No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Origin of rabbit (Oryctolagus cuniculus) in China: Evidence from mitochondrial DNA control region sequence analysis
Abstract
A fragment of mitochondrial DNA (mtDNA) control region (approximately 700 bp) was sequenced in 104 individuals from 20 breeds (three Chinese domestic breeds, five recently derived breeds and 12 introduced breeds) of domestic rabbits, Oryctolagus cuniculus. Nineteen sites were polymorphic, with 18 transitions and one insertion/deletion, and eight haplotypes (A1, A2, A3, A4, A5, A6, A7 and A8) were identified. Haplotype A1 was the most common and occurred in 89 individuals. In the 25 Chinese rabbits, only haplotype A1 was observed, while four haplotypes (A1, A3, A5 and A6) were found in 26 recently derived individuals. Haplotype A2 was shared by seven individuals among three introduced strains. The other six haplotypes accounted for 0.96-1.92% of the animals. Combined with the published sequences of European rabbits, a reduced median-joining network was constructed. The Chinese rabbit mtDNAs were scattered into two clusters of European rabbits. These results suggest that the (so-called) Chinese rabbits were introduced from Europe. Genetic diversity in Chinese rabbits was very low.
... Domesticated rabbits are descendants of the European rabbit, Oryctolagus cuniculus, which exists in both wild and domestic forms [1,2]. e Iberian Peninsula is recorded to be the origin of domesticated rabbits, and two subspecies, Oryctolagus cuniculus cuniculus and Oryctolagus cuniculus algirus, coexist, with the former occurring in the north eastern part and the latter in the south west [3,4]. ...
... All domesticated rabbits are reported to belong to lineage B. Similarly, analyses based on immunoglobulin genes revealed a clear structuring into two mitochondrial clades, A and B [16]. Long et al. [2] determined diversity and origin of 104 rabbits from 20 rabbit by evaluating a 700 bp fragment of the mtDNA control region. e breeds comprised of three Chinese domestic breeds, twelve introduced breeds, and five derived breeds eir study obtained four new haplotypes that had previously not been reported and reported that the Chinese rabbits originated from European rabbits, hence share the same center of origin. ...
... [19]. For comparison, mtDNA sequences of wild and domesticated rabbits from several locations were included in the data analysis [2]. Mitochondrial DNA haplotypes and their distribution in various regions, number of polymorphic sites, haplotype diversity, and nucleotide diversity were determined using DnaSP version 5.10.01 [20]. ...
To evaluate the origin, genetic diversity, and population structure of domesticated rabbits in Kenya, a 263-base pair region of mtDNA D-loop region of 111 rabbits sampled from Kakamega, Vihiga, and Bungoma counties in the western region, Laikipia and Nyandarua counties in the central region, and Kitui, Machakos, and Makueni in the eastern region of the country were analyzed. The average haplotype (0.40702) and nucleotide (0.01494) diversities observed were low, indicating low genetic diversity of domesticated rabbits in Kenya. This study resolved 5 unique haplotypes in the mtDNA D-loop region. A population genetic structure distinguishing Europe grouping and domesticated rabbits in Kenya was obtained on incorporating 32 known haplotypes. Domesticated rabbits in Kenya clustered together with rabbits from other geographic regions, suggesting common origin. The results suggested that the Kenyan domesticated rabbits may have originated from Europe. Integration of exotic breeds into breeding programmes could have contributed to the low genetic diversity. These results provide useful information for breeding and conservation decisions by the relevant stakeholders in the agriculture industry in Kenya.
... It is also a method for finding out the control region (D-loop), haplotypes information and identifying relations among haplotypes by analysing software sequences (Achilli et al., 2008). Over the last three decades, mtDNA has been widely used in rabbit diversity studies (Ennafaa et al., 1987;Long et al., 2003;Mougel et al., 2003;Nguyen et al., 2018;Owuor et al., 2019). These genetic studies have focused on the European geographical expansion reported by Christensen and Peng (2012), and Valvo et al. (2017) mentioned that mtDNA is used to identify the primary origins for domestic rabbits. ...
... We found that rabbit haplotypes were shown in two maternal lineages (Figure 3) based on mtDNA, which agreed with Watson and Davis (2019). Furthermore, all rabbits tested and most of the published sequences were located in second lineages, which is consistent with Long et al. (2003) and Owuor et al. (2019). ...
