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Agriculture is the largest sector of Pakistan economy and is currently contributing 21.8 percent to the gross domestic product.Among agriculture Livestock is the most important sub-sector which contributes 51.8 percent to the agriculture value added. Livestock also contributes significantly towards national exports and 8.5 - 9.0 percent of total exports. (Economic survey of pakistan 2008-09). This sector provides raw material for the industry. It serves as a social safety for the rural poor as they can use it as source of earning at the time of their need. 44.7% people are raising 2 to 3 cattle/buffaloes and 5 to 6 sheeps/goats in their backyards and are deriving 20 to 25 percent income from it. All this take part in enhancing livestock role in agriculture.(Bhattacharya, S. 2008)
Livestock include cattle, buffaloes, sheep, goats, camels, horses, asses and mules. These animals contributes to meat, milk and many more purposes. During the last five years, the combined population of cattle, buffalo, sheep and goat increased from 113 million, 1998-99, to 225 million, 2008-09, indicating a total increase of 12 million or 24 lac heads per annum. (Source: Economic Survey 2008-09)
Among livestock animals Cattle are the most common type of large domesticated animals. About 800 breeds of cattle are recognized all over the world, some which adapted to the local climate, others which were bred by humans for specialized purposes. (Purdy, Herman Breeds Of Cattle 2008 ,2nd ed). Breeds fall into two main categories. Bos indicus (or Bos taurus indicus) cattle, also called zebu, are adapted to hot climates. Bos taurus (or Bos taurus taurus) are the typical cattle of Europe, north-eastern Asia, and parts of Africa and are adapted to cooler climates. Hybrids of Taurus/indicus are widely bred in many warmer regions, having combined characteristics of both types. In some parts of the world further species of cattle are found (both as wild and domesticated animals), and some of these are related so closely to taurine and indicus cattle that interspecies hybrids have been bred. (Breeds of cattle by Oklahoma State University OSU 2006).
Cattle belongs to subfamily Bovinae, and are the most widespread species of the genus Bos, and are most commonly classified as Bos primigenius. Cattle are raised as livestock animal for meat, milk and for draft purpose .Other products include leather and dung for manure or fuel. In some countries, such as India, cattle are sacred. It is estimated that there are 1.3 billion cattle in the world today. In 2009, cattle became the first livestock animal to have its genome mapped.
Among cattle breeds our main emphasis is on Red Sindhi and Tharparkar. Some breeds are used for multiple purposes i.e dairy ,beef, draught, sports etc. These two breeds are used for dual purposes e.g Red Sindhi is for dairy and beef purpose while Tharparkar is for dairy and draught purpose and comes under category of zebu (History and Development of Zebu Cattle in the United States James O. Sanders J Anim Sci 1980. 50:1188-1200). Zebu cattle originated in Southwest Asia and that their descendants were non-humped, they have evolved from three breeds of Indian cattle. Zebu cattle belong to the Bos primigenius species of cattle. They were taken to Africa at an early date and within the last 100 years, have been exported to Brazil and the US.
Zebu cattle are usually red or grey in colour, are horned, have loose skin, large ears and have a hump above their shoulders. This breed is popular for its milk, meat and for draft purpose. In India they are sacred and are only used for draft and milk. In Brazil and other meat producing countries they are produced largely for their beef as they cope better than european breeds in sub-tropical environments. Today the Zebu is present on all continents, mainly in India and Brazil, which has the largest commercial herd in the world, with 155 million head. India has over 270 million Zebu and the United States has over 2 million Zebu.
Red Sindhi are the most popular of all Zebu dairy breeds. This breed is originated in the Sindh province of Pakistan. They are widely kept for milk production across India, Pakistan, Bangla Desh, Sri Lanka, and other countries. They have been used for crossbreeding with temperate (European) origin dairy breeds in many countries to combine their tropical adaptations (heat tolerance, tick resistance, disease resistance, fertility at higher temperatures, etc.) with the higher milk production found in temperate regions. It has been crossed with Jerseys in many places, including India, the United States, Australia, Sri Lanka, etc. Other breeds it has been crossed with include Holstein-Friesian, Brown Swiss and Danish Red. It has also been used to improve beef and dual purpose cattle in many tropical countries, as it is sufficiently meaty to produce good beef calves in such crosses and the high milk production helps give a fast growing calf which is ready for market at one year. It is somewhat smaller than the very similar Sahiwal and produces a little less milk per animal as a result. The resulting cows have characters of both; which are three-quarters Sahiwal and one-quarter Red Sindhi, can not be distinguished from pure Sahiwal cattle. The Red Sindhi range in color from a deep reddish brown to a yellowish red, but most commonly a deep red. They are distinguished from the other dairy breed of Sindh, the Tharparkar or White Sindhi, both by color and form, the Red Sindhi is smaller, rounder, with a more typical dairy form, and with short, curved horns, while the Tharparkar are taller with a shape more typical of Zebu draft breeds, and with longer, lyre shaped horns.
