Genetic interaction involving photoperiod-responsive Hd1 promotes early flowering under long-day conditions in rice (original) (raw)
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Photoperiodic control of flowering is one of the most significant components of the interaction between plants and their environment. Hd1 promotes floral transition from vegetative to reproductive growth under short-day (SD) conditions. An indel-specific functional marker in Hd1 first exon was developed and tested in a collection of 44 rice indica cultivars with different flowering times to evaluate its association with the trait. Results showed that the Hd1 indel-specific marker produced three allelic forms A, B and C as expected, with frequencies of 43.2, 47.7 and 9.1 percent, respectively. A high negative correlation (r=-0.556) was detected between flowering time and functional Hd1 indel. Interval mapping (IM) analysis showed that Hd1 had a negative additive effect (~4.5 days) on flowering time and the gene explained 27.4 percent of phenotypic variation of the trait. Our results indicated the role of Hd1 in determining the time of flowering in rice and suggest applicability of Hd1 indel-specific marker in molecular breeding of early flowering.
2020
Background Plant domestication/adaptation is a good model for evo-devo studies. Mutations that caused morphological and physiological change, followed by human selection, finally led to improvement of phenotypes suitable for different kinds of environments. Originating from the Yangtze Valley, rice is a facultative short-day plant. Rice spread southward thousands of years ago, but one of the new traits beneficial to crop yield would be loss of sensitivity to photoperiod. That is, if rice could be cultivated 2 or 3 seasons each year, the production would at least double. Results We used the sequence information for Heading date 1 (Hd1) gene to reveal the relationship of sequence changes and flowering phenotypes of rice in different regions. Seven loss-of-function hd1 haplotypes were reported previously. By data mining the genome sequencing information in the public domain, we discovered another 3 types. Allele haplotypes are present in sub-tropical and tropical regions, which indicat...
The effects of the photoperiod-insensitive alleles, se13, hd1 and ghd7, on yield components in rice
Molecular Breeding, 2014
Flowering time is closely associated with grain yield in rice (Oryza sativa L.). In temperate regions, seasonal changes in day length (known as the photoperiod) are an important environmental cue for floral initiation. The timing of flowering is important not only for successful reproduction, but also for determining the ideal balance between vegetative growth and reproductive growth duration. Recent molecular genetics studies have revealed key flowering time genes responsible for photoperiod sensitivity. In this study, we investigated the effect of three recessive photoperiod-insensitive alleles, se13, hd1 and ghd7, on yield components in rice under Ehd1deficient genetic background conditions to ensure vegetative growth of each line. We found that se13bearing plants had fewer panicles, hd1-bearing plants showed decreased grain-filling percentage, and ghd7bearing plants appeared to have fewer grains per panicle and fewer secondary branches. Our results indicate that the pleiotropic effects of photoperiodinsensitive genes on yield components are independent of short vegetative growth. This will provide critical information which can be used to create photoperiod-insensitive varieties that can be adapted to a wide range of latitudes.
Mechanisms Of Photoperiod In Regulation Of Rice Flowering
A study on the photoperiodic control of flower in rice is advancing and rice has become an of short day plant. Many genes used in flowering time determination in rice have been identified by many methods. The conclusion from these molecular studies is a remarkable conservation of genes which play an important role in the control of flowering time in rice. The rice photoperiod sensitivity gene Hd3a was originally detected as a heading date related quantitative trait locus found on chromosome 6 of rice. High resolution linkage mapping of Hd3a was carried using a huge segregating population derived from advanced backcross progeny between a japonica variety, Nipponbare, and an indica variety, Kasalath. Researchers revealed that there are three (3) pathways for the day length regulation of flowering in rice, short day activation pathway and long day suppression pathway lastly the long day activation pathway. Some genes where used in multiple pathways and others are specific to a particular pathway. There regulation also depends on the developmental stages. Rice may be an ideal plant to study the night break effect on flowering. In the near future there is need for better understand the controlled of flowering in rice at the genetic level.
Regulatory Genes and Enzymatic Complex of Flowering Time in Rice
Plant Breeding and Biotechnology
Flowering time (heading date) of the rice plant is considered an important agronomic trait for environmental adaptation and grain yield. It is controlled by multiple genes and is regulated by different environmental factors, such as day length, temperature, soil moisture, etc. So far, approximately 125 genes regulating flowering process and floral organ identity or development directly or indirectly have been reported in rice. Among these genes, Heading date 3a (Hd3a), RICE FLOWERING LOCUS T1 (RFT1), Heading date 5 (Hd5), MORF-RELATED GENE702 (MRG702), Casein kinases, CKI and CK2, Pseudo-Response Regulator 37 (PRR37), Hd gene family have been reported as the key genes regulating flowering time in rice; however, their functions are mostly interrelated. Hd3a and RFT1 that encode florigens, are known as the floral transition genes in rice. In rice, florigen immediately induces downstream genes in the shoot apical meristem (SAM) to start the transition from vegetative to reproductive phase. RFT1 gene regulates flowering time with pivotal action while Hd3a, regulates under long day conditions. The Hd5 gene regulates flowering time in variation of early heading for adaptation depending on environmental signals. MRG702, a reader protein, promotes flowering. Casein kinases, CKI and CK2 directly influence the function of the early heading regulator PRR37. Hd16/CKI hinders flowering time in the Ehd1-concerned pathway through phosphorylation of Ghd7 and PRR37. Natural variants of Hd1, PRR37, Ghd7, DTH8, Hd6, and Hd16 were found in the rice varieties that are cultivated presently in Asia and Europe, and their variants play significant roles in the down streaming of Ehd1 expression to delay flowering time in natural long day (LD) conditions.
