基于DNA池测序法筛选奶牛高信息量SNP标记的可行性

doi:10.3724/SP.J.1005.2014.0691

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HEREDITAS(Beijing) ›› 2014, Vol. 36 ›› Issue (7): 691-696.doi: 10.3724/SP.J.1005.2014.0691

• Research Articles • Previous Articles Next Articles

Direct sequencing of DNA pooling for screening highly informative SNPs in dairy cattle

Qin Chu¹, Dong Li², Shiyu Hou³, Wanhai Shi⁴, Lin Liu⁴, Yachun Wang²

1. Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China;
2. Key Laboratory of Agricultural Animal and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
3. Anshan Hengli Dairy Cattle Farm, Liaoning 114200, China;
4. Beijing Dairy Cattle Center, Beijing 100192, China

Received:2013-12-04 Online:2014-07-20 Published:2014-06-23

Abstract

Abstract: In this study, 139 bovine single nuclear polymorphisms (SNPs) were firstly selected and then directly sequenced using DNA pooling. Based on the ratio of two signal peak values, 92 SNPs with the ratio over 1/2 were considered as potential highly informative markers. To further verify the reliability of screening system, 59 SNP markers were genotyped in 122 Holstein cattle using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) method. The results showed that 56 SNPs had a call rate higher than 85%. The minor allele frequency (MAF) of these 56 markers ranged from 0.27 to 0.5, with an average of 0.41; and in which 54 markers had a MAF over 0.3, covering 96.4% of this group of markers (54/56). Our findings indicate that direct sequencing of DNA pooling is a useful and efficient tool for identifying highly informative SNPs.

Key words: dairy cattle, DNA pooling, single nuclear polymorphism, matrix-assisted laser desorption/ionisation time-of- flight mass spectrometry (MALDI-TOF MS), minor allele frequency

Qin Chu, Dong Li, Shiyu Hou, Wanhai Shi, Lin Liu, Yachun Wang. Direct sequencing of DNA pooling for screening highly informative SNPs in dairy cattle[J]. HEREDITAS(Beijing), 2014, 36(7): 691-696.

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Direct sequencing of DNA pooling for screening highly informative SNPs in dairy cattle

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