Divergence in homoeolog expression of the grain length-associated gene GASR7 during wheat allohexaploidization

Abstract

Hexaploid wheat has triplicated homoeologs for most of the genes that are located in subgenomes A, B, and D. GASR7, a member of the Snakin/GASA gene family, has been associated with grain length development in wheat. However, little is known about divergence of its homoeolog expression in wheat polyploids. We studied the expression patterns of the GASR7 homoeologs in immature seeds in a synthetic hexaploid wheat line whose kernels are slender like those of its maternal parent (Triticum turgidum, AABB, PI 94655) in contrast to the round seed shape of its paternal progenitor (Aegilops tauschii, DD, AS2404). We found that the B homoeolog of GASR7 was the main contributor to the total expression level of this gene in both the maternal tetraploid progenitor and the hexaploid progeny, whereas the expression levels of the A and D homoeologs were much lower. To understand possible mechanisms regulating different GASR7 homoeologs, we firstly analyzed the promoter sequences of three homoeologous genes and found that all of them contained gibberellic acid (GA) response elements, with the TaGASR7B promoter (pTaGASR7B) uniquely characterized by an additional predicted transcriptional enhancer. This was confirmed by the GA treatment of spikes where all three homoeologs were induced, with a much stronger response for TaGASR7B. McrBC enzyme assays showed that the methylation status at pTaGASR7D was increased during allohexaploidization, consistent with the repressed expression of TaGASR7D. For pTaGASR7A, the distribution of repetitive sequence-derived 24-nucleotide (nt) small interfering RNAs (siRNAs) were found which suggests possible epigenetic regulation because 24-nt siRNAs are known to mediate RNA-dependent DNA methylation. Our results thus indicate that both genetic and epigenetic mechanisms may be involved in the divergence of GASR7 homoeolog expression in polyploid wheat.

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

“…Many of the methylation differences in the duplicate soybean genes can be attributed to transposon insertions that are present in one member of the pair Kim et al, 2015). These studies along with data from specific wheat (Triticum aestivum) loci (Shitsukawa et al, 2007;Hu et al, 2013;Zhang et al, 2015) and maize (West et al, 2014) suggest that DNA methylation does not play a major global role in differentiating subgenomes, but it can contribute to locus-specific divergence of retained duplicates.…”

Subgenome‐specific assembly of vitamin E biosynthesis genes and expression patterns during seed development provide insight into the evolution of oat genome

“…Because VTE4 catalyses the conversion of γ and δ forms of both T and T3 into α and β forms, the elevated levels of VTE4_1 transcripts are consistent with the relative abundance of the forms of vitamin E in oat seeds: α‐T3 > αT > βT3 > βT (Gutierrez‐Gonzalez et al ., ). Unequal contributions from homeologs in polyploids have been previously shown in wheat (Akhunova et al ., ; Zhang et al ., ), cotton (Adams et al ., ) and rapeseed (Xu et al ., ) and are commonly due to mutations in regulatory regions or epigenetic changes in both methylation patterns and histone modifications. In addition to VTE4_1, the other enzyme with homeologs exhibiting a high correlation ( r = 0.97–1) with T, T3 and total vitamin E forms is HPPD.…”

Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)

“…10 gene had functions that affect the TGW, PH and SL during the maturity stage. To date, some grain weight genes have been isolated, such as Ppd-D1 [56], CKX6-D1 [57], GS1a [11], GW2 [8, 58–59], GS-D1 [60], Sus [9, 61], GASR7 [62–63], TEF-7 [64], CWI [65], and 1-FEH-w3 [66–67]. Using sequence comparison and the analysis of protein domains with PROSITE (http://prosite.expasy.org/), we found that TaSnRK2 .…”