Mitochondrial DNA (mtDNA) and cytochrome b (cyt b) gene sequences were used to determine the status of genetic diversity and phylogeny for 132 individuals from local rabbit breeds in Egypt and Spain. The Egyptian local rabbit breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS). However, the Spanish local rabbit breed was Spanish common rabbit (SCR). Previous breeds were compared with European Wild Rabbit taken from Albacete, Spain (EWR). A total of 353 mutations, 290 polymorphic sites, 14 haplotypes, 0.06126 haplotype diversity and-1.900 (P<0.05) for Tajima's D were defined in this study. Haplotype A mostly occurred in 83.3% of Egyptian rabbits and 11.7 % of EWR, while haplotype B occurred in 63.8% of Spanish rabbits and 36.2% of the EGS breed. A total of 47 domestic and wild Oryctolagus cuniculus published sequences were used to investigate the origin and relation among the rabbit breeds tested in this study. The most common haplotype (A) was combined with 44.7% of published sequences. However, haplotype B was combined with 8.5%. Haplotypes of Egyptian, SCR and EWR were scattered in cluster 1, while we found only one EGS haplotype with two haplotypes of EWR in cluster 2. Our results assumed that genetic diversity for ERB, EBB and SCR was very low. Egyptian breeds and SCR were introduced from European rabbits. We found that ERB and EBB belong to one breed.
... After the initial domestication in France, more than 200 modern breeds or populations have been recognized worldwide and all of them show a considerable phenotypic variation [3,4]. In China, there are approximately 20 indigenous and recently imported rabbit breeds, which are widely kept for their meat, fur and wool [5]. Compared to the indigenous rabbit breeds, these imported breeds are more prevalent in the Chinese rabbit industry because of their better production performances on the important economic traits [6]. ...
... Therefore, sustainable development of the Chinese rabbit industry significantly depends on a sufficient amount of genetic resources available, especially for these indigenous breeds. Although the genetic diversity and population structure of Chinese indigenous rabbits has been studied in a few sporadic reports on the basis of microsatellite markers [26,27] and mitochondrial DNA [5], a genome-wide systematic investigation still remains to be addressed. In China, Sichuan and Fujian are the representative provinces of rabbit raising with a long history, both of them also have the well-known indigenous breeds, such as Sichuan White and Fujian Yellow rabbits. ...
There are a few well-known indigenous breeds of Chinese rabbits in Sichuan and Fujian provinces, for which the genetic diversity and population structure have been poorly investigated. In the present study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) approach to comprehensively discover genome-wide SNPs of 104 rabbits from four Chinese indigenous breeds: 30 Sichuan White, 34 Tianfu Black, 32 Fujian Yellow and eight Fujian Black. A total of 7,055,440 SNPs were initially obtained, from which 113,973 high-confidence SNPs (read depth ≥ 3, calling rate = 100% and biallelic SNPs) were selected to study the genetic diversity and population structure. The mean polymorphism information content (PIC) and nucleotide diversity (π) of each breed slightly varied with ranging from 0.2000 to 0.2281 and from 0.2678 to 0.2902, respectively. On the whole, Fujian Yellow rabbits showed the highest genetic diversity, which was followed by Tianfu Black and Sichuan White rabbits. The principal component analysis (PCA) revealed that the four breeds were clearly distinguishable. Our results first reveal the genetic differences among these four rabbit breeds in the Sichuan and Fujian provinces and also provide a high-confidence set of genome-wide SNPs for Chinese indigenous rabbits that could be employed for gene linkage and association analyses in the future.
... In consistent with Long et al. (2003), all rabbits tested haplotypes (A -N) in this study and most of published sequences were located in the second lineages. On the other hand, it was noticed that the first linkage contained wild rabbits only. ...
... us structure in Iberian Peninsula. The results divided O.cuniculus to two main subspecies in the first, is O.c. algirus, which is found in North and East Iberian peninsula; and the other is O.c. cuniculus which is found in South and west. The same results were confirmed by Queney et al. (2001),Geraldes et al., (2005), andFerrnand and Branco (2006).Long et al. (2003) used mtDNA marker to investigate the relationship among Chinese rabbit breeds, commercial rabbit breeds and some wild rabbit populations. The neighborhood joining and network trees were drown according mtDNA sequences. The strong relationship between Chinese rabbits and O.c. cuniculus was found in previous study. Both of commercial and ...
