Molecular Markers and Their Potentials in Animal Breeding and Genetics

Nigerian J. Anim. Sci. 2018, 20 (3): 29-48

Molecular markers and their Potentials in Animal Breeding and Genetics

Salisu, I. B1,2*, Olawale, A. S2, Jabbar, B2, Koloko, B. L2, Abdurrahaman, S. L1, Amin, A. B1, and Ali, Q2.

1Department of Animal Science, Faculty of Agriculture, Federal University Dutse, PMB 7156 Dutse, Jigawa State-Nigeria. 2Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan, 87-West Canal Bank Road Lahore-53700, Pakistan.

Corresponding Author: [email protected] *Phone No.: +2347066006080, or +923174632425,

Target Audience: Breeders, Government policy makers, academics

Abstract

Over the centuries, livestock improvements largely depend on the selective breeding of the individual animals with superior phenotype. The advent of DNA markers in recent years allowed for easy selection of a number of valuable traits more directly. Molecular markers have played a significant role in animal breeding and genetics by providing the opportunities in maximizing selection particularly for those traits that have low heritability or traits for which measurement of phenotype is difficult, expensive, or only possible in late life. Different types of molecular markers such as restriction fragment length polymorphisms (RFLPs), microsatellites (SSR), and single nucleotide polymorphisms (SNPs), have been widely used in molecular breeding as they can be amplified easily through polymerase chain reaction (PCR) and could be employed to estimate the genetic diversity within or between the breeding populations. These markers can be used simply as reference points in transgenic breeding to identify the animals with specific transgenes or to select the genes/genomic regions that affect economic traits through marker- assisted selection. Hence, the overall improvement in livestock species is greatly aided through the use of molecular markers.

Keywords: Molecular marker; livestock breeding; MAS; selection; Polymorphisms

Description of Problem 3).However, in this practice, there are so many Animal breeding in its conventional form, obstacles, especially in relation to genotype x largely depend on the phenotypic selection of environment (GE) interactions. Conventional an animal with superior trait within breeding strategies in livestock production segregating populations derived from crosses. consume much of the times and do not Other technologies, such as artificial consider all sources of genetic variability insemination, multiple ovulation, and embryo efficiently. Likewise, in those traits which are transfer that aided reproduction have been sex-limited, lowly heritable or late-expressed employed and there has been a significant traits, the effect of conventional breeding is change in the productivity of animals from the limited and in most cases, the techniques that selective breeding of animals(1, 2 and were employed in the selection of phenotype

Salisu et al are usually expensive. In order to improve the substitution) between different genotypes or animal breeding program, it is therefore alleles of a gene for a particular sequence of important to balance molecular genetic DNA in a given population or gene pool.(3, techniques with conventional animal breeding 14). techniques (4, 5 and 6). Recent advancement in They have characteristic biological the area of molecular biology and molecular attributes that can be determined and measured technology has made it possible to disclose a in various parts of the body such as the blood large number of genetic polymorphisms at the or tissue at any given stage of animal DNA level. As such, scientists and researchers development (15, 16). and they are not utilized them confidently as markers in order influenced by environment, pleiotropic, or any to determine the genetic basis for the observed epistatic effects (17). phenotypic variability (7). The unique genetic For effective utilization in marker assisted attributes as well as methodological merit of breeding an ideal DNA marker according to genetic markers, make them essential and (18) should meet the following criteria amenable, to a larger extent, for scientific depending upon the utilization and species research that is related to genetic when involved: compared to other genetic markers (8-11). In  High level of polymorphism (That is term of the direct application, these DNA concurrent existence of a trait at the markers covered wide range of area some of same population of two or more which include: estimation of genetic distance, discontinues variants or genotypes.) determination of twin zygosity and  Even distribution across the whole freemartinism, parentage determination, gene genome (not clustered in certain mapping, sexing of pre-implantation embryos regions) and disease carrier identification (12).  Co-dominance in expression (Various Molecular markers can be used simply as form of marker must be identified in a reference points in transgenic breeding and to diploid organism so that heterozygotes point out the animals with specific transgenes. can be differentiated from The overall improvement in livestock species homozygotes) is therefore achieved greatly by the application  Clear distinct allelic features (so that of molecular markers (3). the different alleles can be easily identified) Genetic marker  Single copy and no pleiotropic effect Genetic marker is a general term used for  Low cost to use (or cost-efficient any observable or assayable phenotype or the marker development and genotyping) genetic basis for assessing of the detected  Easy assay/detection and automation phenotypic variability. Genetic markers are  High availability (un-restricted use) mainly classified based on physically and suitability to be evaluated traits (morphological and productive duplicated/multiplexed (so that the traits), or based on gene product (biochemical data can be accumulated and shared markers), and finally based on DNA analysis between laboratories) (molecular markers) (13).Molecular marker  Genome-specific in nature (especially also known as DNA marker and is defined as a with polyploids) segment of DNA indicating mutations or  There should be no any detrimental variations, which can be employed to detect effect on phenotype polymorphism (base deletion, insertion and

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Classifications of Molecular Markers cut with restriction enzymes or is PCR Botstein et al (19), were the first to used amplified (14). DNA restriction fragment length polymorphism (RFLP) in human linkage Restriction Fragment Length Polymorphisms mapping, since then significant progress has (RFLPs); been made in the development and Restriction Fragment Length enhancement of molecular techniques that Polymorphisms (RFLPs) was the first form of assist in finding the markers of interest simply DNA marker utilized to construct the first true on a large scale, this has resulted in extensive genomic map (20).This hybridization based and successful utilization of DNA markers in marker technology employed synthetic human genetics, animal genetics and breeding, oligonucleotides as probes, which are labelled plant genetics breeding, as well as germplasm fluorescently to hybridize DNA (13). RFLP characterization and management. New technology was first developed by Botstein powerful and easily available technique are and his co-workers since 1980. This recently introduced to discover more types of technology used the restriction enzymes that DNA markers. Different types of molecular cleave the DNA at distinct site to observe the markers used to identify the DNA differences at the level of DNA structure (21). polymorphism in livestock are commonly Differences are marked by using RFLP when classified into three main groups base on the the length of DNA segments are different, this methods applied for their identification (14). imply that the RE (restriction enzymes) cleave I. Non PCR-based or Hybridization- the DNA at specific locations. The change or based Molecular Markers. The most polymorphism that take place as result of common example of this type of mutation indicate creation or removal of the marker is Restriction Fragment Length RE site and produce new RE site. The Polymorphisms [RFLPs]. variations are determined by using II. PCR-based DNA Markers these hybridization probe. In RFLP analysis, the includes; Random Amplified Length choice of the DNA probe is very crucial. Gel Polymorphic DNAs [RAPDs], Simple electrophoresis is needed for the identification Sequence Repeats or microsatellites of RFLPs to separate the DNA fragments of [SSRs], Amplified Fragment Length various lengths and to transfer the fragments Polymorphisms [AFLPs]. into a nylon membrane in which the III. DNA Chip and Sequencing-based radioactive labelled probe is applied to observe DNA Markers. Single nucleotide the segments of DNA exposed to an X-ray Polymorphisms [SNPs] is an example Film (22).This technique is normally employed of these types of markers. in hybridization definition of nucleic acid, detection and diagnosis, description of I. Hybridization-based Molecular polymorphisms on the gene construction of a Markers genetic linkage map and recombinant DNA In hybridization based molecular marker technology in livestock species (6). technologies, cDNA, cloned DNA elements, or Some of the advantages RPLPs markers synthetic oligonucleotides are used as probes, include; Production of co-dominant markers which are tagged with radioisotope or with which enable the separation of homozygotic conjugated enzymes that catalyze a coloured and heterozygotic conditions in a diploid reaction, to hybridize DNA. The DNA is either organism. Selective neutrality, stability and reproducibility are the other outstanding

