"Perfect" markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat

PCR-based markers were developed to detect the point mutations responsible for the two major semi-dwarfing genes Rht-B1b ( Rht1) and Rht-D1b ( Rht2) in wheat. These markers were validated by testing 19 wheat varieties of known Rht genotype. They included Rht-B1b and Rht-D1b dwarfs, double-mutant varieties and tall wheats. These were correctly genotyped with the Rht-B1b and Rht-D1b-specific primers, as well as markers specific for the tall alleles Rht-B1a and Rht-D1a. Using a family of doubled-haploid lines segregating for Rht-B1b and Rht-D1b, the markers were mapped to the expected homoeologous regions of chromosomes 4B and 4D, respectively. Both markers were strongly correlated with a reduction in height, accounting for 23% ( Rht-B1b) and 44% ( Rht-D1b) of the phenotypic variance in the population. These markers will have utility in marker-assisted selection of the Rht-B1b and Rht-D1b genes in wheat breeding programs.     

Control of late maturity alpha-amylase in wheat by the dwarfing gene Rht-D1b and genes on the 1B/1R translocation

The occurrence of late maturity alpha-amylase (LMA) was investigated using two doubled haploid wheat populations segregating for the dwarfing gene Rht-D1b and the 1B/1R translocation. Genotypes were assessed in the field and in controlled environments where a cold-shock treatment was used to induce LMA. Results from field-grown genotypes from the cross Spark × Rialto suggest that the absence of Rht-D1b or the presence of the 1B/1R translocation increases the expression of LMA.These two genetic factors were found to act independently and to have a positive interaction (complementary epistasis). In Option × Potent genotypes fixed for Rht-D1b, the 1B/1R effect was similar to that seen in the equivalent Spark × Rialto genotypes. Under controlled environment conditions, genotypes with the 1B/1R translocation showed a higher occurrence of LMA under both control and cold-shock conditions. 1B/1R was present in the majority of genotypes expressing LMA under control and cold-shock conditions. The results point to the novel finding that the 1B/1R translocation increases the expression of alpha-amylase in LMA-prone germplasm independently of effects of Rht-D1b, whereas previously it had been thought to act by a modification of the Rht-D1b effect.     

A tandem segmental duplication (TSD) in green revolution gene Rht-D1b region underlies plant height variation

? Rht-D1c (Rht10) carried by Chinese wheat (Triticum aestivum) line Aibian 1 is an allele at the Rht-D1 locus. Among the Rht-1 alleles, little is known about Rht-D1c although it determines an extreme dwarf phenotype in wheat. ? Here, we cloned and functionally characterized Rht-D1c using a combination of Southern blotting, target region sequencing, gene expression analysis and transgenic experiments. ? We found that the Rht-D1c allele was generated through a tandem segmental duplication (TSD) of a >?1?Mb region, resulting in two copies of the Rht-D1b. Two copies of Rht-D1b in the TSD were three-fold more effective in reducing plant height than a single copy, and transformation with a segment containing the tandemly duplicated copy of Rht-D1b resulted in the same level of reduction of plant height as the original copy in Aibian 1. ? Our results suggest that changes in gene copy number are one of the important sources of genetic diversity and some of these changes could be directly associated with important traits in crops.     

Characterization of cis-regulatory elements of the homeobox gene Xanf-1

Investigation of molecular mechanisms underlying early patterning of the nervous system is an important task of modern developmental biology. Previously, we identified a novel homeobox gene, Anf, that is expressed in the most anterior zone at the beginning of neuroectoderm specification. The expression pattern of Anf corresponds to primordia of the telencephalon and the rostral part of the diencephalon. In the present work, we investigated cis-regulation of expression of the Xenopus laevis Anf, Xanf-1. Two elements, highly conserved in Xenopus, chick and human, were identified within the Xanf-1 promoter region. The first element, located near position -500, is necessary for overall enhancement of the Xanf-1 expression. The second element, near position -200, is crucial for maintenance of the Xanf-1 expression at moderate levels and also for specific localization of the expression in the anterior neuroectoderm. Thus, the distal part of this element is responsible for suppression of Xanf-1 posterior to the normal expression domain of this gene. The data obtained corroborate with the Nieuwkoop two-signal model of neural induction. This model states that at the first step of induction, all neuroectoderm acquires potencies to develop toward forebrain structures, but later these potencies are suppressed in posterior regions.     

Haplotype variation of Green Revolution gene Rht-D1 during wheat domestication and improvement

Green Revolution made a substantial contribution to wheat yields worldwide in the 1960 s and 1970 s. It is of great importance to analyze the haplotype variation of Rht-D1, the Green Revolution gene, during wheat(Triticum aestivum L.)domestication and breeding to understand its evolution and function in wheat breeding history. In this study, the Rht-D1 and its flanking regions were sequenced and single nucleotide polymorphisms were detected based on a panel of 45 accessions of Aegilops tauschii, 51 accessions of landraces and 80 accessions of commercial varieties. Genetic diversity in the wild accessions was much higher than that in the varieties and higher than that reported previously. Seven haplotypes(Hapl I to Hapl VII) of Rht-D1 were identified and their evolutionary relationships were proposed. In addition to the well-known Green Revolution allele Rht-D1b, Hapl VII(an allele Rht-D1k) was identified in early breeding varieties, which reduced plant height by 16%. The results suggested that Rht-D1k had been used in breeding before the Green Revolution and made a great contribution to wheat production worldwide.Based on the breeding history and molecular evidence, we proposed that the wheat Green Revolution in China and International Maize and Wheat Improvement Center(CIMMYT)occurred independently.     

Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus

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Dissection of cis-regulatory elements of the Drosophila gene Serrate

 The Drosophila gene Serrate encodes a membrane spanning protein, which is expressed in a complex pattern during embryogenesis and larval stages. Loss of Serrate function leads to larval lethality, which is associated with several morphogenetic defects, including the failure to develop wings and halteres. Serrate has been suggested to act as a short-range signal during wing development. It is required for the induction of the organising centre at the dorsal/ventral compartment boundary, from which growth and patterning of the wing is controlled. In order to understand the regulatory network required to control the spatially and temporally dynamic expression of Serrate, we analysed its cis-regulatory elements by fusing various genomic fragments upstream of the reporter gene lacZ. Enhancer elements reflecting the expression pattern of endogenous Serrate in embryonic and postembryonic tissues could be confined to 26 kb of genomic DNA, including 9 kb of transcribed region. Expression in some embryonic tissues is under the control of multiple enhancers located in the 5’ region and in intron sequences. The data presented here provide the tools to unravel the genetic network which regulates Serrate during different developmental stages in diverse tissues. Received: 27 March 1998 / Accepted: 17 May 1998     

Evolution of cis-regulatory elements in duplicated genes of yeast

An increasing number of studies report that functional divergence in duplicated genes is accompanied by gene expression changes, although the evolutionary mechanism behind this process remains unclear. Our genomic analysis on the yeast Saccharomyces cerevisiae shows that the number of shared regulatory motifs in the duplicates decreases with evolutionary time, whereas the total number of regulatory motifs remains unchanged. Moreover, genes with numerous paralogs in the yeast genome do not have especially low number of regulatory motifs. These findings indicate that degenerative complementation is not the sole mechanism behind expression divergence in yeast. Moreover, we found some evidence for the action of positive selection on cis-regulatory motifs after gene duplication. These results suggest that the evolution of functional novelty has a substantial role in yeast duplicate gene evolution.     

水稻胚乳特异表达基因的挖掘及顺式元件分析

本研究旨在利用计算机方法对水稻胚乳特异性表达基因进行挖掘和功能分析,及特异性顺式调控元件的预测。我们将基因在不同组织中的表达信号谱看作多维空间内的向量,利用向量夹角余弦法计算其与理想状态下该基因在某一组织特异表达向量的相似度,以此来判断组织特异性表达基因。本文通过对水稻芯片数据的大规模分析,共挖掘出了127个在水稻胚乳中特异表达基因。并对其启动子进行顺式元件预测,发现两个与胚乳特异表达相关的顺式调控元件,其保守序列分别为CATGCATSCM和GATCGATCGR。与已知功能的顺式元件比较显示,前者为种子特异基因表达相关的RY repeat元件,而后者则与元件RNFG1相似,但其具体功能尚不明确。     

Semi-dwarfing Rht-B1 and Rht-D1 loci of wheat differ significantly in their influence on resistance to Fusarium head blight

Fusarium head blight (FHB) is an important disease of wheat worldwide. Soissons is one of the most resistant varieties grown in UK. The current study was undertaken to identify QTL for FHB resistance in Soissons and to determine whether the semi-dwarfing alleles Rht-B1b and Rht-D1b have a similar influence on susceptibility to FHB. A Soissons (Rht-B1b; Rht-D1a) × Orvantis (Rht-B1a; Rht-D1b) doubled haploid (DH) population was assessed for FHB resistance in three trials. Soissons contributed a single, stable major FHB QTL linked to the Rht-D1 locus. In contrast, the Rht-B1b allele (contributed by Soissons) conferred no negative effect on FHB resistance, even conferring a very minor positive effect in one trial. The influence of the Rht-B1b and Rht-D1b alleles on FHB resistance was further investigated using both Mercia and Maris Huntsman near-isogenic lines. Under high disease pressure both Rht-B1b and Rht-D1b significantly decreased Type 1 resistance (resistance to initial infection). However, whilst Rht-D1b has no effect on Type 2 resistance (resistance to spread of the fungus within the spike), Rht-B1b significantly increased Type 2 resistance. Our study demonstrates that the choice of semi-dwarfing gene used in plant breeding programmes may be a significant consideration where resistance to FHB is an important breeding target.     

Wild-type alleles of Rht-B1 and Rht-D1 as independent determinants of thousand-grain weight and kernel number per spike in wheat

The utilization of dwarfing genes Rht-B1b and Rht-D1b in wheat significantly increased grain yield and contributed to the “green revolution”. However, the benefit of Rht-B1b and Rht-D1b in drought environments has been debated. Although quantitative trait loci (QTL) for kernel number per spike (KN) and thousand-grain weight (TGW) have been found to be associated with Rht-B1 and Rht-D1, the confounding effect of environmental variation has made a direct association difficult to find. In this study, we used a doubled haploid population (225 lines) of Westonia × Kauz, in which both Rht-B1b (Kauz) and Rht-D1b (Westonia) segregated. The purpose of the study was to determine the interaction of Rht-B1 and Rht-D1 with grain yield components, namely KN and TGW, and to investigate genotype-by-environment interactions in glasshouse and field trials conducted in 2010 and 2011 in Western Australia. A genetic map of 1,156 loci was constructed using 195 microsatellite markers, two gene-based markers for Rht-B1 and Rht-D1, and 959 single nucleotide polymorphisms. The major QTL for TGW and KN were strongly linked to Rht-B1 and Rht-D1 loci and the positive effects were associated with the wild-type alleles, Rht-B1a and Rht-D1a. The major QTL of TGW were on chromosome 2D and 4B. The significant genetic effects (14.6–22.9 %) of TGW indicated that marker-assisted selection for TGW is possible, and markers gwm192a (206 bp) or gwm192b (236 bp) can be used as indicators of high TGW. For KN, one major QTL was detected on chromosome 4D in the analysis across three environments. The association of the wild-type alleles Rht-B1a and Rht-D1a in drought environments is discussed.