Genome-Wide Selective Analysis of Boer Goat to Investigate the Dynamic Heredity Evolution under Different Stages

Yuan, Ying; Zhang, Weiyi; Liu, Chengli; He, Yongmeng; Zhang, Haoyuan; Xu, Lu; Yang, Bo; Zhao, Yongju; Ma, Yue; Chu, Mingxing; Zhao, Zhongquan; Huang, Yongfu; Han, Yilin; Zeng, Yan; Ren, Hangxing; Wang, Gaofu; Guang‐Xin, E

doi:10.3390/ani12111356

Cited by 5 publications

(3 citation statements)

References 53 publications

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“…The population structure analysis indicated a consistent clustering pattern based on PCA, NJ phylogenetic trees and admixture analyses. It has been noted that in the experimental samples, apart from the wild goat population, IBE, the other six domestic goat populations were clustered into four groups, which is generally in agreement with their economic traits [47].…”

Section: Population Structure and Linkage Disequilibriumsupporting

confidence: 62%

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Zhao,

Huang,

Chen

et al. 2024

Animals

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Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.

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Section: Population Structure and Linkage Disequilibriumsupporting

confidence: 62%

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Zhao,

Huang,

Chen

et al. 2024

Animals

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“…As we are aware, the Boer goat is recognized globally as one of the finest meat goat breeds, originating from the Republic of South Africa (Yuan et al., 2022). Owing to its exceptional meat production performance, it has been introduced by numerous countries.…”

Section: Discussionmentioning

confidence: 99%

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

Ma,

Li,

et al. 2023

Food and Energy Security

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The Longnan goat (LN) is a local breed discovered during the third census of China's livestock and poultry genetic resources. In order to thoroughly comprehend the population traits, this research examined a total of 70 animals from three different goat populations, namely the LN goat, Nanjiang Brown goat (NJ), and Boer goat (Boer). Specific‐Locus Amplified Fragment Sequencing was employed to analyze genetic diversity, population structure, and selective sweep patterns. Additionally, individual DNA fingerprints were generated to provide detailed genetic profiles for each subject. A total of 643,868 single nucleotide polymorphisms (SNPs) were detected, with a majority located in intergenic and intronic regions. Genetic diversity analysis uncovered lower diversity within the LN population compared to the other two populations. The analysis of population structure unveiled significant genetic distance between LN and both NJ and Boer populations, with distinct clustering patterns observed. Moreover, genetic differentiation coefficients (FST) of 0.1019 and 0.0854 were determined between LN and Boer, as well as LN and NJ, respectively, indicating substantial genetic differentiation. Selective sweep analysis, combining FST and π ratio, identified several genes associated with growth and development, reproduction, hair color, and immunity that may serve as valuable candidates for marker‐assisted breeding. Furthermore, identification of 47,541 runs of homozygosity (ROHs) revealed non‐uniform distribution across chromosomes, with the highest frequency on chromosome 1 and the lowest on chromosome 27. Correlations between different inbreeding coefficients varied, with the highest observed between FHOM and FGRM, and the lowest between FROH >1.5Mb and FROH <500kb. A total of 46 candidate genes were annotated within high‐frequency ROH islands, primarily associated with biological processes such as reproduction, growth and development, and immunity. Finally, a DNA fingerprint, consisting of 371 highly polymorphic SNPs, was generated and presented in the form of a two‐dimensional code for convenient access. Based on the population structure analysis, LN goats have been found to have a distant genetic distance and a higher degree of differentiation from both the Boer and NJ populations. Evaluation of genetic diversity parameters and ROH analysis indicates that the LN population exhibits lower genetic diversity and shows signs of inbreeding. Our findings offer theoretical support for the identification of genetic resources within this population.

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“…Single nucleotide polymorphism (SNP), as the third-generation DNA molecular marker, has the advantages of dense distribution, low typing error, genetic stability and low cost. It is widely used in evolutionary research [ 3 , 4 , 5 , 6 , 7 , 8 ] and genetic relationship identification [ 9 , 10 , 11 , 12 , 13 , 14 ]. One study revealed the genetic diversity of the global goat population and highlighted the migratory routes after domestication based on a 50K SNP chip [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Family Structure and Paternity Test of Tan Sheep in Yanchi Area, China

Qian

et al. 2022

Animals

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Tan sheep is a special breed of locally protected sheep in China, one of the best quality meat sheep in the world. Due to the unclear pedigree of the rams on the Ningxia Tan sheep breeding farm, we investigated 74 rams in the field and explored a new method for family division. Genomic DNA was extracted from the blood of breeding rams. Using Plink software, GCTA tools and R language, we analyzed the genetic structure, kinship, and inbreeding coefficient of the breeding sheep, which revealed the genetic relationship between the individuals. The results showed that there was no obvious clustering phenomenon in the PCA, and the genetic background of the samples was similar. The G matrix and IBS distance matrix indicated that most individuals were far away from each other. Paternity testing identified 24 pairs of unknown parent–child pairs, and all the Tan sheep could be divided into 12 families, which provided a reference for sheep breeding. The average inbreeding coefficient based on the ROH of this population was 0.049, so there was a low degree of inbreeding and the rams in the field were able to maintain high genetic diversity. Overall, we explored a more accurate method through paternity and kinship analysis; it provides a scientific basis for pedigree construction, which has an important application value for Tan sheep breeding.

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Genome-Wide Selective Analysis of Boer Goat to Investigate the Dynamic Heredity Evolution under Different Stages

Cited by 5 publications

References 53 publications

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

Analysis of Family Structure and Paternity Test of Tan Sheep in Yanchi Area, China

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