Several quantitative trait genes(QTGs)related to rice heading date,a key factor for crop development and yield,have been identified,along with complex interactions among genes.However,a comprehensive genetic interacti...Several quantitative trait genes(QTGs)related to rice heading date,a key factor for crop development and yield,have been identified,along with complex interactions among genes.However,a comprehensive genetic interaction network for these QTGs has not yet been established.In this study,we use 18K-rice lines to identify QTGs and their epistatic interactions affecting rice heading date.We identify 264 pairs of interacting quantitative trait loci(QTL)and construct a comprehensive genetic network of these QTL.On average,the epistatic effects of QTL pairs are estimated to be approximately 12.5%of additive effects of identified QTL.Importantly,epistasis varies among different alleles of several heading date genes.Additionally,57 pairs of interacting QTGs are also significant in their epistatic effects on 12 other agronomic traits.The identified QTL genetic interactions are further validated using near-isogenic lines,yeast two-hybrid,and split-luciferase complementation assays.Overall,this study provides a genetic network of rice heading date genes,which plays a crucial role in regulating rice heading date and influencing multiple related agronomic traits.This network serves as a foundation for understanding the genetic mechanisms of rice quantitative traits and for advancing rice molecular breeding.展开更多
Heading date is one of the most important agronomic traits that directly affect rice yield and determines the regional adaptability in specific growing environments.As a short-day plant,rice can grow under long-day(LD...Heading date is one of the most important agronomic traits that directly affect rice yield and determines the regional adaptability in specific growing environments.As a short-day plant,rice can grow under long-day(LD)conditions due to the synergistic regulation of many photosensitive genes.Using a set of chromosome segment substitution lines(CSSLs)with the indica cultivar Huanghuazhan(HHZ)as the recipient parent and Basmati Surkh 89-15(BAS)as the donor parent,we identified a QTL locus.展开更多
QTLs for heading date of rice （Oryza sativa L.） with additive, epistatic, and QTL × environment （QE） interaction effects were studied using a mixed-model-based composite interval mapping （MCIM） method and a...QTLs for heading date of rice （Oryza sativa L.） with additive, epistatic, and QTL × environment （QE） interaction effects were studied using a mixed-model-based composite interval mapping （MCIM） method and a double haploid （DH） population derived from IR64/Azucena in two crop seasons. Fourteen QTLs conferring heading date in rice, which were distributed on ten chromosomes except for chromosomes 5 and 9, were detected. Among these QTLs, eight had single-locus effects, five pairs had double-locus interaction effects, and two single-loci and one pair of double-loci showed QTL × environment interaction effects. All predicted values of QTL effects varied from 1.179 days to 2.549 days, with corresponding contribution ratios of 1.04%-4.84%. On the basis of the effects of the QTLs, the total genetic effects on rice heading date for the two parents and the two superior lines were predicted, and the putative reasons for discrepancies between predicted values and observed values, and the genetic potentiality in the DH population for improvement of heading date were discussed. These results are in agreement with previous results for heading date in rice, and the results provide further information, which indicate that both epistasis and QE interaction are important genetic basis for determining heading date in rice.展开更多
Heading date determines the seasonal and regional adaptation of rice(Oryza sativa L.)varieties and is mainly controlled by photoperiod sensitivity(PS).The core heading date genes Hd1,Ghd7,DTH8,and PRR37 act synergisti...Heading date determines the seasonal and regional adaptation of rice(Oryza sativa L.)varieties and is mainly controlled by photoperiod sensitivity(PS).The core heading date genes Hd1,Ghd7,DTH8,and PRR37 act synergistically in regulating the PS.In this study,we systematically analyze the heading date,PS,and agronomic traits of eight homozygous lines with various combinations of Hd1,Ghd7,and DTH8 alleles in the prr37 background under long-day(LD)and short-day(SD)conditions,respectively.We find that Hd1 alone promotes heading,regardless of the day length.However,under LDs,Hd1 suppresses flowering,in coordination with functional Ghd7 or with Ghd7 and DTH8.These loci cooperate to negatively regulate the Ehd1-Hd3 a/RFT1 pathway and delay heading.Under SDs,Hd1 competes with various heading suppressors to promote heading.Therefore,the dual function of Hd1 is vital for PS.The lines carrying Hd1 alone show reduced plant height with fewer primary and secondary branches in panicles.Lines carrying Ghd7 and DTH8(with hd1)show delayed heading and improve agronomic traits.Overall,our results reveal the regulation of rice PS flowering by the core heading date genes and their effects on agronomic traits,providing valuable information for the selection of rice varieties for adaptation to different light and temperature conditions.展开更多
Previous study showed that a linkage drag between a blast resistance gene Pi25（t） and QTLs conditioning spikelet fertility （qSF-6） and number of filled grains per panicle （qNFGP-6） was detected on the short arm ...Previous study showed that a linkage drag between a blast resistance gene Pi25（t） and QTLs conditioning spikelet fertility （qSF-6） and number of filled grains per panicle （qNFGP-6） was detected on the short arm of chromosome 6. A larger population was used for further verification, and the results confirmed the linkage drag between the blast resistance gene and QTL conditioning spikelet fertility, other than QTL conditioning number of filled grains per panicle. Breakdown or avoidance of the linkage drag could be achieved by selection against the genotype background of a heading-date gene （qHD-7） that resided in the region between RM2 and RM214 on chromosome 7. For further validation, two lines with almost identical genotypes on all chromosomal regions except the Pi25（t） region on chromosome 6 were chosen to develop a new population The results showed that qSF-6 could be further subdivided into qSF-6-1 and qSF-6-2. When the genotype of the region between RM2 and RM214 was from rice variety Zhong 156, the linkage drag between Pi25（t） and qSF-6-2 was detected and the allele of qSF-6-2 from rice variety Gumei 2 reduced the spikelet fertility. When the genotype of the region between RM2 and RM214 was from Gumei 2, no linkage drag was detected. This indicates that the linkage drag between the blast resistance gene and the QTL conditioning spikelet fertility could be broken down or avoided under a certain background genotype selection against heading-date and provides a marker aided solution for high level of blast resistance and yield breeding in rice and other crops as well.展开更多
