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Mining and identification of SNP markers associated with growth traits in the clam Meretrix meretrix
Dai, Ping1,2; Wang, Hongxia2; Liu, Baozhong2,3
2017-06-01
Source PublicationAQUACULTURE INTERNATIONAL
Volume25Issue:3Pages:1185-1196
SubtypeArticle
AbstractSelecting fast-growing strains is the most common objective of genetic breeding programs. In this study, we sought to mine the growth-associated single nucleotide polymorphisms (SNPs) in the commercially cultured clam Meretrix meretrix by candidate gene association analysis. Fifty potentially growth-associated contigs based on their functional annotation were chosen as candidates from our EST database, and 240 SNPs were predicted from these contigs. Seventy-one predicted SNPs and five novel SNPs were identified by pooled DNA sequencing in both a fast-growing population (09SPSB) and a control population (09G(3)SB). Among these SNPs, 24 were also identified in an independent population (CP). Through multiplex SNaPshot genotyping, 16 of the 24 SNPs were used in the marker-trait association analysis between 09SPSB and 09G(3)SB. The results showed that seven SNPs in five contigs were significantly associated with clam shell length (P < 0.05). With bidirectional selective genotyping in the CP, three of the seven growth-associated SNPs were further confirmed. Annotations of these SNP-containing contigs provided some clues of these genes functioning in growth. After a haplotype association analysis, we found four haplotypes with significantly different frequencies between 09SPSB and 09G(3)SB (P < 0.001). Through a generalized multifactor dimensionality reduction (GMDR) analysis, we found several gene-gene interaction models, of which the two-factor model (SNPg5/SNPg16) was the best one. These obtained markers will be useful in further quantitative trait loci identification and marker-assisted selection in M. meretrix.
KeywordGmd Growth Marker-trait Association Meretrix Meretrix Snps
DOI10.1007/s10499-016-0106-x
Indexed BySCI
Language英语
WOS IDWOS:000401852200012
Citation statistics
Document Type期刊论文
Version出版稿
Identifierhttp://ir.qdio.ac.cn/handle/337002/136876
Collection实验海洋生物学重点实验室
Affiliation1.Chinese Acad Fishery Sci, Key Lab Sustainable Utilizat Marine Fisheries Res, Minist Agr, Yellow Sea Fisheries Res Inst, Qingdao 266071, Peoples R China
2.Chinese Acad Sci, Key Lab Expt Marine Biol, Inst Oceanol, Qingdao 266071, Peoples R China
3.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Dai, Ping,Wang, Hongxia,Liu, Baozhong. Mining and identification of SNP markers associated with growth traits in the clam Meretrix meretrix[J]. AQUACULTURE INTERNATIONAL,2017,25(3):1185-1196.
APA Dai, Ping,Wang, Hongxia,&Liu, Baozhong.(2017).Mining and identification of SNP markers associated with growth traits in the clam Meretrix meretrix.AQUACULTURE INTERNATIONAL,25(3),1185-1196.
MLA Dai, Ping,et al."Mining and identification of SNP markers associated with growth traits in the clam Meretrix meretrix".AQUACULTURE INTERNATIONAL 25.3(2017):1185-1196.
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