Abstract
The pedigree file of the Boer and Nubian goat breeds in Mexico was constructed using the national database provided by the Asociación Mexicana de Criadores de Ganado Caprino de Registro. Field technicians routinely updated the goat national database by recording information from flocks participating in the performance-recording system. Information on animal identification number, parents, birth date, sex, breed, and farm of origin were used to undertake pedigree analyses using the ENDOG program (version 4.8). This paper presents a pedigree data file, tables and figures of characteristics of pedigree data, pedigree analyses, pedigree integrity, effective population size and genetic conservation index. The data can be used to estimate other population parameters, to monitor the genetic diversity of the Boer and Nubian goat breeds in Mexico, and also to design balanced breeding programs, maintaining genetic variation at reasonable levels and maximizing genetic progress in these populations.
Keywords: Pedigree analysis, Inbreeding, Effective population size, Population structure
Specifications Table
| Subject | Animal breeding and genetics |
| Specific subject area | Pedigree analyses to assess genetic diversity and population structure |
| Type of data | Tables and Figures |
| How data were acquired | During the 2018 genetic evaluation, genealogical information for the Boer and Nubian breeds was extracted from the performance-recording database provided by the Asociación Mexicana de Criadores de Ganado Caprino de Registro. |
| Data format | Raw, Analyzed, Filtered |
| Parameters for data collection | Field data was obtained from goat production units participating in the performance recording system of the Asociación Mexicana de Criadores de Ganado Caprino de Registro. |
| Description of data collection | Technical personnel from the Asociación Mexicana de Criadores de Ganado Caprino de Registro regularly visit purebred goat production units in Mexico. During such visits they physically evaluate the animals subjected to registration, they also collect and verify their pedigree and productive information. Animals that comply with the inspection parameters, genealogical and productive information, become part of the national breeding flock of their respective breed. Field data from all participating flocks is then concentrated and managed by the Asociación Mexicana de Criadores de Ganado Caprino de Registro, which then extends the animal registration certificates to individual goat breeders. The Asociación Mexicana de Criadores de Ganado Caprino de Registro provides the national database to Universidad Autónoma Chapingo for genetic evaluation purposes, and on a yearly basis, breeding values for growth traits are estimated and published. |
| Data source location | Laboratorio de Evaluaciones Genéticas, Universidad Autónoma Chapingo, Departamento de Zootecnia, Posgrado en Producción Animal, km 38.5 carretera México-Texcoco, Chapingo, Estado de México. |
| Data accessibility | Data is with this article. |
Value of the Data
|
1. Data
Individual records containing animal identification number, identification of parents, animal birth date, sex, breed, and farm of origin were obtained from the national database of the Boer and Nubian breeds in Mexico (Appendix A). Pedigree data for Boer and Nubian breeds comprised 141 and 99 flocks, respectively, that were distributed across 15 states in the country, but mainly distributed in the states of Nuevo León, San Luis Potosí, Sinaloa, Coahuila, Zacatecas and Jalisco (Fig. 2, Fig. 3). The majority of flocks were managed mostly on semi-intensive systems on native and cultivated pastures; supplementation with mineral salts and concentrate feed was provided in certain periods of the year depending on the availability of forage. Flocks’ reproduction took place mostly through controlled natural mating. Breeding was all-year-round, but the highest frequency of mating was from September to December; 90% of kidding were presented from January to April. Kids were naturally reared and suckling lasted three months, on average. The conformation of the pedigree file in both breeds predominantly represents the last ten years (Fig. 1). The characteristics of the pedigree files for the total and reference populations (kids born from 2013 to 2017 were considered as the reference population for both breeds) of Boer and Nubian goat breeds in Mexico are described in Table 1.
Fig. 2.
Population distribution of the reference population for Boer goats in Mexico.
Fig. 3.
Population distribution of the reference population for Nubian goats in Mexico.
Fig. 1.
Number of animals registered by birth year for Boer and Nubian goats in Mexico.
Table 1.
Characteristics of pedigree dataa for the total and reference populations of Boer and Nubian goats in Mexico.
| Parameter | Boer | Nubian |
|---|---|---|
| Total number of animals | 18,947 (4758) | 13,744 (2825) |
| Number of animals with progeny | 7738 (566) | 4837 (308) |
| Number of animals without progeny | 11,209 (4192) | 8907 (2517) |
| Number of animals with both parents known | 12,290 (3824) | 10,361 (2436) |
| Animals with both parents unknown | 4004 (129) | 1677 (27) |
| Number of animals with one parent known | 2653 (805) | 1706 (362) |
| Total number of bucks | 2006 (77) | 943 (22) |
| Total number of does | 5732 (489) | 3894 (286) |
| Number of animals with unknow buck | 5061 (553) | 2556 (278) |
| Number of animals with unknow doe | 5600 (510) | 2504 (138) |
| Average kids per buck | 6.92 (17.27) | 11.86 (14.82) |
| Maximum kids per buck | 239 (94) | 389 (64) |
| Average kids per doe | 2.33 (2.07) | 2.89 (2.06) |
Values without brackets correspond to the total population (in brackets are values for the reference population).
Breed differences in number of offspring per parent are illustrated in Fig. 4. Most of the bucks and does used for breeding purposes produce less than three kids.
Fig. 4.
Frequency of parents by classes of number of offspring for Boer and Nubian goats in Mexico.