This thesis includes three studies to characterize, evaluate and invisitgate originality of local rabbit genetic resources in Egypt by using genetic markers. In the 1st study, 19 microsatellite loci were used to identify the genetic diversity for 3 Egyptian and one Spanish local rabbit breeds. Egyptian breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS), while Spanish rabbits belong to a local domestic variety (Spanish Common rabbit, SCR) used in backyard raising. The previous breeds were compared with European Wild rabbits (EWR). This study indicated that lower genetic diversity exists in ERB, EBB and SCR than EGS and EWR. Results also suggested that ERB and EBB belong to one breed. The phylogenetic analysis confirmed that there is separation between domestic rabbit breeds and wild rabbit or recently domesticated in this study. The objective of the 2nd study was to identify the genetic diversity of different populations of native Middle-Egypt rabbit (NMER) in North Upper Egypt province by using microsatellite polymorphism. Nineteen microsatellite loci were used in the study and an area of 231 km was surveyed, as native rabbits covered 14 points belonging to four Northern Upper Egypt governorates (South Giza, Fayoum, Beni Suef and Menya). Among NMER populations, Menya population gave the highest diversity. In contrast, South Giza population showed the lowest. Analysis results showed 2 main NMER rabbit groups: the Northern group (South Giza and Fayoum) and the Southern group (Beni Suef and Minya). This study provides an overview of genetic diversity of NMER populations in the Northern Upper Egypt province for to designate priorities for conservation of NMER. The goal of 3rd study was to invistigate the maternal origin of 132 individuals belonging to rabbit breeds from Egypt and Spain, by using 450 base pairs (bp) of mitochonderial DNA (mtDNA) cytochrome b (cyt b) gene sequencing. A total of 353 mutations, 290 polymorphic sites, 14 haplotypes (A: N), 0.06126 haplotype diversity and 1.900 for Tajima’s D were defined in this study (P<0.05). Haplotype A mostly occurred in 35.7% of Egyptian rabbits and 16.7% of EWR, while haplotype B occurred in 66.7% of Spanish rabbits and 33.3% of the EGS breed. The number of 46 published sequences for domestic and wild Oryctolagus cuniculus were used to investigate the origin and relation among tested rabbit breeds in this study. The most common haplotype (A) was combined with 43.5% of published sequences, while haplotype B was combined with only 4.3%. All haplotypes in this study were located in the same linkage (B) and distributed in 2 clusters. Analysis of mtDNA confirmed the limitation of genetic diversity for ERB, EBB and SCR, and that ERB and EBB belong to one breed. Further, this study proves for the first time that Egyptian breeds and Spanishbreed were originated from European rabbits.
... The haplotype diversity in the five breeds under study revealed six haplotypes with common haplotype 2 in the five breeds (Table 2). The results of haplotype diversity and nucleotide diversity were identified as low (Table 3), in agreement with the results reported in Spanish, Italian, Kenyan rabbits and three Egyptian breeds (Pierpaoli et al., 1999;Long et al., 2003;Owuor et al., 2019;Emam et al., 2020). Their studies indicated that the low genetic diversity due to domestication and high selection pressure during commercial animal production leads to an inherent decrease in breed variability. ...
Rabbit breeds in Egypt are local and adapted foreign breeds that have been imported since the middle of the last century. Stressful environmental conditions including climatic changes, exposure to diseases and breeding selection have an influence on how gene flow has shaped the genetic diversity of the breeds. Mitochondrial DNA D-loop is a genetic marker used to trace the geographic distribution of genetic variation for the investigation of expansions, migrations and other gene flow patterns. The study aimed to determine the genetic diversity of the mitochondrial DNA D-loop (mtDNA D-loop) in Black Baladi, Red Baladi, Gabali, APRI line and New Zealand breeds to gather the scientific data required to create a proper conservation and sustainable management plan. Blood samples were taken from animals unrelated to each other. A 332-bp of mtDNA D-loop was successfully amplified and alignment sequences were deposited in the GenBank database. The results detected six haplotypes in the five breeds. Haplotype diversity within individual breeds varied from 0 (Red Baladi) to 0.551±0.114 (Gabali). The nucleotide diversity (π) value was relatively low (0.001-0.006), with greater values in APRI and New Zealand. Pairwise distances between breeds yielded varying values ranging from 0 to 0.254, and the values between the Red Baladi and other breeds were comparatively high, with pairwise distances from 0.172 to 0.254. The phylogenetic analysis involved 74 nucleotide sequences of the Egyptian rabbit and thirty-one sequences retrieved from GenBank of the reference samples of different haplogroups. The results of the phylogenetic analysis correlated to the reference mtDNA GenBank database showed that the five Egyptian rabbit breeds were grouped into haplotypes A, B and K. The results of the genetic diversity using mtDNA shed light on the importance of the local breed’s genetic diversity information and revealed unique mtDNA haplotypes, which is an important finding for breeding strategies designed to conserve genetic variants and provide sustainable management.
... For instance, Sichuan grey rabbits (SG) and Sichuan white rabbits (SW) are small breeds with a slow growth rate [2]. China has more than 20 indigenous and imported rabbit breeds, which are used to produce meat and fur [3]. Although the production performance of local rabbit breeds in China is generally lower than that of imported rabbit breeds, indigenous breeds have advantages in disease resistance and meat quality. ...
