Data from: A gene for genetic background in Zea mays: fine-mapping enhancer of teosinte branched1.2 to a YABBY class transcription factor

The effects of an allelic substitution at a gene often depend critically
on genetic background, i.e., the genotypes at other genes in the genome.
During the domestication of maize from its wild ancestor (teosinte), an
allelic substitution at teosinte branched (tb1) caused changes in both
plant and ear architecture. The effects of tb1 on phenotype were shown to
depend on multiple background loci, including one called enhancer of tb1.2
(etb1.2). We mapped etb1.2 to a YABBY class transcription factor
(ZmYAB2.1) and showed that the maize alleles of ZmYAB2.1 are either
expressed at a lower level than teosinte alleles or disrupted by
insertions in the sequences. tb1 and etb1.2 interact epistatically to
control the length of internodes within the maize ear, which affects how
densely the kernels are packed on the ear. The interaction effect is also
observed at the level of gene expression, with tb1 acting as a repressor
of ZmYAB2.1 expression. Curiously, ZmYAB2.1 was previously identified as a
candidate gene for another domestication trait in maize, nonshattering
ears. Consistent with this proposed role, ZmYAB2.1 is expressed in a
narrow band of cells in immature ears that appears to represent a
vestigial abscission (shattering) zone. Expression in this band of cells
may also underlie the effect on internode elongation. The identification
of ZmYAB2.1 as a background factor interacting with tb1 is a first step
toward a gene-level understanding of how tb1 and the background within
which it works evolved in concert during maize domestication.

一个基因上的等位基因替换（allelic substitution）的效应通常极大程度上依赖于遗传背景，即基因组中其他基因的基因型。在从野生祖先大刍草（teosinte）驯化玉米的过程中，大刍草分枝基因（teosinte branched 1，tb1）上的一次等位基因替换，改变了植株与果穗的结构。研究表明，tb1对表型的效应依赖于多个背景位点，其中一个被命名为tb1增强子位点2（enhancer of tb1.2，etb1.2）。我们将etb1.2定位到一个YABBY类转录因子（YABBY class transcription factor）ZmYAB2.1，并证实玉米的ZmYAB2.1等位基因要么表达水平低于大刍草等位基因，要么因序列内插入突变而功能受损。tb1与etb1.2存在上位性互作，共同调控玉米果穗内的节间长度，进而影响籽粒在果穗上的排列密度。该互作效应在基因表达层面同样得以观测到：tb1可作为ZmYAB2.1表达的抑制因子。值得注意的是，ZmYAB2.1此前已被鉴定为玉米另一驯化性状——不脱粒果穗（nonshattering ears）的候选基因。与这一推定功能相符的是，ZmYAB2.1在未成熟果穗的一窄层细胞中表达，该区域似乎对应残迹离层（脱粒相关脱落区）。这部分细胞中的表达或许也是其调控节间伸长效应的分子基础。鉴定出作为tb1互作背景因子的ZmYAB2.1，是从基因层面解析玉米驯化过程中tb1及其发挥作用的遗传背景如何协同演化的第一步。