Sample Pedigree Chart of a Horn Hereford Beef Cattle Breeds of Beef Cattle and Their Characteristics

Asian-Australas J Anim Sci. 2015 Jul; 28(7): 911–921.

African Indigenous Cattle: Unique Genetic Resources in a Speedily Irresolute Earth

Olivier Hanotte

¹School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, Great britain.

Immature-Jun Kwon

²Interdisciplinary Plan in Bioinformatics, Seoul National University, Seoul 151-742, Korea.

Seoae Cho

³CHO&KIM genomics, Seoul 151-919, Korea.

Abstract

At least 150 indigenous African cattle breeds accept been named, but the majority of African cattle populations remain largely uncharacterized. Every bit cattle breeds and populations in Africa adapted to diverse local environmental conditions, they caused unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we observe a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now establish all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain also few while paradoxically the demand of livestock products is continually increasing. Many African ethnic breeds are endangered now, and their unique adaptive traits may exist lost forever. This paper reviews the unique known characteristics of ethnic African cattle populations while describing the opportunities, the necessity and urgency to understand and utilise these resources to respond to the needs of the people of the continent and to the do good of African farmers.

Keywords: Africa, Cattle, Climate, Indigenous Genetic Resource

INTRODUCTION

Once humans started domesticating animals, livestock populations take continually been influenced through selective breeding in response to the needs of the owners as well as through natural pick to conform to the local agro-surroundings. Animal breeding was initially practiced to obtain usable products or services and for socio-cultural (e.g. religions, aesthetic) reasons (Flint and Woolliams, 2008). Although ancient convenance schemes might have existed, knowledge-based selective breeding was showtime practiced by the Romans (Buffum, 1909). Now, with recent technological developments, both phenotypes measurements and genomic information are now beingness used for genetic improvements (Flint and Woolliams, 2008). In particular, methods for obtaining genomic information of animals are developing quickly (e.1000. genome-wide genotyping and sequencing), thus opening new opportunities for genomic option (Habier et al., 2007; Hayes et al., 2013).

However, the commercial livestock sector is facing several new challenges. Demand for livestock products is continuously increasing, but long-term sustainability of the intensive livestock sector is questionable (Otten and Van den Weghe, 2011). Climate change is putting new pressures on livestock production, while livestock themselves are contributing through greenhouse emissions to the climate modify (Houghton et al., 1992; Nardone et al., 2010). Moreover, indigenous livestock, although adapted to the local environments, are poor milk and meat producers compared to the commercial breeds raised in the extensive organisation (Renaudeau et al., 2012).

Arising from the higher up concerns and the need to bridge the huge productivity gaps in developing countries, catalyzed past rapid changes in the production systems, more than ever indigenous livestock genetic resources, which institute the largest proportion of livestock in those countries, are increasingly being eroded through poorly planned crossbreeding and breed replacements. In procedure, we might exist losing unique genetic attributes, especially those responsible for adaptations to the past, current, and even future African environmental challenges, such as parasitic infectious diseases, heat and drought tolerance etc. Here, we summarize the adaptation of indigenous African cattle emphasizing the importance and demand to unravel and characterize these cattle at genome level.

THE ORIGIN OF AFRICAN CATTLE

Currently, about 180 breeds of cattle have been recognized in sub-Saharan Africa; 150 breeds of indigenous cattle and recently introduced exotic and commercial composites (Rege, 1999; Rege et al., 2006). Nonetheless, oft the genetic distinctiveness betwixt these cattle breeds remain largely unknown and it may be more appropriate to talk nearly African cattle populations or ecotypes. Phenotypically humped cattle or zebu cattle (Bos indicus) constitute the majority of African cattle (Hanotte et al., 2000). They are adapted to local environmental weather condition that are generally unsuitable to exotic breeds of European origin (e.yard. high temperatures, long menstruum of drought, vector-born disease). African indigenous taurine cattle Bos taurus (humpless cattle) are now institute nearly exclusively in West Africa, while commercial taurine breeds and their crossbreed are found about in every part of the continent, although their populations are relatively depression compared to the indigenous breeds. Beside these two main types of cattle, the continent is home to sanga and zenga, which are crossbreds between the indigenous taurine and zebu (sanga), and zebu and sanga (zenga), with the latter having college zebu genetic background than the former (Rege, 1999). It should be noted, that all African cattle do bear a taurine mitochondrial Deoxyribonucleic acid, in others words they are no pure zebu Bos indicus on the African continent.