The domestic rabbit (Oryctolagus cuniculus f. domesticus) is a very important variety in biomedical research and agricultural animal breeding. Due to the different geographical areas in which rabbit breeds originated, and the long history of domestication/artificial breeding, rabbits have experienced strong selection pressure, which has shaped many traits of most rabbit varieties, such as color and weight. An efficient genome-wide single-nucleotide polymorphism (SNP) detection strategy is genotyping-by-sequencing (GBS), which has been widely used in many organisms. This study attempted to explore bi-allelic SNPs associated with fur color and weight-related traits using GBS in five rabbit breeds. The data consisted of a total 831,035 SNPs in 150 individuals from Californian rabbits (CF), German Zika rabbits (ZK), Qixing rabbits (QX), Sichuan grey rabbits (SG), and Sichuan white rabbits (SW). In addition, these five breeds of rabbits were obviously independent populations, with high genetic differentiation among breeds and low genetic diversity within breeds. A total of 32,144 SNP sites were identified by selective sweep among the different varieties. The genes that carried SNP loci in these selected regions were related to important traits (fur color and weight) and signal pathways, such as the MAPK/ERK signaling pathway and the Hippo signaling pathway. In addition, genes related to fur color and weight were identified, such as ASIPs, MITFs and KITs, ADCY3s, YAPs, FASs, and ACSL5s, and they had more SNP sites. The research offers the foundation for further exploration of molecular genetic markers of SNPs that are related to traits.
... Rabbits (Oryctolagus cuniculus) are recently domesticated animals with an estimated history of approximately 1400 years [1]. In China, there are approximately 20 indigenous and recently imported rabbit breeds, mainly distributed in Sichuan, Shandong, Henan, and other provinces [2]. Over time, the Chinese indigenous rabbit has evolved features such as roughage resistance and high disease resistance, and these rabbits are widely used for meat, fur and wool [3,4]. ...
Background
Chinese indigenous rabbits have distinct characteristics, such as roughage resistance, stress resistance and environmental adaptability, which are of great significance to the sustainable development of the rabbit industry in China. Therefore, it is necessary to study the genetic diversity and population structure of this species and develop genomic resources.
Results
In this study, we used restriction site-associated DNA sequencing (RAD-seq) to obtain 1,006,496 SNP markers from six Chinese indigenous rabbit breeds and two imported rabbit breeds. Jiuyishan and Fujian Yellow rabbits showed the highest nucleotide diversity (π) and decay of linkage disequilibrium (LD), as well as higher observed heterozygosity (Ho) and expected heterozygosity (He), indicating higher genetic diversity than other rabbits. The inbreeding coefficient (FIS) of New Zealand rabbits and Belgian rabbits was higher than that of other rabbits. The neighbour-joining (NJ) tree, principal component analysis (PCA), and population structure analysis of autosomes and Y chromosomes showed that Belgian, New Zealand, Wanzai, Sichuan White, and Minxinan Black rabbits clustered separately, and Fujian Yellow, Yunnan Colourful, and Jiuyishan rabbits clustered together. Wanzai rabbits were clearly separated from other populations (K = 3), which was consistent with the population differentiation index (FST) analysis. The selection signature analysis was performed in two populations with contrasting coat colours. With Sichuan White and New Zealand rabbits as the reference populations and Minxinan Black and Wanzai rabbits as the target populations, 408, 454, 418, and 518 genes with a selection signature, respectively, were obtained. Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the genes with a selection signature. The results showed that the genes with a selection signature were enriched in the melanogenesis pathway in all four sets of selection signature analyses.
Conclusions
Our study provides the first insights into the genetics and genomics of Chinese indigenous rabbit breeds and serves as a valuable resource for the further effective utilization of the species.
... There are more than 20 indigenous and imported rabbit breeds in China, which are bred for the production of their meat, fur, and wool [16]. The production performance of Chinese indigenous rabbit breeds is generally lower than that of imported breeds, but indigenous breeds have advantages in adaptability, disease resistance, meat quality, and coat color. ...
Pigmentation genes such as MC1R, MITF, TYR, TYRP1, and MLPH play a major role in rabbit coat color. To understand the genotypic profile underlying coat color in indigenous Chinese rabbit breeds, portions of the above-mentioned genes were amplified and variations in them were analyzed by DNA sequencing. Based on the analysis of 24 Tianfu black rabbits, 24 Sichuan white rabbits, 24 Sichuan gray rabbits, and 24 Fujian yellow rabbits, two indels in MC1R, three SNPs in MITF, five SNPs (single nucleotide polymorphisms) in TYR, one SNP in TYRP1, and three SNPs in MLPH were discovered. These variations have low-to-moderate polymorphism, and there are significant differences in their distribution among the different breeds (p < 0.05). These results provide more information regarding the genetic background of these native rabbit breeds and reveal their high-quality genetic resources.
... We extracted genomic DNA from each fecal sample using a QIAamp DNA Stool Mini Kit (Qiagen, Venlo, the Netherlands). We amplified a portion of the mtDNA control region using the primers L15438 (5 0 -GCTGATATTCTACT-TAAACTA-3 0 ) and H16138 (5 0 -AGGGTCTTCAT-TAGGTGCTCGTCT-3 0 ) designed by Long et al. (2003). We carried out polymerase chain reaction (PCR) amplification following the standard protocol for the Qiagen Multiplex PCR kit (Qiagen). ...
