Genetic Diversity Of Five Populations Of The Nigerian Local Breeds Of Goat Using Random Amplified Polymorphic DNA (RAPD) Markers

Project and Seminar Material for Agricultural Engineering AE

Genetic Diversity Of Five Populations Of The Nigerian Local Breeds Of Goat Using Random Amplified Polymorphic DNA (RAPD) Markers


Abstract


Genetic diversity and genetic distance of five populations of the Nigerian breeds of goat were investigated using random amplified polymorphic DNA markers. Five breeds of goat were used for the study and each breed constituted a population, hence, the five populations considered in the study. The populations were: Sokoto Red (SR), Sahel (SH), Kano Brown (KB), Bornu White (BW) and West African Dwarf (WAD) goats. The experiment was conducted within four geographical zones of Nigeria: South east, North west, North east and North central. One hundred and twenty (120) blood samples were randomly collected from various locations across the four geographical zones in Nigeria. The samples were collected from the stocks at the central markets, which served as collection point from all the localities and from household goat keepers.

Varying numbers of sample sizes (Sokoto Red = 23, Kano Brown = 21, Bornu White = 23, WAD = 26 and Sahel = 27) were collected from each breed. The blood samples were collected from the jugular vein of the animals through a process known as venipuncture. Approximately, 5 ml of blood was collected aseptically from each animal into an EDTA container, using 23 gauge sterile needle and syringe, and was stored at -20oC using (ethylene-di-amine-tetra-acetic acid, EDTA) as anticoagulant containers. The DNA samples were isolated and purified from the 120 blood samples following protocol as recommended by (ZYMO RESEARCH CORPORATION, e-mail: info@zymoresearch.com).

The RAPD-PCR reaction followed the procedure described by El Hentati et al., (2012). Seven random primers were used for this study but only three (3) primers produced clearly polymorphic and reproducible bands whereas four (4) failed to produce any band. Allele frequency per population per loci under consideration exceeded the minimum allele frequency (MAF) limit 10%. Level of polymorphism per primer varied from 43 – 80%. Total of 20 scoreable bands were obtained and thirteen (13) out of which were polymorphic to arrive at a total of 65% polymorphism. Genetic diversity of the studied populations was measured with three indices: (Nei’s genetic diversity, Shannon’s information index, Observed and Effective number of alleles).

Observed number of allele (Na) was 2.0000 across the populations while Effective number of alleles (Ne) varied from 1.9003 in WAD to 1.9900 in Sahel population. However, SR, KB and BW had Ne values of 1.9897, 1.9287 and 1.9836 respectively. Nei’s heterozygosity varied across the populations with highest values 0.4975 and 0.4974 obtained in Sahel and Kano Brown respectively whereas lowest value 0.4736 was obtained in WAD. Shannon’s Information index followed similar trend across with average of 0.6822. The mean of coefficient of gene differentiation Gst was (0.0139) and mean of gene flow Nm across populations was (35.3710). The highest genetic similarity (0.9995) and lowest genetic distance (0.0005) was recorded between Sokoto Red and Sahel, while the lowest similarity (0.9505) and highest genetic distance (0.0507) was recorded between Bornu White and WAD. Populations with higher similarity indicated that they are of closer descent and closer geographical locations.

The unweighted pair group method of arithmetic means (UPGMA) dendrogram based on Nei’s genetic distance clearly separated the five populations into two clusters. The closest relationship was observed between Sokoto Red, Sahel and Bornu White goat populations/breeds and the farthest relationship was observed between WAD and Sokoto Red populations. It was concluded that the high similarity obtained in this study was as a result of loss of heterozygosis in the populatons of Nigerian breeds of goat which may have originated among mates in each population/breed. However, the results of this experiment can offer some crucial scientific data useful for breeding programme of Nigerian breeds of goats.Genetic diversity and genetic distance of five populations of the Nigerian breeds of goat were investigated using random amplified polymorphic DNA markers.

Five breeds of goat were used for the study and each breed constituted a population, hence, the five populations considered in the study. The populations were: Sokoto Red (SR), Sahel (SH), Kano Brown (KB), Bornu White (BW) and West African Dwarf (WAD) goats. The experiment was conducted within four geographical zones of Nigeria: South east, North west, North east and North central. One hundred and twenty (120) blood samples were randomly collected from various locations across the four geographical zones in Nigeria. The samples were collected from the stocks at the central markets, which served as collection point from all the localities and from household goat keepers. Varying numbers of sample sizes (Sokoto Red = 23, Kano Brown = 21, Bornu White = 23, WAD = 26 and Sahel = 27) were collected from each breed. The blood samples were collected from the jugular vein of the animals through a process known as venipuncture.

Approximately, 5 ml of blood was collected aseptically from each animal into an EDTA container, using 23 gauge sterile needle and syringe, and was stored at -20oC using (ethylene-di-amine-tetra-acetic acid, EDTA) as anticoagulant containers. The DNA samples were isolated and purified from the 120 blood samples following protocol as recommended by (ZYMO RESEARCH CORPORATION, e-mail: info@zymoresearch.com). The RAPD-PCR reaction followed the procedure described by El Hentati et al., (2012). Seven random primers were used for this study but only three (3) primers produced clearly polymorphic and reproducible bands whereas four (4) failed to produce any band. Allele frequency per population per loci under consideration exceeded the minimum allele frequency (MAF) limit 10%. Level of polymorphism per primer varied from 43 – 80%. Total of 20 scoreable bands were obtained and thirteen (13) out of which were polymorphic to arrive at a total of 65% polymorphism. Genetic diversity of the studied populations was measured with three indices: (Nei’s genetic diversity, Shannon’s information index, Observed and Effective number of alleles).

Observed number of allele (Na) was 2.0000 across the populations while Effective number of alleles (Ne) varied from 1.9003 in WAD to 1.9900 in Sahel population. However, SR, KB and BW had Ne values of 1.9897, 1.9287 and 1.9836 respectively. Nei’s heterozygosity varied across the populations with highest values 0.4975 and 0.4974 obtained in Sahel and Kano Brown respectively whereas lowest value 0.4736 was obtained in WAD. Shannon’s Information index followed similar trend across with average of 0.6822. The mean of coefficient of gene differentiation Gst was (0.0139) and mean of gene flow Nm across populations was (35.3710). The highest genetic similarity (0.9995) and lowest genetic distance (0.0005) was recorded between Sokoto Red and Sahel, while the lowest similarity (0.9505) and highest genetic distance (0.0507) was recorded between Bornu White and WAD. Populations with higher similarity indicated that they are of closer descent and closer geographical locations.

The unweighted pair group method of arithmetic means (UPGMA) dendrogram based on Nei’s genetic distance clearly separated the five populations into two clusters. The closest relationship was observed between Sokoto Red, Sahel and Bornu White goat populations/breeds and the farthest relationship was observed between WAD and Sokoto Red populations. It was concluded that the high similarity obtained in this study was as a result of loss of heterozygosis in the populatons of Nigerian breeds of goat which may have originated among mates in each population/breed. However, the results of this experiment can offer some crucial scientific data useful for breeding programme of Nigerian breeds of goats.


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