The wild auroch, Bos primigenius, is the progenitor of all taurine and zebu cattle (Edwards et al., 2007). They are described by Julius Caesar in his report of the Gallic Wars as "…a little below the elephant in size, and of the appearance, colour, and shape of a bull". Three subspecies of auroch are recognized. According to fossil tape, Northern Africa was the habitat of B. p. africanus from Middle Pleistocene onwards (Linseele, 2004), B. p. primigenius was widely distributed in western Eurasia, while the supposedly wild ancestor of zebu B. p. nomadicus inhabited Southern asia (Stock and Gifford-Gonzalez, 2013).

Estimates of divergent time for Bos taurus and Bos indicus from a mutual antecedent are all pre-Neolithic ranging from to ~ 2 millions to ~ 330,000 years ago depending of the genetic markers and the scale rate of the molecular clock (Hiendleder et al., 2008; Ajmone-Marsan et al., 2010). It remains unclear whether or non African cattle were domesticated on the African continent. It was originally thought that it might have been the instance following molecular show indicating the presence of a "unique" African mitochondrial DNA D-loop haplogroup (Loftus et al., 1994) and archaeological remains of ancient cattle husbandry in the Due east of the Sahara desert (Wendorf and Schild, 1994). Even so, the close sequence similarity betwixt cattle D-loop mtDNA haplogroups (Troy et al., 2001) and more recently, a study using the total cattle mitochondrial Dna sequences (Bonfiglio et al., 2012), showing that the diversity of African mitochondrial DNA is largely embedded within the mitochondrial Dna diversity of Near East cattle, support that the maternal ancestor of African domestic cattle may take originate from the same center of cattle domestication and/or auroch populations than the European taurine, in the Fertile Crescent. All the same, a genome-wide study using single nucleotide polymorphic makers indicates the presence in African cattle of a unique genetic background which was postulated to accept originated from the African auroch through a male person mediated introgression procedure (Decker et al., 2014).

Archaeological and molecular data let making inferences about the history of African cattle, including their possible migration routes within the African continent (Figure 1; Hanotte et al., 2002; ILRI, 2006; Stock and Gifford-Gonzalez, 2013). Humpless Bos taurus are considered the earliest African cattle as supported past archaeological show and pictorial accounts (e.g. Sahara rock paintings) (Cringe and MacDonald, 2000). The humpless longhorns might have been introduced first, followed by humpless shorthorns cattle about 2,500 years later (Epstein, 1971; Rege, 1999). However, it should even so be pointed out that the two waves scenario of taurine inflow into Africa is nevertheless to be supported by any molecular evidence. Hanotte et al. (2002) showed that African Bos taurus cattle expanded from the northeastern part of the continent to the Westward and East Africa (Hanotte et al., 2002). After the initial taurine cattle dispersion, zebu cattle were introduced into the continent, likely in two waves (Hanotte et al., 2002). It is possible that the first African cattle reaching the Southern function of the continent were zebu-introgressed taurine cattle (Epstein and Mason, 1971; Hanotte et al., 2002), Although zebu cattle were probably present in Africa earlier than 2000 BC, the first wave of zebu introduction through the Horn of the continent, is thought to be primarily associated with the development of the Swahili-Arabs culture along the East African coast from the 7th century AD. The second wave of Bos indicus, possibly followed the rinderpest epidemics of 19th century, which wiped out well-nigh of African cattle population.