Under good management conditions the Red Sindhi averages over 1700 kg of milk after suckling their calves but under optimum conditions there have been milk yields of over 3400 kg per lactation.
The Tharparkar a Bos indicus breed used for milk production and as draft animals. The Tharparkar came into prominence during the first World War when some animals were taken to supply milk for the Near East army camps. (Genus Bos: Cattle Breeds of the World, 1985)
In India and abroad, these cattle are known as Tharparkar since they come from the district of that name in the Province of Sind. The Tharparkar is, however, known differently in its own region. In its native tract and the areas neighboring on it, the breed is called Thari, after the desert of Thar; and it is also occasionally known as Cutchi, because the breed is also found on the borders of Cutch which adjoins Tharparkar to the south. In the past these cattle have been known as White or Gray Sindhi, since they are native to the Province of Sind and similar in size the Red Sindhi: this name, however, is no longer used. The Thari is not a homogeneous breed, but that it has the influence of the Kankrej, Red Sindhi, Gir and Nagori breeds. Average animals of the Tharparkar breed are deep, strongly built, medium-sized, with straight limbs and good feet, and with an alert and springy carriage. Thari cattle are said to be very hardy and resistant to several tropical diseases but definite date is lacking. Although animals of the breed are excellent foragers and can stand the rigors of climatic and environmental conditions, they have not been used primarily as a source of meat, and breeders have given little attention to meat qualities. (Joshi, N.R., Phillips, R.W. (1953) Zebu Cattle of India and Pakistan, FAO Agriculture Studies No. 19, Publ. by FAO, Rome, 256 pp).
Present study is designed to characterize these two Pakistani cattle breeds (Red Sindhi and Tharparkar) genetically, it is essential to understand their genetic architecture and relationship among different breeds. This depends on the knowledge of their genetic structure based on molecular markers like D-loop and Cytochrome b region of mitochondrial DNA. Mitochondrial DNA (mtDNA) and cytochrome b gene is widely used as molecular tool in phylogeography and in the inference of human evolutionary history, in detection of the domestication of livestock and in forensic science. In humans and other vertebrates the popularity of mtDNA can be partially attributed to an assumption of strict maternal inheritance, such that there is no recombination between mitochondrial lineages Hence the presents study is designed to see the evulotionary relationship of two Pakistani cattle breeds (Red Sindhi and Tharparkar) with the following objectives:
To identify breed differences of two Pakistani cattle breeds (Red Sindhi and Tharparkar) through Single Nucleotide Polymorphisms (SNPs) detection in mitochondrial D-loop and Cytochrome b region.
To study the evulotionary relationship of two Pakistani cattle breeds (Red Sindhi and Tharparkar).
To study the non coding and coding region of mitochondrial D- loop and cytochrome b gene respectively
REVIEW OF LITERATUR
Hauswirth et al., (1980) We have determined the location of the genes specifying the large and small ribosomal RNAs by hybridization analysis and electron microscopic observations of R-loop forms By Using a physical map of bovine mitochondrial DNA which was derived from the liver of a single Holstein cow. By using electron microscopy, the position of the origin of DNA replication (D-loop) has been located and also the direction of D-loop expansion and the polarity of the large and small ribosomal RNA genes were determined.
