QTL analysis for flowering time using backcross population between Oryza sativa Nipponbare and O. rufipogon

In the near future, global average temperature is expected to increase due to the accumulation of greenhouse gases, and increased temperatures will cause severe sterility in many crop species. In rice, since wild species show high genetic variation, they may have the potential to improve the flowering characters of cultivars. In this study, we investigated flowering characters under natural conditions by comparing an Asian wild rice accession of Oryza rufipogon W630 (originated from Myanmar) with a Japanese rice cultivar, O. sativa Japonica cv. Nipponbare. Further, QTL analysis for days to heading (DH) and spikelet opening time (SOT: the time of day when the spikelet opens) was carried out using BC(2)F(8) backcross population derived from the cross between them. Regarding DH, four QTLs were detected, and two of them were found to have wild alleles with strong effects leading to longer days to heading during the Japanese summer. These wild alleles may be used to produce late-heading cultivars that do not flower during the high summer temperatures anticipated in the future. As for SOT, two parameters of SOTb (beginning time when the first spikelet opens) and SOTm (median time when 50% of the spikelets open) were recorded and the time differences from Nipponbare were investigated. Two QTLs on chromosomes 5 and 10 and two QTLs on chromosomes 4 and 5 were detected for SOTb and SOTm, respectively. The wild alleles were responsible for early spikelet opening time at all loci. If the wild alleles detected in this study have the same effects in the genetic background of other cultivars, they will be very useful in producing early-flowering rice cultivars that complete fertilization in the morning before the temperature rises.     

Analysis of quantitative trait loci affecting chlorophyll content of rice leaves in a double haploid population and two backcross populations

Chlorophyll content, one of the most important physiological parameters related to plant photosynthesis, is usually used to predict yield potential. To map the quantitative trait loci (QTLs) underlying the chlorophyll content of rice leaves, a double haploid (DH) population was developed from an indica/japonica (Zhenshan 97/Wuyujing 2) crossing and two backcross populations were established subsequently by backcrossing DH lines with each of their parents. The contents of chlorophyll a and chlorophyll b were determined by using a spectrophotometer to directly measure the leaf chlorophyll extracts. To determine the leaf chlorophyll retention along with maturation, all measurements were performed on the day of heading and were repeated 30 days later. A total of 60 QTLs were resolved for all the traits using these three populations. These QTLs were distributed on 10 rice chromosomes, except chromosomes 5 and 10; the closer the traits, the more clustering of the QTLs residing on common rice chromosomal regions. In general, the majority of QTLs that specify chlorophyll a content also play a role in determining chlorophyll b content. Strangely, chlorophyll content in this study was found mostly to be lacking or to have a negative correlation with yield. In both backcross F₁ populations, overdominant (or underdominant) loci were more important than complete or partially dominant loci for main-effect QTLs and epistatic QTLs, thereby supporting previous findings that overdominant effects are the primary genetic basis for depression in inbreeding and heterosis in rice.     

Epistatic interactions in genetic regulation of t-PA and PAI-1 levels in a Ghanaian population

The proteins, tissue plasminogen activator (t-PA) and plasminogen activator inhibitor 1 (PAI-1), act in concert to balance thrombus formation and degradation, thereby modulating the development of arterial thrombosis and excessive bleeding. PAI-1 is upregulated by the renin-angiotensin system (RAS), specifically by angiotensin II, the product of angiotensin converting enzyme (ACE) cleavage of angiotensin I, which is produced by the cleavage of angiotensinogen (AGT) by renin (REN). ACE indirectly stimulates the release of t-PA which, in turn, activates the corresponding fibrinolytic system. Single polymorphisms in these pathways have been shown to significantly impact plasma levels of t-PA and PAI-1 differently in Ghanaian males and females. Here we explore the involvement of epistatic interactions between the same polymorphisms in central genes of the RAS and fibrinolytic systems on plasma t-PA and PAI-1 levels within the same population (n = 992). Statistical modeling of pairwise interactions was done using two-way ANOVA between polymorphisms in the ETNK2, RENIN, ACE, PAI-1, t-PA, and AGT genes. The most significant interactions that associated with t-PA levels were between the ETNK2 A6135G and the REN T9435C polymorphisms in females (p = 0.006) and the REN T9435C and the TPA I/D polymorphisms (p = 0.005) in males. The most significant interactions for PAI-1 levels were with REN T9435C and the TPA I/D polymorphisms (p = 0.001) in females, and the association of REN G6567T with the TPA I/D polymorphisms (p = 0.032) in males. Our results provide evidence for multiple genetic effects that may not be detected using single SNP analysis. Because t-PA and PAI-1 have been implicated in cardiovascular disease these results support the idea that the genetic architecture of cardiovascular disease is complex. Therefore, it is necessary to consider the relationship between interacting polymorphisms of pathway specific genes that predict t-PA and PAI-1 levels.     