An external file that holds a picture, illustration, etc. Object name is ajas-28-7-911f1.jpg

Approximate migration route and the origin of Africa domestic cattle (adapted and modified from ILRI, 2006. Safeguarding livestock diversity: the time is now). Circumvolve regions represent the expected center of cattle domestication. Migration road from the outside Africa and within Africa was shown past colour arrows, and the colour of arrow represents the migration time and its origin.

TYPES OF INDIGENOUS CATTLE AND THEIR GEOGRAPHIC DISTRIBUTION

Primary groups of African cattle

Indigenous African cattle can be broadly classified into four categories: humpless Bos taurus, humped Bos indicus, sanga (African humpless Bos taurus×humped Bos indicus hybrid), and zenga, defined every bit sanga×zebu backcross. In addition to these four categories, other African cattle breeds take been recently derived through recent crossbreeding with exotic (Rege and Tawah, 1999).

African Bos taurus includes 2 groups, humpless shorthorns and longhorns. They mostly inhabit West and Fundamental Africa. Both these groups are small in size and their productivity is lower compared to most of the zebu cattle populations in tropical areas (Rege, 1999). However, they take unique evolutionary adaptation to harsh climate (Hansen, 2004) and diverse endemic diseases (Murray et al., 1984; Mattioli et al., 2000). One of these adaptations is their documented tolerance to trypanosomosis (Roberts and Gray, 1973), a parasitic disease due to infection with Trypanosoma sp. whose vector is the tsetse fly.

Zebu cattle (Bos indicus), are the majority of cattle types in Africa. They have a fatty thoracic hump on their shoulders and a large dewlap. The zebu is normally susceptible to trypanosomosis (Murray et al., 1982) however, tolerance to the affliction has been documented in the Orma Boran, an E African zebu brood (Njogu et al., 1985). They are adapted to dry out environmental conditions and high temperatures and are known to be more resistant to tick infestation compared to Bos taurus cattle (Mattioli et al., 2000). African zebu cattle inhabit western and eastern parts of Africa. Their large body size and loftier product levels in tsetse-gratis areas accept made them more highly-seasoned to the local farmers, and therefore partly explain their abundance and broad distributions in Africa.

The sanga is an intermediate type of cattle, which is a cross between Bos taurus and Bos indicus. They are humped only the hump is cervico-thoracic rather than thoracic. They inhabit eastern and southern Africa and are known to be well adapted to seasonally harsh atmospheric condition (Okello and Sabiiti, 2006). It is idea that sanga cattle were derived past hybridization between taurine cattle and zebu around 700 AD (Hanotte et al., 2002). Crossbreeding between sanga cattle, and newly introduced zebu led to a new cattle type called "Zenga" (Rege, 1999). Zenga are found in eastern Africa.

Although, African cattle genetic diversity remains big, cattle populations or breeds go on to face up extinction. Co-ordinate to Rege (1999), 22% of African cattle breeds accept already become extinct in the last century and 32% of indigenous African cattle breeds are in danger of extinction (Rege, 1999). Moreover, some breeds that are critically endangered have fewer than one,000 animals, such equally the Republic of ghana Dwarf Muturu (humpless shorthorns), Mkalama Dun (Small East African Zebu), Pare (Small Eastward African Zebu), Chagga (Small-scale East African Zebu), Baria (Small E African Zebu), Nkone (South African sanga), Pedi (South African sanga), and Shangan (South African sanga) (Rege, 1999). To recoup for the relatively lower production potential of indigenous cattle, crossbreeding of these cattle with exotic breeds, is ordinarily proficient, with minimal inside breed selection programme for the indigenous breeds. The end result is a continuous erosion and loss of cattle diversity, including for adaptive traits, before these genetic resources are fully characterized. There is therefore an urgent demand to comprehensively characterize the African cattle populations, in social club to objectively inform their utilization and conservation earlier they disappear (Hanotte et al., 2010).

