期刊
AQUACULTURE REPORTS
卷 20, 期 -, 页码 -出版社
ELSEVIER
DOI: 10.1016/j.aqrep.2021.100691
关键词
Shrimp; SNP array; Linkage disequilibrium; Effective population size
类别
资金
- Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior-Brazil (CAPES) [001]
- OPUMARSA (Santa Elena, Ecuador)
The inclusion of genomic information has accelerated genetic gain in shrimp breeding. Evaluating LD decay is crucial for assessing the feasibility of genomic selection. A study using a 50K SNP array tool characterized genomic diversity and LD in a farmed shrimp population.
The inclusion of genomic information became a reality in shrimp breeding and it is expected to accelerate the genetic gain over time. The decay of linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs) is an important measure to evaluate the feasibility of implementing genomic selection. The aim of this study was to evaluate the use of a novel 50 K SNP array tool to characterize the genomic diversity, LD and effective population size (N-e) in a farmed shrimp population. A total of 96 animals (40 sires and 56 dams) were genotyped using the novel Illumina AquaArray HD (50 K) vannamei (R). Quality control (QC) of genomic data was performed and three different minor allele frequency (MAF) exclusion thresholds were applied: < 0.10 (QC1), < 0.05 (QC2) and < 0.01 (QC3). After QC, 34,425, 39,091 and 42,789 SNPs were retained for QC1, QC2 and QC3, respectively, validating the high informativeness of this SNP array to this particular shrimp breeding population. The population showed a considerable high overall heterozygosity in comparison to other aquaculture species meaning that genetic diversity is stable despite selection. The principal component analysis revealed three genetically distant groups with the first two principal components explaining 27.7 % of total variation. LD decayed rapidly in the first 30Kb of distance between markers from 0.20 to 0.07 and then decreased to 0.02 in the long-range distance. These results suggest a relatively recent incorporation of animals from different populations in the broodstock. N-e size reduced from 7,871 to 301 animals in 827 generations for QC1, 8,253 to 305 animals for QC2 and 8,957 to 315 animals for QC3, both in 899 generations. Contemporary N-e was close to 86 for all QCs. The level of LD estimated suggests that genomic selection and genome-wide association studies are feasible in shrimp by using this SNP array.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据