Diversified mechanisms for regulating flowering time in a short-day plant rice

Flowering in rice is influenced by not only endogenous factors that comprise an autonomous pathway, but also environmental effects, such as photoperiod, water availability, and temperature just before floral initiation. Recent molecular genetics studies have elucidated the functional roles of genes involved in the photoperiod pathway, e.g., photoreceptors, circadian clock components, and short-day (SD) promotion factors. Although these molecular players are well conserved between rice andArabidopsis, their actual genetic functions are distinct. This is exemplified byHd1 (aCO counterpart) and phytochromes, in particular, ricePHYA. Hd1 has a dual role in regulating flowering time and the expression ofHd3a (anFT counterpart) repression under long-day (LD) conditions while promotion under SDs. Models have been proposed to explain these photoperiod-dependent antagonistic activities. Some regulatory factors are present in only one of the model systems, e.g.,FLC inArabidopsis orEhd1 in rice. Furthermore, epistatic relationships vary among such flowering regulators asHd3a (FT), OsMADS50 (SOCT), andOsMADS14 (AP1). Further experiments to probe these differences will be essential to enlarging our understanding of the diversified flowering regulation mechanisms in rice.     

Mapping loci controlling vernalization requirement and flowering time in Brassica napus

Rapeseed cultivars (Brassica napus L.) can be classified into annual and biennial groups according to their requirement for vernalization in order to induce flowering. The genetic control of these phenotypic differences is not well understood, but this information could be valuable for the design of breeding approaches to accelerate rapeseed improvement. In order to map loci controlling this variation, a doubled haploid population, derived from a cross between annual and biennial cultivars, was evaluated for vernalization requirement and days-to-flowering in a replicated field experiment using three treatments: no vernalization, 4 weeks of vernalization and 8 weeks of vernalization. A linkage map of 132 RFLP loci was used to locate loci controlling these traits. Marker segregation in one region of linkage group 9 was strongly associated with the annual/biennial growth habit in the unvernalized treatment and with days-to-flowering in all three treatments. Two other regions with smaller effects on days-to-flowering were also identified.     

Quantitative trait loci for flowering time and inflorescence architecture in rose

The pattern of development of the inflorescence is an important characteristic in ornamental plants, where the economic value is in the flower. The genetic determinism of inflorescence architecture is poorly understood, especially in woody perennial plants with long life cycles. Our objective was to study the genetic determinism of this characteristic in rose. The genetic architectures of 10 traits associated with the developmental timing and architecture of the inflorescence, and with flower production were investigated in a F ₁ diploid garden rose population, based on intensive measurements of phenological and morphological traits in a field. There were substantial genetic variations in inflorescence development traits, with broad-sense heritabilities ranging from 0.82 to 0.93. Genotypic correlations were significant for most (87%) pairs of traits, suggesting either pleiotropy or tight linkage among loci. However, non-significant and low correlations between some pairs of traits revealed two independent developmental pathways controlling inflorescence architecture: (1) the production of inflorescence nodes increased the number of branches and the production of flowers; (2) internode elongation connected with frequent branching increased the number of branches and the production of flowers. QTL mapping identified six common QTL regions (cQTL) for inflorescence developmental traits. A QTL for flowering time and many inflorescence traits were mapped to the same cQTL. Several candidate genes that are known to control inflorescence developmental traits and gibberellin signaling in Arabidopsis thaliana were mapped in rose. Rose orthologues of FLOWERING LOCUS T (RoFT), TERMINAL FLOWER 1 (RoKSN), SPINDLY (RoSPINDLY), DELLA (RoDELLA), and SLEEPY (RoSLEEPY) co-localized with cQTL for relevant traits. This is the first report on the genetic basis of complex inflorescence developmental traits in rose.     