Main subgroups of African cattle

The humpless Bos taurus includes two groups, humpless longhorns and humpless shorthorns. They are currently constitute in West and Central Africa (Rege et al., 2006). Sanga cattle are mainly kept in eastern and southern Africa, but they are also found in Central Africa. The distribution of the five African cattle groups including the recent derived breeds is shown at Figure ii (Rege, 1999; Hanotte et al., 2002; Rege et al., 2006).

An external file that holds a picture, illustration, etc. Object name is ajas-28-7-911f2.jpg

Distributions of ethnic cattle in sub-Saharan Africa. Marks on the map stand for African cattle distribution, and each mark shows the type of cattle which inhabit the region. Cattle of North Africa and imported commercial cattle breeds are not shown in this figure.

Overall, cattle population density is highest in the East African highlands compared to other regions, a legacy of the history of cattle introduction and human migration on the African continent (Figure 1). The two waves of Bos indicus migration led to a dominance of zebu type cattle among the Eastward African ethnic cattle, thus replacing nearly, if not all, Eastward African Bos taurus cattle (Payne, 1964; Epstein and Stonemason, 1971; Hanotte et al., 2002). Together, Y chromosome, autosomal and mtDNA studies clarify the introgression pattern of zebu cattle (Bradley et al., 1994; Hanotte et al., 1997, 2002; Porto-Neto et al., 2013). All genetic evidence suggests that zebu introgression on the Africa continent was primarily a male person zebu process. While this might be expected for a polygenous species like cattle, it is however surprising that not a single zebu mitochondrial Deoxyribonucleic acid have been and then far been identified on the African continent. The reason(due south) are unclear. Maybe, zebu mitochondrial Deoxyribonucleic acid haplotypes might have been selected against in crossbreed cattle living on the African continent. Further studies are therefore needed.

Admixture analyses of African cattle using microsatellite data have revealed a gradient of Bos indicus introgression across the African continent (Hanotte et al., 2002), with the level of zebu introgression decreasing from eastern to western Africa (Hanotte et al., 2002; Freeman et al., 2006). Moreover, cattle that inhabit subtropical areas of West and Central Africa barely accept any zebu beginnings. Given the susceptibility of near zebu cattle populations to trypanosomosis, tsetse-infested areas in subtropical areas virtually likely prevented introgression of zebu ancestry into these populations (MacHugh et al., 1997).

CHARACTERISTICS OF AFRICAN INDIGENOUS CATTLE

African indigenous cattle breeds have unique morphological features which distinguishes them from other cattle. These include horn shape and size (e.g. Ankole and Kuri) (Rege et al., 2006; Ndumu et al., 2008; Kugonza et al., 2011; Terefe et al., 2015). In addition to concrete features, not-visible traits such as disease resistance, climatic stress resistance and productivity traits also differ among breeds. These characteristics are largely the upshot of natural and human selection. Some breeds are already known for their unique adaptive attributes (due east.thousand. Muturu) or adept economic performances (due east.g. Kenya Boran).

One of the well-known outstanding features of African cattle is trypanosomosis resistance. Trypanosomosis is a tsetse-transmitted disease in vertebrates. In cattle the master pathogenic trypanosomes are Trypanosoma congolense and T. vivax. Non-African cattle breeds are highly susceptible to trypanosomes infection. The African Bos taurus are tolerant while African Bos indicus are susceptible although not as susceptible as the not-African Bos taurus and Bos indicus exotic breeds. For instance, the North'Dama cattle (a long humpless longhorns), which are found in central and West Africa, are trypanotolerant (Mattioli et al., 2000), which has led to an overall population increase and expansion of their geographical range (Rege and Tawah, 1999). Other studies accept reported that the Sheko cattle (an East African humpless shorthorns) shows also resistance to trypanosomosis (Lemecha et al., 2006). Unfortunately today, this cattle brood is rapidly disappearing as issue of beingness increasingly being crossed with trypanosusceptible zebu cattle. Although zebu cattle are unremarkably susceptible to trypanosomosis, some zebu breeds that inhabit tsetse-infested regions, such as the Nuba Mountain Zebu, Mongolla or the Orma Boran, and the Mursi have been reported to take relatively reasonable levels of tolerance to trypanosomosis, as a result of local evolutionary adaptation (Ruttledge, 1928; Rege and Tawah, 1999; Terefe et al., 2015). Also, the Bovino de Tete, which is a zenga type of cattle found in Mozambique and the Alur cattle found in the Democratic Republic of Congo, are also thought to show some level of trypanotolerance (Lemecha et al., 2006).

