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Plant height is an important agronomic trait with a significant impact on grain yield, as demonstrated by the positive effect of the REDUCED HEIGHT (RHT) dwarfing alleles (Rht1b) on lodging and harvest index in the "Green Revolution" wheat varieties. However, these gibberellic acid (GA)-insensitive alleles also reduce coleoptile length, biomass production, and yield potential in some environments, triggering the search for alternative GA-sensitive dwarfing genes. Here we report the identification, validation, and characterization of the gene underlying the GA-sensitive dwarfing locus RHT25 in wheat. This gene, designated as PLATZ-A1 (TraesCS6A02G156600), is expressed mainly in the elongating stem and developing spike and encodes a plant-specific AT-rich sequence- and zinc-binding protein (PLATZ). Natural and induced loss-of-function mutations in PLATZ-A1 reduce plant height and its overexpression increases plant height, demonstrating that PLATZ-A1 is the causative gene of RHT25. PLATZ-A1 and RHT1 show a significant genetic interaction on plant height, and their encoded proteins interact with each other in yeast and wheat protoplasts. These results suggest that PLATZ1 can modulate the effect of DELLA on wheat plant height. We identified four natural truncation mutations and one promoter insertion in PLATZ-A1 that are more frequent in modern varieties than in landraces, suggesting positive selection during wheat breeding. These mutations can be used to fine-tune wheat plant height and, in combination with other GA-sensitive dwarfing genes, to replace the GA-insensitive Rht1b alleles and search for grain yield improvements beyond those of the Green Revolution varieties.

Key messageThis study identified Rht25, a new plant height locus on wheat chromosome arm 6AS, and characterized its pleiotropic effects on important agronomic traits. Understanding genes regulating wheat plant height is important to optimize harvest index and maximize grain yield. In modern wheat varieties grown under high-input conditions, the gibberellin-insensitive semi-dwarfing alleles Rht-B1b and Rht-D1b have been used extensively to confer lodging tolerance and improve harvest index. However, negative pleiotropic effects of these alleles (e.g., poor seedling emergence and reduced biomass) can cause yield losses in hot and dry environments. As part of current efforts to diversify the dwarfing alleles used in wheat breeding, we identified a quantitative trait locus (QHt.ucw-6AS) affecting plant height in the proximal region of chromosome arm 6AS (

Wheat vernalization requirement is mainly controlled by the VRN1, VRN2, VRN3, and VRN4 genes. The first three have been cloned and have homoeologs in all three genomes. VRN4 has been found only in the D genome (VRN-D4) and has not been cloned. We constructed a high-density genetic map of the VRN-D4 region and mapped VRN-D4 within a 0.09 cM interval in the centromeric region of chromosome 5D. Using telocentric 5D chromosomes generated from the VRN-D4 donor Triple Dirk F, we determined that VRN-D4 is located on the short arm. The VRN-D4 candidate region is colinear with a 2.24 Mb region on Brachypodium distachyon chromosome 4, which includes 127 predicted genes. Ten of these genes have predicted roles in development but we detected no functional polymorphisms associated to VRN-D4. Two recombination events separated VRN-D4 from TaVIL-D1, the wheat homolog of Arabidopsis vernalization gene VIL1, confirming that this gene is not a candidate for VRN-D4. We detected significant interactions between VRN-D4 and other four genes controlling vernalization requirement (Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3), which confirmed that VRN-D4 is part of the vernalization pathway and that it is either upstream or is part of the regulatory feedback loop involving VRN1, VRN2 and VRN3 genes. The precise mapping of VRN-D4 and the characterization of its interactions with other vernalization genes provide valuable information for the utilization of VRN-D4 in wheat improvement and for our current efforts to clone this vernalization gene.