Hauswirth et al., (1984) Heterogenity of Mitochondrial DNA was observed by using Mitochondrial DNA from bovine tissue contains heterogeneous sequences located within an evolutionary conserved cytosine homopolymer sequence near the 5' end of the D-loop region. This part of the mammalian mitochondrial genome is known to contain the origin of heavy strand DNA synthesis and the major transcriptional promoter for each strand. Nucleotide sequence analysis of cloned DNA and electrophoretic analysis of appropriate small fragments from animal tissue reveal a population of length polymorphs containing from 9 to 19 cytosine residues. No individual length species represents more than 40% of the population. These data imply mtDNA sequence heterogeneity, which most likely occurs intracellularly as well. The localization of variability to a homopolymer run suggests that replication slip-page generated the sequence population. We also report that when recombinant clones containing this region are repeatedly passaged in E. coli, they begin to regenerate length variation similar to that seen in animal mtDNA.
King et al., (1987) The genomes of mammalian mitochondria are duplex DNA circles which is conserved region. The two major transcriptional promoters and the origin of DNA replication for one DNA strand are located in a single region which contains no structural genes and occupies about 6% of the genome. This region is called the displacement loop (D-loop) region since it is often triplex structure in which the heavy strand of the genome has been partially replicated. The promoters and the sites of initiation of D-loop DNA synthesis have been mapped in the human and mouse genomes and may show limited sequence conservation. We have mapped these sites in the bovine mitochondrial genome. Some features are conserved between all three species. The lack of sequence homology is in contrast to the greater than 80% sequence conservation which has been reported in portions of the D-loop region which are located distal to the origin of DNA replication and far from the transcriptional promoters. These results imply that closely related species may have developed different means of controlling mitochondrial gene expression.
Suzuki et al., (1993) To obtain information on maternal phylogenetic relationships between West African N'Dama (Bos taurus) and East African Zebu (B. indicus) cattle a study of polymorphisms of mitochondrial DNA(mtDNA) was carried out. A relatively large sample size was made possible by using polymerase chain reaction (PCR) amplification of DNA prepared from small blood samples to generate fragments of two known polymorphic mtDNA regions, one within the gene encoding subunit 5 of NADH dehydrogenase and one encompassing the entire D-loop. This approach allowed us to achieve a higher resolution restriction analysis on mtDNA from more animals and is more appropriate method than conventional methods. PCR-amplified mtDNA of 58 animals from five populations was examined at 26 restriction sites by 16 enzymes. In this way 154 nucleotides of mtDNA were scanned for polymorphism. Six polymorphic sites were located by this means, five of which were within the D-loop and one of which was within the NADH dehydrogenase 5 gene. None of the polymorphisms observed could be considered typical of breed or type.
Eledath et al., (1996) To characterize 16 Holstein maternal lines we use allele-specific polymerase chain reaction (ASPCR) and single-strand conformation polymorphism (SSCP). These methods detect polymorphic nucleotides at eight different positions in the displacement loop (D-loop) of bovine mitochondrial DNA (mtDNA) 16022, 16057, 16074, 16231, 16247, 106, 169 and 363. ASPCR analysis of the maternal lines showed variations at nucleotide positions 106, 169, and 363 of the mtDNA. Within-line variation was observed in five maternal lines for nucleotide 363. SSCP analysis of the mtDNA D-loop region revealed variations that classified the maternal lines into six different genotypes. Based upon the variations observed by ASPCR and SSCP analysis, the animals representing the 16 maternal lines could be assigned to 10 different genotypic groups. These procedures provide a rapid, simple, non-radioactive, and reliable method of detecting polymorphism in the D-loop region of bovine mtDNA.
Janecek et al.,(1996) Nucleotide sequence evolution of the mitochondrial cytochrome c oxidase subunit II (COII) gene was used to examine the molecular phylogenetics and evolution of the Bovinae, a subfamily within the mammalian order Artiodactyla ( hoofed mammals of the order Artiodactyla, which includes cattle, deer, camels, hippopotamuses, sheep, ...). The COII gene was sequenced in representatives of three bovine tribes (Bovini, Boselaphini, and Tragelaphini) and the outgroup taxon Capra (subfamily Caprinae). COII data also supported a close relationship between African and Asian buffaloes. Analysis of nucleotide substitutions in the COII gene prompted a system of differential weighting of nucleotide substitutions for inferring phylogenetic relationships across the range of divergence times examined here (2-20 million years). Rates of evolution in the COII gene are examined and compared to evolutionary rates in mtDNA tRNA/rRNA genes and the D-loop among other artiodactyl taxa.