Tick infestation represents another major claiming for African cattle. Unlike trypanosomosis, African Bos indicus cattle are believed to be more resistant to infestation past cattle ticks compared to taurine animals (Piper et al., 2009). However, among African taurine cattle, the North'Dama and Ankole (humpless longhorns) take been reported to be resistant to tick infestation (Mattioli et al., 2000). In addition, Tswana cattle (South African sanga), from Botswana, have very loftier tolerance to heavy tick challenges (Rege et al., 2006). The Tswana is also known to have resistance to the endemic heartwater disease, every bit exercise Landim cattle (Southward African sanga) from Mozambique (Asselbergs et al., 1993).

Singled-out evolutionary history betwixt Bos taurus and B. indicus accept resulted in different degree of thermos-tolerance at the cellular and physiological levels (Hansen, 2004). Bos indicus breeds can effectively regulate their torso temperature against thermal stress and are better adapted to hot atmospheric condition than Bos taurus breeds (Hansen, 2004). In add-on, several breeds of zebu and zenga are able to withstand very harsh environmental conditions, and those characteristics have arisen through evolutionary adaptation. For examples, Karamajong Zebu cattle (Large East African Zebu) in Uganda are well adapted to very dry out climates and they tin can survive if they are able to drink merely once every two days (Thomas, 1943). Turkana cattle (Large East African Zebu) in Kenya, which are classified in the same subgroup of cattle, are thought to be able to survive on very poor pasture, scarce water and have skilful walking abilities (Rege et al., 2006). Angoni cattle (Small East African Zebu) in Zambia and Ugogo Grey cattle (Small East African Zebu) in Tanzania are adapted to browsing during the long dry out seasons (Felius, 1995; Rege and Tawah, 1999). In the case of Landim cattle (South African Sanga) in Mozambique, they are thought to have resistance to hot, humid weather as well equally extended dry periods and foot and mouth affliction (Felius, 1995; Rege et al., 2006; Machiel, et al, 2013). In Africa, cattle breeds have adapted to hot and dry weather, but others have adapted to fifty-fifty cold and moisture conditions, such as Jem-Jem cattle (Small East African Zebu) in Federal democratic republic of ethiopia (Rege and Tawah, 1999).

African cattle continue to play a major role in the socioeconomic development and nutritional security of the people of the continent (Table one). It is likely that some the earliest African societies depended only on livestock given their nomadic lifestyle (Marshall and Hildebrand, 2002). Pastoralism remains an of import activity in the continent today, and exemplified past the Fulani, Maasai and the Tuaregs communities. Across the continent, cattle remain major socio-cultural assets and they play important social-cultural roles in many African societies (e.g. marriage, initiation). Likewise these major socio-cultural roles, African cattle represent a major source of animal protein (dairy product and beef), provide typhoon power, thus support crop farming, and fertilizer through manure, which is as well used every bit fuel by some communities.