Main-effect QTL, epistatic effects and their interactions with environment are important genetic components of quantitativetraits. In this study, we analyzed the QTL, epistatic effects and QTL by environment interacti...Main-effect QTL, epistatic effects and their interactions with environment are important genetic components of quantitativetraits. In this study, we analyzed the QTL, epistatic effects and QTL by environment interactions (QE) underlying plantheight and heading date, using a doubled-haploid ( DH) population consisting of 190 lines from the cross between anindica parent Zhenshan 97 and a japonica parent Wuyujing 2, and tested in two-year replicated field trials. A geneticlinkage map with 179 SSR (simple sequence repeat) marker loci was constructed. A mixed linear model approach wasapplied to detect QTL, digenic interactions and QEs for the two traits. In total, 20 main-effect QTLs, 9 digenic interactionsinvolving 18 loci, and 5 QTL by environment interactions were found to be responsible for the two traits. No interactionswere detected between the digenic interaction and environment. The amounts of variations explained by QTLs of maineffect were 53.9% for plant height and 57.8% for heading date, larger than that explained by epistasis and QEs. However,the epistasis and QE interactions sometimes accounted for a significant part of phenotypic variation and should not bedisregarded.展开更多
CONSTANS,CO-like,and TOC1(CCT)family genes play important roles in regulating heading date,which exerts a large impact on the regional and seasonal adaptation of rice.Previous studies have shown that Grain number,plan...CONSTANS,CO-like,and TOC1(CCT)family genes play important roles in regulating heading date,which exerts a large impact on the regional and seasonal adaptation of rice.Previous studies have shown that Grain number,plant height,and heading date2(Ghd2)exhibits a negative response to drought stress by directly upregulating Rubisco activase and exerting a negative effect on heading date.However,the target gene of Ghd2 regulating heading date is still unknown.In this study,CO3 is identified by analyzing Ghd2 ChIP-seq data.Ghd2 activates CO3 expression by binding to the CO3 promoter through its CCT domain.EMSA experiments show that the motif CCACTA in the CO3 promoter was recognized by Ghd2.A comparison of the heading dates among plants with CO3 knocked out or overexpressed and double-mutants with Ghd2 overexpressed and CO3 knocked out shows that CO3 negatively and constantly regulates flowering by repressing the transcription of Ehd1,Hd3a,and RFT1.In addition,the target genes of CO3 are explored via a comprehensive analysis of DAP-seq and RNA-seq data.Taken together,these results suggest that Ghd2 directly binds to the downstream gene CO3,and the Ghd2eCO3 module constantly delays heading date via the Ehd1-mediated pathway.展开更多
Heading date in rice is a typical quantitative trait controlled by multiple quantitative trait loci （QTLs）. It is mainly regulated by environmental factors such as photoperiod and temperature （Izawa, 2007）. Many Q...Heading date in rice is a typical quantitative trait controlled by multiple quantitative trait loci （QTLs）. It is mainly regulated by environmental factors such as photoperiod and temperature （Izawa, 2007）. Many QTLs for heading date have been identified using different mapping populations and methods （http：// www.gramene.org/qtl）. Up to date, several major heading date QTLs have been cloned by map-based cloning strategy （Yano et al., 2000; Takahashi et al., 2001; Kojima et al., 2002; Doi et al., 2004; Xue et al., 2008; Wei et al., 2010; Yan et al.,展开更多
Grain yield and heading date are key factors determining the commercial potential of a rice variety. Mapping of quantitative trait loci （QTLs） in rice has been advanced from primary mapping to gene cloning, and head...Grain yield and heading date are key factors determining the commercial potential of a rice variety. Mapping of quantitative trait loci （QTLs） in rice has been advanced from primary mapping to gene cloning, and heading date and yield traits have always attracted the greatest attention. In this review, genomic distribution of QTLs for heading date detected in populations derived from intra-specific crosses of Asian cultivated rice （Oryza sativa） was summarized, and their relationship with the genetic control of yield traits was analyzed. The information could be useful in the identification of QTLs for heading date and yield traits that are promising for the improvement of rice varieties.展开更多
Aegilops umbellulata(UU)is a wheat wild relative that has potential use in the genetic improvement of wheat.In this study,46 Ae.umbellulata accessions were investigated for stripe rust resistance,heading date(HD),and ...Aegilops umbellulata(UU)is a wheat wild relative that has potential use in the genetic improvement of wheat.In this study,46 Ae.umbellulata accessions were investigated for stripe rust resistance,heading date(HD),and the contents of iron(Fe),zinc(Zn),and seed gluten proteins.Forty-two of the accessions were classified as resistant to stripe rust,while the other four accessions were classified as susceptible to stripe rust in four environments.The average HD of Ae.umbellulata was significantly longer than that of three common wheat cultivars(180.9 d vs.137.0 d),with the exception of PI226500(138.9 d).The Ae.umbellulata accessions also showed high variability in Fe(69.74-348.09 mg kg^(-1))and Zn(49.83-101.65 mg kg^(-1))contents.Three accessions(viz.,PI542362,PI542363,and PI554399)showed relatively higher Fe(230.96-348.09 mg kg^(-1))and Zn(92.46-101.65 mg kg^(-1))contents than the others.The Fe content of Ae.umbellulata was similar to those of Ae.comosa and Ae.markgrafii but higher than those of Ae.tauschii and common wheat.Aegilops umbellulata showed a higher Zn content than Ae.tauschii,Ae.comosa,and common wheat,but a lower content than Ae.markgrafii.Furthermore,Ae.umbellulata had the highest proportion of γ-gliadin among all the species investigated(Ae.umbellulata vs.other species=mean 72.11%vs.49.37%;range:55.33-86.99%vs.29.60-67.91%).These results demonstrated that Ae.umbellulata exhibits great diversity in the investigated traits,so it can provide a potential gene pool for the genetic improvement of these traits in wheat.展开更多
