Population genetic analysis of the domestic Bactrian camel in China by RAD-seq

Molecular Characterization of Tick-borne Pathogens in Bactrian Camels and Ticks from Gansu Province, China

PURPOSE

Ticks are dangerous ectoparasites for humans and other animals, and tick-borne pathogens of Bactrian camels have been epidemiologically surveyed in Gansu Province, China. We aimed to determine the current distribution of tick-borne pathogens among Bactrian camels in Gansu during August 2013 using molecular tools.

METHODS

All ticks underwent morphological identification. We extracted DNA from the blood samples and ticks, screened them for Theileria, Babesia, Anaplasma, and Ehrlichia using standard or nested PCR with specific primers.

RESULTS

All ticks collected from the skin were identified as Hyalomma asiaticum. The blood and tick samples harbored similar pathogens, including the Theileria species, T. annulata, T. luwenshuni, T. uilenbergi, and T. capreoli, the Anaplasma species A. bovis and uncultured Anaplasma, the Ehrlichia species E. canis and uncultured Ehrlichia, and a new haplotype of Babesia species.

CONCLUSION

Our findings of anaplasmataceae and piroplasmida in Bactrian camels in Gansu provide a theoretical basis for deeper investigation into the epidemiology of tick-borne pathogens in these camels.

Genetic Diversity and Population Structure of Hemiculter leucisculus (Basilesky, 1855) in Xinjiang Tarim River

Hemiculter leucisculus is an invasive fish and widely distributed in the Xinjiang Tarim River. In this study, RAD-seq was used to explore the genetic diversity and population subgroup structure of H. leucisculus in the Tarim River and develop relevant Simple Sequence Repeat (SSR) markers. The study collected 40 samples distributed at four different sites of the Tarim River. A total of 7,291,260 single nucleotide polymorphisms (SNPs) were obtained. The genetic diversity results showed that the population genetic diversity level of H. leucisculus was low. The population pairwise F_ST values ranged from 0.231 to 0.258, indicating that there was moderate genetic differentiation among these populations. AMOVA showed that the genetic variation within populations accounted for 92.31% of the total variation. The principal component analysis (PCA) and neighbor joining (NJ) tree revealed that the four populations could be separated into two clusters (upper-middle and downstream populations) and the individuals from Taitema Lake (TTMH) showed differences and had a bigger geographic distance than the others. There is the probability that the H. leucisculus from Bosten Lake entered Taitema Lake to breed and then expanded into the Tarim River due to the water diversion projects in location. In addition, 147,705 SSRs loci were detected and 22,651 SSR primer pairs were developed. This study will contribute to providing valuable molecular data for the management of wild populations, marker-assisted selection and resource exploitation of H. leucisculus.

Genome-wide SNP analysis reveals the selection signatures of two indigenous buffalo breeds in Sichuan

Sichuan Province spawned abundant of indigenous buffalo varieties, which probably harbor valuable gene resources beneficial to the genetic improvement of buffalo. However, limited genetic information was publicly available. To better understand their selection signatures between different populations, we performed a restriction site-associated DNA sequencing (RADseq) to explore genome-wide SNPs among two indigenous breeds of Sichuan buffaloes. As a result, a total of 2,110,077 high-quality SNPs were finally obtained. Population genetic analysis indicated a obviously genetic differentiation between two breeds. The detection of selective genes showed that 995 and 910 protein-coding genes underwent positive selection in Yibin buffalo (GYBS) and Dechang buffalo (XCS). Further functional analysis revealed distinctly discrepant selection in two breeds. Candidate genes that positively selected from Yibin buffaloes have mainly occurred in functions closely related to meat quality, complex living environment adaption capability, and disease resistance. While they were significantly enriched in cell proliferation and cell components in Dechang buffalo, indicating the selection pressure primarily derived from the requirement of organism growth and development speed during breed formation. Our dataset constitutes a promising reservoir of genome-wide SNP markers of Sichuan buffaloes and provides potentially traits selected in different local populations. Such comprehensive genetic resources offer an unprecedented opportunity for genetic association analysis of economically important traits and precision breeding programs in buffaloes.

Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F₂ birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F₂ birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail.

Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F₂ females were produced by full-sib mating of F₁ birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.