The distribution of number of animals by inbreeding level and sex is presented in Table 2. The largest number of inbred animals were observed in the Nubian population, most of them were concentrated in the low levels of inbreeding (≤6.25%). On the other hand, for Boer, the largest number of inbred animals was concentrated in the class from 6.25 to 14.9%. In the last 8 (Boer) and 10 (Nubian) years there was an increase in the number of inbred animals (Fig. 5, Fig. 6). Nonetheless, the average inbreeding coefficient in inbred animals during this period was relatively stable.
Table 2.
Numbera and sex of animals for different inbreeding levels for the total and reference populations in Boer and Nubian goats in Mexico.
| Inbreeding level | Boer |
Nubian |
||||
|---|---|---|---|---|---|---|
| Males | Females | Total, per level | Males | Females | Total, per level | |
| 0.00% | 6575 (1712) | 10,590 (2122) | 17,165 (3834) | 4436 (900) | 6154 (988) | 10,590 (1888) |
| 0.01–6.24% | 250 (180) | 314 (209) | 564 (389) | 863 (287) | 1100 (328) | 1963 (615) |
| 6.25–14.99% | 302 (164) | 491 (189) | 793 (353) | 396 (92) | 463 (101) | 859 (193) |
| 15.00–29.99% | 107 (66) | 301 (101) | 408 (167) | 104 (44) | 218 (84) | 322 (128) |
| 30.00% or higher | 4 (4) | 13 (11) | 17 (15) | 4 (0) | 6 (1) | 10 (1) |
| Total, inbred animals | 663 (414) | 1119 (510) | 1782 (924) | 1367 (423) | 1787 (514) | 3154 (937) |
| Total | 7238 (2126) | 11,709 (2632) | 18,947 (4758) | 5803 (1323) | 7941 (1502) | 13,744 (2825) |
Values without brackets corresponding to the total population (in brackets corresponding to the reference population).
Fig. 5.
Number of inbred individuals (bars) and average inbreeding coefficient in inbred animals (line) for each year of birth for the Boer breed.
Fig. 6.
Number of inbred individuals (bars) and average inbreeding coefficient in inbred animals (line) for each year of birth for the Nubian breed.
The pedigree structure showed that around 70% of the animals had identification of parents, almost 60% had identification of grandparents, and about 40% had identification of great-grandparents for the Boer breed (Fig. 7). For the Nubian breed, around 80% of animals had identification of parents, more than 70% had identification of grandparents and 60% had identification of great-grandparents (Fig. 8). In summary, the Pedigree Completeness Index in the first generation was 88.8 (Boer) and 92.6% (Nubian) for the reference population and 71.9 (Boer) and 81.6% (Nubian) for the total population. There were not big differences in the genealogy recording regarding mother or father side.
Fig. 7.
Percent of known ancestors for total and reference (in brackets) populations in the pedigree of the Boer breed. GGS = great-grand sire; GGD = great-grand dam.
Fig. 8.
Percent of known ancestors for total and reference (in brackets) populations in the pedigree of the Nubian breed. GGS = great-grand sire; GGD = great-grand dam.
In general, since 2003 and 2005 (for Nubian and Boer, respectively) the effective population size showed an erratic pattern over the years. However, it remained over 50 (Fig. 9), indicating an acceptable level of genetic diversity for these two goat populations. On the other hand, for both breeds the average genetic conservation index (GCI) showed positive trends over the years (Fig. 10).
Fig. 9.
Effective population size (Ne) by birth year for Boer and Nubian goats in Mexico.
Fig. 10.
Evolution of average Genetic Conservation Index (GCI) through the studied period for the Boer and Nubian breeds in Mexico.
The following figures provide the number of most influential ancestors that explained the genetic diversity in the total and reference populations for the Boer (Fig. 11) and Nubian (Fig. 12) goat breeds. A less genetic contribution of ancestors was detected in the Nubian than in the Boer population.
Fig. 11.
Cumulative genetic contribution of ancestors to the total and reference populations for the Boer breed.
Fig. 12.
Cumulative genetic contribution of ancestors to the total and reference populations for the Nubian breed.
2. Experimental design, materials, and methods
Pedigree analyses were performed using the ENDOG (version 4.8) program [1] with the procedures: pedigree content, founders, generations intervals, and offspring analysis. The results were obtained from the following output tables:
Midef: the inbreeding coefficient (), relatedness coefficient (), and number of generations for each individual in the dataset.
GCI: the genetic conservation index computed for each animal as proposed by Alderson [2].
PediCont and PediContRef: the frequency of the contribution of given ancestor in the pedigree to the 5th parental generation for the whole pedigree or for a given reference population.
PedKnow and PedKnowRef: the completeness index for the whole pedigree or for a given reference population.
GenInterv and GeIntRef: average generation intervals and reproductive ages for each path parent–son, for the whole population or for a given reference population.
Ancestors and AncestorsRef: contribution to the population [3] for the whole population or for a predefined reference population.
NeOffs_Year: the estimates of effective population size by years.
Acknowledgments
The unrestricted access to its national database for the Boer and Nubian goat breeds is highly appreciated of the Asociación Mexicana de Criadores de Ganado Caprino de Registro.
Footnotes
Supplementary data to this article can be found online at https://doi.org/10.1016/j.dib.2020.105270.
Conflict of Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Appendix A. Supplementary data
The following are the Supplementary data to this article:
References
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