RNA-Seq identifies SNP markers for growth traits in rainbow trout.
RNA-Seq identifies SNP markers for growth traits in rainbow trout.
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DOI：
10.1371/journal.pone.0036264
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Yao J
中科院分区：
文献类型：
--
作者：
Salem M;Vallejo RL;Leeds TD;Palti Y;Liu S;Sabbagh A;Rexroad CE 3rd;Yao J
快速生长是一个重要的和高度期望的性状，它影响着食用动物生产的盈利能力，其中饲料成本占生产成本的最大比例。传统的基于表型的选择通常用于选择生长性状;然而，遗传改良在几代人中是缓慢的。单核苷酸多态性（SNPs）解释了个体间90%的遗传差异;因此，它们最适合用于遗传评估和采用分子遗传学进行选择性育种的策略。在编码序列内或附近发现的SNP特别令人感兴趣，因为它们更可能改变蛋白质的生物学功能。我们的目的是利用SNPs来识别与生长遗传变异相关的标记和基因。RNA-Seq全转录组分析的汇集的cDNA样本从人口的虹鳟鱼选择改善增长与遗传学的队列（10条鱼从1个全同胞家庭）确定SNP标记与生长速度。等位基因不平衡（快速生长样品的等位基因频率与缓慢生长样品的等位基因频率之间的比率）在得分>5.0时被认为是扩增，并且<0.2时被认为是杂合性丢失。SNPs的子集（n = 54）进行了验证和评估与生长性状在778个人的三代父母/后代面板代表40个家庭。 22个SNP标记和1个线粒体单倍型与生长性状显著相关。在其他具有重要商业价值的水产养殖种群中证实了48个标记的多态性。许多标记被聚类到代谢能产生途径的基因中，是遗传选择的合适候选者。该研究表明，在不同群体的低序列覆盖率下，RNA-Seq是识别SNP的快速有效手段，表型之间存在等位基因不平衡。该技术适用于缺乏完整和注释良好的基因组参考序列的非模式物种的标记开发。
Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs) explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth. RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample) were considered at scores >5.0 as an amplification and <0.2 as loss of heterozygosity. A subset of SNPs (n = 54) were validated and evaluated for association with growth traits in 778 individuals of a three-generation parent/offspring panel representing 40 families. Twenty-two SNP markers and one mitochondrial haplotype were significantly associated with growth traits. Polymorphism of 48 of the markers was confirmed in other commercially important aquaculture stocks. Many markers were clustered into genes of metabolic energy production pathways and are suitable candidates for genetic selection. The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes. This technique is suitable for marker development in non-model species lacking complete and well-annotated genome reference sequences.
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影响因子：
30.8
作者：
Goering, Harald H. H.;Curran, Joanne E.;Blangero, John
通讯作者：
Blangero, John
影响因子：
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作者：
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DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
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作者：
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通讯作者：
HOCHBERG, Y
影响因子：
2.5
作者：
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通讯作者：
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影响因子：
30.8
作者：
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通讯作者：
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