Mapping quantitative trait loci affecting susceptibility to Marek's disease virus in a backcross population of layer chickens

Marek's disease (MD), caused by the oncogenic MD avian herpes virus (MDV), is a major source of economic losses to the poultry industry. A reciprocal backcross (BC) population (total 2052 individuals) was generated by crossing two partially inbred commercial Leghorn layer lines known to differ in MDV resistance, measured as survival time after challenge with a (vv+) MDV. QTL affecting resistance were identified by selective DNA pooling using a panel of 198 microsatellite markers covering two-thirds of the chicken genome. Data for each BC were analyzed separately, and as a combined data set. Markers showing significant association with resistance generally appeared in blocks of two or three, separated by blocks of nonsignificant markers. Defined this way, 15 chromosomal regions (QTLR) affecting MDV resistance, distributed among 10 chromosomes (GGA 1, 2, 3, 4, 5, 7, 8, 9, 15, and Z), were identified. The identified QTLR include one gene and three QTL associated with resistance in previous studies of other lines, and three additional QTL associated with resistance in previous studies of the present lines. These QTL could be used in marker-assisted selection (MAS) programs for MDV resistance and as a platform for high-resolution mapping and positional cloning of the resistance genes.     

Association between molecular markers and blast resistance in an advanced backcross population of rice

An advanced backcross population consisting of 80 BC₃F₃ lines derived from rice vars. Vandana/Moroberekan was analysed for blast resistance and genotyped with 50 candidate genes and 23 simple sequence repeat (SSR) markers. Six candidate defence response genes [thaumatin, three nucleotide-binding site-leucine-rich repeat sequences from maize and two resistance gene analogue (RGA) markers] and one SSR marker (RM21) were significantly associated with partial blast resistance in rice (P=0.01). These markers accounted for phenotypic variation ranging from 9.6% to 29.4% and contributed to 76% of the total variation of percentage diseased leaf area (DLA) observed under natural infection. Four candidate genes (oxalate oxidase, 14-3-3 protein and two RGA markers) and four SSR markers (RM21, RM168, RM215 and RM250) were significantly associated with resistance to a single pathogen isolate, PO6-6. Among these, two markers were for DLA, five for lesion number and one for lesion size. These markers accounted for 9.1–28.7% of the phenotypic variation. A moderate correlation (r=0.48, P<0.01) was found between the level of partial resistance measured in the greenhouse and that measured under natural conditions. Analysis of BC₃F₄ progeny using genotypes of BC₃F₃ confirmed the phenotypic contribution of these markers. Cluster analysis of DNA profiles showed that the BC₃ population was genetically similar (>85%) to the recurrent parent Vandana. Although no obvious relationship between DNA profiles and resistant phenotypes was observed, three lines (VM19, VM46 and VM76) in a cluster with high similarity to Vandana (89–96%) expressed a high level of partial blast resistance in the field. Analysis of disease progress in the field confirmed the performance of selected lines based on greenhouse and nursery analyses. The advanced backcross progeny with resistance phenotypes tagged by markers will be useful for accumulating blast resistance in upland rice.Communicated by G. Wenzel     

Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome

Genetic architecture of flowering time in maize was addressed by synthesizing a total of 313 quantitative trait loci (QTL) available for this trait. These were analyzed first with an overview statistic that highlighted regions of key importance and then with a meta-analysis method that yielded a synthetic genetic model with 62 consensus QTL. Six of these displayed a major effect. Meta-analysis led in this case to a twofold increase in the precision in QTL position estimation, when compared to the most precise initial QTL position within the corresponding region. The 62 consensus QTL were compared first to the positions of the few flowering-time candidate genes that have been mapped in maize. We then projected rice candidate genes onto the maize genome using a synteny conservation approach based on comparative mapping between the maize genetic map and japonica rice physical map. This yielded 19 associations between maize QTL and genes involved in flowering time in rice and in Arabidopsis. Results suggest that the combination of meta-analysis within a species of interest and synteny-based projections from a related model plant can be an efficient strategy for identifying new candidate genes for trait variation.     