The activation of the meristem identity gene VERNALIZATION1 (VRN1) is a critical regulatory point in wheat (Triticum spp.) flowering. In photoperiod-sensitive wheat varieties, VRN1 is expressed only under long days (LDs), but mutants carrying deletions in a regulatory element in its promoter show VRN1 transcription and early spike development under short days (SDs). However, complete spike development is delayed until plants are transferred to LDs, indicating the existence of an additional regulatory mechanism dependent on LDs. We show here that exogenous gibberellin (GA) application accelerates spike development under SDs, but only in wheat lines expressing VRN1. The simultaneous presence of GA and VRN1 results in the up-regulation of the floral meristem identity genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1-1 and LEAFY, whereas inhibition of GA biosynthesis with paclobutrazol precludes the LD induction of these two genes. The inductive role of GA on wheat flowering is further supported by the up-regulation of GA biosynthetic genes in the apices of plants transferred from SDs to LDs and in photoperiod-insensitive and transgenic wheat plants with increased FLOWERING LOCUS T transcription under SDs. The up-regulation of GA biosynthetic genes was not observed in the leaves of the same genetic stocks. Based on these observations, we propose a model in which FLOWERING LOCUS T is up-regulated in the leaves under LDs and is then transported to the shoot apical meristem, where it simultaneously induces the expression of VRN1 and GA biosynthetic genes, which are both required for the up-regulation of the early floral meristem genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1-1 and LEAFY and the timely development of the wheat spike.

Abstract Background More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppressed in the genome via small non-coding RNAs (sRNAs). sRNAs guide silencing of TEs at the transcriptional (mainly 24-nt sRNAs) and post-transcriptional (mainly 21-nt sRNAs) levels. In this study, we report the distribution of these two types of sRNAs among the different classes of wheat TEs, the regions targeted within the TEs, and their impact on the methylation patterns of the targeted regions. Results We constructed an sRNA library from hexaploid wheat and developed a database that included our library and three other publicly available sRNA libraries from wheat. For five completely-sequenced wheat BAC contigs, most perfectly matching sRNAs represented TE sequences, suggesting that a large fraction of the wheat sRNAs originated from TEs. An analysis of all wheat TEs present in the Triticeae Repeat Sequence database showed that sRNA abundance was correlated with the estimated number of TEs within each class. Most of the sRNAs perfectly matching miniature inverted repeat transposable elements (MITEs) belonged to the 21-nt class and were mainly targeted to the terminal inverted repeats (TIRs). In contrast, most of the sRNAs matching class I and class II TEs belonged to the 24-nt class and were mainly targeted to the long terminal repeats (LTRs) in the class I TEs and to the terminal repeats in CACTA transposons. An analysis of the mutation frequency in potentially methylated sites revealed a three-fold increase in TE mutation frequency relative to intron and untranslated genic regions. This increase is consistent with wheat TEs being preferentially methylated, likely by sRNA targeting. Conclusions Our study examines the wheat epigenome in relation to known TEs. sRNA-directed transcriptional and post-transcriptional silencing plays important roles in the short-term suppression of TEs in the wheat genome, whereas DNA methylation and increased mutation rates may provide a long-term mechanism to inactivate TEs.

Plant height is an important agronomic trait with a significant impact on grain yield, as demonstrated by the positive effect of the REDUCED HEIGHT(RHT) dwarfing alleles (Rht1b) on lodging and harvest index in the "Green Revolution" wheat varieties. However, these gibberellic acid (GA)-insensitive alleles also reduce coleoptile length, biomass production, and yield potential in some environments, triggering the search for alternative GA-sensitive dwarfing genes. Here we report the identification, validation, and characterization of the gene underlying the GA-sensitive dwarfing locus RHT25 in wheat. This gene, designated as PLATZ-A1 (TraesCS6A02G156600), is expressed mainly in the elongating stem and developing spike and encodes a plant-specific AT-rich sequence- and zinc-binding protein (PLATZ). Natural and induced loss-of-function mutations in PLATZ-A1 reduce plant height and its overexpression increases plant height, demonstrating that PLATZ-A1 is the causative gene of RHT25. PLATZ-A1 and RHT1 show a significant genetic interaction on plant height, and their encoded proteins interact with each other in yeast and wheat protoplasts. These results suggest that PLATZ1 can modulate the effect of DELLA on wheat plant height. We identified four natural truncation mutations and one promoter insertion in PLATZ-A1 that are more frequent in modern varieties than in landraces, suggesting positive selection during wheat breeding. These mutations can be used to fine-tune wheat plant height and, in combination with other GA-sensitive dwarfing genes, to replace the GA-insensitive Rht1b alleles and search for grain yield improvements beyond those of the Green Revolution varieties. [ABSTRACT FROM AUTHOR]