Salisu et al qualities of these markers. However, Randomly Amplified Polymorphic DNA Application of RPLPs required higher quality (RAPD): and larger quantities of the starting DNA Random Amplified Polymorphic DNA which is not always available. Additionally, also called arbitrarily primed PCR (AP-PCR), the technique involved, is labor intensive and or as a DNA amplification fingerprinting time consuming. Moreover, RFLPs are limited technique (DAF) and was introduced in 1990. with regard to identification of the whole This technology utilizes an in-vitro genome variation in animals and due low amplification to randomly amplify the variability found in farm animals by unknown loci of nuclear DNA with a matching inbreeding, renders many RFLPs sites un pair of short oligo-primers, (8-10 base pairs) in useful (14). length (25, 26). Multiple primers in the range of (5 to 21) nucleotides are mostly used and II. PCR-based molecular markers has proven to be successful when detection is Following the emergence of AFLP, new combined with polyacrylamide gel advanced technologies which utilizes PCR electrophoresis. The amplified products range also emerged in 1990 (23). from less than 10 to over a 100 depending PCR is a laboratory technique that upon the ratio and primer/template involves the synthesis of nucleic acid simply combination (14).RAPD technology had been by replicating a specific region of the target used to estimates the genetic differences within DNA (24).The technique uses two or between the certain taxa of interest by oligonucleotide primers that flank the desire evaluating the occurrence or lack of each DNA segment which is amplified after a product, which is directed by modification in series of repeated cycles. During the cycling the DNA sequence at each locus. Scientist process, the DNA is denatured by high have also reported the application RAPD temperature and the primers anneals to their markers for stock identification of Nemipterus complementary sequences at a temperature japonicas(27). lower than that of denaturation. A thermophilic The simple procedure of RAPD involves; DNA polymerase is then used to completed  DNA extraction (highly quality DNA) extension of the annealed primers. As the  Addition of single random primer, extension products themselves are also  Amplification by (PCR, complementary to primers, successive cycles  Separation DNA fragments via of amplification basically twofold the target electrophoresis for amount of generated DNA in the preceding  Ethidium bromide staining and cycle and the result is an exponential visualization of RAPD PCR fragments accumulation of a particular target fragment. under UV light Genomic DNA from two distinct  Determination of different fragment individual frequently produces different size by comparing with known amplification and a specific fragment produced molecular marker using gel analysis from one individual but not for other represent software. DNA polymorphism and can be employed as As compared to RFLP, RAPD technique genetic markers. The obtained pattern of offers a quick, simple, cheap but an efficient replicated bands could be used for genomic technique of producing molecular information. fingerprint (25). Being highly polymorphic, only very small quantity of DNA is needed to be amplified by PCR technique in the absence of DNA

Salisu et al sequence information. This is the major reason  Adapters ligation (enzyme adapters), why RAPD technique has been used  Pre-PCR amplification of the digested successfully in various phylogenetic and fragments; pre-selective amplification taxonomic researches (14). using EcoRI primer + A and MseI primer However, one major disadvantage of + C RAPD technique is that the RAPD primers are  Selective PCR by labeled pair of primer very sensitive to PCR conditions and this may (primer + three base pairs; for used lead to poor reproducibility with respect to labeled, reverse unlabeled) other methods. Additionally, the result of  Analysis of fragment using automated amplification profile by each primer frequently sequencing machine following gel covers numerous different loci within the electrophoresis. A programs such as Gene genome, which essentially is unable to Mapper (AFLP,2005) can be used for the distinguish between heterozygous and analysis of the electrophoretograms (11). homozygous individuals (28). AFLP technique offer an effective, fast and cost-effective means for detecting a large Amplified Fragment Length Polymorphism number of polymorphic genetic markers which (AFLP); are very consistent and reproducible, and are AFLP method is a simple and capable of being genotyped automatically. inexpensive finger printing technique which The technique is considered as the most provide more valuable information by effective method for molecular producing multi-locus and consistent genomic epidemiological studies of pathogenic fingerprints (29). the basic idea behind AFLP microorganisms and it is also used extensively polymorphism was the insertion and deletion in forensic science. or substitution of nucleotides between and at The AFLP technology has been widely restriction sites. The base substitutions are utilized in identification of genetic normally done at primer binding sites during polymorphisms, evaluating and characterizing PCR as in the case of RAPD. This technique is breed resources, measuring the correlation distinctive, as it enables the binding of among breeds, constructing genetic maps and adaptors of known sequences to DNA identifying genes in the main species farm segments that are produced through the animals (30-35). Apart from microsatellites, complete digestion of genomic DNA. This AFLP technology remained the best molecular ensure easy separation of the generated DNA system for population genetics and genome fragments following amplification the subset typing (14). Despites the outstanding features of entire fragments. Though, the main goal of of AFLP, yet the technique has some AFLP is the same as that of RFLP that is limitations some of which include; demanding polymorphism, however as an alternative of more DNA (300-1000ng per reaction) and method of analyzing one locus at a time, it is technically more difficult as compared to permits concurrent study of many loci (30, 31). RAPD. however, the recent availability of kits and automation will possibly bring the The major steps involve in AFLP techniques technique into a higher level of applicability are; (36).  Extraction of highly quality DNA, Microsatellite marker/ single sequence repeat  Digestion of DNA using restriction (SSR) enzymes (enzyme mixture, commonly Microsatellites are polymorphic loci Eco RI + MseI), present in DNA and contain 1-6-nucleotide