Janecek et al., (1996) To examine relationships between yield traits and mtDNA polymorphism we use two independent data files from the breeding herd of Iowa State University and six North Carolina herds were used.Maternal lineages were established. Data from Iowa State University were 1476 records from 602 cows from 29 maternal lineages. Eleven sites of polymorphism were found. An animal model for gene substitution was used to examine the relationship between sequence differences and yield traits. Traits analyzed were mature. Effects of sequence differences were significant for most traits. Sequence information from the D-loop was available for 12 lineages from North Carolina. The effect of polymorphism at 4 sites was examined using 1472 records from 668 cows. No significant relationships existed between any of the traits and D-loop polymorphism, but results suggested that an association might exist between polymorphism and concentrations of milk yield, fat percentage, and energy. Whenever a significant relationship was detected, the effect of mutation (rare genotype) was detrimental.
Lau et al., (1998) Sequenced mitochondrial DNA (mt DNA) for 303 bp of the Cytochrome b gene for 54 animals from 14 populations, and for 158 bp of the D-loop region for 80 animals from 11 populations of swamp and river buffalo. The phylogenetic relationships among the 33 D-loop haplotypes, with a cluster of 11 found in swamp buffalo only. The time of divergence of the swamp and river types, estimated from the D-loop data, was 28000 to 87000 years ago. They hypothesized that the species originated in the mainland South-East Asia, and that was spread north to China and west to the Indian subcontinent, where the river type evolved and domesticated. Following domestication in China, the domesticated swamp buffalo spread through two separate routes, through Taiwan and the Philippines to the eastern islands of Borneo and Sulawesi, and south through mainland south-east Asia and then to the western islands of Indonesia.
Lau et al., (1998) Mitochondrial DNA (mtDNA) and cytochrome b gene of swamp and river buffalo was sequenced for 303bp of 54 animals from 14 population. We obtained five polymorphic sites. Only one cytochrome b haplotype is found in river buffalo and four in swamp buffalo. These sites are result of transversion substitution. An additional site is found which is result of transition substitution. out of these four one is found in each population.out of 33 D.loop haplotype 11 is found in swamp buffalo.This shows that the evolution of swamp and river buffalo is from swamp like animal. These two buffalos are different from each other by two nucleotide positions.
Mirol et al., (2003) A portion of the mitochondrial D-loop was sequenced in 36 animals from five Creole cattle populations in Argentina and four in Bolivia. Sequence comparisons revealed three main groups: two with the characteristics of European breeds and a third showing the transitions representative of the African taurine breeds. The African sequences were found in two populations from Argentina and three populations from Bolivia. The most probable explanation for the finding is that animals could have been moved from Africa to Spain during the long-lasting Arabian occupation that started in the seventh century, and from the Iberian Peninsula to America eight centuries later. However, since African haplotypes were not found in the Spanish sample, the possibility of cattle transported directly from Africa cannot be disregarded.
Sultana et al., (2004) Mitochondrial DNA (mtDNA) of 30 Pakistani goat is sequenced and we obtained 22 new haplotypes ; mt-lineage A it has further two clusters A1 and A2.17bp deletion and 76bp insertion was observed in 232 pakistani goats.This shows high diversity of mtDNA gene.
Kierstein et al., (2004) We analyzed the entire mitochondrial D-loop region of 80 water buffaloes of four different breeds, i.e., 19 swamp buffaloes and 61 river buffaloes. Sampled in Brazil and Italy. We detected 36 mitochondrial haplotypes with 128 polymorphic sites. Pooled with published data of South-East Asian and Australian water buffaloes we show evidence that both river and swamp buffaloes decent from one domestication event, probably in the Indian subcontinent. However, the today swamp buffaloes have an unravelled mitochondrial history, which can be explained by introgression of wild water buffalo mtDNA into domestic stocks.
Lei et al., (2004) The complete mitochondrial D-loop sequences in 22 individuals from 8 cattle breeds in China were analyzed. Comparisons of these 22 sequences revealed 66 polymorphic sites, 5 types of mutation and 19 mitochondrial haplotypes, the percentage of haplotype was 86.36%, showing that abundant mitochondrial genetic diversity exists in Chinese cattle. The lowest average percentage of mtDNA D-loop nucleotide variation was in Xizhen cattle, Mongolian cattle, Holstein, Qinchuan cattle. The molecular phylogenetic tree of mtDNA D-loop of 8 Chinese cattle breeds was constructed by Neighbor-Joining method. The NJ tree indicated that these mtDNA sequences fell into 3 distinct haplotype groups, it also suggested in molecular level that there were probably 3 maternal origins, of which the main origins of Chinese cattle were from Bos taurus and Bos indicus.
