.其中分支α中包含除南滚河种群外的4个地理种群,分支β仅含有南滚河种群,表明南滚河种群与其他4个地理种群间存在明显分化.遗传多样性分析结果表明,中国境内的亚洲象种群的遗传多样性水平较低,分析原因认为是栖息地破碎化阻断了种群间有效的基因交流.     

Genetic diversity and structure in a natural Hordeum chilense population based on gliadin analysis

Hordeum chilense Roem. et Schult. is a South American wild barley that occurs exclusively in Chile and Argentina, where it is a component of natural pastures. This species has been crossed with durum and bread wheats to obtain a new amphiploid, named tritordeum, which presents agronomic traits of a new crop. The knowledge of the reproductive system is very important for the management of any species with breeding purposes. In this work with this finality, two hundred seventy seeds of 32 original spikes from a natural population were analysed for the variation of gliadin by A-PAGE. The data suggested that 98% of the genetic diversity appeared between spikes whereas only the 2.0% was within spikes. Only four out of 32 analysed spikes showed certain level of heterozygosity for the ω-gliadins. The Wright's fixation index for this population was established in F = 0.993 and the cross-fertilisation rate was equal to 0.4%, which suggested that H. chilense is an autogamous species.     

Microsatellite analysis revealed genetic diversity and population structure among Chinese cashmere goats

Most cashmere goats are found in northern China and Mongolia. They are regarded as precious resources for their production of high quality natural fibre for the textile industry. It was the first time that the genetic diversity and population structure of nine Chinese cashmere populations has been assessed using 14 ISAG/FAO microsatellite markers. In addition, two Iranian populations and one West African goat population were genotyped for comparison. Results indicated that the genetic diversity of Chinese cashmere goats was rich, but less than those of the Iranian goat populations. All pairwise F_ST values between the Chinese cashmere goat populations reached a highly significant level (P < 0.001), suggesting that they should all be considered as separate breeds. Finally, clustering analysis divided Chinese cashmere goats into at least two clusters, with the Tibetan Hegu goats alone in one cluster. An extensive admixture was detected among the Chinese goat breeds (except the Hegu), which have important implications for breeding management.     

Association analysis,genetic diversity and structure analysis of tobacco based on AFLP markers

Knowledge in the area of genetic diversity could aid in providing useful information in the selection of material for breeding such as hybridization programs and quantitative trait loci mapping. To this end, 50 Nicotiana tabacum genotypes were genotyped with 21 primer combination of amplified fragment length polymorphism (AFLP). A total of 480 unambiguous DNA fragments and 373 polymorphic bands were produced with an average of 17.76 per primer combination. Also, the results revealed high polymorphic rate varing from 52.63 to 92.59 %, demonstrating that AFLP technique utilized in this research can be a powerful and valuable tool in the breeding program of N. tabacum. Cluster analysis based on complete linkage method using Jaccard’s genetic distance, grouped the 50 tobacco genotypes into eight clusters including three relatively big clusters, one cluster including Golden gift, Burly 7022 and Burly Kreuzung, one cluster consisting of two individuals (Pereg234, R9) and three single-member clusters (Pennbel69, Coker176 and Budisher Burley E), Recent genotypes showed high genetic distance from other genotypes belonging to cluster I and II. Association analysis between seven important traits and AFLP markers were performed using four statistical models. The results revealed the model containing both the factors, population structure (Q) and general similarity in genetic background arising from shared kinship (K), reduces false positive associations between markers and phenotype. According to the results nine markers were determined that could be considered to be the most interesting candidates for further studies.     

Amplified fragment length polymorphism analysis of the population structure and genetic diversity of Phoebe zhennan (Lauraceae), a native species to China

Phoebe zhennan S. Lee et F. N. Wei (Lauraceae), is the main source of Gold Phoebe, a rare and extremely valuable wood in China. However it has undergone a dramatic decline. In this study, we used 12 amplified fragment length polymorphism primer combinations to assay 92 accessions, which were highly representative of the entire P. zhennan germplasm. It revealed that P. zhennan consisted of three genetic populations, named as SCZ (central Sichuan), CQH (eastern Sichuan, Chongqin, Hubei and Hunan) and YG (Yunnan and Guizhou), probably owing to natural selection caused by topography differences. The CQH population further diverged into two geographical sub-populations: CD-CQ (SCD and west region of Chongqin) and HB-HN (eastern side of Chongqin, Hubei and Hunan). The loci were moderately polymorphic (40.4%). The genetic distance between SCZ and YG was the highest, between CD-CQ and HB-HN the lowest. Pairwise fixation indices (Ф_PT) between any inferred populations were significant. This rare species exhibited low genetic diversity; therefore, the results provided significant data related to the conservation and management of P. zhennan. That is, with this genetic information, land managers are equipped with better tools allowing them to more effectively protect this species and its limited genetic diversity.     