Table 1

Examples of ethnic cattle breeds with unusual characteristics in sub-Saharan Africa (DAGRIS 2007)

Group	Breed name	Characteristics
Humpless Longhorns	Kuri	First-class swimmers, intolerant to heat and sunlight
Humpless Longhorns	N'Dama	Tolerance to trypanosomosis and cattle ticks
Humpless Shorthorns	Savanna Muturu	Sexual dimorphism on trunk size, well-fleshed torso
Humpless Shorthorns	Sheko	Tolerance to trypanosomosis
Large E African Zebu	Barka	Agile disposition
	Karamajong zebu	Adapted to a very dry climate
	Kenyan Boran	Walking power, highly adapted to harsh conditions, herd instinct, mothering ability, longevity, large sexual practice dimorphism
	Orma Boran	Tolerance to trypanosomosis
	Turkana	survive on very poor pasture and scarce water, walking ability
Pocket-sized East African Zebu	Angoni	Adjusted to browsing during dry out flavour, variable glaze color and size of horns
	Arsi	Poor milkers, extremely active and often very aggressive
	Jem-Jem	Well adapted to the moisture and cold climate
	Mongolla	Expected tolerance to trypanosomosis, well fleshed
	Nuba Mount Zebu	Dwarf, tolerance to trypanosomosis
	Ogaden	Proficient dairy and beefiness characteristics
	Ugogo Grey	Adapted to browsing during dry season
W African Zebu	Azaouak	Very well adjusted to drought
	Red Fulani	Nervous and intractable temperament, poor milkers
	Sudanese Fulani	Good walking power
	White Fulani	Good dairy and beef characteristics
	Yola	Expected tolerance to trypanosomosis, highly variable conformation
Due east African Sanga	Bahima^*	Susceptible to rinderpest and trypanosomosis
Due east African Sanga	Raya-Azebo	Good draught power
South African Sanga	Afrikaner	Walking and grazing ability, good mothering power, longevity
	Barotse	Docile temperament making it a good work animal
	Landim^*	Well adapted to hot, humid weather as well as dry periods, very resistant to Foot and Oral fissure Disease
	Mashona	Loftier fertility, stiff maternal instinct, docile disposition
	Nguni	Loftier fertility, early sexual maturity, good foraging and walking power, good mothering ability
	Tswana	Tolerance to ticks, resistance to the endemic heartwater
	Tuli	Loftier fertility, good mothering ability, low dogie mortality
Zenga	Alur	Thought to have trypanotolerance
	Arado	Docile, good piece of work animal, low milk yield
	Bovines of Tete	Thought to have trypanotolerance
	Fogera	Docile temperament
	Horro	Calm disposition, variable milk production
Recently derived breeds	Borgou	Sexual dimorphism

Although African indigenous breeds mostly perform poorly compared to commercial cattle breeds, the latter having been continuously selected for specific productivity traits (east.thou. Angus cattle for beef production, Holstein-Friesian cattle for milk), some ethnic African breeds are known to accept both expert dairy and beef characteristics (Collier and Gunning, 1999; Ndumu et al., 2008; Kugonza et al., 2011). For example, the White Fulani cattle (W African Zebu), which inhabit Cameroon in the Central African Republic and Nigeria, testify proficient performance both as a dairy and beef breed (Pullan and Grindle, 1980). Other well-known beefiness-dairy cattle are Ogaden cattle (Small Due east African Zebu) (Rege and Tawah, 1999), Jiddu cattle (Zenga) (Box, 1968), and Fogera cattle (Zenga) (Gebremedhin et al., 2007). While the Kenana and Butana cattle from Sudan are amid the all-time milk producing zebu breeds (Musa et al., 2005).

For commercial cattle breeds artificial selection and direction interventions have resulted in markedly productivity improvements and by extension, economical performance but at the cost of reduced genetic diversity and in some example fertility (Pryce et al., 2004; De Roos et al., 2008). In contrast, almost African cattle breeds have not been selected consistently for productivity gains. Rather the primary selection focus has been on survival, in ofttimes unpredictable, harsh and changing environmental conditions. Although some chemical element of artificial selection pressures take been practical equally illustrated by the high cultural value of some African breeds (e.chiliad. Ankole) (Ndumu et al., 2008; Kugonza et al., 2011).

