von Korff Maria, Radovic Slobodanka, Choumane Wafaa, Stamati Konstantina, Udupa Sripada M, Grando Stefania, Ceccarelli Salvatore, Mackay Ian, Powell Wayne, Baum Michael, Morgante Michele
International Center for Agricultural Research in the Dry Areas, PO Box 5466, Aleppo, Syria.
Plant J. 2009 Jul;59(1):14-26. doi: 10.1111/j.1365-313X.2009.03848.x. Epub 2009 Feb 26.
In the present study, we analysed allele-specific expression (ASE) in the selfing species barley to assess the frequency of cis-acting regulatory variation and the effects of genetic background, developmental differences and drought stress on allelic expression levels. We measured ASE ratios in 30 genes putatively involved in stress responses in five hybrids and their reciprocals, namely Hordeum spontaneum 41-1/Alexis (HAl), Hordeum spontaneum 41-1/Arta (HAr), Sloop/WI3408 (SW), Tadmor/Sloop (TS) and Tadmor/WI3408 (TW). In order to detect cis-acting variation related to drought and developmental changes, the barley hybrids were grown under control and water-limited conditions, and leaf tissue was harvested at two developmental stages. The analysis demonstrated that more than half of the genes measured (63%) showed allelic differences in expression of up to 19-fold due to cis-regulatory variation in at least one cross by treatment/stage combination. Drought stress induced changes in allelic expression ratios, indicating differences between drought responsive cis-elements. In addition, ASE differences between developmental stages suggested the presence of cis-acting elements interacting with developmental cues. We were also able to demonstrate that the levels and frequency of allelic imbalance and hence differences in cis-regulatory elements are correlated with the genetic divergence between the parental lines, but may also arise as an adaptation to diverse habitats. Our findings suggest that cis-regulatory variation is a common phenomenon in barley, and may provide a molecular basis of transgression. Differential expression of near-isogenic members of the same gene family could potentially result in hybrid lines out performing their parents in terms of expression level, timing and response to developmental and environmental cues. Identification and targeted manipulation of cis-regulatory elements will assist in breeding improved crops with a better adaptation to changing environments.
在本研究中，我们分析了自花授粉物种大麦中的等位基因特异性表达（ASE），以评估顺式作用调控变异的频率，以及遗传背景、发育差异和干旱胁迫对等位基因表达水平的影响。我们测量了五个杂种及其反交组合中30个推测参与胁迫反应的基因的ASE比率，这五个组合分别是：野生大麦41-1/亚历克西斯（HAl）、野生大麦41-1/阿尔塔（HAr）、斯卢普/ WI3408（SW）、塔德莫尔/斯卢普（TS）和塔德莫尔/ WI3408（TW）。为了检测与干旱和发育变化相关的顺式作用变异，将大麦杂种种植在对照和水分受限条件下，并在两个发育阶段采集叶片组织。分析表明，所测量的基因中超过一半（63%）由于至少一个杂交组合中处理/阶段组合的顺式调控变异，表现出高达19倍的等位基因表达差异。干旱胁迫诱导了等位基因表达比率的变化，表明干旱响应顺式元件之间存在差异。此外，发育阶段之间的ASE差异表明存在与发育线索相互作用的顺式作用元件。我们还能够证明，等位基因不平衡的水平和频率以及顺式调控元件的差异与亲本系之间的遗传差异相关，但也可能是对不同生境的一种适应而产生。我们的研究结果表明，顺式调控变异在大麦中是一种常见现象，可能为杂种优势提供分子基础。同一基因家族近等基因成员的差异表达可能会使杂交系在表达水平、时间以及对发育和环境线索的响应方面表现优于其亲本。鉴定和顺式调控元件的靶向操作将有助于培育出更能适应不断变化环境的改良作物。