Assessment of genetic diversity and population structure in mungbean

This study was carried out to assess the genetic diversity and to analyze the population genetic structure for a total of 692 mungbean accessions preserved at National Agrobiodiversity Center (NAC) of the Rural Development Administration (RDA), Korea. Mungbean accessions were collected from 27 countries in nine different geographic regions, and were genotyped using 15 microsatellite markers, which were developed in our previous study. A total of 66 alleles were detected among 692 accessions at all the loci with an average of 4.4 alleles per locus. All the microsatellite loci were found to be polymorphic. The expected heterozygosity (H _E ) and polymorphism information content (PIC) ranged from 0.081 to 0.588 (mean = 0.345) and from 0.080 to 0.544 (mean = 0.295), respectively. Of the 66 alleles, 17 (25.8%) were common (frequency range between 0.05 and 0.5), 15 (22.7%) were abundant (frequency range > 0.5), and 34 (51.5%) were rare (frequency range < 0.05). Locus GB-VR-7 provided the highest number of rare alleles(eight), followed by GB-VR-91(six) and GB-VR-113(four). Country-wide comparative study on genetic diversity showed that accessions from the USA possessed the highest genetic diversity (PIC) followed by Nepal, Iran, and Afghanistan. And region-wide showed that accessions from Europe possessed the highest average genetic diversity, followed by accessions from the USA, South Asia, West Asia, and Oceania. Twenty-seven countries were grouped into seven clades by phylogenetic relationship analysis, but clustering pattern did not strictly follow their geographical origin because of extensive germplasm exchange between/among countries and regions. As a result of a model-based analysis (STRUCTURE) of microsatellite data, two distinct genetic groups were identified which shared more than 75% membership with one of the two genetic groups. However the genetic group pattern did not reflect their geographical origin. The Duncan’s Multiple Range Test among these two genetic groups and an admixed group, with a mean of 16 phenotypic traits, showed significant difference in 12 quantitative and qualitative traits on the basis of ANOVA. These 15 newly developed SSR markers proved to be useful as DNA markers to detect genetic variation in mungbean germplasm for reasonable management and crossbreeding purposes.     

Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).     

Characterization of genetic diversity and population structure in wheat using array based SNP markers

Genetic diversity is crucial for successful adaptation and sustained improvement in crops. India is bestowed with diverse agro-climatic conditions which makes it rich in wheat germplasm adapted to various niches. Germplasm repository consists of local landraces, trait specific genetic stocks including introgressions from wild relatives, exotic collections, released varieties, and improved germplasm. Characterization of genetic diversity is done using morpho-physiological characters as well as by analyzing variations at DNA level. However, there are not many reports on array based high throughput SNP markers having characteristics of genome wide coverage employed in Indian spring wheat germplasm. Amongst wheat SNP arrays, 35K Axiom Wheat Breeder’s Array has the highest SNP polymorphism efficiency suitable for genetic mapping and genetic diversity characterization. Therefore, genotyping was done using 35K in 483 wheat genotypes resulting in 14,650 quality filtered SNPs, that were distributed across the B (~?50%), A (~?39%), and D (~?10%) genomes. The total genetic distance coverage was 4477.85 cM with 3.27 SNP/cM and 0.49 cM/SNP as average marker density and average inter-marker distance, respectively. The PIC ranged from 0.09 to 0.38 with an average of 0.29 across genomes. Population structure and Principal Coordinate Analysis resulted in two subpopulations (SP1 and SP2). The analysis of molecular variance revealed the genetic variation of 2% among and 98% within subpopulations indicating high gene flow between SP1 and SP2. The subpopulation SP2 showed high level of genetic diversity based on genetic diversity indices viz. Shannon’s information index (I)?=?0.648, expected heterozygosity (He)?=?0.456 and unbiased expected heterozygosity (uHe)?=?0.456. To the best of our knowledge, this study is the first to include the largest set of Indian wheat genotypes studied exclusively for genetic diversity. These findings may serve as a potential source for the identification of uncharacterized QTL/gene using genome wide association studies and marker assisted selection in wheat breeding programs.