Sung et al.,(2005) To determine the origin and genetic diversity of Chinese cattle, we analyzed the complete mtDNA D-loop sequences of 84 cattle from 14 breeds/populations from southwest and west China, together with the available cattle sequences in GenBank. Our results showed that the Chinese cattle samples converged into two main groups, which correspond to the two species Bos taurus and Bos indicus. Although a dominant lineage was clearly discerned in both B. taurus and B. indicus mtDNAs, network analysis of the lineages in each of the two species further revealed multiple clades that presented regional difference. The B. taurus samples in China could be grouped into clades T2, T3, and T4, whereas B. indicus harbored two clades I1 and I2. Age estimation of these discerned clades showed a time range of 14,100-44,500 years .It is suggested that B. indicus contributed more to the cattle from south and southwest China. The genetic diversity of Chinese cattle varied among the breeds studied.
Lai et al., (2005) This study determined yak's complete sequence of mitochondrial DNA control region (D-loop) of 35 individuals in 5 yak breeds at the first time. The result showed that the length of D-loop in yak was 891 -895 bp. There were 55 polymorphic sites .24 haplotypes was defined in this study, in which haplotype H4 and H6 were major haplotypes of Chinese yak. The results indicated that the genetic diversity of Chinese yak was very abundant. Analysis of molecular variance and network construction results indicated that there was significant divergence among Chinese yak breeds. The network construction indicated that Chinese yak had been divided into 2 types and had probably 2 maternal origins or 2 domesticated places.
David et al., (2006) Mitochondria are vital organelles that perform a variety of fundamental functions ranging from the synthesis of ATP and also involved in programmed cell death(apoptosis). It has six compartments: outer membrane, inner boundary membrane, intermembrane space, cristal membranes, intracristal space,and matrix, mitochondria have a complex, internal structure. Mitochondria contain their own DNA (mtDNA), encoding a small number of vital genes. Glycolysis occurred in mitochondria and provide energy for life due to its compartmentalization.
Lei et al., (2006) 231 samples of mitochondrial D-loop were used to explore the origin and genetic diversity of Chinese cattle through sequencing. Four of the previously identified mitochondrial DNA lineages (T1-T4) were identified in the Bos taurus type, including lineage T1, which was found for the first time in Chinese cattle. Two lineages (I1 and I2) were identified in the Bos indicus type. Our results support the suggestion that the Yunnan-Guizhou Plateau is the domestication site of Chinese zebu. We also found evidence that Tibetan cattle originated from taurine and zebu cattle. It was possible to divide Chinese cattle in this study into two major groups: northern and southern cattle.
Schlumbaum et al., (2006) Analysis of nucleotide diversity within the mitochondrial D-loop revealed high haplotype diversity and similar diversity to a European cattle reference group. Mitochondrial T3 haplotypes radiated star-like from two similarly frequent haplotypes, possibly indicating two different expansion routes. The breed structure of Evolène cattle can be explained either by an introduction of diverse female lineages from the domestication centre or by later admixture.
Liu et al., (2006) Mitochondrial D-loop sequences in 82 individual cattle from 4 breeds were analyzed. The results revealed 31 mitochondrial haplotypes and 65 polymorphic sites. The nucleotide diversity and haplotype diversity (H) estimated from mtDNA D-loop region in 4 cattle breeds in Guizhou showing that abundant mitochondrial genetic diversity exists in Guizhou cattle breeds. The Neighbor-Joining (NJ) molecular phylogenyetic tree of mtDNA D-loop of 4 Guizhou cattle breeds was constructed according to the 31 haplotypes. The NJ tree indicated that the origin of cattle breeds was from Bos taurus and Bos indicus which had nearly the same influence on cattle breeds in Guizhou.
Lei et al., (2007) The phylogeny of water buffalos is still controversy because the domestic buffalo is derived from man selection. For more study about Mitochondrial D.loop we analyse 80 baffalo samples; 61 river and 19 swamp buffalos.we detect 36 Mitochondrial sites and 128 polymorphic sites. Result showed that both buffalos are domesticated from single domesticated event.