Population fragmentation can reduce genetic diversity and increase the extinction risk of island endemic mammals, especially those with low dispersal ability. However, the intra‐island genetic structure and demographic history of mammals have not yet been well evaluated, especially on small geographic scales. We performed a genetic analysis of isolated island populations of the Amami rabbit (Pentalagus furnessi) on Tokunoshima Island using mitochondrial D‐loop region sequences and 8 nuclear microsatellite markers. Using data from fecal samples, we detected 2 genetic groups that corresponded with the northern and southern forested areas of the island based on the mitochondrial and nuclear genomes. We detected some admixture between the 2 groups in the nuclear genomes but did not detect gene flow between the 2 groups in the mitochondrial genomes. Although genetic diversity was higher in the southern population than in the northern population, the fixation index showed higher levels of inbreeding in the southern area with a signal of a recent bottleneck. We inferred the divergence time between the northern and southern groups (∼4,320 years ago) using approximate Bayesian computations. These genetic structure patterns may have been generated by a combination of the demographic history of the species in relation to the geology of the island, human activities in the stone age, deforestation due to sugar plantations (beginning approximately 300 years ago), and recent human activities. This study highlights the importance of considering genetic structure in relation to complex factors within a single‐island habitat for appropriate genetic management of endemic mammals on islands. © 2018 The Wildlife Society.
... Mitochondrial DNA (mtDNA) is informative for indicating genetic diversity and phylogenetic analysis of animals because of its specific characteristics, such as small molecular weight, high variability and maternal transmission (Long et al. 2003;Achilli et al. 2012;Dadi et al. 2012;Imes et al. 2012;Melo-Ferreira et al. 2012). Because of length variation and little selective pressure, D-loop sequence accumulates much more mutations than the rest of the molecule and provides extensive polymorphism information, making it a useful tool for studying short-term evolutionary phenomena. ...
Recently, the number of Tibetan mastiffs, which is a precious germplasm resource and cultural heritage, is decreasing sharply. Therefore, the genetic diversity of Tibetan mastiffs needs to be studied to clarify its phylogenetics relationships and lay the foundation for resource protection, rational development and utilization of Tibetan mastiffs. We sequenced hypervariable region I of mitochondrial DNA (mtDNA) of 110 individuals from Tibet region and Gansu province. A total of 12 polymorphic sites were identified which defined eight haplotypes of which H4 and H8 were unique to Tibetan population with H8 being identified first. The haplotype diversity (Hd: 0.808), nucleotide diversity (Pi: 0.603%), the average number of nucleotide difference (K: 3.917) of Tibetan mastiffs from Gansu were higher than those from Tibet region (Hd: 0.794; Pi: 0.589%; K: 3.831), which revealed higher genetic diversity in Gansu. In terms of total population, the genetic variation was low. The median-joining network and phylogenetic tree based on the mtDNA hypervariable region I showed that Tibetan mastiffs originated from grey wolves, as the other domestic dogs and had different history of maternal origin. The mismatch distribution analysis and neutrality tests indicated that Tibetan mastiffs were in genetic equilibrium or in a population decline.
... This is well illustrated by the lack of consistency among runs using lower values of K in the STRUCTURE analysis and the lack of identifiable structure in the scatter plot of the DAPC. Even though we mainly used European and North American rabbit breeds in the present study, both historical records [10] and genetic studies in other non-European breeds [66] have shown that domestic breeds worldwide were derived very recently from European breeds. Perhaps more likely, and as suggested by Parker et al [34] based on similar results in dogs, the process of breed formation is likely to have not followed a bifurcating tree model and most breeds originated from crosses among multiple breeds. ...
Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of similar to 20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the FST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.
... The sequence divergence of mitochondrial DNA (mtDNA) has been used to delineate the historical divergence of genetic groups and haplotype frequencies have revealed recent animal movements among local populations (Moritz 1994). MtDNA sequencing is also being increasingly used to investigate the relationships, origins and diversity of domesticated animal species, including rabbits, pigs, goats, buffalos and horses (Kierstein et al. 2004; Kim et al. 1999 Long et al. 2003; Manjunath et al. 2004; Wang et al. 2000). In contrast, similar studies of aquaculture species are rare (Nguyen et al. 2004 ), perhaps reflecting their more limited relevance due to the short history of domestication for most species. ...
As part of a study of genetic variation in the Vietnamese strains of the common carp (Cyprinus carpio L.) using direct DNA sequencing of mitochondrial control and ATPase6/8 gene regions, samples from a number of other countries were analyzed for comparison. Results show that the levels of sequence divergence in common carp is low on a global scale, with the Asian carp having the highest diversity while Koi and European carp are invariant. A genealogical analysis supports a close relationship among Vietnamese, Koi, Chinese Color and, to a lesser extent, European carp. Koi carp appear to have originated from a strain of Chinese red carp. There is considerable scope to extend this research through the analysis of additional samples of carp from around the world, especially from China, in order to generate a comprehensive global genealogy of common carp strains.