Salisu et al repeats which are arranged head to tail without application of MALDITOF (Matrix Assisted interruption by any other base or motif and are Laser Desorption Ionisation Time of Flight) dispersed throughout the genome (37). or they mass spectrometry, as a swift and promising are DNA segments characterized by a different way of differentiating polymorphic DNA number of copies (usually 5-50) of sequence fragments (44). Their co-dominant nature motifs of around two to five (2-5) bases coupled with high mutation rate make them the (known as repeat unit) (38). They are highly most precious marker in the estimation of polymorphic and plentiful, usually found in genetic diversity within and between breed non-coding regions of genes (39-41). The most (45). common dinucleotide motif in mammals is Recently microsatellites markers are the (CA)n, where n is the number of repeats (42). most valuable genetic markers in livestock In avian species, the frequency of (CA) ≥10 is genetic characterization studies (46, 47). These evaluated at once every 140 to 180 kb, and that markers offers a series of benefits over other of (CA) ≥14 is one every 350 to 450 kb(43). types of markers, specifically, that multiple Microsatellites loci are also termed as short SSR alleles can be identified at a single locus tandem repeats (STR's), simple sequence by utilizing simple PCR based screen, very repeats (SSR's) and simple sequence tandem less amounts of DNA are essential for repeats (SSTR). Scientists have also suggested screening, and analysis is amenable to the terms minisatellites and macro satellites to automated allele identification and sizing (48). define the regions with increasing larger repeat Greater understanding of genomes and units and overall lengths. The microsatellites genomics has been achieved through the and minisatellites altogether make up the studies of the potential biological function and variable number of tandem repeats (VNTRs). evolutionary relevance of microsatellites (49). The lengths of a specific microsatellite Microsatellites markers were mainly sequences tend to be highly variable among considered to be evolutionally neutral (39). individuals. These variations make up the More recent data assumes that they molecular alleles (14). Microsatellite-derived microsatellites can possibly play a significant markers exhibit a powerful way of mapping role in genome evolution (41) and provide genes controlling more valuable traits. As soon points of recombination. They are presumed to as the simple repeat region is identified, by take part in gene expression, regulation and sequencing its immediate flanking regions, function (50, 51) and have been found to specific primers can be designed for PCR and hybridize nuclear proteins and function as for genotyping. Normally, the size of a transcriptional activating elements (52), microsatellite PCR product is obtained by scilicet they suggested to have an important electrophoresis in a denaturing polyacrylamide functional role. The option of microsatellites gel. One of the two primers employed in the marker in livestock improvement than RFLP PCR is often labelled with a fluorescent or marker, is due the large variety of its radioactive tag. This technique of detection molecular applications which includes, genetic usually works better but suffers from an characterization studies, analysis of population inherent weakness in determining the size of structure (53), estimation of genetic variability DNA accurately. More recently, there is an and inbreeding (54),determination of paternity alternative to the gel-based approach to (55), phylogenetic relationships among determine the size of DNA products; there are populations (56), disease diagnostics, forensic a series of technological advancement based analysis, development of genetic map on mass spectrometry. One new trend is the (quantitative trait loci) and Marker assisted

Salisu et al breeding among others (9, 27, 57-59). for the genetic and genomic analysis of farm However, one of the major drawback of this animals (63). technique is that it is very expensive and time- There are four major reasons for the consuming. Moreover, Heterozygotes can increasing interest in the utilization of SNPs as mistakenly be classifying as homozygote when markers for genetic analysis. Initially, they are there is occurrence of null-alleles as result of widespread and provide more potential mutations in the primer annealing sites. The markers near or in any locus of interest than accurate scoring of polymorphisms can also be other types of polymorphism such as complicated due to shutter bands. microsatellites. For instance, in human microsatellite markers are helpful in genomic DNA there appears to be an SNP identifying neutral biodiversity however, they approximately every 1000 bases (64). cannot tell about the information concerning Secondly, some SNPs are located within the the functional traits biodiversity (14). coding regions and directly influence the protein function. These SNPs may be directly III. DNA chip and sequencing-based responsible for some of the differences among molecular Markers the individuals in economical traits. Thirdly, Single nucleotide polymorphisms (SNPs SNPs are inherited more stable than Single nucleotide polymorphism is a microsatellites, this attributes make them more variation in DNA sequence which occur due to promising as long-term selection markers. a substitution in the nucleotide at a particular Lastly, SNPs are more reliable than location in the genome. (38) In other words, microsatellites for high throughput genetic SNP marker is just a one base replacement in a analysis, using DNA microarray technology sequence of DNA (6). SNPs comprise more (65). However, SNPs are generally biallelic than 90% of all variances between the systems, meaning that there are usually only individuals; thus, they are the excellent genetic two alleles in a population. As a result, the variation resource for population studies and information content per SNP marker is less genome mapping (60). Genomic selection by than multiallelic microsatellite markers. means of the SNP markers is a powerful novel SNPs can be detected by a series of tool for genetic selection (61). These type of techniques. The common gel-based approach marker are becoming highly attractive in employs the standard molecular techniques, i.e molecular marker development due to their sequencing, PCR, restriction digests and abundance in the genome of any organism different forms of gel electrophoresis, such as (coding and non-coding regions), and ability to denaturing gradient gel electrophoresis identifying hidden polymorphism which is not (DGGE), single-strand conformation commonly recognized by other genetic polymorphism (SSCP) and cleavage fragment markers and techniques (62). Currently, there length polymorphism (CFLP) (66-69),also have been a series of progress in complete introduced a well-designed method, cleaved genome sequencing, in the development of amplified polymorphic sequence (CAPS) that next generation sequencing technologies and utilized mismatch PCR primers to produce high throughput genotyping new restriction site on one of the alleles. Other platform. Improvement in these technologies technique includes the PCR-based TaqMan has resulted in the development of the high- assay (64), the high-performance liquid density single nucleotide polymorphism (HD- chromatography-based WAVE DNA fragment SNP) arrays as an up-to-the-minute implement analysis system(70), and MALDI-TOF mass spectrometry, including the utilization of

Salisu et al peptide nucleic acid probes (71). One mass Even though, such chips can give the desire spectrometry approach employs a distinct genotypes that improve the precision of primer to extend into the SNP site using di- genomic evaluation by better tracking of the deoxynucleotides. The SNP is defined by the loci responsible for genetic variation (75). SNP particular di-deoxynucleotide incorporated chips are recently available for human, ovine, (72). All these methods require previous bovine, canine, porcine and equine species knowledge of the sequence of the polymorphic (76). However, for the application of DNA site. chips technology into large scale genotyping of One way to detect polymorphisms with a animal, there are series of major technical less mismatches of nucleotide, is the random problems that need to be taken into account amplified polymorphic DNA (RAPD) assay (77). These include the presence of secondary (73). This assay uses short oligonucleotide structures in the target and the difficulty that is primers of arbitrary sequence to amplify associated with optimizing hybridization distinct regions of the genome. Typically, only conditions over the complete array as result of one 10-mer oligonucleotide of a particular differences in annealing temperature among arbitrary sequence is used in each PCR. RAPD oligonucleotides. The preparation of labelled polymorphisms are detected after gel genomic DNA segment with adequately high electrophoresis as the presence or absence of specific activity for hybridization to particular fragments between the individual immobilized oligonucleotides can also be animals. The disappearance of a particular problematic, especially if a high number of fragment is the result of sequence differences loci are to be screened altogether. The major in one or both of the priming sites which keeps challenge, however, is to find out valuable oligonucleotide from annealing and subsequent SNPs that can estimate the breeding value of polymerization. A typical arbitrary an animal. Recently, the association of ten oligonucleotide will produce up to a twelve or pharmaceutical companies and The Welcome more discrete DNA bands. Trust have announced an initiative to produce The utilization of DNA microarray or a human SNP map. While detecting the ‘DNA-on-Chip’ technology to detect SNPs is a presence of a known SNP is relatively simple, potentially strong tool for high throughput the major antagonist in this desirous attempt DNA screening (64). Through this technique, must hence be the identification of new SNPs sequences up to 40000 can be screened on a at regular intervals throughout the human single slide at one time. Study have also shown genome (78). It is therefore improbable that that, 2.3 Mb of genomic DNA scanned were SNP mapping in farm animals will ever be successfully identified up to 3241 candidate carried out on this scale in the anticipated SNPs, using more than 100 tiling future. Nonetheless, DNA microarrays and microarrays.(65). In July 2010, Illumina SNP development are extremely applicable for released two new genotyping SNP chips future selection of livestock. In similar manner including a low-density chip (Bovine3K) that microsatellites have substituted RFLPs, having 2,900 SNP (74) and a larger density SNPs are anticipated to replace microsatellites chip (BovineHD) having up to 777,962 SNP as the technique of choice for detection of and in January 2011, another a high density DNA polymorphisms. chip with 648,855 SNP was released (74).

