Genetic diversity and population structure analysis of eight local chicken breeds of Southern Xinjiang

Azimu, W.; Manatbay, B; Li, Y; Kaimaerdan, D; Wang, H E; Reheman, Aikebaier; Muhatai, Geminguli

doi:10.1080/00071668.2018.1523537

Cited by 17 publications

(14 citation statements)

References 27 publications

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“…Genetic diversity, an effective monitor for conservation purposes, within Chinese indigenous chicken populations has been evaluated using microsatellites (Abiye Shenkut et al. 2015; Azimu et al. 2018), random-amplified polymorphic DNA (Lynch and Milligan 1994), amplified fragment length polymorphisms (Christian 2004), and genome-wide single-nucleotide polymorphisms (SNPs) (Chen et al.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds

Nie

Almeida

Jia

et al. 2019

Genome Biology and Evolution

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The conservation and development of chicken have received considerable attention, but the admixture history of chicken breeds, especially Chinese indigenous breeds, has been poorly demonstrated. In this study, we aimed to evaluate the genetic diversity and population structure of eight chicken breeds (including conserved chicken breeds) from different geographic origin and to identify admixture within these breeds using a 600-K single-nucleotide polymorphism panel for genotyping. Using the genotype of 580,961 single-nucleotide polymorphism markers scored in 1,200 animals, we evaluated the genetic diversity (heterozygosity and proportion of polymorphic markers), linkage disequilibrium decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance), and migration events (TreeMix and f-statistics) of the eight domesticated chicken breeds. The results of population analytical methods revealed patterns of hybridization that occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture, followed by trade, have been important forces in shaping the genomic variation in modern Chinese chicken. Moreover, isolation by distance might play a critical role in shaping the genomic variation within Eurasia continent chicken breeds. Moreover, genetic information provided in this study is valuable resources for production applications (genomic prediction, and breeding strategy) and scientific research (genetic basis detection, studying evolution, or domestication).

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds

Nie

Almeida

Jia

et al. 2019

Genome Biology and Evolution

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“…Generally speaking, the higher the population genetic variation is, the higher is the population genetic richness. Thus, the PIC is often used as an indicator [ 32 , 33 ]. With the exception of g.29121 A > G, the other eight SNPs have reached the Hardy–Weinberg balance, which suggested that these SNPs of cattleyak were not strongly selected and might not be influenced by mutation, selection and genetic drift.…”

Section: Discussionmentioning

confidence: 99%

Polymorphisms of SORBS1 Gene and Their Correlation with Milk Fat Traits of Cattleyak

Yang

Min

Zhu

et al. 2021

Animals

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This study aimed to find the SNPs in the SORBS1 gene of cattleyak, analyze the relationship between its polymorphisms and the milk fat traits, and find potential molecular markers for the milk fat traits of cattleyak. The polymorphism of the SORBS1 gene in 350 cattleyak from Hongyuan County (Sichuan, China) were detected by PCR and DNA sequencing, and the correlation between these SNPs and the milk production traits of cattleyak was analyzed. The results showed that there were nine SNPs in the CDS and their adjacent non-coding regions of the SORBS1 gene, and all SNPs have three genotypes. The correlation analysis found that the genotypes with superior milk fat traits in the other eight alleles were homozygous genotypes with a high genotype frequency except the g.96284 G > A (c.3090 G > A) (p < 0.05). However, at locus g.96284 G > A, the milk fat percentage, monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs) and saturated fatty acids (SFAs) of the GA genotype were significantly higher than that of GG and AA genotypes (p < 0.05). Among these SNPs, three SNPs (g.6256 C > T (c.298 C > T), g.24791 A > G (c.706 A > G) and g.29121 A > G (c.979 A > G)) caused the amino acids change. The genotypes of the three SNPs consist of three haplotypes and four diplotypes. The amino acid mutation degree of diplotype H1–H1 (CCAAAA) was the highest, and its milk fat percentage, MUFAs, PUFAs and SFAs were also the highest (p < 0.05). Taken together, we found nine SNPs in the SORBS1 gene that are closely related to the milk fat traits of cattleyak. Moreover, the mutation of amino acids caused by SNPs had positive effects on the milk fat traits of cattleyak. H1-H1 is the dominant diplotype which significantly related to the milk fat traits of cattleyak. This study provides a new molecular marker and theoretical basis for screening the milk fat traits of cattleyak.

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“…Marker mikrosatelit sering diaplikasikan untuk studi keragaman genetik, hubungan filogenetik, struktur genetik populasi, dan analisis quantitative trait loci (QTLs) (Abebe et al 2015;Azimu et al 2018;De Carvalho et al 2020;Habimana et al 2020;Hariyono et al 2019;Zhang et al 2021). Marker mikrosatelit juga telah diaplikasikan untuk studi keragaman genetik sapi lokal di Indonesia (Utomo et al 2011;Merliana et al 2014;Septian et al 2015;Sutarno et al 2015;Mansur et al 2016;Agung et al 2019;Margawati et al 2019;Jakaria et al 2020).…”

Section: Definisi Dan Keunggulanunclassified

Application of Microsatellite Markers for Genetic Diversity Analysis of Indonesian Local Cattle

Hariyono

2022

WARTAZOA

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Animal genetic resources (AnGR), including cattle, have been valuable national assets that need to be preserved and developed. There are at least 16 recognized breeds of cattle that have been registered as local and new breeds by the Ministry of Agriculture of the Republic of Indonesia. Conservation and development programs of these local cattle breeds require basic information regarding their genetic diversity, relationships, and structures. There are several types of DNA markers that can be used for genetic diversity analysis, such as microsatellite markers. Microsatellites or short tandem repeats (STRs) are a group of DNA sequences consisting of tandemly repeated units (1–6 bp), which are abundant throughout the genome and can be found in both coding and non-coding regions. The primary advantages of microsatellites are that they are inherited in a Mendelian pattern (codominant markers), high polymorphism rates, and high abundances throughout the genome. The aim of this review is to discuss the application of microsatellite markers for genetic diversity analysis in Indonesian local cattle based on 3 indices: number alleles per locus, expected heterozygosity (He), and polymorphisms information content (PIC). There are at least 28 microsatellite markers that have been studied in Indonesian local cattle, with the number of alleles per locus ranging from 2 to 32, He values ranging from 0.100 to 0.985, and PIC values from 0.095 to 0.935. Based on the PIC values, several microsatellites are classified as highly informative, e.g. BM1824, ILST6, TGLA126, TGLA53, TGLA227, TGLA122, ETH225, INRA23, SPS113, SPS115, BM1818, CSSM66, ETH10, INRA005, INRA037, ETH185, HEL017, and ILSTS029. Therefore, these microsatellite markers can be potentially used for future genetic diversity analysis of other breeds of cattle.

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Genetic diversity and population structure analysis of eight local chicken breeds of Southern Xinjiang

Cited by 17 publications

References 27 publications

Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds

Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds

Polymorphisms of SORBS1 Gene and Their Correlation with Milk Fat Traits of Cattleyak

Application of Microsatellite Markers for Genetic Diversity Analysis of Indonesian Local Cattle

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