... Some alleles were shared by all 13 breeds, while others were specific to one or several breeds. MQ and XH sheep have private alleles which may be useful as biomarkers for breed origin Long et al. 2003). Most loci were polymorphic for all breeds, but some were monomorphic in specific breeds. ...
With the establishment of modern sheep production systems in China, various forms of hybridization with Western breeds and
between native breeds have been utilized for genetic improvement. At the same time, the progressive destruction or deterioration
of sheep habitat has accompanied urbanization in China. Together these factors have accelerated the loss of genetic diversity,
or even resulted in the extinction of some indigenous breeds. It is therefore important that efficient strategies for surveillance,
evaluation, conservation and utilization of available genetic resources are developed for this species. In this study, a total
of 30 microsatellite markers were used to assess genetic diversity for 12 native breeds and one Western sheep breed in Northern
China. The high polymorphism information contents at the 30 markers, varying from averages of 0.519 to 0.666 for the 13 breeds,
imply the retention of natural variation from source populations in the domestic breeds from different geographic regions
in China. Analysis of genetic differentiation revealed substantial divergence among these breeds. Neutrality tests indicated
that more than one third of the 30 loci were in departure from neutrality, implying that some evolutionary forces (e.g. selection
and migration) had acted on these populations. Phylogenetic and phylogeographic analyses displayed a remarkable degree of
consistency between geographic origins, breeding histories and the pattern of genetic differentiation.
... Direct DNA sequencing is being increasingly used to investigate the taxonomy, genealogical relationships, origins and diversity of domesticated animal species including pigs (Kim et al. 2002a), cattle (Kim et al. 2002b), rabbits (Long et al. 2003), buffalo (Kierstein et al. 2004) and goats (Manjunath et al. 2004). In contrast, similar studies of aquaculture species are rare (Nguyen et al. 2004), perhaps reflecting their more limited relevance because of the short history of domestication for such species. ...
Direct sequencing of mitochondrial DNA (mtDNA) D-loop (745 bp) and MTATPase6/MTATPase8 (857 bp) regions was used to investigate genetic variation within common carp and develop a global genealogy of common carp strains. The D-loop region was more variable than the MTATPase6/MTATPase8 region, but given the wide distribution of carp the overall levels of sequence divergence were low. Levels of haplotype diversity varied widely among countries with Chinese, Indonesian and Vietnamese carp showing the greatest diversity whereas Japanese Koi and European carp had undetectable nucleotide variation. A genealogical analysis supports a close relationship between Vietnamese, Koi and Chinese Color carp strains and to a lesser extent, European carp. Chinese and Indonesian carp strains were the most divergent, and their relationships do not support the evolution of independent Asian and European lineages and current taxonomic treatments.
This chapter discusses the origin and the history of the domestic rabbit. All varieties of domestic rabbits used in modern biomedical research were developed from the European rabbit, Oryctolagus cuniculus. The European rabbit possesses a mixture of features that make it an appealing model for in vivo research: an intermediate body size, tractable disposition, ability to breed readily in captivity, and a short generation time. Given its obvious utility as a research subject, the European rabbit is richly represented in the scientific literature from the Age of Enlightenment onward. When breed standards improved and production facilities moved from the backyard to commercial rabbitries, rabbits were increasingly accepted as research models. The obvious physical and behavioral differences between European rabbits and other leporids ultimately led to the recognition of Oryctolagus as a separate genus, with O. cuniculus as the only member species. The role of the European rabbit as a game species, agricultural commodity, research model, invasive pest, endangered species, and companion animal has increased.
Both wild and domestic rabbits belong to the species Oryctolagus cuniculus. Although rabbits provide value through meat and fur production, and they serve as an important biomedical animal model, research
in rabbits have been hampered because of a lack of genomic resources. With the recent development of a rabbit linkage map
containing cytogenetically anchored linkage data, large-insert BAC libraries, and some sequencing data, it is anticipated
that genomic-based studies using rabbits will increase over the next decade.
A characterization was conducted on mitochondrial DNA (mtDNA) molecules extracted separately from 107 European rabbits (Oryctolagus cuniculus) both wild and domestic, 13 European hares (Lepus capensis), and 1 eastern cottontail (Sylvilagus floridanus). Experimentally this study took into account restriction site polymorphism, overall length variation of the noncoding region, and numbers of repeated sequences. Nucleotide divergences indicate that the mtDNAs from the three species derived from a common ancestor some 6–8 million years (Myr) ago. Every animal appeared heteroplasmic for a set of molecules with various lengths of the noncoding region and variable numbers of repeated sequences that contribute to them. This systematic heteroplasmy, most probably generated by a rate of localized mtDNA rearrangements high enough to counterbalance the cellular segregation of rearranged molecules, is a shared derived character of leporids.
The geographic distribution of mtDNA polymorphism among wild rabbit populations over the western European basin shows that two molecular lineages are represented, one in southern Spain, the second over northern Spain, France, and Tunisia. These two lineages derived from a common ancestor some 2 Myr ago. Their present geographical distribution may be correlated to the separation of rabbits into two stocks at the time of Mindel glaciation.