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Figure 1. Summary of the various molecular markers technologies

Salisu et al Table 1.0 Common type of molecular markers and their important features FEATURES RFLP RAPD AFLP SSR SNP DNA Require (μg) 10 0.02 0.5-1.0 0.05 0.05 PCR based No Yes Yes Yes Yes Number of Polymorph loci 1-3 1.5-50 20-100 1-3 1 analysed Type of polymorphism Single base Single base Single base Change in Single change, change, change, repeat nucleotide insertion, insertion, insertion, length change, deletion deletion deletion insertion, deletion Dominance Co-dominant Dominant Dominant/C Co- Co-dominant o-dominant dominant Reproducibility High Unreliable High High High Ease of use Not easy Easy Easy Easy Easy Automation Low Moderate Moderate High High Cost per analysis High Low Moderate Low Low Developmental cost High Low Moderate High High Need for sequence data Yes No No yes Yes Accuracy Very High Very Low Medium High Very High Radioactive detection Usually yes No No No Yes Genomic abundance High Very High Very High Medium Medium Part of genome surveyed Low copy Whole Whole Whole Whole coding genome genome genome genome regions Level of polymorphism 1 Low Low to Low to High High moderate moderate Effective multiplex ratio 2 Low Medium High Medium Medium Marker index 3 Low Medium High Medium Medium Inheritance Co-dominant Dominant Dominant Co- Co- Dominant Dominant Detection of alleles Yes No No Yes Yes Utility for genetic mapping Species Cross Cross Species Species specific specific specific specific specific Utility in Marker assisted Moderate Low to Low to High Low to selection Moderate moderate moderate Cost and labour involved in High Low to Low to High High generation Moderate moderate 1Level of polymorphism (average heterozygosity) is an average of the probability that two alleles taken at random can be distinguished; 2Effective multiplex ratios is the number of polymorphic loci analysed per experiment in the germplasm tested; 3Marker index is the product of the average expected heterozygosity and the effective multiplex ratio. Adapted from: (1, 23, 79-82).

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Potentials applications of Molecular between populations and make it possible to Markers in Live Stock Improvement genetically examine differences and determine Through conventional breeding special genomic attributes of indigenous techniques, molecular markers can play a very livestock populations (88-90). significant role for the improvement of livestock. These roles could be categorized as Parentage determination immediate (short range) or long term The knowledge on mating system of applications. (10). species is important for successful breeding management because breeding value is usually Immediate applications: estimated from off-springs and relatives. To Molecular markers have various determine genetic relatedness among immediate applications some of which individuals and assess kinship molecular includes: Estimation of genetic distance, marker are used as tools for investigating parentage determination, determination of twin issues such as identifying the paternity of zygosity and freemartinism, sexing of pre- animals generated through multiple-sire implantation embryos, disease carrier pasture mating. five microsatellite loci were identification, and gene mapping as well as used to verify the genetic information of marker-assisted selection (12). The short range parentage in an ex situ population of marabou applications of molecular markers were briefly storks and interpret behavior during the descried in the following sub-suctions below: breeding season using genetic pedigree (91). Scientist have proven the feasibility of using These short range application can be parentage tests to correctly identify animals describing briefly in the following sub-suctions generated by multiple sire mating (92, 93). below: Sexing of pre-implantation embryos Estimation of genetic Diversity: Determination of the sex of the pre- Diversity among organisms is as a result implanted embryos is important for the of variations in DNA sequences and management and breeding of livestock as well environmental effects. Genetic distance a as for the prenatal diagnosis of livestock measure of overall evolutionary divergence disorders. The genetic sex of an individual between species, breeds, strains. Among depends on whether the X-bearing ovum is various markers, microsatellites are the most fertilized by a Y or X- bearing spermatozoa. popular markers in livestock genetic Among several established protocols for characterization studies (47). Due to their high sexing farm animals, Molecular markers are mutation rate and codominant nature that allow used to determine sex of pre-implantation the estimation of within and between breed embryos, based on the identification of the Y genetic diversity. The relationships between chromosome, such as SRY, ZFY and TSPY populations and individuals are estimated genes. Study have showed that TSPY was a through the genetic distances (83-87). Genetic good male-specific marker, the usefulness of distance is measure based on polymorphic which was enhanced by the high copy number characters at the different levels of the gene (94). Scientist have reported the (morphological, biochemical, cellular and simultaneous amplification of sequences DNA level). Currently single nucleotide corresponding to both X- and Y- amylogenic polymorphism (SNPs) is used to determine the gene to establish a reliable, reproducible and genetic variation and relationships within and efficient PCR-based goat sexing system (95).

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Disease carrier identification improvements includes; Quantitative trait loci Genetic diseases resulted from vertical (QTL) mapping through linkage. Such transmission of defective genes to the mapping information if obtain, especially for offspring, when this allele is recessive, those loci that influence the trait performance heterozygotic (carrier) animals have a normal or vulnerability/tolerant to disease, can be phenotype but can pass the genetic defect to employed in breeding programmes either by their off-springs, the defective allele carries a manipulations within the breed E.g. Marker mutation that results in the synthesis of a non- assisted selection of young sires, or between functional protein variant, leading to the breed introgression programmes (99). developmental or metabolic disorders which can lead to significant losses in agricultural Gene mapping yield during animal husbandry. Several The three major applications of molecular molecular markers have been used for early markers have been identified in relation to identification and linked to various disease in gene mapping. Firstly, molecular marker livestock due to DNA polymorphism that allows for direct identification of a desire gene occurs within a gene. It aids the understanding instead of gene product and the identified gene of the molecular mechanism and genetic can be efficiently used as a tool for somatic control of several genetic and metabolic cell hybrid screening. Secondly, through the disorders (96-98). Likewise, allow the use of different DNA probes and easy-to- identification of heterozygous carrier animals screen techniques, a molecular marker can be which are otherwise phenotypically helpful in physical mapping of genes utilizing indistinguishable from normal individual. an in situ hybridization. Finally, molecular Studies on ARMS PCR-based assay for markers offer a sufficient markers system for detection of a novel single-nucleotide construction of genetic map by applying polymorphism in the 5' untranslated region of linkage analysis (100). Markers such as the bovine ITGB6 receptor gene associated RFLPs, which present the evolutionary with foot-and-mouth disease susceptibility conserved cording subsequences are very concluded that SNP G29A mutation in the 5 essentials in comparative mapping methods UTR of the ITGB6 gene (chromosome 2) where polymorphism is not necessary. But associated with resistance to FMD infection in these are usually one locus and di-allelic and the zebu cattle (96). Studies on susceptibility are therefore not essential for linkage analysis. to Para tuberculosis infection demonstrated Conversely, markers such as microsatellite that the TLR2-1903 T/C SNP was significantly which exhibits higher polymorphism associated with resistance to MAP in Holstein- information content than ordinary RFLPs and Friesian cows (97).A correlation study of can be generated more quickly and easily. As CARD15 gene style polymorphism and such, more efforts were put generate gene susceptibility of tuberculosis detected G1596A maps on the basis of such type of markers. polymorphism in the TLR1 gene and found it Additional application of molecular markers to be associated with BTB infection status in obtained via DNA sequences data namely Chinese Holstein cattle (98). ASO (Allele specific oligonucleotide) and STMS (Sequence tagged microsatellite Long term application of molecular site) polymorphic markers are similarly markers; useful in rapid development of gene The most common long term application mapping (99). of molecular markers in livestock