RING finger E3 ligases play an important role in regulating plant growth and development by mediating substrate degradation.In this study,we identified TaGW2L,encoding a Grain width and weight2(GW2)-like RING finger E...RING finger E3 ligases play an important role in regulating plant growth and development by mediating substrate degradation.In this study,we identified TaGW2L,encoding a Grain width and weight2(GW2)-like RING finger E3 ligase,as a novel positive regulator of heading date in wheat(Triticum aestivum L.).TaGW2L exhibited high amino acid sequence similarities with TaGW2 homoeologs,particularly in the conserved RING finger domain.Expression analysis indicated that TaGW2L was constitutively expressed in various wheat tissues.TaGW2L showed transactivation activity in yeast and could interact with the ubiquitin-conjugating enzymes E2_(s).An in vitro ubiquitination assay verified that TaGW2L possessed a similar E3 ligase activity to TaGW2.Overexpression of the TaGW2L-7A homoeolog in wheat led to a significantly earlier heading date under both natural conditions and long-day conditions.Transcriptome analysis revealed that multiple known genes positively regulating wheat heading were significantly upregulated in the TaGW2L-7A-overexpression plants compared with the wild-type control.Together,our findings shed light on the role of TaGW2L in wheat heading date and provide potential applications of TaGW2L for the adaptation improvement of crops.展开更多
Plant height and heading date are important agronomic traits in wheat(Triticum aestivum L.)that affect final grain yield.In wheat,knowledge of pseudo-response regulator(PRR)genes on agronomic traits is limited.Here,we...Plant height and heading date are important agronomic traits in wheat(Triticum aestivum L.)that affect final grain yield.In wheat,knowledge of pseudo-response regulator(PRR)genes on agronomic traits is limited.Here,we identify a wheat TaPRR95 gene by genome-wide association studies to be associated with plant height.Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height,particularly the peduncle,with an earlier heading date.The longer peduncle is mainly caused by the increased cell elon-gation at its upper section,whilst the early heading date is accompanied by elevated expression of flow-ering genes,such as TaFT and TacO1.A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAAVAux genes for auxin signaling inpr95abad plants that may act as a regulatory mechanism to promote robust plant growth.A haplotype analysis identifies a TaPRR95-B haplotype(Hap2)to be closely associated with reduced plant height and increased thousand-grain weight.Moreover,the Hap2 frequency is higher in cultivars than that in landraces,suggesting the artifi-cial selection on the allele during wheat breeding.These findings suggest that TaPRR95 is a regulator for plant height and heading date,thereby providing an important target for wheat yield improvement.展开更多
Heading date(or flowering time),an important agronomic trait in crop species,is closely associated with regional adaptation and yield.Members of the Pseudo-Response Regulator(PRR)family play key roles in regulating fl...Heading date(or flowering time),an important agronomic trait in crop species,is closely associated with regional adaptation and yield.Members of the Pseudo-Response Regulator(PRR)family play key roles in regulating flowering.However,their role and molecular mechanism controlling heading date in rice is not very clear.Here,we identified rice OsPRR protein,OsPRR59,which delayed heading under longday conditions.OsPRR59 positively regulates yield by affecting plant height,secondary branches number per panicle,grain number per panicle,seed setting rate,and grain weight per plant.OsPRR59 is expressed in most tissues and its protein is localized to the nucleus.We also found that OsPRR59 directly binds to the promoter of Ehd3 to inhibit its expression.Compared with the WT,osprr59 ehd3 showed a significantly delayed heading phenotype,as did the ehd3 mutant.This was opposite to the phenotype of the osprr59 mutant,confirming that Ehd3 acted downstream of OsPRR59 in regulating rice flowering.Our results identified a direct regulator of Ehd3,and revealed a novel molecular mechanism of clock component OsPRR proteins in regulating heading date and provide a new genetic resource for fine-tuning heading date in rice.展开更多
Heading date of 26 native japonica rice cultivars in southwest China was investigated,and their basic vegetative growth(BVG),photoperiod-sensitivity(PS) and temperature-sensitivity(TS) were analyzed under artificial s...Heading date of 26 native japonica rice cultivars in southwest China was investigated,and their basic vegetative growth(BVG),photoperiod-sensitivity(PS) and temperature-sensitivity(TS) were analyzed under artificial short-day and natural long-day conditions in Nanjing,as well as artificial high-temperature and natural low-temperature conditions in winter in Hainan.The results showed that the PS and TS varied among different cultivars.The BVG of all the japonica cultivars was well situated,but differed within cultivars.Regression analysis showed a significant correlation between heading date and PS,indicating that PS was the main factor affecting heading date of japonica cultivars in southwest China.Genetic analysis was conducted on these 26 cultivars using a set of heading date near isogenic lines as test lines.All the japonica cultivars carried the dominant early-heading gene Ef-1 or Ef-1t,and most of these cultivars carried the dominant photoperiod sensitivity allele E1 or E1t,the PS of which was slightly weaker than E1.For the Se-1 locus,these cultivars mainly carried recessive photoperiod insensitivity gene Se-1e.In addition,the PS of 22 japonica cultivars could be repressed or weakened by the recessive allele hd2,inhibiting the expression of E1 and Se-1.These results indicated that the genotypes of heading date determined different PS and well situated BVG in japonica rice cultivars in southwest China.展开更多
A rice heading-date-related mutant was isolated from a ^60Co-y-ray-induced mutation pool of Zhejing 22, a conventional japonica cultivar in Zhejiang Province, China. The mutant was characterized by a delayed heading d...A rice heading-date-related mutant was isolated from a ^60Co-y-ray-induced mutation pool of Zhejing 22, a conventional japonica cultivar in Zhejiang Province, China. The mutant was characterized by a delayed heading date of almost 20 d longer than the wild type plant. Genetic analysis revealed that the mutation was controlled by a single nuclear-encoded recessive gene that was designed as HD（t） （heading date tentatively）. To isolate the HD（t） gene, a map-based cloning approach was employed using 479 F2 mutant individual plants derived from the cross between the hd（t） mutant （japonica） x Zhenshan 97 （indica）. Finally, the HD（t） gene was mapped to an approximate 53 kb region between the insertion and deletion （InDel） markers of 10-61W and 10-66W on chromosome 10. According to the genome sequence of Nipponbare, the target region contains 11 annotated genes. It is helpful for future cloning of HD（t） gene based on this fine mapping results.展开更多