Halbert et al., (2007) To see introgression in mitochondrial and nuclear domestic cattle (Bos taurus) 11 US federal bison populations were examined . Mitochondrial introgression was examined through polymerase chain reaction methods and confirmed through analysis of D-loop sequences. Nuclear introgression was assessed in 14 chromosomal regions through examination of microsatellite electromorph and sequence differences between bison and domestic cattle. Only one population was identified with domestic cattle mitochondrial DNA introgression. In contrast, evidence of nuclear introgression was found in 7 of the examined populations. The identification of genetically unique and undisturbed populations is critical to species conservation efforts, and this study serves as a model for the genetic evaluation of interspecies introgression.
Lei et al., (2007) Complete mitochondrial D-loop sequences of 119 samples representing seven native types were observed. Two mitochondrial DNA (mtDNA) lineages (lineages A and B) were determined for the Chinese swamp buffalo. Examination of the diversity patterns suggest that lineage A has undergone a population development . Difference of lineages A and B was estimated at 18,000 years ago. Combined analyses of mtDNA sequences from Chinese, Indian, Brazilian/Italian and Southeast Asian/Australian buffalo samples showed independent domestication events in the swamp buffalo from China and the river buffalo from the India subcontinent. Our data support the hypothesis of the evolution of domesticated swamp and river buffalo from ancestral swamp-like animals. These ancestral animals were extensively distributed across mainland Asia and most likely are represented today by the wild Asian buffalo (Bubalus arnee).
Edward et al., (2007) mtDNA of aurochs (Bos primigenius) was sequenced from 59 archaeological skeletal finds. All aurochs belonged to the previously designated P haplogroup, indicating that this represents the Late Glacial Central European signature. The Neolithic and Bronze Age samples all carry P haplotype mitochondrial DNA. Previous work has shown that most ancient and modern European domestic cattle carry haplotypes previously designated T. This in combination with our new finding of a T haplotype in a very Early Neolithic site in Syria. During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare.
Andrea et al., (2007) We classified local cattle breed according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, make the local population. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors are derive from natural selection and breed admixture. While Brazilian Creole breeds gives a little information on their genetic composition.Studty of genetic diversity, phylogenetic relationships and patterns of taurine/zebuine admixture was carried out on ten cattle breeds in Brazil.
Jia et al., (2007) The complete mitochondrial D-loop region from 123 individuals in 12 Chinese cattle breeds and two individuals in Germany Yellow cattle breed was sequenced and analyzed. The results were shown as follows: 93 variations and 57 haplotypes were detected. In the Neighbor-Joining tree, 13 cattle breeds were divided into two main clades, Bos taurus and Bos indicus. The importance of Yunnan cattle in the origin of Chinese cattle was also confirmed based on their abundant haplotypes. Then, a very special haplotype i1 (Haplogroup i1 is a Y chromosome haplogroup associated with the mutations identified known as single nucleotide polymorphisms (SNPs) discovered in 27 Chinese cattle breeds, including i1 breeds in this study and 16 breeds in the GenBank, played the role of a nucleus in Chinese zebu. At the same time, the construction of Chinese zebu core group based on haplotype i1 validated the distinct origin of Bos indicus in Tibet, which was different from that of the other cattle breeds with zebu haplotypes in China.
Guz et al., (2007) mtDNA sequence analysis of yake revealed that there are no differences with cattle in the yak mitochondrial genome organization. Interestingly, within the D-loop, the conserved sequence blocks are less conserved than surrounding regions. Neighbor-Joining (NJ) trees based on single genes, gene sets and genes of mitochondrial genome were constructed. The analysis identified the yak as a sister group of a cattle/zebu clade. Based on substitutions in 22 tRNA genes, 12S rRNA gene and 16S rRNA gene, the dating of divergence between yak and cattle/zebu, and yak and water buffalo, was proposed to have occurred 4.38-5.32 and 10.54-13.85 million years before present, respectively. This is consistent with the paleontologyical data (Paleontology is the study of prehistoric life, including organisms' evolution and interactions with each other). Yak and sheep/goat divergent dating predicts that their divergence occurred at 13.14-27.99 million years before the present day.