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Marker assisted selection (MAS) half-sib families, significant QTL for birth The recent advancement of molecular weight were identified in the centromeric techniques has opened up the introduction of region on specific bovine chromosome (102, genes to animal breeding which were not 103). Marker-assisted selection based on a available before through conventional multi-trait economic index in chicken was also breeding, creating a lot of interest about MAS reported by (104). Studies on genetic (Marker assisted selection). The recent relationships between economic traits and application of molecular genetic technologies genetic markers were conducted in 147 goats increasingly presents the way to choose the demonstrated superior RAPD markers of body breeding animals at an early stage (even weight and Cashmere yield and superior one of embryo); to select for a superior variety of body weight and Cashmere fineness (105). traits (99). Marker assisted selection (MAS) is a novel technique that complement traditional Conclusions and applications breeding methods in which the relative 1. Molecular markers have breeding value of a parent is predicted using revolutionized the agricultural science genotypes of markers associated with the trait including animal breeding and for rapid genetic gains towards achieving long genetics specifically. term animal improvement. It depends on 2. Genetic polymorphism of DNA has identifying association between genetic marker led to the discovery of various marker and linked Quantitative traits loci (QTL) based techniques with a number of on the distance between marker and target applications in the applied livestock traits. Selection for recessive genes and breeding research. However, mutants is faster because an individual’s utilization of these markers for phenotype can be predicted at a very early livestock genetic research largely stage. Sex-limited traits (milk yield, egg relies on the optimal selection of a production), low heritability traits, traits suitable marker technique for a lacking selection response and genetic gain in specified application. conventional selection are easily predicted 3. Molecular markers when compared with Marker assisted selection (MAS). High with the conventional animal breeding linkage disequilibrium, a large population a techniques, provide more accurate large number of markers per chromosome, genetic information and better genomes containing a large number of knowledge of the animal genetic chromosomes high heterozygote frequencies at resources. the relevant genes and markers and markers 4. These markers hold great potentials that are located close to quantitative trait loci for the Nigerian livestock breeding (QTLs) with large effects are expected have programmes. However, various higher response to MAS. QTL involved in bottlenecks such as poor infrastructure, behavior of diary and udder conformation was inadequate capacity and operational identifies on chromosome 6 that could form support, lack of an enabling policy, the the basis of QTL for clinical mastitis (101). statutory and regulatory framework at Body conformation traits such as stature and the country level, which in turn affects body depth affect feed intake and thus milk research institutions could be the production, while udder traits correlate with major reasons that will impede the the incidence of clinical mastitis and the length proper adoption of these techniques. of productive life. By hybridization between

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5. In the near future, it is anticipated that challenges. Online Journal of Animal the development of molecular marker Feed Research, 3(3): p. 149-152. will enormously continue in the 9. Teneva, A., K. Dimitrov, C.V. Petrović, developing countries like Nigeria, so M. Petrović, I. Dimitrova, N. as to serve as an underlying tool for Tyufekchiev, and N. Petrov (2013). geneticists and breeders that will be Molecular genetics and SSR markers as a useful in the production of animals new practice in farm animal genomic with desirable traits for human use. analysis for breeding and control of disease disorders. Biotechnology in References Animal Husbandry, 29(3): p. 405-429. 1. Kumar, P., V. Gupta, A. Misra, D. Modi, 10. Alemayehu, K. and A. Getu (2015). and B. Pandey (2009). Potential of Review on the Role of Molecular molecular markers in plant Genetics in Animal Performance biotechnology. Plant Omics, 2(4): p. 141. Improvement. International Journal of 2. Umesh, S., K. Arun, and A. Khanna Genetics, 5(2): p. 30-38. (2010). Non-genetic factors affecting age 11. Gamaniel, I. and D. Gwaza (2017). at first calving and first lactation traits in Molecular Characterization of Animal Hariana cows. Indian Veterinary Journal, Genetics Resources, its Potential for use 87(1): p. 91-93. in Developing Countries. Journal of 3. Singh, U., R. Deb, R.R. Alyethodi, R. Genetics and Genetic Engineering , 1( 1): Alex, S. Kumar, S. Chakraborty, A. P. 43-57. Sharma (2014). Molecular markers and 12. Deb, R., U. Singh, and S.K. andArjava their applications in cattle genetic Sharma (2012). Molecular marker research: A review. Biomarkers and assisted selection for disease resistance Genomic medicine, 6(2): p. 49-58. breeds of cattle. Agricultural Research 4. Barillet, F. (2007). Genetic improvement Updates,: p. 153. for dairy production in sheep and goats. 13. Teneva, A. and M. Petrović (2010). Small Ruminant Research, 70(1): p. 60- Application of molecular markers in 75. livestock improvement. Biotechnology in 5. Mirkena, T., G. Duguma, A. Haile, M. Animal Husbandry, 26(3-4): p. 135-154. Tibbo, A. Okeyo, M. Wurzinger, and J. 14. Yadav, A.K., S. Tomar, A.K. Jha, and J. Sölkner, (2010). Genetics of adaptation in Singh (2017). Importance of Molecular domestic farm animals: A review. Markers in Livestock Improvement: A Livestock Science, 132(1): p. 1-12. Review. International Journal of 6. Beuzen, N., M. Stear, and K. Chang Agriculture Innovations and Research, 5( (2000). Molecular markers and their use 4): P. 614-621. in animal breeding. The Veterinary 15. Haley, C. and D. De Koning Journal, 160(1): p. 42-52. (2006).Genetical genomics in livestock: 7. Yadav, B. and A. Mitra (1999). One day potentials and pitfalls. Animal Genetics, symposium on emerging DNA 37(s1): p. 10-12. Technologies for the Next Millennium. 16. Deb, R., S. Chakraborty, and U. Singh CCMB/CDFD, Hyderabad, 23: p. 9. (2012).Molecular markers and their 8. Ebegbulem, V. and P. Ozung (2013). application in livestock genomic research. Application of molecular markers in farm Journal of Veterinary animal improvement: Prospects and Science and Technology, 3(2): p. 7579.