NRL3 is essential for the growth and development of rice leaves.In this study,we found that the loss function of NRL3 also delayed heading date under natural long daylight and short daylight conditions.The yeast two-h...NRL3 is essential for the growth and development of rice leaves.In this study,we found that the loss function of NRL3 also delayed heading date under natural long daylight and short daylight conditions.The yeast two-hybrid and the bimolecular fluorescence complementation proved that NRL3interacts with OsK4,a Snf1-related kinase.OsK4 localized to the nucleus and expressed in various rice tissues.The rhythmic expression pattern of Os K4 was similar to NRL3 under long daylight and short daylight conditions.Knock-out mutants of Os K4 exhibited early heading under long daylight conditions,indicating that it acts as a negative regulator of heading date in rice.Interestingly,the OsK4 mutant under the nrl3 mutant background rescued the late heading phenotype of nrl3 under long daylight conditions,suggesting that Os K4 functions downstream of NRL3.Moreover,both NRL3 and Os K4 controlled heading date through regulating the expression of Hd3a and RFT1 genes.These findings shed light on the heading date regulation in rice and provide a sound theoretical base to improve regional adaptability of rice.展开更多
An optimum heading date is essential for sustainable crop productivity and ensuring high yields. In the present study, F2：3 populations were generated by crossing an early-heading accession, Y2280, with a late-headin...An optimum heading date is essential for sustainable crop productivity and ensuring high yields. In the present study, F2：3 populations were generated by crossing an early-heading accession, Y2280, with a late-heading accession, Y2282. The heading dates of the F2 and F3 populations were investigated in a field study. Using publicly available simple sequence repeat （SSR） markers, the early heading date gene HdAey2280 was mapped onto Aegilops tauschfi chromosome 7DS between the flanking markers wmc438 and barc126 at distances of 15 and 9.1 cM, respectively. Further analysis indicated that HdAey2280 is a novel heading date gene. New SSR markers were developed based on the Ae. tauschfi draft genome sequence, resulting in four new markers that were linked to the heading date gene HdAey2280. The closest distance of these markers was 1.9 cM away from the gene. The results collected in this study will serve as a framework for map-based cloning and marker-assisted selection in wheat breeding programs in the future.展开更多
Heading date of rice is a key agronomic trait determining cultivated areas and seasons and affecting yield. In the present study, ifve primary single segment substitution lines with the same genetic background were us...Heading date of rice is a key agronomic trait determining cultivated areas and seasons and affecting yield. In the present study, ifve primary single segment substitution lines with the same genetic background were used to detect quantitative trait loci （QTLs） for heading date in rice. Two QTLs, qHD3 and qHD6 on the short arm of chromosome 3 and the short arm of chromosome 6, respectively, were identiifed under natural long-day （NLD）. Nineteen secondary single segment substitution lines （SSSLs） and seven double segments pyramiding lines were designed to map the two QTLs and to evaluate their epistatic interaction between them. By overlapping mapping, qHD3 was mapped in a 791-kb interval between SSR markers RM3894 and RM569 and qHD6 in a 1 125-kb interval between RM587 and RM225. Results revealed the existence of epistatic interaction between qHD3 and qHD6 under natural long-day （NLD）. It was also found that qHD3 and qHD6 had signiifcant effects on plant height and yield traits, indicating that both of the QTLs have pleiotropic effects.展开更多
Heading date(or flowering time)is one of the most important agronomic traits in rice,influencing its regional adaptability and crop yield.Many major-effect genes for rice heading date have been identified,but in pract...Heading date(or flowering time)is one of the most important agronomic traits in rice,influencing its regional adaptability and crop yield.Many major-effect genes for rice heading date have been identified,but in practice they are difficult to be used for rice molecular breeding because of their dramatic effects on heading date.Genes with minor effects on heading date,which are more desirable for fine-tuning flowering time without significant yield penalty,were seldom reported.In this study,we identified a new minor-effect heading date repressor,Delayed Heading Date 4(DHD4).The dhd4 mutant shows a slightly earlier flowering phenotype without a notable yield penalty compared with wild-type plants under natural long-day conditions.DHD4 encodes a CONSTANS-like transcription factor localized in the nucleus.Molecular,biochemical,and genetic assays show that DHD4 can compete with 14-3-3 to interact with OsFD1,thus affecting the formation of the Hd3a-14-3-3-OsFD1 triprotein FAC complex,resulting in reduced expression of OsMADS14 and OsMADS15,and ultimately delaying flowering.Taken together,these results shed new light on the regulation of flowering time in rice and provide a promising target for fine-tuning flowering time to improve the regional adaptability of rice.展开更多
Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using ...Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using whole- genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 （OsPRR37; hereafter PRR37） is respon- sible for the Early heading7-2 （EH7-2）/Heading date2 （Hd2） QTL which was identified from a cross of late-heading rice ＇Milyang23 （M23）＇ and early-heading rice ＇H143＇. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT （CONSTANS, CO-like, and TOC1） domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day condi- tions, and are adapted to the northernmost regions of rice cultivation, up to 53~ N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and GhdT/ Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.展开更多
基金supported by the National Natural Science Foundation of China(32222064 and 32341030)the Natural Science Foundation of Shanghai(22ZR1445800)Zhejiang Provincial Natural Science Foundation of China(LQ24C130008).
