Open Access

Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse

  • Kyoung-Tag Do1,
  • Joon-Ho Lee2,
  • Hak-Kyo Lee2,
  • Jun Kim3 and
  • Kyung-Do Park2Email author
Contributed equally
Journal of Animal Science and Technology201456:28

https://doi.org/10.1186/2055-0391-56-28

Received: 15 September 2014

Accepted: 29 October 2014

Published: 5 December 2014

Abstract

This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that had raced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missing genotype rate of >10%, minor allele frequency of <0.05 and Hardy–Weinberg equilibrium test P-value of <10–6) were excluded after quality control processes. SNPs on the X and Y chromosomes and genotyped individuals with missing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used for the analysis. The measures of the LD, square of correlation coefficient (r2) between SNP pairs, were calculated for each allele and the effective population size was determined based on r2 measures. The polymorphism information contents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline was observed over the first 1 Mb. But r2 decreased more slowly with increasing distance and was constant after 2 Mb of distance and the decline was almost linear with log-transformed distance. The average r2 between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average r2 between all SNP pairs was 0.02. We observed an initial pattern of decreasing Ne and estimated values were closer to 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be large considering Jeju horse’s population size (about 2,000 heads), but it should be interpreted with caution because of the technical limitations of the methods and sample size.

Keywords

Jeju horse Linkage disequilibrium (LD) Effective population size

Background

According to the literature, horses began to be raised in Jeju Island before the Goryo Dynasty. However, historically in 1276 Mongolian Yuan Dynasty of China established a horse ranch in Jeju Island and 160 Mongolian horses were introduced to produce warhorse. Through adaptation to the harsh environment of the Jeju Island and long term isolation, Jeju horses have developed their own conformation. They have several coat colours and body size is smaller than that of Mongolian horse. Since 1960s due to the industrialization and the development of agricultural machines and means of transportation, demand for horses decreased. In 1986, dozens of Jeju horses with pedigree registry were designated as a natural monument (No.347) because of their historical importance. In May, 2000, Livestock Promotion Agency was designated as Jeju horse registration agency and Jeju horse registration started. Currently, about 2,000 heads of Jeju horses are being raised at local ranches. Domestic animals are well suited for genetic studies, since they enable comparisons of populations exposed to different selection criteria and environmental challenges [1, 2]. Jeju horses are very valuable animals to preserve historically and economically and it is very important to investigate unique genetic characteristics of Jeju horses [3, 4]. Jeju horses have been isolated for more than 700 years and it is estimated that their homozygocity of genotype increased by inbreeding and genetic drift. The increase of recessive homozygosity caused inbreeding and decreased growth and reproductive performance [5, 6]. Especially, average withers height of Jeju horse, approximately 122 cm, is shorter than that of Mongolian (140 cm).

As the rapid development of microarray technology, high density whole genome SNPs (SNP chip) became a strong tool for the researches of quantitative and population genetics. Recently, these genome-wide SNPs were commonly used for estimation of historical effective population size in livestock [713] and human [14, 15]. Closely-linked loci give information on population sizes over historical periods of time, while loosely-linked loci estimate population sizes in the immediate past [1618]. Using high density SNPs, LD of many SNP pairs which have either close linkage or loose linkage by the distance between SNPs can be measured and used for estimation of historical effective population size.

This experiment was conducted to investigate the LD in population level and to estimate the effective population size for systemic preservation using genomic information of Juju horses.

Material and methods

Single-nucleotide polymorphism (SNP) data

DNA samples were obtained from 240 Jeju horses (racehorses) that were randomly chosen and had raced at the Jeju racing park and they were genotyped for the initial genome-wide scan using Equine SNP70 BeadChips (Geneseek, Lincoln, NE). Genomic DNA was isolated from nasal area according to the procedure of Performagene™-LIVESTOCK PG-AC1 Reagent Package (DNA Genotek INC, Canada). The quantity and quality of the genomic DNA was evaluated using 0.8% Agarose gel electrophosis and Nanodrop ND-100 electrophotometer. Genotyping was performed using the InfiniumHD iselect Custom BC Neogen_Equine_Community_Array (Illumina, USA), which contained 65,157 SNPs across the whole genome. Genomestudio softwareV.2011.1.9.4 (Illumina, USA) was used to call the genotypes from the samples. The chip includes 65,157 SNPs that are uniformly distributed on the 31 equine autosomes, X and Y chromosomes from the EquCab2 SNP database of the horse genome (Figure 1). We excluded the SNPs with a missing genotype rate of over 10%, minor allele frequency (MAF) of less than 0.05, and Hardy–Weinberg equilibrium (HWE) test P-value of less than 10–6 as a quality control procedure [13]. SNPs on the X and Y chromosomes and genotyped individuals with missing genotype rate over 10% were also excluded, remaining 44,426 autosomal SNPs from 218 heads for further analysis.
Figure 1

Number of SNPs and average distance between adjacent SNPs per chromosome after quality control processes.