Exploring the genomic resources of seven domestic Bactrian camel populations in China through restriction site-associated DNA sequencing

The domestic Bactrian camel is a valuable livestock resource in arid desert areas. Therefore, it is essential to understand the roles of important genes responsible for its characteristics. We used restriction site-associated DNA sequencing (RAD-seq) to detect single nucleotide polymorphism (SNP) markers in seven domestic Bactrian camel populations. In total, 482,786 SNPs were genotyped. The pool of all remaining others were selected as the reference population, and the Nanjiang, Sunite, Alashan, Dongjiang, Beijiang, Qinghai, and Hexi camels were the target populations for selection signature analysis. We obtained 603, 494, 622, 624, 444, 588, and 762 selected genes, respectively, from members of the seven target populations. Gene Ontology classifications and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and the functions of these genes were further studied using Genecards to identify genes potentially related to the unique characteristics of the camel population, such as heat resistance and stress resistance. Across all populations, cellular process, single-organism process, and metabolic process were the most abundant biological process subcategories, whereas cell, cell part, and organelle were the most abundant cellular component subcategories. Binding and catalytic activity represented the main molecular functions. The selected genes in Alashan camels were mainly enriched in ubiquitin mediated proteolysis pathways, the selected genes in Beijiang camels were mainly enriched in MAPK signaling pathways, the selected genes in Dongjiang camels were mainly enriched in RNA transport pathways, the selected genes in Hexi camels were mainly enriched in endocytosis pathways, the selected genes in Nanjiang camels were mainly enriched in insulin signaling pathways, while the selected genes in Qinghai camels were mainly enriched in focal adhesion pathways; these selected genes in Sunite camels were mainly enriched in ribosome pathways. We also found that Nanjiang (HSPA4L and INTU), and Alashan camels (INO80E) harbored genes related to the environment and characteristics. These findings provide useful insights into the genes related to the unique characteristics of domestic Bactrian camels in China, and a basis for genomic resource development in this species.

Development of Genomic Resources and Identification of Genetic Diversity and Genetic Structure of the Domestic Bactrian Camel in China by RAD Sequencing

The domestic Bactrian camel is indispensable to agricultural production in the desertification area of China owning to its endurance to hunger and thirst, cold resistance, drought resistance, and good long-distance transportation. Therefore, it is necessary to investigate the genetic diversity, genetic structure, and genes with important roles in the evolution of this species. In this study, 1,568,087 SNPs were identified in 47 domestic Bactrian camels inhabiting four regions of China, namely Inner Mongolia, Gansu, Qinghai, and Xinjiang, by restriction site associated DNA sequencing (RAD-seq). The SNP data were used for nucleotide diversity analysis (π) and linkage disequilibrium (LD) attenuation analysis to elucidate the genetic diversity of the domestic Bactrian camel in the four regions studied. Results showed that Xinjiang camels had the highest nucleotide diversity and the fastest decay rate of the LD coefficient; therefore, Xinjiang camels had the highest genetic diversity. Structure analysis, principal component analysis (PCA), and phylogenetic tree construction by the neighbor-joining (NJ) method showed that Qinghai camels clustered separately, at a larger phylogenetic distance from camels in the other regions. Through analyses of selection signals, it was found that the number of selected genes shared by Inner Mongolia camels, Qinghai camels, Xinjiang camels, and Gansu camels was 7, 24, 25, and 113, respectively. The shared selected genes of the domestic Bactrian camel in the four regions were further analyzed, and three shared genes (GRIA3, XIAP, and THOC2) of the domestic Bactrian camel in China were identified. Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the shared selected genes of the domestic Bactrian camel in all four regions studied. Across all regions, genes involved in the cellular process were the most abundant subcategory under biological process. Cell and cell part represented the main proportion of genes under cellular component. Binding represented the main molecular function. In addition, the shared selected genes of the domestic Bactrian camel in the four regions of China were significantly enriched in the long-term depression pathway. The research should enable further study of the genetic resources of the domestic Bactrian camel, as well as the conservation of these resources.

Development of Single Nucleotide Polymorphism (SNP) Markers for Analysis of Population Structure and Invasion Pathway in the Coconut Leaf Beetle Brontispa longissima (Gestro) Using Restriction Site-Associated DNA (RAD) Genotyping in Southern China

To determine population genomic structure through high-throughput sequencing techniques has revolutionized research on non-model organisms. The coconut leaf beetle, Brontispa longissima (Gestro), is a widely distributed pest in Southern China. Here, we used restriction site-associated DNA (RAD) genotyping to assess the invasion pathway by detecting and estimating the degree of genetic differentiation among 51 B. longissima accessions collected from Southern China. A total of 10,127 SNPs were obtained, the screened single nucleotide polymorphism (SNP) information was used to construct the phylogenetic tree, FST analysis, principal component analysis, and population structure analysis. Genetic structure analysis was used to infer the population structure; the result showed that all accessions were divided into Hainan population and non-Hainan population. The Hainan population remained stable, only the Sansha population differentiated, and the non-Hainan populations have gradually differentiated into smaller sub-populations. We concluded that there are two sources of invasion of B. longissima into mainland China: Taiwan and Hainan. With the increase of the invasion time, the Hainan population was relatively stable, and the Taiwan population was differentiated into three sub-populations. Based on the unrooted phylogenetic tree, we infer that Taiwan and Hainan are the two invasive base points. The Taiwan population invaded Fujian, Guangdong, and Guangxi, while the Hainan population invaded Yunnan and Sansha. Our results provide strong evidence for the utility of RAD sequencing (RAD-seq) in population genetics studies, and our generated SNP resource could provide a valuable tool for population genomics studies of B. longissima in the future.