文摘Several quantitative trait genes(QTGs)related to rice heading date,a key factor for crop development and yield,have been identified,along with complex interactions among genes.However,a comprehensive genetic interaction network for these QTGs has not yet been established.In this study,we use 18K-rice lines to identify QTGs and their epistatic interactions affecting rice heading date.We identify 264 pairs of interacting quantitative trait loci(QTL)and construct a comprehensive genetic network of these QTL.On average,the epistatic effects of QTL pairs are estimated to be approximately 12.5%of additive effects of identified QTL.Importantly,epistasis varies among different alleles of several heading date genes.Additionally,57 pairs of interacting QTGs are also significant in their epistatic effects on 12 other agronomic traits.The identified QTL genetic interactions are further validated using near-isogenic lines,yeast two-hybrid,and split-luciferase complementation assays.Overall,this study provides a genetic network of rice heading date genes,which plays a crucial role in regulating rice heading date and influencing multiple related agronomic traits.This network serves as a foundation for understanding the genetic mechanisms of rice quantitative traits and for advancing rice molecular breeding.
基金supported by the Zhejiang Provincial Natural Science Foundation of China(Grant Nos.LZ24C130004 and LQ24C130008)。
文摘Heading date is one of the most important agronomic traits that directly affect rice yield and determines the regional adaptability in specific growing environments.As a short-day plant,rice can grow under long-day(LD)conditions due to the synergistic regulation of many photosensitive genes.Using a set of chromosome segment substitution lines(CSSLs)with the indica cultivar Huanghuazhan(HHZ)as the recipient parent and Basmati Surkh 89-15(BAS)as the donor parent,we identified a QTL locus.
文摘QTLs for heading date of rice （Oryza sativa L.） with additive, epistatic, and QTL × environment （QE） interaction effects were studied using a mixed-model-based composite interval mapping （MCIM） method and a double haploid （DH） population derived from IR64/Azucena in two crop seasons. Fourteen QTLs conferring heading date in rice, which were distributed on ten chromosomes except for chromosomes 5 and 9, were detected. Among these QTLs, eight had single-locus effects, five pairs had double-locus interaction effects, and two single-loci and one pair of double-loci showed QTL × environment interaction effects. All predicted values of QTL effects varied from 1.179 days to 2.549 days, with corresponding contribution ratios of 1.04%-4.84%. On the basis of the effects of the QTLs, the total genetic effects on rice heading date for the two parents and the two superior lines were predicted, and the putative reasons for discrepancies between predicted values and observed values, and the genetic potentiality in the DH population for improvement of heading date were discussed. These results are in agreement with previous results for heading date in rice, and the results provide further information, which indicate that both epistasis and QE interaction are important genetic basis for determining heading date in rice.
基金supported by grants from the National Natural Science Foundation of China (31921004 and 31871596)the Major Program of Guangdong Basic and Applied Research (2019B030302006)the Laboratory of Lingnan Modern Agriculture Project (NT2021002)
文摘Heading date determines the seasonal and regional adaptation of rice(Oryza sativa L.)varieties and is mainly controlled by photoperiod sensitivity(PS).The core heading date genes Hd1,Ghd7,DTH8,and PRR37 act synergistically in regulating the PS.In this study,we systematically analyze the heading date,PS,and agronomic traits of eight homozygous lines with various combinations of Hd1,Ghd7,and DTH8 alleles in the prr37 background under long-day(LD)and short-day(SD)conditions,respectively.We find that Hd1 alone promotes heading,regardless of the day length.However,under LDs,Hd1 suppresses flowering,in coordination with functional Ghd7 or with Ghd7 and DTH8.These loci cooperate to negatively regulate the Ehd1-Hd3 a/RFT1 pathway and delay heading.Under SDs,Hd1 competes with various heading suppressors to promote heading.Therefore,the dual function of Hd1 is vital for PS.The lines carrying Hd1 alone show reduced plant height with fewer primary and secondary branches in panicles.Lines carrying Ghd7 and DTH8(with hd1)show delayed heading and improve agronomic traits.Overall,our results reveal the regulation of rice PS flowering by the core heading date genes and their effects on agronomic traits,providing valuable information for the selection of rice varieties for adaptation to different light and temperature conditions.
基金supported by the Science and Technology Program of Zhejiang Province, China (Grant No. 2005C24007)National High Technology Research and Development Program of China (Grant Nos. 2006AA10Z1E8 and 2006AA100101)
文摘Previous study showed that a linkage drag between a blast resistance gene Pi25（t） and QTLs conditioning spikelet fertility （qSF-6） and number of filled grains per panicle （qNFGP-6） was detected on the short arm of chromosome 6. A larger population was used for further verification, and the results confirmed the linkage drag between the blast resistance gene and QTL conditioning spikelet fertility, other than QTL conditioning number of filled grains per panicle. Breakdown or avoidance of the linkage drag could be achieved by selection against the genotype background of a heading-date gene （qHD-7） that resided in the region between RM2 and RM214 on chromosome 7. For further validation, two lines with almost identical genotypes on all chromosomal regions except the Pi25（t） region on chromosome 6 were chosen to develop a new population The results showed that qSF-6 could be further subdivided into qSF-6-1 and qSF-6-2. When the genotype of the region between RM2 and RM214 was from rice variety Zhong 156, the linkage drag between Pi25（t） and qSF-6-2 was detected and the allele of qSF-6-2 from rice variety Gumei 2 reduced the spikelet fertility. When the genotype of the region between RM2 and RM214 was from Gumei 2, no linkage drag was detected. This indicates that the linkage drag between the blast resistance gene and the QTL conditioning spikelet fertility could be broken down or avoided under a certain background genotype selection against heading-date and provides a marker aided solution for high level of blast resistance and yield breeding in rice and other crops as well.
基金We gratefully acknowledge Prof.Zhu Jun for kind pro-V1sion of software QTLMapper 1.0.The work was in part supported by the National High Tech R&D Pro-gram of China(863 Program)the National Natural Sci-ence Foundation of China and the National Program on Key Basic Research Project of China(973 Program).
