QTL mapping in autotetraploids using SNP dosage information.
QTL mapping in autotetraploids using SNP dosage information.
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DOI：
10.1007/s00122-014-2347-2
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发表时间：
2014-09
影响因子：
5.4
通讯作者：
Bryan, Glenn J.
中科院分区：
文献类型：
--
作者：
Hackett, Christine A.;Bradshaw, John E.;Bryan, Glenn J.
通过分析同源四倍体中SNP剂量得到的密集连锁图提供了关于数量性状基因座的位置和遗传模型的详细信息。 测序和基因分型技术的最新发展使研究人员能够生成高密度的单核苷酸多态性（SNP）基因型数据用于作图研究。对于多倍体物种，SNP基因型是关于等位基因剂量的信息，并且Hackett等人（PLoS ONE 8：e63939）提出了关于剂量信息如何用于同源四倍体物种中F1群体的连锁图构建和数量性状基因座（QTL）定位的理论。在这里，QTL定位使用剂量信息探索模拟表型性状的中度遗传力和可能的非加性效应。不同的映射策略进行了比较，在添加剂和更复杂的模型，模型拟合作为一个单一的步骤或通过迭代重新加权建模。我们建议在没有迭代重新加权的情况下拟合加性模型，然后探索在最可能的位置估计的基因型均值的非加性模型。我们应用这一策略重新分析了190个F1个体的马铃薯群体的高遗传力性状：花色、成熟度、高度和对晚疫病（Phytophthora infestans（Mont.）de Bary）和马铃薯胞囊线虫（Globodera pallida）的基因组DNA序列，使用3839个SNP的图谱。详细的连锁图提高了QTL定位的近似置信区间，揭示了每个QTL的遗传模型的更多信息。对于几个报道的QTL，可以鉴定候选SNP，并用于提出候选性状基因。我们的结论是，高标记密度是信息的遗传模型在基因座的大的影响，但需要更大的群体来检测较小的QTL。本文的在线版本（doi：10.1007/s 00122 -014-2347-2）包含补充材料，可供授权用户使用。
Dense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci. Recent developments in sequencing and genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, the SNP genotypes are informative about allele dosage, and Hackett et al. (PLoS ONE 8:e63939,) presented theory about how dosage information can be used in linkage map construction and quantitative trait locus (QTL) mapping for an F1 population in an autotetraploid species. Here, QTL mapping using dosage information is explored for simulated phenotypic traits of moderate heritability and possibly non-additive effects. Different mapping strategies are compared, looking at additive and more complicated models, and model fitting as a single step or by iteratively re-weighted modelling. We recommend fitting an additive model without iterative re-weighting, and then exploring non-additive models for the genotype means estimated at the most likely position. We apply this strategy to re-analyse traits of high heritability from a potato population of 190 F1 individuals: flower colour, maturity, height and resistance to late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematode (Globodera pallida), using a map of 3839 SNPs. The approximate confidence intervals for QTL locations have been improved by the detailed linkage map, and more information about the genetic model at each QTL has been revealed. For several of the reported QTLs, candidate SNPs can be identified, and used to propose candidate trait genes. We conclude that the high marker density is informative about the genetic model at loci of large effects, but that larger populations are needed to detect smaller QTLs. The online version of this article (doi:10.1007/s00122-014-2347-2) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
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DOI：
10.1007/s004380050800
发表时间：
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期刊：
MOLECULAR AND GENERAL GENETICS
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