Zea mays Transcriptome or Gene expression

Combining dissimilar parents often leads to increased vigor in the hybrid offspring. “Heterosis” describes both this behavior and its underlying Mendelian and non-Mendelian interactions [1], although its molecular basis remains largely unknown. Recent comparisons of small RNA (sRNA) profiles from parents and their heterotic progeny identified correlations between interparental 24-nucleotide (24-nt) RNA variation and non-additive 24-nt RNA changes in the resulting hybrid [2,3]. 24-nt RNAs guide de novo cytosine methylation, and several proteins are required for their biogenesis, including a Snf2-like ATPase: required to maintain repression1 (RMR1) [4]. We found height variation between heterotic hybrids +/- RMR1 activity, implicating a role for RMR1 in heterosis. Based on the published correlations mentioned above [2,3], we hypothesized that RMR1-loss reduces parental sRNAs, altering their relative ratios and changing the sRNA profiles in the resulting hybrid from those of a standard hybrid (from +RMR1 parents). To probe this hypothesis, we profiled sRNAs from parents and hybrids +/- RMR1 function, limiting the parental diversity to only portions of chromosomes 6 and 9. Our analysis will address how RMR1 loss changes hybrid sRNAs in the presence and absence of underlying genetic variation and help to determine how this loss results in different phenotypic outcomes from heterotic crosses. 1. Shull (1948) Genetics 2. Groszmann et al (2011) PNAS 3. Barber et al (2012) PNAS 4. Hale et al (2007) PLoS Biology Overall design: We used an interchange chromosome (T6-9 043-1) introgressed into B73 (~95% B73) to create a local region of genetic diversity when crossed as a female parent to 100% B73 individual. Small RNAs from immature cobs were sequenced from both of these parents and their resulting hybrid (2 samples each). Additionally, a similar cross where the T6-9 containing female parent lacked RMR1 activity (rmr1-1 / rmr1-1) was used to generate a counterpart hybrid whose small RNAs were also profiled (2 samples) from immature cobs. Finally, small RNAs from 2 immature cobs of an unrelated rmr1 heterozygote (again highly introgressed into B73) were sequenced as well.

将遗传背景差异较大的亲本进行杂交，通常可使杂交后代获得更强的生长活力。杂种优势（Heterosis）一词既指代这一现象，也涵盖其背后的孟德尔式与非孟德尔式互作机制[1]，尽管其分子基础至今尚未完全阐明。既往针对亲本及其杂种优势后代的小RNA（small RNA, sRNA）表达谱对比研究已证实，亲本间24核苷酸（24-nucleotide, 24-nt）RNA的差异与杂交后代中24-nt RNA的非加性表达变化存在相关性[2,3]。24-nt RNA可介导从头胞嘧啶甲基化，其生物发生过程需要多种蛋白参与，包括一类类Snf2 ATP酶：维持沉默因子1（required to maintain repression1, RMR1）[4]。本研究发现，携带/不携带RMR1活性的杂种优势杂交组合间存在株高差异，提示RMR1在杂种优势形成中发挥一定作用。基于前文提及的已有研究相关性结论[2,3]，本研究提出假说：RMR1功能缺失会减少亲本sRNA的积累，改变亲本sRNA的相对比例，进而使杂交后代的sRNA表达谱与由携带RMR1活性的亲本产生的标准杂交种的sRNA表达谱产生差异。为验证这一假说，本研究对携带/不携带RMR1功能的亲本及其杂交后代的sRNA进行了表达谱分析，且将亲本间的遗传差异限定在第6号和第9号染色体的部分区域内。本研究的分析将阐明：在存在或不存在基础遗传变异的情况下，RMR1功能缺失如何改变杂交后代的sRNA表达谱，并有助于揭示该功能缺失如何导致杂种优势杂交组合产生不同的表型结果。
1. 舒尔（Shull, 1948）《遗传学（Genetics）》
2. 格罗兹曼等（Groszmann et al, 2011）《美国国家科学院院刊（PNAS）》
3. 巴伯等（Barber et al, 2012）《美国国家科学院院刊（PNAS）》
4. 黑尔等（Hale et al, 2007）《公共科学图书馆·生物学（PLoS Biology）》
实验整体设计：本研究使用导入B73遗传背景（约95%序列来自B73）的易位染色体（interchange chromosome, T6-9 043-1）作为母本，与100%遗传背景为B73的个体进行杂交，以创造局部遗传差异区域。分别对这两个亲本及其杂交后代的未成熟雌穗进行小RNA测序，每个组设置2个生物学重复样本。此外，本研究还设置了另一组相似杂交组合：将携带T6-9易位染色体且RMR1活性缺失的母本（rmr1-1 / rmr1-1）与100% B73个体杂交，获得对应的杂交后代，并对其未成熟雌穗的小RNA进行表达谱分析（2个生物学重复样本）。最后，本研究还对1个无关的rmr1杂合子（同样高度导入B73遗传背景）的2个未成熟雌穗样本进行了小RNA测序。