Linkage disequilibrium (LD)

The measures of the LD were square of correlation coefficient (r2) between SNP pairs and calculated for each allele at locus A with each allele at locus B [7, 19].
r 2 = D 2 P A P a P B P b
(1)

Where D = PAB-PAPB and PA, Pa, PB and Pb are the frequencies of alleles A, a, B and b, respectively.

Effective population size

The effective population size was determined based on r2 measures. Because LD breaks down more rapidly over generations for loci further apart, LD at large distances reflects Ne at recent generations.
E r 2 = 1 1 + 4 N e c
(2)
Where, Ne is effective population size and c is the recombination distance (in Morgans) between the SNPs. Equation (2) can be rearranged as follows [17, 2022]:
2 e = r c 2 - 1 - 1 2 c
(3)

Where, Ne is the effective population size t generations ago, c is the distance between markers in Morgans, r2c is the mean value of r2 for markers c Morgans apart, and c = (2 t)-1. Megabase to centimorgan conversion rate was applied for generation grouping based on the result of Corbin et al. [21]. The estimation of LD measure and effective population size was used programs that we developed by GNU Fortran.

Results and discussion

Single-nucleotide polymorphism (SNP) data

Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs were excluded after quality control processes (missing genotype rate of >10%, minor allele frequency of <0.05 and Hardy–Weinberg equilibrium test P-value of <10–6) and finally, 44,426 (71.9%) SNPs were selected and used for the analysis. The minor allele frequencies (MAF) in each chromosome followed a uniform distribution and averaged to be 0.24 and the average χ2 value (p-value) of Hardy-Weinberg disequilibrium (HWE) test, polymorphism information contents (PIC) and expected heterozygosity (HE) were 1.32 (0.25), 0.27 and 0.34, respectively. The number of SNPs per autosome ranged from 452 to 3,509 and average distance between adjacent SNPs was 50.4 kb (Table 1), and their relationships are shown in Figure 1. The frequency of adjacent SNP pairs which are aparted between 10 Mb (Mega base pairs = 1,000,000 bp) and 100 Mb was 27,289 (61.4%), and that of adjacent SNP pairs less than 10 Mb was 14,764 (24.9%).
Table 1

Simple statistics for single-nucleotide polymorphism (SNP) data by chromosome

Chromosome

No. of SNPs

Mean

No. of SNP pairs

Mean

Distance1

MAF2

HE3

r-square4

 

r-square5

1

3,509

53.0

0.24

0.33

0.25

6,154,786

0.02

2

2,463

49.1

0.25

0.34

0.29

3,031,953

0.02

3

2,234

53.5

0.25

0.34

0.27

2,494,261

0.02

4

2,185

49.7

0.24

0.33

0.28

2,386,020

0.02

5

1,909

52.2

0.25

0.34

0.26

1,821,186

0.02

6

1,762

48.1

0.24

0.33

0.25

1,551,441

0.02

7

1,887

52.2

0.24

0.33

0.28

1,779,441

0.02

8

1,946

48.2

0.25

0.34

0.27

1,892,485

0.03

9

1,767

47.2

0.26

0.34

0.29

1,560,261

0.03

10

1,688

49.7

0.24

0.33

0.27

1,423,828

0.03

11

1,332

46.0

0.24

0.34

0.27

886,446

0.03

12

622

53.0

0.25

0.34

0.21

193,131

0.03

13

826

51.4

0.24

0.33

0.20

340,725

0.03

14

1,954

47.7

0.24

0.34

0.28

1,908,081

0.03

15

1,841

49.6

0.24

0.33

0.26

1,693,720

0.02

16

1,775

49.2

0.24

0.33

0.25

1,574,425

0.02

17

1,598

50.5

0.25

0.33

0.31

1,276,003

0.03

18

1,532

53.8

0.24

0.33

0.27

1,172,746

0.02

19

1,225

48.9

0.24

0.33

0.26

749,700

0.03

20

1,252

51.0

0.25

0.34

0.26

783,126

0.02

21

1,257

45.6

0.24

0.33

0.25

789,396

0.03

22

1,036

48.1

0.24

0.34

0.24

536,130

0.02

23

1,097

50.4

0.25

0.34

0.28

601,156

0.03

24

1,039

44.5

0.25

0.34

0.25

539,241

0.03

25

737

53.2

0.24

0.33

0.25

271,216

0.03

26

684

61.0

0.24

0.33

0.22

233,586

0.03

27

778

51.1

0.25

0.34

0.25

302,253

0.03

28

867

52.9

0.24

0.33

0.27

375,411

0.03

29

579

58.0

0.24

0.33

0.23

167,331

0.03

30

593

50.7

0.24

0.33

0.23

175,528

0.03

31

452

55.1

0.25

0.33

0.20

101,926.