     

RAPD analysis of genetic diversity and population genetic structure of Stipa krylovii Reshov. in Inner Mongolia steppe

Random amplified polymorphic DNA (RAPD) analysis was used to characterize the genetic diversity and population genetic structure of Stipa krylovii populations in Inner Mongolia steppe of North China. Thirteen 10 bp oligonucleotide primers, which generated 237 RAPD bands, were used to analyze 90 plants of five populations from three regions, meadow steppe, typical steppe and desert steppe, from the east to the west. The genetic diversity of Stipa krylovii that was revealed by observed number of alleles (na), expected number of alleles (ne), Nei's diversity index (h), Shannon's diversity index (H), amplificated loci, polymorphic loci and the percentage of polymorphic loci (PPB) increased from the east to the west. The Pearson's correlation analysis between genetic diversity parameters and ecological parameters indicated that the genetic diversity of Stipa krylovii was associated with precipitation and cumulative temperature variations along the longitude (humidity were calculated by precipitation and cumulative temperature). Dendrogram based on Jaccard's genetic distance showed that the individuals from the same population formed a single sub-group. Although most variation (56.85%) was within populations, there was high genetic differentiation among populations of Stipa krylovii, high differentiation within and between regions by AMOVA analysis. Either Nei's unbiased genetic distance (G(ST)) or gene flow (Nm) among pairwise populations was not correlated with geographical distance by Mantel's test (P > 0.05), suggesting that there was no consistency with the isolation by distance model in these populations. Natural selection may have played a role in affecting the genetic diversity and population structure, but habitat destruction and degradation in northern grassland in China may be the main factor responsible for high genetic differentiation among populations, within and among regions.     

RAPD analysis of genetic diversity and population genetic structure of Stipa krylovii reshov. in Inner Mongolia steppe

Random amplified polymorphic DNA (RAPD) analysis was used to characterize the genetic diversity and population genetic structure of Stipa krylovii populations in Inner Mongolia steppe of North China. Thirteen 10-bp oligonucleotide primers, which generated 237 RAPD bands, were used to analyze 90 plants of five populations from three regions, meadow steppe, typical steppe and desert steppe, from the east to the west. The genetic diversity of Stipa krylovii that was revealed by observed number of alleles (na), expected number of alleles (ne), Nei’s diversity index (h), Shannon’s diversity index (H), amplificated loci, polymorphic loci and the percentage of polymorphic loci (PPB) increased from the east to the west. The Pearson’s correlation analysis between genetic diversity parameters and ecological parameters indicated that the genetic diversity of Stipa krylovii was associated with precipitation and cumulative temperature variations along the longitude (humidity were calculated by precipitation and cumulative temperature). Dendrogram based on Jaccard’s genetic distance showed that the individuals from the same population formed a single subgroup. Although most variation (56.85%) was within populations, there was high genetic differentiation among populations of Stipa krylovii, high differentiation within and between regions by AMOVA analysis. Either Nei’s unbiased genetic distance (G _ST) or gene flow (Nm) among pairwise populations was not correlated with geographical distance by Mantel’s test (P > 0.05), suggesting that there was no consistency with the isolation by distance model in these populations. Natural selection may have played a role in affecting the genetic diversity and population structure, but habitat destruction and degradation in northem grassland in China may be the main factor responsible for high genetic differentiation among populations, within and among regions. The text was submitted by the authors in English.     

Microsatellite markers of genetic diversity and population structure of Carica papaya

We assessed the genetic diversity of 96 papaya accessions by molecular characterisation using microsatellite markers. Fifteen polymorphic primers were selected. Accessions, which were classified as Common, Formosa and Solo according to fruit types, were evaluated for allele frequency, heterozygosity, polymorphism information content (PIC), inbreeding coefficient (f) and the genetic diversity structure. Fifteen primers amplified 68 alleles with an average of 4.53 per locus. PIC values ranged from 0.19 to 0.69. The observed heterozygosity (H_O) was low for all selected microsatellites. High f estimates (0.58) and excess of homozygotes indicated inbreeding, mainly caused by the tendency to select hermaphrodite plants for succeeding generations. Analysis of molecular variance showed that most of the variation (98%) resides within subpopulation. The genetic analysis based on Bayesian statistics proved to be sensitive enough to detect relationships among the papaya accessions, grouping them into six clusters, irrespective of their classification types.     