Abstract Background More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppressed in the genome via small non-coding RNAs (sRNAs). sRNAs guide silencing of TEs at the transcriptional (mainly 24-nt sRNAs) and post-transcriptional (mainly 21-nt sRNAs) levels. In this study, we report the distribution of these two types of sRNAs among the different classes of wheat TEs, the regions targeted within the TEs, and their impact on the methylation patterns of the targeted regions. Results We constructed an sRNA library from hexaploid wheat and developed a database that included our library and three other publicly available sRNA libraries from wheat. For five completely-sequenced wheat BAC contigs, most perfectly matching sRNAs represented TE sequences, suggesting that a large fraction of the wheat sRNAs originated from TEs. An analysis of all wheat TEs present in the Triticeae Repeat Sequence database showed that sRNA abundance was correlated with the estimated number of TEs within each class. Most of the sRNAs perfectly matching miniature inverted repeat transposable elements (MITEs) belonged to the 21-nt class and were mainly targeted to the terminal inverted repeats (TIRs). In contrast, most of the sRNAs matching class I and class II TEs belonged to the 24-nt class and were mainly targeted to the long terminal repeats (LTRs) in the class I TEs and to the terminal repeats in CACTA transposons. An analysis of the mutation frequency in potentially methylated sites revealed a three-fold increase in TE mutation frequency relative to intron and untranslated genic regions. This increase is consistent with wheat TEs being preferentially methylated, likely by sRNA targeting. Conclusions Our study examines the wheat epigenome in relation to known TEs. sRNA-directed transcriptional and post-transcriptional silencing plays important roles in the short-term suppression of TEs in the wheat genome, whereas DNA methylation and increased mutation rates may provide a long-term mechanism to inactivate TEs.

Spike fertility index (SF) is a trait easily measured at maturity and strongly associated with the number of grains per unit area. In order to identify genomic regions involved in SF control, a biparental (Baguette 10 × Klein Chajá) population of 80 recombinant inbred lines (RIL) was used. Seven field trails were conducted to determine the SF BLUP value per RIL. RILs were genotyped using a commercial chip (Axiom® 35K SNP Wheat Breeder's Array, Affimetrix). A linkage map was constructed with 857 SNP markers, and SF QTL mapping was performed. The narrow-sense heritability of SF was 0.89. Three genomic regions (QTL) associated with SF were found on chromosomes 2D, 4A, and 7A. The proportion of genetic variation explained by these three QTL was 32%, with no significant epistatic interaction between QTL. [ABSTRACT FROM AUTHOR]

The activation of the meristem identity gene VERNALIZATION1 (VRN1) is a critical regulatory point in wheat (Triticum spp.) flowering. In photoperiod-sensitive wheat varieties, VRN1 is expressed only under long days (LDs), but mutants carrying deletions in a regulatory element in its promoter show VRN1 transcription and early spike development under short days (SDs). However, complete spike development is delayed until plants are transferred to LDs, indicating the existence of an additional regulatory mechanism dependent on LDs. We show here that exogenous gibberellin (GA) application accelerates spike development under SDs, but only in wheat lines expressing VRN1. The simultaneous presence of GA and VRN1 results in the up-regulation of the floral meristem identity genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1-1 and LEAFY, whereas inhibition of GA biosynthesis with paclobutrazol precludes the LD induction of these two genes. The inductive role of GA on wheat flowering is further supported by the up-regulation of GA biosynthetic genes in the apices of plants transferred from SDs to LDs and in photoperiod-insensitive and transgenic wheat plants with increased FLOWERING LOCUS T transcription under SDs. The up-regulation of GA biosynthetic genes was not observed in the leaves of the same genetic stocks. Based on these observations, we propose a model in which FLOWERING LOCUS T is up-regulated in the leaves under LDs and is then transported to the shoot apical meristem, where it simultaneously induces the expression of VRN1 and GA biosynthetic genes, which are both required for the up-regulation of the early floral meristem genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1-1 and LEAFY and the timely development of the wheat spike [ABSTRACT FROM AUTHOR]