From an test of microsatellite DNA variation, African cattle breeds are reported to have college genetic diversity than cattle breeds in other regions (MacHugh et al., 1997; Loftus et al., 1999; Ndumu et al., 2008). Linkage disequilibrium (LD), the nonrandom association of alleles at two or more loci (Falconer, 1981), values for African cattle breeds (eastward.g. North'Dama, East African Shorthorn Zebu) tends besides to exist lower compared to other cattle breeds (Goddard and Hayes, 2009; Mbole-Kariuki et al., 2014). Lower LD values in African cattle breeds could bespeak that African cattle have oftentimes larger gene pools equally genetic resource than other cattle breeds, such as Holstein or Angus breeds.

GENOMICS STUDIES OF AFRICAN CATTLE

Until now African indigenous cattle are relatively less intensively studied at the genome level. However, the situation is expected to change rapidly with several ongoing studies. All published African genome broad analyses accept used and so far the Illumina 50K bead single nucleotide polymorphisms (SNPs) chips. Decker et al. (2014) studied on worldwide patterns of ancestry, difference, and admixture in domesticated cattle and African Bos taurus cattle populations. Every bit mentioned in a higher place they identified unique African cattle autosomal groundwork, which may have originated from local auroch introgression. Although, alternative caption are possible (due east.thousand. genetic migrate and/or ascertainment bias of the SNPs bit). Makina et al. (2014) take reported the genome wide genetic diversity of 4 indigenous South African breeds, while the detailed genetic architecture and population construction of an Due east African Shorthorn Zebu cattle population has been reported (Mbole-Kariuki et al., 2014), with Murray et al. (2013) showing show of inbreeding likewise equally outbreeding low in the same population. Due west African cattle take besides been studied (Gautier et al., 2010), including the first evidence of adaptive genetic divergence in African cattle through "genome-broad" SNPs analysis (Gautier et al., 2009).

No African cattle genome of reference have withal been published. However, two European taurine cattle genome of reference are today bachelor but no zebu B. indicus genome. Besides, there are no publically bachelor African taurine genome of reference. Given the mixed breed nature of most African cattle population and the presence of a unique African taurine lineage on the continent, the availability of these reference genomes are important for genomic studies of African cattle.

Genome sequencing of African cattle will permit = the development of African cattle specific genomic tools (east.thou. African cattle high density SNPS chips), which could be used in genome broad selection breeding approaches (genome selection). Such chips could also exist used for the identification of unique African cattle genomic regions and ultimately the causative mutation of major African cattle adaptive traits.

As a result, future African cattle population would exist expected to have loftier 'functional' genetic diversity, while being adapted to their local environments. There accept been many trials to meliorate productivities of African cattle through crossbreeding. Nevertheless, such breeding improvement strategy has faced many challenges including adverse nutritional and climatic conditions (Scholtz and Theunissen, 2010). Moreover, African indigenous cattle are endangered of extinction due to rash crossbreeding with exotic breeds (Rege, 1999). According to Reist-Marti, Simianer (2003), variety of many of African taurine and zebu already reached marginal variety of endangerment, and future multifariousness is expected to be a half of current multifariousness in 20–50 years (Reist-Marti et al., 2003). Thus, deeper genetic studies on African indigenous cattle would be needed to amend cattle breed against hereafter climate changes and preserve current African indigenous cattle equally valuable genetic resources.

Phenotypes are controlled by genes (Crick, 1970), and phenotypic variation among organisms sometimes reveals evolutionary adaptations or artificial pick (Glazier et al., 2002). Cattle phenotypes may be nether the genetic control of a unmarried or a few loci with major result (e.g. coat color ) or multiple loci each explaining a minor proportion of the observed phenotypic variances (e.g. productivity traits such as milk yield and growth rates) (Ashwell et al., 2004; (Goddard and Hayes, 2009). The after are referred every bit quantitative trait loci or QTLs. Many QTLs take been mapped in cattle ((Hu et al., 2013), including disease tolerance in indigenous African cattle (Hanotte et al., 2003), and QTL association analysis is used in modern breeding technology for genetic improvement (Kim et al., 2003; Khatkar, 2004).

