Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
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DOI：
10.1534/genetics.116.192823
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发表时间：
2017-04
期刊：
影响因子：
3.3
通讯作者：
Mott R
中科院分区：
文献类型：
--
作者：
Imprialou M;Kahles A;Steffen JG;Osborne EJ;Gan X;Lempe J;Bhomra A;Belfield E;Visscher A;Greenhalgh R;Harberd NP;Goram R;Hein J;Robert-Seilaniantz A;Jones J;Stegle O;Kover P;Tsiantis M;Nordborg M;Rätsch G;Clark RM;Mott R
结构重排会对定量表型产生意想不到的影响。令人惊讶的是，这些重排也可以被认为是……为了了解结构变异的群体遗传学及其对表型的影响，我们开发了一种方法来绘制在低覆盖率测序的群体中分离的结构变异。我们避免直接调用结构变体。相反，某个位点存在潜在结构变异的证据是通过异常映射到该位点的短读计数的变化来表明的。这些结构变异性状被视为数量性状并进行遗传图谱绘制，类似于基因表达研究。一个基因座的结构变异性状与远处基因座的基因型之间的关联表明了转座的起源和目标。利用来自 488 个重组近交拟南芥基因组的超低覆盖率 (0.3×) 群体序列数据，我们鉴定了 6502 个分离结构变异。值得注意的是，其中 25% 是转位。虽然许多结构变异无法精确描述，但我们通过聚合酶链式反应验证了 44 个预测转座断点中的 83%。我们表明，特定的结构变异可能是导致发芽和抵抗真菌 Albugo laibachii（分离株 Nc14）感染的数量性状位点的原因。此外，我们还表明，读数映射异常导致的表型遗传力不同于标准遗传变异，并且在发芽和抽苔时间方面超过了标准遗传变异。结构变异内的基因也更有可能被沉默或失调。这种方法补充了在较少个体中进行高覆盖率测序的结构变异发现的流行策略。它通常适用于低覆盖率测序的大群体，并且特别适合于定位转座。
Structural Rearrangements can have unexpected effects on quantitative phenotypes. Surprisingly, these rearrangements can also be considered as... To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between a structural variant trait at one locus, and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3×) population sequence data from 488 recombinant inbred Arabidopsis thaliana genomes, we identified 6502 segregating structural variants. Remarkably, 25% of these were transpositions. While many structural variants cannot be delineated precisely, we validated 83% of 44 predicted transposition breakpoints by polymerase chain reaction. We show that specific structural variants may be causative for quantitative trait loci for germination and resistance to infection by the fungus Albugo laibachii, isolate Nc14. Further we show that the phenotypic heritability attributable to read-mapping anomalies differs from, and, in the case of time to germination and bolting, exceeds that due to standard genetic variation. Genes within structural variants are also more likely to be silenced or dysregulated. This approach complements the prevalent strategy of structural variant discovery in fewer individuals sequenced at high coverage. It is generally applicable to large populations sequenced at low-coverage, and is particularly suited to mapping transpositions.
影响因子：
3.3
作者：
Lai AG;Denton-Giles M;Mueller-Roeber B;Schippers JH;Dijkwel PP
通讯作者：
Dijkwel PP