Next Article in Journal
The Use of Infrared Thermography (IRT) as Stress Indicator in Horses Trained for Endurance: A Pilot Study
Previous Article in Journal
Effect of Anacardic Acid against Thiram Induced Tibial Dyschondroplasia in Chickens via Regulation of Wnt4 Expression
Article Menu
Issue 3 (March) cover image

Export Article

Open AccessArticle
Animals 2019, 9(3), 83; https://doi.org/10.3390/ani9030083

Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle

1
Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
2
National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
3
Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally this work.
Received: 18 January 2019 / Revised: 21 February 2019 / Accepted: 22 February 2019 / Published: 6 March 2019
(This article belongs to the Section Animal Genetics and Genomics)
  |  
PDF [1663 KB, uploaded 6 March 2019]
  |  

Simple Summary

Evaluation of the population structure and linkage disequilibrium can offer important insights to fully understand the genetic diversity and population history of cattle, which can enable us to appropriately design and implement GWAS and GS in cattle. In this study, we characterized the extent of genome-wide LD and the haplotype block structure, and estimated the persistence of phase of Chinese indigenous cattle with Illumina BovineHD BeadChip. According to our study, 58K, 87K, 95K, 52K, and 52K markers would be necessary for SCHC, NCC, SWC, SIM, and WAG, respectively, in the implementation of GWAS and GS and combining a multipopulation with high persistence of phase is feasible for the implication of genomic selection for Chinese beef cattle.

Abstract

Understanding the linkage disequilibrium (LD) across the genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design and implement the genome-wide association (GWAS) and genomic selection (GS) in beef cattle. We estimated the extent of genome-wide LD, haplotype block structure, and the persistence of phase in 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r2 between adjacent SNPs were 0.60, 0.67, 0.58, 0.73, and 0.71 for South Chinese cattle (SCHC), North Chinese cattle (NCC), Southwest Chinese cattle (SWC), Simmental (SIM), and Wagyu (WAG). The highest correlation (0.53) for persistence of phase across groups was observed for SCHC vs. SWC at distances of 0–50 kb, while the lowest correlation was 0.13 for SIM vs. SCHC at the same distances. In addition, the estimated current effective population sizes were 27, 14, 31, 34, and 43 for SCHC, NCC, SWC, SIM, and WAG, respectively. Our result showed that 58K, 87K, 95K, 52K, and 52K markers were required for implementation of GWAS and GS in SCHC, NCC, SWC, SIM, and WAG, respectively. Also, our findings suggested that the implication of genomic selection for multipopulation with high persistence of phase is feasible for Chinese cattle. View Full-Text
Keywords: linkage disequilibrium; effective population size; persistence of phase; haplotype block structure; Chinese cattle linkage disequilibrium; effective population size; persistence of phase; haplotype block structure; Chinese cattle
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material

SciFeed

Share & Cite This Article

MDPI and ACS Style

Xu, L.; Zhu, B.; Wang, Z.; Xu, L.; Liu, Y.; Chen, Y.; Zhang, L.; Gao, X.; Gao, H.; Zhang, S.; Xu, L.; Li, J. Evaluation of Linkage Disequilibrium, Effective Population Size and Haplotype Block Structure in Chinese Cattle. Animals 2019, 9, 83.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Animals EISSN 2076-2615 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top