文摘Main-effect QTL, epistatic effects and their interactions with environment are important genetic components of quantitativetraits. In this study, we analyzed the QTL, epistatic effects and QTL by environment interactions (QE) underlying plantheight and heading date, using a doubled-haploid ( DH) population consisting of 190 lines from the cross between anindica parent Zhenshan 97 and a japonica parent Wuyujing 2, and tested in two-year replicated field trials. A geneticlinkage map with 179 SSR (simple sequence repeat) marker loci was constructed. A mixed linear model approach wasapplied to detect QTL, digenic interactions and QEs for the two traits. In total, 20 main-effect QTLs, 9 digenic interactionsinvolving 18 loci, and 5 QTL by environment interactions were found to be responsible for the two traits. No interactionswere detected between the digenic interaction and environment. The amounts of variations explained by QTLs of maineffect were 53.9% for plant height and 57.8% for heading date, larger than that explained by epistasis and QEs. However,the epistasis and QE interactions sometimes accounted for a significant part of phenotypic variation and should not bedisregarded.
基金supported by the Natural Science Foundation of China(U20A2031)the Earmarked Fund for China Agricultural Research System(CARS-01).
文摘CONSTANS,CO-like,and TOC1(CCT)family genes play important roles in regulating heading date,which exerts a large impact on the regional and seasonal adaptation of rice.Previous studies have shown that Grain number,plant height,and heading date2(Ghd2)exhibits a negative response to drought stress by directly upregulating Rubisco activase and exerting a negative effect on heading date.However,the target gene of Ghd2 regulating heading date is still unknown.In this study,CO3 is identified by analyzing Ghd2 ChIP-seq data.Ghd2 activates CO3 expression by binding to the CO3 promoter through its CCT domain.EMSA experiments show that the motif CCACTA in the CO3 promoter was recognized by Ghd2.A comparison of the heading dates among plants with CO3 knocked out or overexpressed and double-mutants with Ghd2 overexpressed and CO3 knocked out shows that CO3 negatively and constantly regulates flowering by repressing the transcription of Ehd1,Hd3a,and RFT1.In addition,the target genes of CO3 are explored via a comprehensive analysis of DAP-seq and RNA-seq data.Taken together,these results suggest that Ghd2 directly binds to the downstream gene CO3,and the Ghd2eCO3 module constantly delays heading date via the Ehd1-mediated pathway.
基金supported by grants from the Ministry of Science and Technology of China(No. 2010CB125901)the National Natural Science Foundation of China(No.31271315)the Bill & Melinda Gates Foundation
文摘Heading date in rice is a typical quantitative trait controlled by multiple quantitative trait loci （QTLs）. It is mainly regulated by environmental factors such as photoperiod and temperature （Izawa, 2007）. Many QTLs for heading date have been identified using different mapping populations and methods （http：// www.gramene.org/qtl）. Up to date, several major heading date QTLs have been cloned by map-based cloning strategy （Yano et al., 2000; Takahashi et al., 2001; Kojima et al., 2002; Doi et al., 2004; Xue et al., 2008; Wei et al., 2010; Yan et al.,
基金funded by the Chinese High-Yielding Transgenic Program (Grant No. 2011ZX08001-004)the National High-Tech Research and Development Program (Grant No. 2011AA10A101)the Research Funding of China National Rice Research Institute(Grant No. 2009RG002)
文摘Grain yield and heading date are key factors determining the commercial potential of a rice variety. Mapping of quantitative trait loci （QTLs） in rice has been advanced from primary mapping to gene cloning, and heading date and yield traits have always attracted the greatest attention. In this review, genomic distribution of QTLs for heading date detected in populations derived from intra-specific crosses of Asian cultivated rice （Oryza sativa） was summarized, and their relationship with the genetic control of yield traits was analyzed. The information could be useful in the identification of QTLs for heading date and yield traits that are promising for the improvement of rice varieties.
基金supported by the National Natural Science Foundation of China(31771783)the Key Research and Development Program of Sichuan Province,China(2021YFYZ0002)the Sichuan Science and Technology Program,China(2018HH0130 and 2022YFH0105)。
文摘Aegilops umbellulata(UU)is a wheat wild relative that has potential use in the genetic improvement of wheat.In this study,46 Ae.umbellulata accessions were investigated for stripe rust resistance,heading date(HD),and the contents of iron(Fe),zinc(Zn),and seed gluten proteins.Forty-two of the accessions were classified as resistant to stripe rust,while the other four accessions were classified as susceptible to stripe rust in four environments.The average HD of Ae.umbellulata was significantly longer than that of three common wheat cultivars(180.9 d vs.137.0 d),with the exception of PI226500(138.9 d).The Ae.umbellulata accessions also showed high variability in Fe(69.74-348.09 mg kg^(-1))and Zn(49.83-101.65 mg kg^(-1))contents.Three accessions(viz.,PI542362,PI542363,and PI554399)showed relatively higher Fe(230.96-348.09 mg kg^(-1))and Zn(92.46-101.65 mg kg^(-1))contents than the others.The Fe content of Ae.umbellulata was similar to those of Ae.comosa and Ae.markgrafii but higher than those of Ae.tauschii and common wheat.Aegilops umbellulata showed a higher Zn content than Ae.tauschii,Ae.comosa,and common wheat,but a lower content than Ae.markgrafii.Furthermore,Ae.umbellulata had the highest proportion of γ-gliadin among all the species investigated(Ae.umbellulata vs.other species=mean 72.11%vs.49.37%;range:55.33-86.99%vs.29.60-67.91%).These results demonstrated that Ae.umbellulata exhibits great diversity in the investigated traits,so it can provide a potential gene pool for the genetic improvement of these traits in wheat.
