三江黄牛全基因组数据分析

doi:10.3864/j.issn.0578-1752.2017.01.016

Abstract

Abstract: 【Objective】 The objective of this paper is to study the genetic diversity of Sanjiang cattle group and discuss its genetic variation at the genome level.【Method】Fifty individual genomic DNA were extracted and mixed with isocratic and equal volumes, then the DNA pool of the mixed samples were constructed. Genomic DNA was interrupted randomly by using CovarisS2 and the DNA fragments of 500 bp were recovered by electrophoresis, and DNA library was constructed at last. Finally, the sequencing data were obtained through the Illumina HiSeq 2000. The short reads were mapped to bovine reference genome (UMD 3.1) to detect the genomic mutations of Sanjiang cattle using BWA software. The analysis of the re-sequencing data was implemented using SAMtools, Picard-tools, GATK, Reseqtools, the SNPs and indels were annotated based on the Ensembl, DAVID and dbSNP database. 【Result】A total of 77.8 Gb of sequence data were generated by whole-genome sequencing analysis, 99.31% of the reference genome sequence was covered with an mapping depth of 25.32-fold, 778 403 444 reads and 77 840 344 400 bases were obtained, of which 673 670 505 reads and 67 341 451 555 bases covered 86.55% and 86.51% of bovine reference genomes (UMD 3.1) respectively, paired-end reads mapping were 635 242 898 (81.61%), paired-end bases mapping were 63 512 636 924 (81.59%). A total of 20 477 130 SNPs and 1 355 308 small indels were identified, of which 2 147 988 SNPs (2.4%) and 90 180 (6.7%) indels were found to be new. Of the total number of SNPs, 989 686 (4.83%) homozygous SNPs and 19 487 444 (95.17%) heterozygous SNPs were discovered, homozygous/heterozygous SNPs was 1﹕19.7. Transitions were 14 800 438, transversions were 6 680 058, transition/transversion (TS/TV) was 2.215. SNPs of splice site mutations were 727, the number of SNPs which the start codon converts into no stop codon were 117, SNPs of premature stop codon were 530, the number of SNPs which stop codon converts into no stop codon were 88. A total of 57 621 non-synonymous SNPs and 83 797 synonymous SNPs were detected, the ratio was 0.69. Non-synonymous SNPs were detected in 9,017 genes, 567 genes were assigned as trait-associated genes, which included meat quality, disease resistance, milk production, growth rate, fecundity with the number of 471, 77, 21, 10, and 8 respectively, the function of some genes were overlap. In detection of indels, 693 180 (51.15%) were deletions and 662 148 (48.85%) were insertions, 161 198 (11.89%) were homozygous and 1 194 110 (88.11%) were heterozygous. Most variations were located in intergenic regions and introns. Heterozygosity (H), nucleotide diversity (Pi) and theta W of Sanjiang cattle genome-wide were 7.6 × 10^-3, 0.0039, 0.0040, respectively, which indicated that Sanjiang cattle have an abundant genetic diversity. The Tajima'D of Sanjiang cattle population was-0.06 832, which speculated that the population exists an unbalanced selection.【Conclusion】Results of this research will provide valuable genomic data for further investigations of the genetic mechanisms underlying traits of interest and protection of Sanjiang cattle breeds genetic diversity.

Key words: Sanjiang Cattle, genome, next generation sequencing, SNP, indel

SONG NaNa, ZHONG JinCheng, CHAI ZhiXin, WANG Qi, HE ShiMing, WU JinBo, JIAN ShangLin, RAN Qiang, MENG Xin, HU HongChun. The Whole Genome Data Analysis of Sanjiang Cattle[J].Scientia Agricultura Sinica, 2017, 50(1): 183-194.

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