Finally the distribution of mtDNA diversity exhibits a mosaic pattern both at inter- and intrapopulation levels.
Unlabelled:
We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform.
Availability:
http://www.megasoftware.net.
Contact:
s.kumar@asu.edu
New data on mitochondrial DNA polymorphism in Oryctolagus cuniculus confirm the existence of 2 maternal lineages which are geographically well separated. They provide evidence in favour of northern Spain (and possibly southern France) as a refuge area for rabbit populations during the last major glaciation. Osteological analysis leads to the discrimination of populations and the recognition of discrete qualitative characters, which provide additional markers to describe population diversity. Characterization of different domains of mtDNA from ancient bones was used as a tool to resolve the general question of the origin of present populations. Results obtained from ancient and present rabbits living in Zembra (Tunisia) showed that the present-day population has descended from animals present on the island some 2 000 years ago. Archaeozoological data provide evidence for their introduction by Bronze Age, Punic or Roman people.
The mitochondrial genetic variability in European rabbit (Oryctolagus cuniculus) populations present in Europe and North Africa from 11,000 years ago to the present day has been analyzed using ancient DNA techniques. DNA was extracted from 90 rabbit bones found in 22 archaeological sites dated between the Mesolithic and recent times. Nucleotide sequences present in a variable 233-bp domain of the cytochrome b gene were compared to those present in modern-day rabbits. The results show that the structure of ancient populations of wild rabbit exhibited remarkable stability over time until the Middle Ages. At this time, a novel type of mtDNA molecule abruptly appears into most wild populations studied from France. This mtDNA type corresponds to that currently present in the domestic breeds of rabbit examined so far. The relative rapidity by which this mtDNA type established and its absence in all sites examined before 1,700 years ago lend support to the hypothesis that between 2,000 and 1,000 years ago, man may have favored the development, into all regions of France, of animals carrying this particular mtDNA molecule. The origin of such animals has still to be found: animals previously living outside of France or within France but in very restricted areas? This event was concomitant with the documented establishment of warrens after the tenth century A.D. in Europe.
Analysis of variation in the hypervariable region of mitochondrial DNA (mtDNA) has emerged as an important tool for studying human evolution and migration. However, attempts to reconstruct optimal intraspecific mtDNA phylogenies frequently fail because parallel mutation events partly obscure the true evolutionary pathways. This makes it inadvisable to present a single phylogenetic tree at the expense of neglecting equally acceptable ones. As an alternative, we propose a novel network approach for portraying mtDNA relationships. For small sample sizes (< approximately 50), an unmodified median network contains all most parsimonious trees, displays graphically the full information content of the sequence data, and can easily be generated by hand. For larger sample sizes, we reduce the complexity of the network by identifying parallelisms. This reduction procedure is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes. As a spin-off, our approach can also assist in identifying sequencing errors, which manifest themselves in implausible network substructures. We illustrate the advantages of our approach with several examples from existing data sets.
In rabbit we observed heteroplasmy at an exceptionally high level, the heterogeneity occurring within the non-coding region of the DNA. Mitochondrial DNA (mt DNA) was cloned in pBR322 and the nucleotide sequence analysis of an EcoRI-Hind III fragment encompassing the non-coding region revealed that although there are common features with other mammalian mtDNAs (termed large central-conserved-sequence block, conserved-sequence blocks 1, 2 and 3 and termination-associated elements) the non-coding region shows an unusual organization; two stretches of tandem repeats of 20 bp and 153 bp are present in a part containing the origin of H-strand replication (OH) and probably the promoters for transcription as judged from other vertebrates. The long repeats are located between tRNA(Phe) and conserved sequence block 3 and the short repeats are located between conserved sequence blocks 1 and 2. When cloned in Escherichia coli (recA or recBC sbcb) DNA fragments containing the short repeats show length differences corresponding to various copy numbers of repeats. Electrophoretic analysis of the appropriate restriction fragments of rabbit mtDNA reveals extended intra- and inter-individual length heterogeneity. Both sets of repeats are involved in the generation of heterogeneity and are present in variable copy numbers from one mtDNA molecule to another. Moreover, rearrangement of the motives of the short repeat are observed to different extents in the mtDNA from one animal to another. The occurrence, maintenance and possible involvement of these repeated sequences, capable of forming stable secondary structures, are discussed in relation to their location in the region of control signals.