基金supported by the National Natural Science Foundation of China (32172045, 31671687)the National Key Research and Development Program of China (2016YFD0100302)the Agricultural Science and Technology Innovation Program of the CAAS
文摘RING finger E3 ligases play an important role in regulating plant growth and development by mediating substrate degradation.In this study,we identified TaGW2L,encoding a Grain width and weight2(GW2)-like RING finger E3 ligase,as a novel positive regulator of heading date in wheat(Triticum aestivum L.).TaGW2L exhibited high amino acid sequence similarities with TaGW2 homoeologs,particularly in the conserved RING finger domain.Expression analysis indicated that TaGW2L was constitutively expressed in various wheat tissues.TaGW2L showed transactivation activity in yeast and could interact with the ubiquitin-conjugating enzymes E2_(s).An in vitro ubiquitination assay verified that TaGW2L possessed a similar E3 ligase activity to TaGW2.Overexpression of the TaGW2L-7A homoeolog in wheat led to a significantly earlier heading date under both natural conditions and long-day conditions.Transcriptome analysis revealed that multiple known genes positively regulating wheat heading were significantly upregulated in the TaGW2L-7A-overexpression plants compared with the wild-type control.Together,our findings shed light on the role of TaGW2L in wheat heading date and provide potential applications of TaGW2L for the adaptation improvement of crops.
基金We are grateful for the funding from STI 2030-Major Projects(2023ZD0406802)the National Natural Science Foundation of China(32072066,32172050,3220151460)+2 种基金Hainan Yazhou Bay Seed Lab(B21HJ0215)CAAS Agricultural Science and Technology Innovation Program(CAAS-ZDRW202002,CAAS-ZDRW202201)Hebei Natural Science Foundation(C2021205013).
文摘Plant height and heading date are important agronomic traits in wheat(Triticum aestivum L.)that affect final grain yield.In wheat,knowledge of pseudo-response regulator(PRR)genes on agronomic traits is limited.Here,we identify a wheat TaPRR95 gene by genome-wide association studies to be associated with plant height.Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height,particularly the peduncle,with an earlier heading date.The longer peduncle is mainly caused by the increased cell elon-gation at its upper section,whilst the early heading date is accompanied by elevated expression of flow-ering genes,such as TaFT and TacO1.A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAAVAux genes for auxin signaling inpr95abad plants that may act as a regulatory mechanism to promote robust plant growth.A haplotype analysis identifies a TaPRR95-B haplotype(Hap2)to be closely associated with reduced plant height and increased thousand-grain weight.Moreover,the Hap2 frequency is higher in cultivars than that in landraces,suggesting the artifi-cial selection on the allele during wheat breeding.These findings suggest that TaPRR95 is a regulator for plant height and heading date,thereby providing an important target for wheat yield improvement.
基金supported by the National Natural Science Foundation of China(31771886 and 31771764)China Postdoctoral Science Foundation(2019T120164)Central Public-interest Scientific Institution Basal Research Fund(Y2020YJ10)。
文摘Heading date(or flowering time),an important agronomic trait in crop species,is closely associated with regional adaptation and yield.Members of the Pseudo-Response Regulator(PRR)family play key roles in regulating flowering.However,their role and molecular mechanism controlling heading date in rice is not very clear.Here,we identified rice OsPRR protein,OsPRR59,which delayed heading under longday conditions.OsPRR59 positively regulates yield by affecting plant height,secondary branches number per panicle,grain number per panicle,seed setting rate,and grain weight per plant.OsPRR59 is expressed in most tissues and its protein is localized to the nucleus.We also found that OsPRR59 directly binds to the promoter of Ehd3 to inhibit its expression.Compared with the WT,osprr59 ehd3 showed a significantly delayed heading phenotype,as did the ehd3 mutant.This was opposite to the phenotype of the osprr59 mutant,confirming that Ehd3 acted downstream of OsPRR59 in regulating rice flowering.Our results identified a direct regulator of Ehd3,and revealed a novel molecular mechanism of clock component OsPRR proteins in regulating heading date and provide a new genetic resource for fine-tuning heading date in rice.
基金supported by the National Natural Science Foundation of China(Grant No.30871497)the National High Technology Research and Development Program of China(Grant No.2009AA101101)the Program of Introducing Talents of Discipline to University(Grant No.B08025)
文摘Heading date of 26 native japonica rice cultivars in southwest China was investigated,and their basic vegetative growth(BVG),photoperiod-sensitivity(PS) and temperature-sensitivity(TS) were analyzed under artificial short-day and natural long-day conditions in Nanjing,as well as artificial high-temperature and natural low-temperature conditions in winter in Hainan.The results showed that the PS and TS varied among different cultivars.The BVG of all the japonica cultivars was well situated,but differed within cultivars.Regression analysis showed a significant correlation between heading date and PS,indicating that PS was the main factor affecting heading date of japonica cultivars in southwest China.Genetic analysis was conducted on these 26 cultivars using a set of heading date near isogenic lines as test lines.All the japonica cultivars carried the dominant early-heading gene Ef-1 or Ef-1t,and most of these cultivars carried the dominant photoperiod sensitivity allele E1 or E1t,the PS of which was slightly weaker than E1.For the Se-1 locus,these cultivars mainly carried recessive photoperiod insensitivity gene Se-1e.In addition,the PS of 22 japonica cultivars could be repressed or weakened by the recessive allele hd2,inhibiting the expression of E1 and Se-1.These results indicated that the genotypes of heading date determined different PS and well situated BVG in japonica rice cultivars in southwest China.
基金supported by the Chinese Ministry of Agriculture(Grant Nos.200803034 and 2011ZX08001001)the Zhejiang Provincial and the National Natural Science Foundation of China(Grant Nos.Y3080361 and 31071207)+2 种基金the Science and Technology Department of Zhejiang Province,China(Grant No.2004C12020)the Special Fund for Agro-scientific Research in the Public Interest(Grant No.201103007)the Special Fund of Zhejiang Academy of Agricultural Science,China
文摘A rice heading-date-related mutant was isolated from a ^60Co-y-ray-induced mutation pool of Zhejing 22, a conventional japonica cultivar in Zhejiang Province, China. The mutant was characterized by a delayed heading date of almost 20 d longer than the wild type plant. Genetic analysis revealed that the mutation was controlled by a single nuclear-encoded recessive gene that was designed as HD（t） （heading date tentatively）. To isolate the HD（t） gene, a map-based cloning approach was employed using 479 F2 mutant individual plants derived from the cross between the hd（t） mutant （japonica） x Zhenshan 97 （indica）. Finally, the HD（t） gene was mapped to an approximate 53 kb region between the insertion and deletion （InDel） markers of 10-61W and 10-66W on chromosome 10. According to the genome sequence of Nipponbare, the target region contains 11 annotated genes. It is helpful for future cloning of HD（t） gene based on this fine mapping results.