Caixetal et al., (2007) Mitochondrial DNA (mtDNA) is unusual in its rapid rate of evolution and high level of intraspecies sequence variation. To explore that how mtDNA population rate is so rapid we have determined here the nucleotide sequence of all or part of the D-loop region in 14 maternally related Holstein cows. Four different D-loop sequences can be distinguished in the mtDNA of these animals. One explanation is that multiple mitochondrial genotypes existed in the maternal germ line and that expansion or segregation of one of these genotypes during oogenesis or early development led to the rapid genotypic shifts observed.
Laisj et al., (2007) In order to clarify the origin and genetic diversity of yak in China, we analysed mitochondrial DNA (mtDNA) control region sequences in 52 individuals from four domestic yak breeds, as well as from a hybrid between yak and cattle. Twenty-five samples were further selected for partial cytochrome b sequencing based on control region sequence information. Two yak samples shared sequences with Chinese cattle (Bos taurus); the remaining yak mtDNAs converged into two major clades in the phylogenetic analysis. Genetic diversity varied substantially among the breeds, with the hybrid yak demonstrating the highest diversity. Our results suggest that the Chinese yak was domesticated from two distinct materinal lineage sources or from a heterogeneous pool containing both divergent lineages, with occasional gene introgression from cattle.
Tsai et al., (2008) We studied the complete mitochondrial DNA D-loop structure of pigeon. Amplification three partial fragments of the D-loop and then combing the three fragments to cover the full length of the D-loop were done. Ten samples from pigeons were collected and were successfully amplified and sequenced. Repetitive sequences of a VNTR and an STR were both observed at the 3'-end of D-loop region. DNA sequence data revealed polymorphic sequences including SNPs, VNTR and STR within the D-loop. Each sample was different due to four genotyping procedures, SNPs, VNTRs and STRs. The polymorphic nature of the D-loop can be a valuable method for maternal identification and genetic linkage of pigeon in particular forensic science investigations.
Cortes et al., (2008) To clarify the genetic diversity and the mitochondrial DNA (mtDNA) diversity of the Lidia cattle breed, 521-bp D-loop fragment was sequenced in 527 animals. Haplotype T3 was the most common, followed by the African T1 haplotype, very low frequencies were recorded for haplotypes T and T2. Haplotype T3 was present in all those analysed; in five it was the only one present, and in only one lineage (Miura) was its frequency lower than that of T1. T1, a haplotype reported in Criollo breeds and to date in only a single European breed, was found in a single animal. Network analysis of the Lidia breed revealed the presence of two major haplotypes: T3 and T1. The Lidia breed appears to be more closely related to prehistoric Iberian and Italian than to British aurochs.
Xin et al., (2009). We analysed six Y-STR loci (UMN0929, UMN0108, UMN0920, INRA124, UMN2404 and UMN0103) using 576 unrelated males and 10 females of the Qinchuan cattle population in Chinese Shaanxi Province. Allele frequency, gene diversity, the polymorphic information content, and the number of effective gene were calculated. All loci are identified according to the Hardy-Weinberg equilibrium (P > 0.05). The population data were compared with published data of other cattle breeds. It suggested that Qinchuan cattle were originated from Bos Taurus. It gives information about individual identification, paternity testing, and origin analysis of Qinchuan cattle breed.
Chuan et al.,(2009) The complete D-loop region of mitochondrial DNA from 206 individuals in 16 Chinese indigenous cattle breeds was sequenced and analyzed to detect variability of D-loop region of mitochondria DNA. Results showed 101 variations and 99 haplotypes were found, in which 73 haplotypes were of Bos taurus and the other 26 haplotypes were of Bos indicus. According to the phylogenetic tree, 16 cattle breeds were divided into two groups, Bos taurus and Bos indicus. Based on the Network graphics, the 73 haplotypes of Bos taurus were classified into 3 groups and the 26 haplotypes of Bos indicus were classified into 5 groups. It was concluded that those purine C decrease was possibly originated in Chinese Bos indicus. There was only 16% of H3 haplotype sequences similar to the sequence of Nellore, and 84% of those sequences had purine C variation in Chinese indigenous cattle breeds through the analysis on their common H3 haplotypes.