Salisu et al

17. Agarwal, M., N. Shrivastava, and H. Padh 25. Welsh, J. and M. McClelland (1990). (2008).Advances in molecular marker Fingerprinting genomes using PCR with techniques and their applications in plant arbitrary primers. Nucleic acids research, sciences. Plant cell reports, 27(4): p. 617- 18(24): p. 7213-7218. 631. 26. Williams, J.G., A.R. Kubelik, K.J. Livak, 18. Jonah, P., L. Bello, O. Lucky, A. Midau, J.A. Rafalski, and S.V. Tingey (1990). and S. Moruppa (2011).The importance DNA polymorphisms amplified by of molecular markers in plant breeding arbitrary primers are useful as genetic programmes. Global Journal of Science markers. Nucleic acids research, 18(22): Frontier Research, 11(5): p. 4-12. p. 6531-6535. 19. Botstein, D., R.L. White, M. Skolnick, 27. Mudasir, H., M. Sawant, R. Pawar, A. and R.W. Davis (1980).Construction of a Pawsae, and F. Bhat (2016). Stock genetic linkage map in man using identification of Nemipterus japonicus restriction fragment length along west coast of India using RAPD polymorphisms. American journal of markers. Skuast Journal of Research, human genetics, 32(3): p. 314. 18(2): p. 130-137. 20. Williams, J (2005).The use of marker- 28. Bardakci, F (2001). Random amplified assisted selection in animal breeding and polymorphic DNA (RAPD) markers. biotechnology. Revue Scientifique et Turkish Journal of Biology, 25(2): p. 185- Technique-Office International des 196. Epizooties, 24(1): p. 379. 29. Vos, P., R. Hogers, M. Bleeker, M. 21. Mburu, D. and O. Hanotte (2005). A Reijans, T.v.d. Lee, M. Hornes, M. practical approach to microsatellite Kuiper (1995). AFLP: a new technique genotyping with special reference to for DNA fingerprinting. Nucleic acids livestock population genetics. A manual research, 23(21): p. 4407-4414. prepared for the IAEA/ILRI training 30. Jun, R., H. Lu-Sheng, G. Evens, A. Hua- course on molecular characterisation of Shui, G. Jun, C. Ke-Fei, and D. Neng- small ruminant genetic resources of Asia Shui (2004). AFLP markers for genomic 22. Ngo, T.T. and D. Narinesingh (2007). DNA fingerprinting in pigs. Chinese Kosmotropes enhance the yield of Journal of Agricultural Biotechnology, antibody purified by affinity 1(1): p. 9-12. chromatography using immobilized 31. Negrini, R., I. Nijman, E. Milanesi, K. bacterial immunoglobulin binding Moazami‐ Goudarzi, J. Williams, G. proteins. Journal of Immunoassay and Erhardt, D. Bradley, (2007). Immunochemistry, 29(1): p. 105-115. Differentiation of European cattle by 23. Farooq, S. and F. Azam (2002). AFLP fingerprinting. Animal Genetics, Molecular markers in plant breeding-II. 38(1): p. 60-66. Some pre-requisites for use. Pakistan 32. Ajmone‐ Marsan, P., R. Negrini, E. journal of biological Sciences, 5(10): p. Milanesi, R. Bozzi, I. Nijman, J. Buntjer, 1141-1147. J. Lenstra (2002). Genetic distances 24. Mullis, K.B. and F.A. Faloona (1989). within and across cattle breeds as Specific synthesis of DNA in vitro via a indicated by biallelic AFLP markers. polymerase-catalyzed chain reaction, in Animal Genetics, 33(4): p. 280-286. Recombinant DNA Methodology. 33. Negrini, R., E. Milanesi, R. Bozzi, M. Elsevier. p. 189-204. Pellecchia, and P. Ajmone‐ Marsan

Salisu et al

(2006). Tuscany autochthonous cattle microsatellite linkage map of the porcine breeds: an original genetic resource genome. Genetics, 136(1): p. 231-245. investigated by AFLP markers. Journal of 43. Primmer, C.R., T. Raudsepp, B.P. Animal Breeding and Genetics, 123(1): p. Chowdhary, A.P. Møller, and H. Ellegren 10-16. (1997). Low frequency of microsatellites 34. De Marchi, M., C. Dalvit, C. Targhetta, in the avian genome. Genome Research, and M. Cassandro (2006). Assessing 7(5): p. 471-482. genetic diversity in indigenous Veneto 44. Braun, A., D.P. Little, D. Reuter, B. chicken breeds using AFLP markers. Müller-Mysok, and H. Köster (1997). Animal genetics, 37(2): p. 101-105. Improved analysis of microsatellites 35. Buntjer, J., M. Otsen, I. Nijman, M. using mass spectrometry. Genomics, Kuiper, and J. Lenstra (2002). Phylogeny 46(1): p. 18-23. of bovine species based on AFLP 45. McCouch, S.R., X. Chen, O. Panaud, S. fingerprinting. Heredity, 88(1): p. 46. Temnykh, Y. Xu, Y.G. Cho, M. Blair 36. Karp, A.(1997). Molecular tools in plant (1997). Microsatellite marker genetic resources conservation: a guide to development, mapping and applications the technologies. Bioversity International. in rice genetics and breeding. Plant 37. Bidichandani, S.I., T. Ashizawa, and P.I. molecular biology, 35(1-2): p. 89-99. Patel (1998). The GAA triplet-repeat 46. Civanova, K., L. Putnova, and J. Dvorak expansion in Friedreich ataxia interferes (2006). Analysis of microsatellite set for with transcription and may be associated biodiversity studies in horses. Acta with an unusual DNA structure. The fytotechnica et zootechnica : p. 39-40. American Journal of Human Genetics, 47. Sunnucks, P. (2000). Efficient genetic 62(1): p. 111-121. markers for population biology. Trends in 38. Scherf, B.D. and D. Pilling (2015). The ecology & evolution, 15(5): p. 199-203. Second Report on the State of the World's 48. Schlötterer, C. (2000). Evolutionary Animal Genetic Resources for Food and dynamics of microsatellite DNA. Agriculture. Chromosoma, 109(6): p. 365-371. 39. Awadalla, P. and K. Ritland (1997). 49. Subramanian, S., R.K. Mishra, and L. Microsatellite variation and evolution in Singh (2003). Genome-wide analysis of the Mimulus guttatus species complex microsatellite repeats in humans: their with contrasting mating systems. abundance and density in specific Molecular Biology and Evolution, 14(10): genomic regions. Genome biology, 4(2): p. 1023-1034. p. R13. 40. Duran, C., N. Appleby, D. Edwards, and 50. Gupta, M., Y.-S. Chyi, J. Romero- J. Batley (2009). Molecular genetic Severson, and J. Owen (1994). markers: discovery, applications, data Amplification of DNA markers from storage and visualisation. Current evolutionarily diverse genomes using Bioinformatics, 4(1): p. 16-27. single primers of simple-sequence 41. Moxon, E.R. and C. Wills, DNA repeats. Theoretical and applied genetics, microsatellites: agents of evolution? 89(7-8): p. 998-1006. Scientific American, 1999. 280(1): p. 94- 51. Kashi, Y., D. King, and M. Soller (1997). 99. Simple sequence repeats as a source of 42. Rohrer, G.A., L.J. Alexander, J.W. Keele, quantitative genetic variation. Trends in T.P. Smith, and C.W. Beattie (1994). A genetics, 13(2): p. 74-78.