基金supported by the China National Natural Science Foundation(Grant No.31871597)the Key Research and Development Program of Zhejiang Province,China(Grant No.2021C02063-2)+2 种基金the Key Research and Development Program of China National Rice Research Institute(Grant No.CNRRI-2020-02)the Science and Technology Project of Jiangxi Provincial Department of Education,China(Grant No.GJJ180217)the Project supported by Jiangxi Youth Science Foundation,China(Grant No.20202BAB215001)。
文摘NRL3 is essential for the growth and development of rice leaves.In this study,we found that the loss function of NRL3 also delayed heading date under natural long daylight and short daylight conditions.The yeast two-hybrid and the bimolecular fluorescence complementation proved that NRL3interacts with OsK4,a Snf1-related kinase.OsK4 localized to the nucleus and expressed in various rice tissues.The rhythmic expression pattern of Os K4 was similar to NRL3 under long daylight and short daylight conditions.Knock-out mutants of Os K4 exhibited early heading under long daylight conditions,indicating that it acts as a negative regulator of heading date in rice.Interestingly,the OsK4 mutant under the nrl3 mutant background rescued the late heading phenotype of nrl3 under long daylight conditions,suggesting that Os K4 functions downstream of NRL3.Moreover,both NRL3 and Os K4 controlled heading date through regulating the expression of Hd3a and RFT1 genes.These findings shed light on the heading date regulation in rice and provide a sound theoretical base to improve regional adaptability of rice.
基金financially supported by the National HighTech R&D Program of China (2011AA100104)
文摘An optimum heading date is essential for sustainable crop productivity and ensuring high yields. In the present study, F2：3 populations were generated by crossing an early-heading accession, Y2280, with a late-heading accession, Y2282. The heading dates of the F2 and F3 populations were investigated in a field study. Using publicly available simple sequence repeat （SSR） markers, the early heading date gene HdAey2280 was mapped onto Aegilops tauschfi chromosome 7DS between the flanking markers wmc438 and barc126 at distances of 15 and 9.1 cM, respectively. Further analysis indicated that HdAey2280 is a novel heading date gene. New SSR markers were developed based on the Ae. tauschfi draft genome sequence, resulting in four new markers that were linked to the heading date gene HdAey2280. The closest distance of these markers was 1.9 cM away from the gene. The results collected in this study will serve as a framework for map-based cloning and marker-assisted selection in wheat breeding programs in the future.
基金financially supported by the National Natural Science Foundation of China (31171529)the Key Technologies R&D Program of China during the 12th Five-Year Plan period (2013BAD01B02-13)the Special Fund for Agro-Scientific Research in the Public Interest of China (201303007)
文摘Heading date of rice is a key agronomic trait determining cultivated areas and seasons and affecting yield. In the present study, ifve primary single segment substitution lines with the same genetic background were used to detect quantitative trait loci （QTLs） for heading date in rice. Two QTLs, qHD3 and qHD6 on the short arm of chromosome 3 and the short arm of chromosome 6, respectively, were identiifed under natural long-day （NLD）. Nineteen secondary single segment substitution lines （SSSLs） and seven double segments pyramiding lines were designed to map the two QTLs and to evaluate their epistatic interaction between them. By overlapping mapping, qHD3 was mapped in a 791-kb interval between SSR markers RM3894 and RM569 and qHD6 in a 1 125-kb interval between RM587 and RM225. Results revealed the existence of epistatic interaction between qHD3 and qHD6 under natural long-day （NLD）. It was also found that qHD3 and qHD6 had signiifcant effects on plant height and yield traits, indicating that both of the QTLs have pleiotropic effects.
基金This research was supported by grants from the Ministry of Agriculture of China for Transgenic Research,China(2016ZX08009-003)the Central Public-Interest Scientific Institution Basal Research Fund,China(Y2020YJ10)+2 种基金the National Natural Science Foundation of China,China(31771764,91935303,31871603,and U1701232)the National Key Research and Development Program of China,China(2016YFD0100403 and 2016YFD0100301)the CAAS Innovation Project,China(CAASZDXT2019003).
文摘Heading date(or flowering time)is one of the most important agronomic traits in rice,influencing its regional adaptability and crop yield.Many major-effect genes for rice heading date have been identified,but in practice they are difficult to be used for rice molecular breeding because of their dramatic effects on heading date.Genes with minor effects on heading date,which are more desirable for fine-tuning flowering time without significant yield penalty,were seldom reported.In this study,we identified a new minor-effect heading date repressor,Delayed Heading Date 4(DHD4).The dhd4 mutant shows a slightly earlier flowering phenotype without a notable yield penalty compared with wild-type plants under natural long-day conditions.DHD4 encodes a CONSTANS-like transcription factor localized in the nucleus.Molecular,biochemical,and genetic assays show that DHD4 can compete with 14-3-3 to interact with OsFD1,thus affecting the formation of the Hd3a-14-3-3-OsFD1 triprotein FAC complex,resulting in reduced expression of OsMADS14 and OsMADS15,and ultimately delaying flowering.Taken together,these results shed new light on the regulation of flowering time in rice and provide a promising target for fine-tuning flowering time to improve the regional adaptability of rice.
文摘Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus （QTL） mapping and candidate gene analysis using whole- genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 （OsPRR37; hereafter PRR37） is respon- sible for the Early heading7-2 （EH7-2）/Heading date2 （Hd2） QTL which was identified from a cross of late-heading rice ＇Milyang23 （M23）＇ and early-heading rice ＇H143＇. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT （CONSTANS, CO-like, and TOC1） domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day condi- tions, and are adapted to the northernmost regions of rice cultivation, up to 53~ N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and GhdT/ Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.