Stock et al., (2009) Mitochondrial DNA has been the traditional marker for the study of animal domestication, as its high mutation rate allows for the accumulation of molecular diversity within the time frame of domestic history. Additionally, it is exclusively maternally inherited and haplotypes become part of the domestic gene pool via actual capture of a female animal rather than by interbreeding with wild populations. Initial studies of British aurochs identified a haplogroup, designated P, which was found to be highly divergent from all known domestic haplotypes over the most variable portion of the D-loop. An additional, separate aurochs haplotype, E. was found by analysis of a large and geographically representative sample of aurochs from northern and central Europe.Until recently, the European aurochs appeared tso have no matrilinear descendants among the publicly available modern cattle control regions sequenced; if aurochs mtDNA was incorporated into the domestic population, aurochs either formed a very small proportion of modern diversity or had been subsequently lost. However, a haplogroup P sequence has recently been found in a modern sample, along with a new divergent haplogroup called Q. Here we confirm the outlying status of the novel Q and E haplogroups and the modern P haplogroup sequence as a descendent of European aurochs, by retrieval and analysis of cytochrome b sequence data from twenty ancient wild and domesticated cattle archaeological samples.
Yang et al., (2009) The complete mitochondrial D-loop region from 187 individuals in 18 Chinese cattle breeds, which include 5 northern breeds, 9 southern breeds, 3 Tibetan breeds and Germany Yellow Cattle(only 2 individuals), was sequenced and analyzed by PCR and sequencing technique. The results showed as follows: The region of D-loop in 186 individuals in 18 breeds ranged from 909 bp to 913 bp. There were totally 97 haplotypes sorted into 62 taurine ones, 34 zebu ones and a yak one. And there were 110 variation sites expanding from the start to the end of the D-loop region, with only 75 ones distinguishing taurine and 43 ones distinguishing zebu. In the Neighbor-Joining tree and network, 18 cattle breeds were mainly divided into two clades, Bos taurus and Bos indicus .The study for Clade proved that Chinese Tibetan cattle had an introgression of yak maternally. This is the first time to detect yak lineage in Chinese cattle based on the complete D-loop sequence6. Analysis showed that Tibetan cattle was an isolated type, not only for zebu but also for taurine.
Zhang et al., (2009) The complete D-loop region of mitochondrial DNA from 206 individuals in 16 Chinese indigenous cattle breeds was sequenced to detect variability of D-loop region of mitochondria DNA for those breeds. The results showed 101 variations and 99 haplotypes were found, in which 73 haplotypes were of Bos taurus and the other 26 haplotypes were of Bos indicus. Based on the Network graphics, the 73 haplotypes of Bos taurus were classified into 3 groups and the 26 haplotypes of Bos indicus were classified into 5 groups. There was only 16% of H3 haplotype sequences similar to the sequence of Nellore, and 84% of those sequences had purine C variation in Chinese indigenous cattle breeds through the analysis on their common H3 haplotypes. It was concluded that those purine C decrease was possibly originated in Chinese Bos indicus.
Jia et al., (2010) We sequenced 856 individual of cattle for D.loop in which 264 were of Chinese cattle and the rest sequences are of cattle from six Asian countries. Our results indicated that cattle from six Asian countries fell into three clades, Bos taurus (taurine), Bos indicus (zebu) and yak. Four main haplogroups T1A, T2, T3 (including T3A and T3B) and T5 were found in taurine, and two haplogroups I1 and I2 in zebu. We also found that I1 and I2 haplogroups were separated by four variable sites rather than five ones and four haplogroups or sub-haplogroups of T1A, T3A, T3B and T5 were found for the first time in these Asian cattle. These data brought us a new insight into cattle's genetic structure in these six Asian countries.
Wang et al., (2010) To determine the origin and genetic diversity of Yunnan gayal and cattle we analysed mtDNA control region sequences of 71 samples and SRY gene (sex determining region Y) sequences of 39 samples, together with the available sequences in GenBank. The neighbour-joining phylogeny and the reduced median network analysis showed that Yunnan gayal originated from the hybridization between male Bos frontalis and female Bos taurus or Bos indicus, and that Yunnan cattle mostly originated from B. indicus, also containing some hybrids of male B. indicus and female B. taurus. The phylogenetic pattern of Yunnan cattle was consistent with the recently described cattle matrilineal pool from China and indicated more contribution to the Yunnan cattle from B. indicus than from B. taurus.