Comparative analysis of genetic diversity and population genetic structure in Abies chensiensis and Abies fargesii inferred from microsatellite markers

Abies chensiensis Tieghem and Abies fargesii Franchet are two closely related tree species of Pinaceae endemic to China. A. chensiensis is usually found scattered in small forest fragments, whereas A. fargesii is a dominant member of coniferous forest. To evaluate the genetic effect of fragmentation on A. chensiensis, a total of 24 populations were sampled from the whole distribution of the two species. Seven nuclear microsatellite loci were employed to analyze comparatively the genetic diversity and population genetic differentiation. Both A. chensiensis and A. fargesii have high level within-population genetic diversity and low inter-population genetic differentiation. Low microsatellite differentiation (2.1%) between A. fargesii and A. chensiensis was observed. But microsatellite marker was able to discriminate most populations of these two species. Compared to A. fargesii, A. chensiensi has lower allelic diversity and higher genetic differentiation among populations. It suggested the existence of negative genetic impacts of habitat fragmentation on A. chensiensis.     

Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella

Electrophoretically demonstrable variation in 12 enzymes was studied in more than 1 600 isolates of Escherichia coli from human and animal sources and in 123 strains of the four species of Shigella. All 12 enzymes were polymorphic; and the number of allozymes (mobility variants), which were equated with alleles, averaged 9.3 per locus in E. coli. For Shigella species, the mean number of alleles was 2.9 per locus. Some 77% of the allozymes recorded in Shigella were shared with E. coli. A total of 302 unique genotypic combinations of alleles over the 12 loci (electrophoretic types, ETs) was distinguished, of which 279 represented E. coli and 23 were Shigella. Among electrophoretic types, mean allelic diversity per locus was 0.52 for E. coli and 0.29 for Shigella. It was estimated that there are, on the average, about 0.3 detectable codon differences per locus between pairs of strains of E. coli and Shigella, which is roughly equivalent to 1.2 amino acid differences per enzyme. Evidence that the enzyme loci studied are a random sample of the genome is provided by a significant positive correlation between estimates of genetic divergence between pairs of strains obtained by DNA reassociation tests and estimates of genetic distance between the same strains based on electrophoresis. A principal components analysis of allozyme profiles revealed that the 302 ETs fall into three overlapping clusters, reflecting strong non-random associations of alleles, largely at four loci. Each of the four ETs of E. coli that have been most frequently recovered from natural populations has an allozyme profile that is very similar to, or identical with, the hypothetical modal ET of one of the groups. ETs of Shigella fall into two of the groups. No biological significance can at present bbe attributed to the genetic structure revealed by Multilocus electrophoretic techniques. The electrophoretic data are fully compatible with other molecular and more conventional evidence of a close affinity between E. coli and Shigella, and they raise questions regarding the present assignments of certain strains to species. In support of evidence from DNA reassociation tests and serotyping, the present study suggests that S. sonnei is homogeneous in chromosomal genotype.     

Genetic diversity and population structure of Chrysichthys nigrodigitatus from Niger Delta based on AFLP analysis

The silver catfish, Chrysichthys nigrodigitatus is an important food fish in the Niger Delta. To understand the genetic variations and population structure in Nigeria’s Niger Delta, eighty-eight individuals collected from 7 locations were analyzed based on amplified fragment length polymorphism (AFLP) analysis. A total of 243 bands were identified using 4 AFLP primer combinations. The average gene diversity was 0.1708 ± 0.1547 and Shannon’s information index was 0.2792 ± 0.2224. The pairwise F_st values ranged from 0.133 to 0.796. The results of AMOVA analysis indicated that 19.03% of the genetic variation was contained among three groups. The gene flow estimates (Nm) demonstrated that different degrees of gene flow existed among populations ranging from 0.064 to 1.630. Two clades were recognized on the UPGMA tree. The results supported that freshwater or brackishwater habitat, limited long-distance dispersal of the adult and juveniles and physical barriers may be responsible for the current genetic structure.