0.03

Overall

44,426

50.4

0.24

0.34

0.26

38,766,939

0.02

1Kilo base pairs (Kb) between adjacent SNPs, 2minor allele frequency, 3Expected heterozygosity, 4between adjacent SNP pairs, 5between all SNP pairs.

Linkage disequilibrium (LD)

The results of this study provide an overview of LD in the Jeju Horse using a high density SNP panel. Linkage disequilibrium decreased with increasing distance between SNP pairs (Figure 2) and the most rapid decline was observed over the first 1 Mb. But r2 decreased more slowly with increasing distance and was constant after 2 Mb of distance and the decline in LD was almost linear with log-transformed distance [21]. The average r2 between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average r2 between all SNP pairs was 0.02 (Table 1).
Figure 2

Trend on r 2 between SNP pairs according to distance with all chromosomes. (Upper) Distance range from 0 to 10 Mb. r2 values averaged using bins of 0.1 Mb. (Lower) Distance range from 0 to 0.5 Mb. r2 values averaged using bins of 0.01 Mb.

According to reports [21, 23] in a sample of 817 and 24 Thoroughbred horses, LD in r2 decreased from 0.6 to 0.2 when the distance between markers increased to 0.5 Mb. The pattern of decline of LD with distance in our population was similar (Figure 2), but the LD observed was lower (0.49 ~ 0.07) when compared with other reports [21, 23].

Validation work by Corbin et al. [21] on their Thoroughbred (817 head) data suggests that our sample size of 218 heads is more accurate to obtain an unbiased result of LD in our population. On the other hand, the pattern and magnitude of decline of LD with distance at less than 10 Mb were almost similar and linkage disequilibrium declined more slowly in Jeju horse population than in Thoroughbred populations [21].

Effective population size

We observed an initial pattern of decreasing Ne and estimated values were closer to 41 at 1 ~ 5 generations ago (Figure 3). This result is in agreement with the previous approach [17] by calculating historical Ne, assuming linear population growth. The observed pattern showed a decrease in Ne upto around 1 ~ 5 generations. Corbin et al. [21] reported the effective population size (Ne) was estimated to be 100 heads at 20 generations in Thoroughbreds and Cunningham et al. [24] calculated the effective number of studbook founders of the Thoroughbred to be 28.2 from pedigree analyses.
Figure 3

Effective population size (N e ) plotted against generations in the past, truncated at 50 generations.

The 41 heads (Ne) estimated in this study seems to be large considering Jeju horse’s population size. Currently, there is about 2,000 Jeju horses in Jeju Island and it may be difficult to interpret inflated Ne. There may be a few speculations, such as an immigration event, a hybridization event or any combination of these. Therefore, it is useful to consider our observation in the context of what is known about the demographic history of Jeju horses. In 1986, 150 Jeju horses with pedigree registry were designated as a natural monument (No.347). In October, 1990, Jeju horse racing park was open and Jeju horse racing started and the names of various horses raised in Jeju was unified to Jeju horse. As the sales of Jeju horse racing park increased, the demand for Jeju horse increased and since the horses raised at ranches were selected as basic registered horses and included to Jeju horse management system, bloods of other breeds might be introduced.

On the other hand, since intensive selection for racing performance of Throughbred has been conducted for long period, the effective population size of Throughbred can be relatively small. However, for Jeju horse, fundamental effective population size can be larger than that of Throughbred since almost no selection has been conducted for Jeju horses. The effective population size (41 heads) estimated at 1 ~ 5 generations should be interpreted with caution because of the technical limitations of the methods and sample size.

Conclusions

Jeju horses are very valuable animals to preserve historically and economically and it is very important to investigate unique genetic characteristics of Jeju horses for the stable maintenance. Also, we should make efforts to prevent inbreeding coefficient increase and to increase effective population size through the reduction of generation interval.

Notes

Declarations

Acknowledgments

This work was supported by the National Research Foundation of Korea Grant funded by the Korean Government (NRF-2013R1A1A2012586). We are grateful to Jeju horse breeder’s Association for helping us.

Authors’ Affiliations

(1)
Department of Equine Sciences, Sorabol College
(2)
The Animal Genomics and Breeding Center, Hankyong National University
(3)
Provincial Livestock Promotion

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© Do et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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