Efficiency of genotyping by sequencing technology and its comparison with single nucleotide polymorphism array in an F2 chickens population

Document Type : Research Paper

Authors

1 PhD student,, Department of Animal Science, Agricultural Faculty, Tarbiat Modares University, Tehran,, Iran.

2 Department of Animal Science, Agricultural Faculty, Tarbiat Modares University, Tehran, Iran.

Abstract

For researches, there is a wide variety of available technologies to collect molecular information in the field of chicken genomics. These technologies, which consist of single-nucleotide polymorphism (SNP) arrays and genotyping by sequencing (GBS), depending on the goals of the study, can have different applications. The aim of this study was to compare the results of markers genotyped by two technologies, namely, 60 K SNP BeadChip and genotyping by sequencing, using data collected on F2 chicken population resulting from a reciprocal crosses between a native bird of Urmia and a fast-growing commercial Arian line. In genotyping by GBS, 882,918 SNPs were identified, of which 815,613 SNPs (92.40%) were located on chromosomes 1 to 28. In 60 K SNP array, the number of SNPs for each sample were 51347, which were distributed on chromosomes 1 to 28. The GBS data identified more markers and haplotype blocks than the 60 K SNP array. The rate of linkage disequilibrium (LD) in the physical distances of 10, 100 and 1000 kbp in GBS was less than that of SNP array. The large variety of SNPs in the GBS resulted in a uniform population structures and kinship. Also, in addition to the high performance for identifying single nucleotide polymorphisms, the technology of GBS also reduced the costs of the genotyping for each sample, therefore, it seems that the use of genotyping by sequencing technology could be a suitable alternative method to the 60 K SNP BeadChip array technology for genome-wide association studies in chicken population.
 
 

Keywords

Main Subjects

Extended Abstract

Introduction

    Nowadays, researchers in the field of agricultural genomics have a wide variety of technologies to collect molecular genetic information. These technologies, which consist of 60k single nucleotide polymorphism (SNP) BeadChip array and Genotyping by Sequencing (GBS), depending on the goals of the researcher's study, can have different applications. The high cost of single nucleotide polymorphism array technology per sample limits their use in research applications, especially for the large-sized populations. The aim of this study was to evaluate the efficiency of the data obtained from the genotyping by sequencing (GBS) technology in an F2 chickens population and compare the results with the data obtained from a 60k SNP BeadChip array.

 

Materials & Methods

    A F1 chicken population was created from a reciprocal crosses between a fast-growing Arian commercial broiler line and an Urmia native fowls. The F1 population were intercrossed randomly to produce 312 F2 chickens in eight half-sib families from five hatches. The Genomic DNA of these birds were extracted from blood samples and then genotyped by a commercial Illumina chicken SNP BeadChip panel in collaboration with Aarhus University, Denmark. Also, 368 birds, including 312 birds from the F2 generation, 37 birds from the F1 generation, and 19 birds from the base population generation were genotyped using genotyping by sequencing technology by The Elshire Group Ltd., New Zealand.

 

Results

    Using genotyping by sequencing technology, 882,918 SNPs were detected, of which 815,613 SNP were located on chromosomes 1 to 28 and 67,305 SNPs on autosomal chromosomes 30 to 33 and sex chromosomes Z and W. For 60k SNP array, 51347 SNP markers, located on chromosomes 1 to 28, were genotyped for each sample. The analysis of the missing genotype in 60k SNP array technology indicated that almost all the birds had all single nucleotide polymorphisms. These results for the missing genotype in the genotyping by sequencing technology were about 54%, which could be reduced by using imputation of missing data. The rate of linkage disequilibrium (LD) in the physical distances of 10 kbp, 100 kbp and 1000 kbp in GBS technology was less than that of SNP array. By increasing the physical distances, the rate of LD decreased. The number of haplotype blocks in the genotyping by sequencing technology (167396) were substantially higher than the 60 kb single nucleotide polymorphism array (6783).  

Conclusion

    In the present study, the diversity of SNPs in the genotyping by sequencing data was very high, creates an acceptable homogeneity of population structure and kinship structures. Since haplotypes blocks have a higher linkage disequilibrium with quantitative trait loci (QTL), it is expected that the genotyping by sequencing technology improve genome-wide association studies (GWAS) due to its higher haplotype blocks. Also, in addition to the high performance in identifying single nucleotide polymorphisms, the technology of GBS also reduced the costs of the genotyping for each sample, therefore, it seems that the use of genotyping by sequencing technology could be a suitable alternative method to the 60k SNP BeadChip array technology for genome-wide association studies in chicken population.

References

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Iranian Journal of animal Science
Volume 55, Issue 4
December 2024
Pages 693-711

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History

  • Receive Date: 19 February 2024
  • Revise Date: 21 April 2024
  • Accept Date: 30 April 2024

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