The association of flowering time quantitative trait loci with duplicated regions and candidate loci in Brassica oleracea.

A population of 150 doubled haploid lines of rapid cycling Brassica oleracea, derived from an F1 from a var. alboglabra x var. italica cross, was scored for flowering time in two trials. Using information on 82 mapped molecular markers, spread evenly across the nine linkage groups, QTL were identified at six locations; one each on linkage groups O2 and O3 and two each on linkage groups O5 and O9. In total, these QTL explained 58 and 93% of the genetical variation in the two trials. Three of these QTL, on linkage groups O2, O3, and O9, were situated in regions showing considerable homology both with each other and with chromosome regions of B. nigra that have been shown to affect flowering time. These same regions are all homologous to a single tract of Arabidopsis chromosome 5, which contains a number of the flowering-related genes, one or more of which may be candidates for the QTL found in Brassica.     

Double loss-of-function mutation in EARLY FLOWERING 3 and CRYPTOCHROME 2 genes delays flowering under continuous light but accelerates it under long days and short days: an important role for Arabidopsis CRY2 to accelerate flowering time in continuous light

The photoperiodic response is one of the adaptation mechanisms to seasonal changes of lengths of day and night. The circadian clock plays pivotal roles in this process. In Arabidopsis, LHY, CCA1, ELF3, and other clock proteins play major roles in maintaining circadian rhythms. lhy;cca1 double mutants with severe defects in circadian rhythms showed accelerated flowering under short days (SDs), but delayed flowering under continuous light (LL). The protein level of the floral repressor SVP increased in lhy;cca1 mutants under LL, and the late-flowering phenotype of lhy;cca1 mutants was partially suppressed by svp, flc, or elf3. ELF3 interacted with both CCA1 and SVP, and elf3 suppressed the SVP accumulation in lhy;cca1 under LL. These results suggest that the unique mechanism of the inversion of the flowering response of lhy;cca1 under LL may involve both the ELF3-SVP/FLC-dependent and -independent pathways. In this work, elf3-1 seeds were mutagenized with heavy-ion beams and used to identify mutation(s) that delayed flowering under LL but not long days (LDs) or SDs even without ELF3. In this screening, seven candidate lines named suppressor of elf3 1 (self1), sel3, sel5, sel7, sel14, sel15, and sel20 were identified. Genetic analysis indicated that sel20 was a new deletion allele of a mutation in the blue light receptor, CRY2. A late-flowering phenotype and decrease of FT expression in the elf3;sel20 double mutant was obvious under LL but not under SDs or LDs. These results indicated that the late-flowering phenotype in the double mutant elf3;sel20 as well as in lhy;cca1 was affected by the presence of darkness. The results suggest that CRY2 may play more essential roles in the acceleration of flowering under LL than LDs or SDs.     

Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations

To understand the types of gene action controlling seven quantitative traits in rice, we carried out quantitative trait locus (QTL) mapping in order to distinguish between the main-effect QTLs (M-QTLs) and digenic epistatic QTLs (E-QTLs) responsible for the trait performance of 254 recombinant inbred lines (RILs) from rice varieties Lemont/Teqing and two backcross hybrid (BCF₁) populations derived from these RILs. We identified 44 M-QTL and 95 E-QTL pairs in the RI and BCF₁ populations as having significant effects on the mean values and mid-parental heterosis of heading date, plant height, flag leaf length, flag leaf width, panicle length, spikelet number and spikelet fertility. The E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both the RI and BCF₁ populations. In both BCF₁ populations, over-dominant (or under-dominant) loci were more important than additive and complete or partially dominant loci for M-QTLs and E-QTL pairs, thereby supporting prior findings that overdominance resulting from epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice.     

