Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL.
Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL.
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DOI：
10.1186/s13059-015-0665-6
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发表时间：
2015-05-12
期刊：
影响因子：
12.3
通讯作者：
Gubler F
中科院分区：
文献类型：
--
作者：
Barrero JM;Cavanagh C;Verbyla KL;Tibbits JF;Verbyla AP;Huang BE;Rosewarne GM;Stephen S;Wang P;Whan A;Rigault P;Hayden MJ;Gubler F
下一代测序技术为识别导致性状变异的遗传成分提供了新的机会。然而，在具有大的多倍体基因组的物种中，例如面包小麦，快速鉴定数量性状基因座（QTL）相关基因的能力仍然是重要的。为了克服这一点，我们引入了一种新的管道，通过RNA测序分析多个近等基因系分离的目标QTL。我们使用这种方法来表征一个主要的和广泛使用的种子休眠QTL位于染色体4AL。它利用大型多亲本作图群体提供的能力和作图分辨率，同时通过在目标QTL区域使用多等位基因对比来降低复杂性。我们的方法确定了两个相邻的候选基因属于ABA诱导的小麦质膜19家族的QTL区域内。其中之一，PM 19-A1，在休眠基因型的籽粒成熟过程中高度表达。第二个，PM 19-A2，显示了序列的变化，导致休眠和非休眠基因型之间的几个氨基酸改变。我们证实PM 19基因是种子休眠的正调控因子。这些强有力的候选人的有效鉴定证明了我们的转录组学管道的实用性，快速QTL基因定位。通过这种方法，我们能够提供一个全面的遗传分析的主要来源的小麦籽粒休眠。对面包小麦和硬粒小麦的进一步分析表明，这个重要的休眠QTL早于六倍体小麦。小麦育种者利用这些基因可以帮助消除小麦收获前发芽。本文的在线版本（doi：10.1186/s13059-015-0665-6）包含补充材料，可供授权用户使用。
Next-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation. However, in species with large polyploid genomes, such as bread wheat, the ability to rapidly identify genes underlying quantitative trait loci (QTL) remains non-trivial. To overcome this, we introduce a novel pipeline that analyses, by RNA-sequencing, multiple near-isogenic lines segregating for a targeted QTL. We use this approach to characterize a major and widely utilized seed dormancy QTL located on chromosome 4AL. It exploits the power and mapping resolution afforded by large multi-parent mapping populations, whilst reducing complexity by using multi-allelic contrasts at the targeted QTL region. Our approach identifies two adjacent candidate genes within the QTL region belonging to the ABA-induced Wheat Plasma Membrane 19 family. One of them, PM19-A1, is highly expressed during grain maturation in dormant genotypes. The second, PM19-A2, shows changes in sequence causing several amino acid alterations between dormant and non-dormant genotypes. We confirm that PM19 genes are positive regulators of seed dormancy. The efficient identification of these strong candidates demonstrates the utility of our transcriptomic pipeline for rapid QTL to gene mapping. By using this approach we are able to provide a comprehensive genetic analysis of the major source of grain dormancy in wheat. Further analysis across a diverse panel of bread and durum wheats indicates that this important dormancy QTL predates hexaploid wheat. The use of these genes by wheat breeders could assist in the elimination of pre-harvest sprouting in wheat. The online version of this article (doi:10.1186/s13059-015-0665-6) contains supplementary material, which is available to authorized users.
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影响因子：
3.3
作者：
Liu, Shubing;Sehgal, Sunish K.;Bai, Guihua
通讯作者：
Bai, Guihua
影响因子：
3.5
作者：
Ayliffe, MA;Steinau, M;Pryor, AJ
通讯作者：
Pryor, AJ
影响因子：
--
作者：
Li, CD;Tarr, A;Appelsa, R
通讯作者：
Appelsa, R
影响因子：
7.4
作者：
Gubler, Frank;Hughes, Trijntje;Jacobsen, John
通讯作者：
Jacobsen, John
影响因子：
4.4
作者：
Gómez-Porras JL;Riaño-Pachón DM;Dreyer I;Mayer JE;Mueller-Roeber B
通讯作者：
Mueller-Roeber B