Salisu et al

52. Li, Y.C., A.B. Korol, T. Fahima, A. journal of tropical medicine and hygiene, Beiles, and E. Nevo (2002). 76(5): p. 888-895. Microsatellites: genomic distribution, 60. Frohlich, T., T. Kirschbaum, U. Thoenes, putative functions and mutational F. Furrer, U. Dietrich-Veenstra, and M. mechanisms: a review. Molecular Seller (2004). The LightTyper ecology, 11(12): p. 2453-2465. Instrument: High-Throughput Genotyping 53. Arora, R. and S. Bhatia (2004). Genetic of Single Nucleotide Polymorphisms. structure of Muzzafarnagri sheep based Biochemica-Mannheim-, (2): p. 9-11. on microsatellite analysis. Small ruminant 61. Seidel, G. (2009). Brief introduction to research, 54(3): p. 227-230. whole-genome selection in cattle using 54. Mateus, J., M. Penedo, V. Alves, M. single nucleotide polymorphisms. Ramos, and T. Rangel Figueiredo (2004). Reproduction, Fertility and Development, Genetic diversity and differentiation in 22(1): p. 138-144. Portuguese cattle breeds using 62. Rasal, K.D., V. Chakrapani, A.K. Pandey, microsatellites. Animal Genetics, 35(2): p. A.R. Rasal, J.K. Sundaray, A. Ninawe, 106-113. and P. Jayasankar (2017). Status and 55. Luikart, G., M.P. Biju Duval, O. Ertugrul, future perspectives of single nucleotide Y. Zagdsuren, C. Maudet, and P. Taberlet polymorphisms (SNPs) markers in (1999). Power of 22 microsatellite farmed fishes: Way ahead using next markers in fluorescent multiplexes for generation sequencing. Gene Reports, 6: parentage testing in goats (Capra hircus). p. 81-86. Animal Genetics, 30(6): p. 431-438. 63. Fan, B., Z.-Q. Du, D.M. Gorbach, and 56. Saitou, N. and M. Nei (1987). The M.F. Rothschild (2010). Development neighbor-joining method: a new method and application of high-density SNP for reconstructing phylogenetic trees. arrays in genomic studies of domestic Molecular biology and evolution, 4(4): p. animals. Asian-Australasian Journal of 406-425. Animal Sciences, 23(7): p. 833-847. 57. Ritz, L., M.L. Glowatzki Mullis, D. 64. Landegren, U., M. Nilsson, and P.-Y. MacHugh, and C. Gaillard (2000). Kwok (1998). Reading bits of genetic Phylogenetic analysis of the tribe Bovini information: methods for single- using microsatellites. Animal genetics, nucleotide polymorphism analysis. 31(3): p. 178-185. Genome research, 8(8): p. 769-776. 58. Thomas, N. and K. Anilkumar (2008). 65. Lipshutz, R.J., S.P. Fodor, T.R. Gingeras, Genetic characteristics of five and D.J. Lockhart (1999). High density microsatellite markers associated with synthetic oligonucleotide arrays. Nature milk production traits in crossbred dairy genetics, 21(1s): p. 20. cattle of kerala. Vet World, 1: p. 245-247. 66. Parsons, B.L. and R.H. Heflich (1997). 59. Montoya, L., M. Gallego, B. Gavignet, R. Genotypic selection methods for the Piarroux, J.-A. Rioux, M. Portus, and R. direct analysis of point mutations. Fisa (2007). Application of microsatellite Mutation Research/Reviews in Mutation genotyping to the study of a restricted Research, 387(2): p. 97-121. Leishmania infantum focus: different 67. Kwok, P.-Y. and X. Chen (1998). genotype compositions in isolates from Detection of single nucleotide variations, dogs and sand flies. The American in Genetic engineering. Springer. p. 125- 134.

Salisu et al

68. Nataraj, A.J., I. Olivos Glander, N. 76. Ajmone-Marsan, P (2011). Use of Kusukawa, and W.E. Highsmith (1999). molecular information for the Single‐ strand conformation characterization and conservation of farm polymorphism and heteroduplex analysis animal genetic resources: results of large for gel‐ based mutation detection. scale international projects and Electrophoresis, An International Journal perspectives offered by new technologies. 20(6): p. 1177-1185. Sustainable conservation of livestock 69. Michaels, S.D. and R.M. Amasino breeds diversity for the,: p. 85. (1998). A robust method for detecting 77. Hacia, J.G (1999). Resequencing and single nucleotide changes as polymorphic mutational analysis using oligonucleotide markers by PCR. The Plant Journal, microarrays. Nature genetics, 21(1s): p. 14(3): p. 381-385. 42. 70. Kuklin, A., K. Munson, D. Gjerde, R. 78. Taillon-Miller, P., E.E. Piernot, and P.-Y. Haefele, and P. Taylor (1997). Detection Kwok (1999). Efficient approach to of single-nucleotide polymorphisms with unique single-nucleotide polymorphism the WAVE™ DNA fragment analysis discovery. Genome research, 9(5): p. system. Genetic testing, 1(3): p. 201-206. 499-505. 71. Ross, P.L., K. Lee, and P. Belgrader, 79. Vignal, A., D. Milan, M. SanCristobal, Discrimination of single-nucleotide and A. Eggen (2002). A review on SNP polymorphisms in human DNA using and other types of molecular markers and peptide nucleic acid probes detected by their use in animal genetics. Genetics MALDI-TOF mass spectrometry. Selection Evolution, 34(3): p. 275. Analytical Chemistry, 1997. 69(20): p. 80. Miah, G., M.Y. Rafii, M.R. Ismail, A.B. 4197-4202. Puteh, H.A. Rahim, K.N. Islam, and M.A. 72. Li, J., J.M. Butler, Y. Tan, H. Lin, S. Latif (2013). A review of microsatellite Royer, L. Ohler, J.A. Monforte (1999). markers and their applications in rice Single nucleotide polymorphism breeding programs to improve blast determination using primer extension and disease resistance. International journal time-of-flight mass spectrometry. of molecular sciences, 14(11): p. 22499- Electrophoresis, 20(6): p. 1258-1265. 22528. 73. Cushwa, W. and J. Medrano (1996). 81. Kalia, R.K., M.K. Rai, S. Kalia, R. Singh, Applications of the random amplified and A. Dhawan (2011). Microsatellite polymorphic DNA (RAPD) assay for markers: an overview of the recent genetic analysis of livestock species. progress in plants. Euphytica, 177(3): p. Animal Biotechnology, 7(1): p. 11-31. 309-334. 74. Wiggans, G., P. VanRaden, and T. 82. Semagn, K., Å. Bjørnstad, and M. Cooper (2011). The genomic evaluation Ndjiondjop, An overview of molecular system in the United States: Past, present, marker methods for plants. African future. Journal of dairy science, 94(6): p. journal of biotechnology, 2006. 5(25). 3202-3211. 83. Beja-Pereira, A., P. Alexandrino, I. 75. VanRaden, P. and M. Tooker (2010). Bessa, Y. Carretero, S. Dunner, N. Gains in reliability from combining Ferrand, A. Sanchez (2003). Genetic subsets of 500, 5,000, 50,000 or 500,000 characterization of southwestern genetic markers. Journal of dairy European bovine breeds: a historical and science, 93: p. 534. biogeographical reassessment with a set