Mapping genetic loci for flowering time,maturity, and photoperiod insensitivity in soybean

Time of flowering and maturity in soybean (Glycine max (L.) Merr) are important reproductive characters of agronomic interest. These traits are useful for developing soybean cultivars with a wider geographical adaptation. The objective of this research was to use molecular markers to identify chromosomal regions that control traits for flowering time, maturity and photoperiod insensitivity in soybean. Two single-cross populations, IX132 (PI 317.336 × `Corsoy') consisting of 101 progeny, and IX136 (PI 317.334B × `Corsoy') consisting of 100 progeny, were used. Days to R1 (the day when 50% of the plants in a plot have an open flower at one of the top nodes with a fully expanded leaf) was observed among F_6:7 RI lines in the field during 1991 and 1992 and in the growth chamber at 12 h and 20 h photoperiods using fluorescent and incandescent lamps. Days to R3 (the number of days after emergence when 50% of the plants in a plot had presented the first 5 mm pod at one of the top four nodes with a fully expanded leaf was observed in the field during 1991 and in the growth chamber with 12 h photoperiod. Days to R7 (the number of days after emergence when 50% of pods in a plot had mature pod color) was observed in the field in 1991. A total of 139 markers (88 RFLPs and 51 SSRs) in the IX132 population and 125 markers (73 RFLPs and 52 SSRs) in the IX136 population were used to map quantitative trait loci (QTL) affecting these traits. Results show that a large-effect QTL for days to R1, R3, and R7, and photoperiod insensitivity was found at the same location on linkage group (LG) C2 in both populations. This result suggests that photoperiod insensitivity, flowering time, and maturity may be controlled by the same gene(s) or by tightly clustered genes in the same chromosomal region. In addition to the large effect QTL, minor QTL were also detected controlling the four traits in both populations. Minor QTL account for as much as 17.8% and 12.1% of phenotypic variance in populations IX132 and IX136, respectively. Thus, time of flowering, maturity, and photoperiod insensitivity in these soybean populations are proposed to be controlled by a major QTL with a large effect and modified by several minor QTL.     

Epistasis and genotype-environment interaction for quantitative trait loci affecting flowering time in Arabidopsis thaliana

A major goal of evolutionary biology is to understand the genetic architecture of the complex quantitative traits that may lead to adaptations in natural populations. Of particular relevance is the evaluation of the frequency and magnitude of epistasis (gene–gene and gene–environment interaction) as it plays a controversial role in models of adaptation within and among populations. Here, we explore the genetic basis of flowering time in Arabidopsis thaliana using a series of quantitative trait loci (QTL) mapping experiments with two recombinant inbred line (RIL) mapping populations [Columbia (Col) x Landsberg erecta (Ler), Ler x Cape Verde Islands (Cvi)]. We focus on the response of RILs to a series of environmental conditions including drought stress, leaf damage, and apical damage. These data were explicitly evaluated for the presence of epistasis using Bayesian based multiple-QTL genome scans. Overall, we mapped fourteen QTL affecting flowering time. We detected two significant QTL–QTL interactions and several QTL–environment interactions for flowering time in the Ler x Cvi population. QTL–environment interactions were due to environmentally induced changes in the magnitude of QTL effects and their interactions across environments – we did not detect antagonistic pleiotropy. We found no evidence for QTL interactions in the Ler x Col population. We evaluate these results in the context of several other studies of flowering time in Arabidopsis thaliana and adaptive evolution in natural populations.     

FPF1 transgene leads to altered flowering time and root development in rice

AtFPF1 (FLOWERING PROMOTING FACTOR 1) is a gene that promotes flowering in Arabidopsis. An expression vector containing AtFPF1 driven by a Ubi-1 promoter was constructed. The gene was introduced into rice callus by Agrobacterium-mediated transformation and fertile plants were obtained. The presence of AtFPF1 in rice plants was confirmed by PCR, Southern and Northern blot analyses, as well as by -glucuronidase assay. The results showed that, as in Arabidopsis, AtFPF1 reduced flowering time in rice. Furthermore, introduction of AtFPF1 enhanced adventitious root formation but inhibited root growth in rice during the seedling stage. The results suggest that AtFPF1 promotes flowering time in both dicots and monocots, and plays a role in the initiation of adventitious roots in rice.Ming-Li Xu and Jia-Fu Jiang contributed equally to this work