2006
A quantitative trait locus (QTL), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the Oryza sativa variety Jefferson and an accession of the wild rice relative Oryza rufipogon. A series of near-isogenic lines (NILs) containing different O. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. In contrast to the late-flowering O. rufipogon parent, O. rufipogon alleles in the substitution lines caused early flowering under both short-and long-day lengths and provided evidence for at least two distinct sub-QTL: dth1.1a and dth1.1b. Potential candidate genes underlying these sub-QTL include genes with sequence similarity to Arabidopsis GI, FT, SOC1, and EMF1, and Pharbitis nil PNZIP. Evidence from families with nontarget O. rufipogon introgressions in combination with dth1.1 alleles also detected an early flowering QTL on chromosome 4 and a late-flowering QTL on chromosome 6 and provided evidence for additional sub-QTL in the dth1.1 region. The availability of a series of near-isogenic lines with alleles introgressed from a wild relative of rice provides an opportunity to better understand the molecular basis of transgressive variation in a quantitative trait.
Proceedings of the National Academy of Sciences, 2009
Rice is a facultative short-day plant, and molecular genetic studies have identified the major genes involved in short-day flowering. However, the molecular mechanisms promoting the diversity of flowering time in cultivated rice are not known. We used a core collection of 64 rice cultivars that represent the genetic diversity of 332 accessions from around the world and studied the expression levels and polymorphisms of 6 genes in the short-day flowering pathway. The RNA levels of Heading date 3a (Hd3a), encoding a floral activator, are highly correlated with flowering time, and there is a high degree of polymorphism in the Heading date 1 (Hd1) protein, which is a major regulator of Hd3a expression. Functional and nonfunctional alleles of Hd1 are associated with early and late flowering, respectively, suggesting that Hd1 is a major determinant of variation in flowering time of cultivated rice. We also found that the type of Hd3a promoter and the level of Ehd1 expression contribute to the diversity in flowering time and Hd3a expression level. We evaluated the contributions of these 3 factors by a statistical analysis using a simple linear model, and the results supported our experimental observations.
International Journal of Molecular Sciences
Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS5...
Euphytica, 2008
Flowering time is aVected not only by photoperiod sensitivity (PS) but also by basic vegetative growth (BVG) and optimum photoperiod (OP), although their developmental and genetic relationships are not well understood. The present study was carried out in rice to examine to what extent these three developmental components are modiWed by the three Xowering time genes, Se1 (= Hd1), Ef1 and e1 (= m-Ef1), which are known to contribute to Xowering time in temperate and tropical regions of rice cultivation. Photoperiodic response curves were estimated under controlled conditions of diVerent growth regimes, using eight near-isogenic lines possessing diVerent combinations of the alleles at the three loci. The results showed that each of the components is greatly aVected by the main eVect of the genes, temperature and their epistasis, indicating that none of the three genes controls Xowering time by altering any single component in PS, BVG or OP. Epistasis was detected more frequently among the three genes than reported before, suggesting that epistasis contributes to Xowering time by changing PS, BVG and OP diVerently. The comparison of the nucleotide sequences suggested that Ef1 is the same as Early heading date 1 (Ehd1). Since the two genes Se1 (= Hd1) and Ef1 (= Ehd1) are known to up-regulate the rice homolog of Arabidopsis FT, it is suggested that the detected epistasis may respond to diverse environments by modulating the CO/FT system conserved in Xowering plants.
Plant and Cell Physiology, 2002
Heading date 3a (Hd3a) has been detected as a heading-date-related quantitative trait locus in a cross between rice cultivars Nipponbare and Kasalath. A previous study revealed that the Kasalath allele of Hd3a promotes heading under short-day (SD) conditions. High-resolution linkage mapping located the Hd3a locus in a ~20-kb genomic region. In this region, we found a candidate gene that shows high similarity to the FLOWERING LOCUS T (FT) gene, which promotes flowering in Arabidopsis. Introduction of the gene caused an early-heading phenotype in rice. The transcript levels of Hd3a were increased under SD conditions. The rice Heading date 1 (Hd1) gene, a homolog of CONSTANS (CO), has been shown to promote heading under SD conditions. By expression analysis, we showed that the amount of Hd3a mRNA is up-regulated by Hd1 under SD conditions, suggesting that Hd3a promotes heading under the control of Hd1. These results indicate that Hd3a encodes a protein closely related to Arabidopsis FT and that the function and regulatory relationship with Hd1 and CO, respectively, of Hd3a and FT are conserved between rice (an SD plant) and Arabidopsis (a long-day plant).