Exploring genetic diversity and population structure of Punjab goat breeds using Illumina 50 K SNP bead chip

Muner, Raja Danish; Moaeen‐ud‐Din, Muhammad; Bilal, G.; Waheed, Hafiz Muhammad; Khan, Muhammad Sajjad; Asad, Muhammad Javaid; Kuthu, Zulfiqar Hussain

doi:10.1007/s11250-021-02825-w

Cited by 12 publications

(6 citation statements)

References 37 publications

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“…The findings from genomic data have become an invaluable resource for effective management of breeding programs in small and endangered populations [ 10 ]. The availability of a medium density single nucleotide polymorphism (SNP) array for goat species [ 11 ] has provided the opportunity to improve the knowledge on the genetic differentiation between goat populations, in particular for local genetic resources [ 12 , 13 , 14 ]. The Italian caprine diversity was previously studied through SNP data analyses [ 1 , 2 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat

Tolone

Sardina

Senczuk

et al. 2022

Animals

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Italy contains a large number of local goat populations, some of which do not have a recognized genetic structure. The “Mascaruna” is a goat population reared for milk production in Sicily. In this study, a total of 72 individuals were genotyped with the Illumina Goat_IGGC_65K_v2 BeadChip with the aim to characterize the genetic diversity, population structure and relatedness with another 31 Italian goat populations. The results displayed a moderate level of genetic variability for Mascaruna, in concordance with the estimated values for Italian goats. Runs of homozygosity islands are linked to genes involved in milk production, immune response and local adaptation. Population structure analyses separated Mascaruna from the other goat populations, indicating a clear genetic differentiation. Although they are not conclusive, our current results represent a starting point for the creation of monitoring and conservation plans. Additional analyses and a wider sampling would contribute to refine and validate these results. Finally, our study describing the diversity and structure of Mascaruna confirms the usefulness of applied genomic analyses as valid tools for the study of the local uncharacterized genetic resources.

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Section: Introductionmentioning

confidence: 99%

Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat

Tolone

Sardina

Senczuk

et al. 2022

Animals

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“…The results indicated that both types of Bactrian Camels exhibit rich genetic diversity and a close genetic relationship, with evident historical genetic exchange between them. The 50K SNP chip was utilized to assess genetic diversity and relationships within the Punjab goat breeds of Pakistan, revealing rich genetic diversity but a high degree of inbreeding within this population [ 20 ]. Whole genome re-sequencing (WGRS) involves high-throughput sequencing of individuals from species with known reference genome species, followed by the study of genetic differences among individuals through analysis of the measured genome data and comparison with the reference sequence [ 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing

Wang,

et al. 2024

BMC Genomics

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Background Inner Mongolia cashmere goat (IMCG), renowned for its superior cashmere quality, is a Chinese indigenous goat breed that has been developed through natural and artificial selection over a long period. However, recently, the genetic resources of IMCGs have been significantly threatened by the introduction of cosmopolitan goat breeds and the absence of adequate breed protection systems. Results In order to assess the conservation effectiveness of IMCGs and efficiently preserve and utilize the purebred germplasm resources, this study analyzed the genetic diversity, kinship, family structure, and inbreeding of IMCGs utilizing resequencing data from 225 randomly selected individuals analyzed using the Plink (v.1.90), GCTA (v.1.94.1), and R (v.4.2.1) software. A total of 12,700,178 high-quality SNPs were selected through quality control from 34,248,064 SNP sites obtained from 225 individuals. The average minor allele frequency (MAF), polymorphic information content (PIC), and Shannon information index (SHI) were 0.253, 0.284, and 0.530, respectively. The average observed heterozygosity (Ho) and the average expected heterozygosity (He) were 0.355 and 0.351, respectively. The analysis of the identity by state distance matrix and genomic relationship matrix has shown that most individuals’ genetic distance and genetic relationship are far away, and the inbreeding coefficient is low. The family structure analysis identified 10 families among the 23 rams. A total of 14,109 runs of homozygosity (ROH) were identified in the 225 individuals, with an average ROH length of 1014.547 kb. The average inbreeding coefficient, calculated from ROH, was 0.026 for the overall population and 0.027 specifically among the 23 rams, indicating a low level of inbreeding within the conserved population. Conclusions The IMCGs exhibited moderate polymorphism and a low level of kinship with inbreeding occurring among a limited number of individuals. Simultaneously, it is necessary to prevent the loss of bloodline to guarantee the perpetuation of the IMCGs’ germplasm resources.

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“…Despite of having rich diversity of goat breeds in the country; no GWAS has been carried out in Pakistani goats regarding growth and conformation traits. However, Punjab goat breeds have been recently documented using 50 K SNP chip 18 . Current study was aimed to fulfill the gap by finding significant genomic regions or SNPs and relevant genes influencing body weight and morphometric measurements among goat breeds of Punjab province.…”

Section: Introductionmentioning

confidence: 99%

Genome wide association study identifies novel candidate genes for growth and body conformation traits in goats

Moaeen‐ud‐Din

Muner²,

Khan³

2022

Sci Rep

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Pakistan is third largest country in term of goat population with distinct characteristics of breeds and estimated population of 78.2 million. Punjab province has 37% of country’s total population with seven important documented goat breeds namely Beetal, Daira Din Pannah, Nachi, Barbari, Teddi, Pahari and Pothwari. There is paucity of literature on GWAS for economically important traits i.e., body weight and morphometric measurements. Therefore, we performed GWAS using 50 K SNP Chip for growth in term of age adjusted body weight and morphometric measurements in order to identify genomic regions influencing these traits among Punjab goat breeds. Blood samples were collected from 879 unrelated animals of seven goat breeds along with data for body weight and morphometric measurements including body length, body height, pubic bone length, heart girth and chest length. Genomic DNA was extracted and genotyped using 50 K SNP bead chip. Association of genotypic data with the phenotypic data was performed using Plink 1.9 software. Linear mixed model was used for the association study. Genes were annotated from Capra hircus genome using assembly ARS1. We have identified a number of highly significant SNPs and respective candidate genes associated with growth and body conformation traits. The functional aspects of these candidate genes suggested their potential role in body growth. Moreover, pleiotropic effects were observed for some SNPs for body weight and conformation traits. The results of current study contributed to a better understanding of genes influencing growth and body conformation traits in goat.

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Exploring genetic diversity and population structure of Punjab goat breeds using Illumina 50 K SNP bead chip

Cited by 12 publications

References 37 publications

Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat

Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat

Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing

Genome wide association study identifies novel candidate genes for growth and body conformation traits in goats

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