Tracing the genes and loci of monogenic traits in African cattle would exist relatively simple (e.thou. Glazier et al., 2002). Withal research on complex traits in African cattle, given their relatively high genetic diversity would exist more than challenging than in inbred cattle that accept depression genetic diversity. In the case of dog species, approximately thirty,000 SNPs are needed for between-breed analyses (Sutter et al., 2004) because dogs are highly inbred animals, and this might exist similar for most commercial livestock (Zajc et al., 1997). In contrast, hundred thousands of SNPs would be needed for complex traits in Bos taurus and Bos indicus subspecies (Goddard and Hayes, 2009). Moreover, data from clan studies with SNPs have articulate limitations for explaining complex traits (Lander and Kruglyak, 1995; Andersson and Georges, 2004; Manolio et al., 2009) even though several phenotypes are determined by but a few genes (Kim et al., 2003; Andersson and Georges, 2004; Schenkel et al., 2006).

The advent of next-generation-sequencing (NGS) applied science (Shendure and Ji, 2008), has fabricated the production of genetic information much easier (Mardis, 2008) and information technology is now possible to apply not only partial genome information just unabridged genomes ones from individuals (Davey et al., 2011).

As already been mentioned, virtually African cattle have a Bos indicus ancestry, and the common ancestor of Bos taurus and Bos indicus dates back to over 330,000 or even 2 meg years ago (Ajmone-Marsan et al., 2010). This could represent a claiming for genomic analyses that utilise the today European taurine cattle genomes of reference. Fortunately, a previous written report using NGS whole genome sequence information showed 92 percent to 99 percent overall alignment rates between Bos indicus and the reference genome for taurine, except for the Y chromosome likely because of its incomplete sequence assembly (Canavez et al., 2012). Thus, major difficulties are not expected when performing resequencing analyses using NGS methods.

Nevertheless, re-sequencing analyses using reference genome of European Bos taurus have clear limitations such equally missing information of unaligned genome regions or inaccurate reflection of structure variations. As an extreme case, single nucleotide substitutions occur at a mean rate of about 1.2% betwixt human and chimpanzee genome (Mikkelsen et al., 2005), but the construction of the genome between homo and chimpanzee differ considerably considering of structural variants including genomic insertion, deletion and even inversions (Newman et al., 2005). These limitations could make exact identification of African cattle genome diversity hard. A complementary method, de-novo genome assembly would therefore assistance overcome limitations in genomic inquiry of African indigenous cattle.

Conclusion

Agro-ecological zones, direct influenced past climate variation are perhaps more diverse on the African continent than on whatsoever other continents. Consequently African indigenous cattle inhabiting these areas are expected to show a mosaic of environmental adaptation cardinal to their survival in local production systems. Identification of these adaptations is not anymore beyond attain thank you to the availability of new genomic tools as well as smarter phenotyping tools and procedures.

The genetic diversity of African indigenous stand for an unique resource and opportunity for tackling the challenges of livestock productivity faced by the African continent, including the increase demand for livestock products and the consequence of climate instability and changes. It is up to us to understand it and to exploit information technology now for the benefit of the African continent and its population.

ACKNOWLEDGMENTS

This work was supported past a grant from the Next-Generation BioGreen 21 Program (Project No. PJ01134905), Rural Development Administration, Democracy of Korea. Nosotros thank Steve Kemp, Tadelle Dessie, Hak-Kyo Lee, Sung-Jong Oh, and Heebal Kim for effective suggestions on the report and for helpful comments on the manuscript.

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