Mining and identification of SNP markers associated with growth traits in the clam Meretrix meretrix

doi:10.1007/s10499-016-0106-x

IOCAS-IR > 实验海洋生物学重点实验室

	Mining and identification of SNP markers associated with growth traits in the clam Meretrix meretrix
	Dai, Ping 1,2; Wang, Hongxia 2; Liu, Baozhong2,3
	2017-06-01
发表期刊	AQUACULTURE INTERNATIONAL
卷号	25 期号:3 页码:1185-1196
文章类型	Article
摘要	Selecting 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.
关键词	Gmd Growth Marker-trait Association Meretrix Meretrix Snps
DOI	10.1007/s10499-016-0106-x
收录类别	SCI
语种	英语
WOS记录号	WOS:000401852200012
引用统计
文献类型	期刊论文
版本	出版稿
条目标识符	http://ir.qdio.ac.cn/handle/337002/136876
专题	实验海洋生物学重点实验室
作者单位	1.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
第一作者单位	中国科学院海洋研究所
推荐引用方式 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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