Salisu et al

of 16 microsatellites. Journal of Heredity, 91. Ferrie, G.M., O.R. Cohen, P. Schutz, 94(3): p. 243-250. K.A. Leighty, C. Plasse, T.L. Bettinger, 84. Ibeagha-Awemu, E.M., O.C. Jann, C. and E.A. Hoffman (2013). Identifying Weimann, and G. Erhardt (2004). parentage using molecular markers: Genetic diversity, introgression and improving accuracy of studbook records relationships among West/Central African for a captive flock of marabou storks cattle breeds. Genetics Selection (Leptoptilus crumeniferus). Zoo biology, Evolution, 36(6): p. 673. 32(5): p. 556-564. 85. Sodhi, M., M. Mukesh, B. Mishra, B. 92. Rosa, A.J., E. Schafhouser, A.T. Hassen, Prakash, S. Ahlawat, and K. Mitkari G.H. Rouse, D.E. Wilson, and J.M. Reecy (2005). Evaluation of genetic (2003). Use of molecular markers to differentiation in Bos indicus cattle determine parentage in multiple sire breeds from Marathwada region of India pastures. Beef Research Report, 19. using microsatellite polymorphism. http://lib.dr.iastate.edu/beefreports_2003/ Animal biotechnology, 16(2): p. 127-137. 19 86. Joshi, M.B., P.K. Rout, A.K. Mandal, C. 93. Zhang, Y., Y. Wang, D. Sun, Y. Yu, and Tyler-Smith, L. Singh, and K. Thangaraj Y. Zhang (2010). 57 Validation of 17 (2004). Phylogeography and origin of Microsatellite Markers for Parentage Indian domestic goats. Molecular Biology Verification and Identity Test in Chinese and Evolution, 21(3): p. 454-462. Holstein Cattle. Asian-Australasian 87. Tapio, M., I. Tapio, Z. Grislis, L.E. Journal of Animal Sciences, 23(4): p. 425. HOLM, S. Jeppsson, J. Kantanen, E. 94. Lemos, D.C., Á.F.L. Rios, L.C. Caetano, Eythorsdottir (2005). Native breeds R.B. Lôbo, R.A. Vila, L. Martelli, E.S. demonstrate high contributions to the Ramos (2005). Use of the TSPY gene for molecular variation in northern European sexing cattle. Genetics and Molecular sheep. Molecular ecology, 14(13): p. Biology, 28(1): p. 117-119. 3951-3963. 95. Chen, A.-q., Z.-r. Xu, and S.-d. Yu 88. Edea, Z., H. Dadi, S.W. Kim, T. Dessie, (2007). Sexing goat embryos by PCR and K.-S. Kim (2012). Comparison of amplification of X-and Y-chromosome SNP variation and distribution in specific sequence of the amelogenin gene. indigenous Ethiopian and Korean Cattle Asian-Australasian journal of animal (Hanwoo) populations. Genomics & sciences, 20(11): p. 1689. informatics, 10(3): p. 200-205. 96. Singh, R., R. Deb, U. Singh, R. Alex, S. 89. Gorbach, D., M. Makgahlela, J. Reecy, S. Kumar, S. Chakraborti, R. Singh (2014). Kemp, I. Baltenweck, R. Ouma, S. Moore Development of a tetra-primer ARMS (2010). Use of SNP genotyping to PCR-based assay for detection of a novel determine pedigree and breed single-nucleotide polymorphism in the 5′ composition of dairy cattle in Kenya. untranslated region of the bovine ITGB6 Journal of animal breeding and genetics, receptor gene associated with foot-and- 127(5): p. 348-351. mouth disease susceptibility in cattle. 90. Lin, B.Z., S. Sasazaki, and H. Mannen Archives of virology, 159(12): p. 3385- (2010). Genetic diversity and structure in 3389. Bos taurus and Bos indicus populations 97. Koets, A., W. Santema, H. Mertens, D. analyzed by SNP markers. Animal Oostenrijk, M. Keestra, M. Overdijk, M. science journal, 81(3): p. 281-289. Nielen (2010). Susceptibility to

Salisu et al

paratuberculosis infection in cattle is body conformation and behavior in cattle. associated with single nucleotide Journal of Heredity, 94(6): p. 496-506. polymorphisms in Toll-like receptor 2 102. Davis, G (1998). The mapping of which modulate immune responses quantitative trait loci for birth weight in a against Mycobacterium avium subspecies tropical beef herd. In Proceedings of the paratuberculosis. Preventive veterinary 6th World congress on genetics Applied medicine, 93(4): p. 305-315. to Livestock Production., 26: p. 441-444. 98. Prajapati, B., J. Gupta, D. Pandey, G. 103. Machado, M.B., M.M. Alencar, A.P. Parmar, and J. Chaudhari (2017). Pereira, H.N. Oliveira, E. Casas, L.L. Molecular markers for resistance against Coutinho, and L.C. Regitano (2003). QTL infectious diseases of economic affecting body weight in a candidate importance. Veterinary world, 10(1): p. region of cattle chromosome 5. Genetics 112. and Molecular Biology, 26(3): p. 259- 99. Naqvi, A (2007). Application of 265. molecular genetic technologies in 104. Lahav, T., G. Atzmon, S. Blum, G. Ben‐ livestock production: potentials for Ari, S. Weigend, A. Cahaner, J. Hillel developing countries. Advances in (2006). Marker‐ assisted selection based Biological Research, 1(3-4): p. 72-84. on a multi‐ trait economic index in 100. O'Brien, S.J (1991). Mammalian genome chicken: experimental results and mapping: lessons and prospects. Current simulation. Animal genetics, 37(5): p. Opinion in Genetics & Development, 482-488. 1(1): p. 105-111. 105. Shen, W., L. Li, Q. Pan, G. Qin, and S. 101. Hiendleder, S., H. Thomsen, N. Reinsch, Geng (2004). Genetic effect of the marker J. Bennewitz, B. Leyhe-Horn, C. Looft, assisted selection on economic traits of C. Kühn (2003). Mapping of QTL for goats. Yi chuan= Hereditas, 26(5): p. 625-630.