Feral rabbit populations in Australia have generally been managed using localized control procedures. While these procedures may result in local extinctions, persistence of populations will depend on the probability of recolonization. Genetic markers developed using temperature gradient gel electrophoresis (TGGE) combined with heteroduplex analysis (HA) of mitochondrial DNA (mtDNA) were used to characterize the degree of subdivision and extent of gene flow within and among rabbit populations distributed over large distances (up to 1000 km) in southern Queensland (QLD) and north-west New South Wales (NSW), Australia. TGGE analyses revealed significant heterogeneity in mtDNA control region haplotype frequencies. From heterogeneity chi 2 tests, it was evident that the differentiation observed was largely attributable to five sites which were located in the semiarid eastern region, whereas haplotype frequencies were homogeneous throughout the arid western region. These results suggest that there are independent population systems within the study area. The extent of gene flow among local populations within each system is related to the spatial configuration of acceptable habitat patches and the persistence of the populations is determined by the probability of recolonization following local extinction. These data suggest that to provide better overall control of rabbit populations, different management strategies may be necessary in arid and semiarid ecosystems. In arid south-west QLD and north-west NSW, where extensive gene flow occurs over large distances, rabbit populations should be managed at a regional level. In semiarid eastern QLD, where gene flow is restricted and populations are more isolated, localized control procedures may provide effective short-term relief. These results indicate that in nonequilibrium systems with patchy distribution of individuals, the interpretation of migration rate from estimates of gene flow obtained using existing genetic models must include an understanding of the spatial and temporal scales over which population processes operate.
The nucleotide sequence of the complete mitochondrial DNA (mtDNA) molecule of the rabbit (Oryctolagus cuniculus, order Lagomorpha) was determined. The length of the molecule is 17,245 nt, but the length is not absolute due to the presence of different numbers of repeated motifs in the control region. The organization and gene contents of the mtDNA of the rabbit conform to those of other eutherian species. The putative secondary structures of the tRNAs of the rabbit have been described. These structures as well as the structure of the L-strand origin of replication comply with those characteristic for eutherians in general. The compositional differences between the two mtDNA strands have also been detailed.
We studied mitochondrial DNA variation in the European rabbit through the examination of restriction fragment length polymorphism in 526 individuals from 20 locations spread across the Iberian Peninsula. Digestion with eight enzymes of a 1120-bp fragment comprising most of the cytochrome b gene resolved 38 different haplotypes. These haplotypes were distributed in two highly divergent clades, with different but overlapping geographical distributions, and with comparable levels of within-clade variation. The overall phylogeographical pattern suggests a history of long-term regional isolation of two groups of rabbit populations, compatible with the recognition of two subspecies within the Iberian Peninsula, followed by recent contact and admixture. The underlying cause is sought in the alternation of glacial and interglacial periods in the late Pleistocene.
The European rabbit: wild population evolution and domestication 6th World Rabbit Congress
- M Monnerot
- O Loreille
- F Mougel
- A M Vachot
- N Dennebouy
- C Callou
- J D Vigne
- J C Mounolou
Monnerot, M., Loreille, O., Mougel, F., Vachot, A.M., Dennebouy, N., Callou, C., Vigne, J.D. & Mounolou, J.C. (1996) The European rabbit: wild population evolution and domestication. 6th World Rabbit Congress, 331–4.
Evolutionnary patterns at the antibody constant region in rabbit (Oryctolagus cuniculus): characterisation of endemic b-locus allotypes and their frequency correlation with major mitochondrial gene types in Spain
- Van
- W Loo
- F Mougel
- M S Sanchez
- C Bouton
- E Castien
- R Soriguer
- R Hamers
- M Monnerot
van der Loo, W., Mougel, F., Sanchez, M.S., Bouton, C., Castien, E., Soriguer, R., Hamers, R. & Monnerot, M. (1997) Evolutionnary patterns at the antibody constant region in rabbit (Oryctolagus cuniculus): characterisation of endemic b-locus allotypes and their frequency correlation with major mitochondrial gene types in Spain. Gibier Faune Sauvage 14, 427–49.
Discussion on the origin of the domestic rabbit in China
- Chen Y.W.
Chen, Y.W. (1984) Discussion on the origin of the domestic rabbit in China. Chinese Journal of Rabbit Farming 2, 37–43 (in Chinese).
Feasibility study on calculating Heterosis by genetic structure of strains
- Z H Ban
- R Y Liu
- C N Xiao
Ban, Z.H., Liu, R.Y., Xiao, C.N. et al. (1996) Feasibility study on calculating Heterosis by genetic structure of strains. Chinese Journal of Rabbit Farming 1, 15–21 (in Chinese).
The history of Chinese rabbit farming
- Chen Y.W.
Chen, Y.W. & Wang, Y.H. (1991) The history of Chinese rabbit farming. Chinese Journal of Rabbit Farming 5, 5–13 (in Chinese).
Evolutionnary patterns at the antibody constant region in rabbit (Oryctolagus cuniculus): characterisation of endemic b‐locus allotypes and their frequency correlation with major mitochondrial gene types in Spain
- Van Der Loo W.
Feasibility study on calculating Heterosis by genetic structure of strains
- Ban Z.H.
The European rabbit: wild population evolution and domestication
- M Monnerot
- O Loreille
- F Mougel
- A M Vachot
- N Dennebouy
- C Callou
- J D Vigne