Photoperiod sensitivity gene controlling heading date in rice cultivars in the northernmost region of Japan

Rice is grown in diverse environments at latitudes ranging from 53^°N to 40^°S. In Japan, Hokkaido is the northernmost rice cultivation region(42–45^°N latitude). Only extremely early maturing (heading) varieties that have extremely low photoperiod sensitivity are adapted to this area. Heading date is the most important trait in adaptation to this particular environment. Also, the efficient manipulation of heading date is a crucial component of rice improvement. To determine the genetic basis for heading date among cultivars grown in Hokkaido, the heading behaviour was analyzed. Clear segregations were observed. To estimate the photoperiod sensitivity of the genes involved, the cultivars and F₁ plants from crosses between the cultivars were grown under different daylength conditions. The results indicated that the genes controlling heading date are photoperiod sensitive, suggesting they play important roles in the northernmost rice cultivation regions in Japan, to which only cultivars with extremely low photoperiod sensitivity are adapted. This revised version was published online in August 2006 with corrections to the Cover Date.     

Inheritance of heading time in spring barley evaluated in multiple environments

The inheritance of heading time of spring barley was studied in three extremely early genotypes IB, RL and ‘Mona’ (M), which is homozygous recessive for the early maturity ea8 (=ea_k) gene conferring extreme earliness under short daylengths and is relatively photoperiod insensitive, and five (GP, MA, PS, NU and BA) spring genotypes that are early to intermediate for heading time. Frequency distributions of F₂ generations grown at Ouled Gnaou, Morocco (32°15′ N), an environment which maximizes differences between photoperiod‐insensitive and photoperiod‐sensitive genotypes, indicated that across populations many loci were segregating in a complex Mendelian manner. IB and RL were both homozygous recessive for the ea8 gene, which conferred an early heading time. RL had partially dominant alleles at second locus (Enea8), which enhanced its earliness. Recovery of only progeny within the parental range of genotypes for heading time from the crosses of RL/M and IB/M suggests that numerous loci remained suppressed, perhaps latent, given their diverse parentage. The ea8 recessive homozygote in RL suppressed another unidentified locus which, when homozygous recessive in the absence of the ea8 recessive homozygote, conferred extreme earliness in one short daylength environment (Ouled Gnaou, Morocco) but was undetected in another environment (Davis, CA, USA). Epistatic gene action and genotype × environment effects strongly influenced heading time. In addition to a genetic system consisting of single‐locus recessive homozygotes conferring photoperiod insensitivity, a second genetic system, based on dominant alleles at one or a few loci, derived from the early heading Finnish landrace ‘Olli’, also confers extremely early heading time under short daylengths and relative photoperiod insensitivity in the genotype GP.     

Development and characterization of chromosome segment substitution lines derived from backcross between japonica donor rice cultivar Yukihikari and japonica recipient cultivar Kirara397

Grain yield-related traits and grain quality-related traits are important for rice cultivars. The quantitative trait loci (QTLs) involved in controlling the natural variation in these traits among closely related cultivars are still unclear. The present study describes the development of a novel chromosome segment substitution line (CSSL) population derived from a cross between the temperate japonica cultivars Yukihikari and Kirara397, which are grown in Hokkaido, the northernmost limit for rice cultivation. Days to heading, culm length, panicle length, panicle number, brown grain weight per plant, thousand brown grain weight, brown grain length, brown grain width, brown grain thickness, apparent amylose content, and protein content were evaluated. Panicle length, brown grain length and amylose content differed significantly in the parental cultivars. Thirty-five significant changes in the evaluated traits were identified in the CSSLs. A total of 28 QTLs were located on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 10, 11 and 12. These findings could be useful for breeding rice cultivars in the northernmost limit for rice cultivation.     

Diallel analysis of floral morphology in radish (Raphanus sativus L.)

Patterns of photoperiodic-response curve (PRC) of heading time in rice were examined using the five near-isogenic lines (NILs) of Taichung 65, in which insensitive alleles was replaced by photosensitive alleles through backcrossings. In the first experiment, the NILs showed the diversified patterns of PRC, depending on genotype, under the controlled conditions (9-, 10-, 12- and 14-h daylengths). In addition, the two NILs with different Se1 alleles showed the different patterns although they showed similar heading times under natural daylength (NDL) conditions. The cryptic difference gives some clues as to the relationship between the patterns and heading-time behaviors under NDL conditions. In the second experiment, behaviors of vegetative and reproductive developments under 20-h daylength condition with high- and low-nutrient conditions were examined to know whether or not they behave as expected from their PRC obtained in the first experiment. Under the extremely long-day condition, the photosensitive alleles brought about long-growth durations where the internal changes for senescence might drastically occur with increases of total number of phytomers (TNP) and decrease potentials for reproductive developments. The nutrient levels might not affect the pattern of internal changes but might affect TNP, depending on genotype, and as a result, the nutrient levels might bring about different developmental fates in the same genotype under the long-day condition. The present results suggest the importance of genotype-by-environment interaction in relation to the cryptic variation of PRC in rice.     

Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region

Plant breeding programs in local regions may generate genetic variations that are desirable to local populations and shape adaptability during the establishment of local populations. To elucidate genetic bases for this process, we proposed a new approach for identifying the genetic bases for the traits improved during rice breeding programs; association mapping focusing on a local population. In the present study, we performed association mapping focusing on a local rice population, consisting of 63 varieties, in Hokkaido, the northernmost region of Japan and one of the northern limits of rice cultivation worldwide. Six and seventeen QTLs were identified for heading date and low temperature germinability, respectively. Of these, 13 were novel QTLs in this population and 10 corresponded to the QTLs previously reported based on QTL mapping. The identification of QTLs for traits in local populations including elite varieties may lead to a better understanding of the genetic bases of elite traits. This is of direct relevance for plant breeding programs in local regions.     

Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido

Improving the eating quality of cooked rice has been one of the most important objectives in rice breeding programs. Eating quality of cooked rice is a complex trait including several components, such as external appearance, taste, aroma, and texture. Therefore, dissection of these components followed by marker-assisted selection of detected QTL(s) may be a useful approach for achieving desirable eating quality in rice breeding. Whiteness of cooked rice (WCR) is an important factor related to the external appearance of cooked rice. WCR is known to be associated with the amylose and protein contents of the endosperm. However, the genetic basis of WCR remains unclear. In this study, we evaluated phenotypic variation in WCR among recently developed rice cultivars from Hokkaido, Japan. Then, we developed doubled haploid lines (DHLs) derived from a cross between two cultivars from Hokkaido, Joiku No. 462 (high WCR) and Jokei06214 (low WCR). Using the DHLs, we detected two QTLs for WCR, qWCR3 and qWCR11, on chromosomes 3 and 11, respectively. We also examined the dosage effect of the two QTLs based on both the categorized segregants in the DHLs and the relationship between the WCR phenotype and inheritance around the QTL regions in cultivars from Hokkaido.     

Genes conferring low seedling reaction to Mexican pathotypes of Puccinia recondita f. sp. tritici,and adult-plant responses of recent wheat cultivars from the former USSR

Fifty-five spring bread wheat (Triticum aestivum L.) cultivars, mostly released between 1975 and 1991 in eight leaf rust-prone spring wheat growing regions of the former USSR, were tested in the seedling growth stage for reaction to 15 Mexican pathotypes of Puccinia recondita f. sp. tritici. In total, seven known and at least two unknown genes were identified, either singly or in combinations: Lr3 (7 cultivars), Lr10 (14), Lr13 (5), Lr14a (1), Lr16 (1), Lr23 (3); the unknown genes were identified in 14 cultivars. The first unknown gene could be either Lr9, Lr19, or Lr25; however, the second unknown gene in 9 cultivars was different from any named gene. Twelve of the 15 pathotypes are virulent for this gene, hence its use in breeding for resistance will be limited. The cultivars were also evaluated at two field locations in Mexico with two pathotypes in separate experiments. The area under the disease progress curve and the final disease rating of the cultivars indicated genetic diversity for genes conferring adult plant resistance. based on the symptoms of the leaf tip necrosis in adult plants, resistance gene Lr34 could be present in at least 20 cultivars. More than half of the cultivars carry high to moderate levels of adult plant resistance and were distributed in each region.     

Photoperiod insensitivity gene essential to the varieties grown in the northern limit region of paddy rice (Oryza sativa L.) cultivation

Summary The release of extremely early maturing varieties has made it possible to cultivate rice in Hokkaido (NL45-42°) in Japan, the northern limit region of paddy rice cultivation. Until then, rice cultivation in this region has been impracticable due to the climate condition, especially short summer and long-day more than 15 hours during summer. Experiment results confirmed that the success of rice cultivation in this area depends on raising photoperiod insensitivity varieties with short basic vegetative growth period. Moreover, in this study, the genetic factors controlling the photoperiod insensitivity of Hokkaido varieties were analyzed by using 8 kinds of tester lines for three loci, E1, E2, and E3, controlling photoperiod sensitivity. It was found out that all the varieties examined carry el, a photoperiod insensitivity allele of E1 locus, but as for the other loci, E2 and E3, the existence of plural alleles were recognized. We have already clarified that almost all the japonica-type varieties grown in Japan (except Hokkaido) and Taiwan carry E1 bringing about strong photoperiod sensitivity. Accordingly, it can be concluded that el is the gene essential to Hokkaido varieties: the interchange of E1 with e1 enabled rice cultivation under long-day condition.     

Effect of Drought on the Gas Exchange,Chlorophyll Fluorescence and Yield of Six Different‐Era Spring Wheat Cultivars

In semi‐arid areas of north‐west China, grain yields of wheat (Triticum aestivum L.) are higher in recently bred cultivars than those released six decades earlier. The gas exchange, chloroplast activity and yield of six spring wheat cultivars grown in the 1950s, Hst and Gs96 (early), in the 1970s, Gy602 and Dx24 (intermediate), and in the 1990s, Gc20 and Lc8275 (modern) were compared with adequate water (WET) and drought stress (DRY) to determine the effects of drought stress among the cultivars. The results showed that in the WET treatment, the modern cultivars had significantly higher rates of leaf gas exchange, photosystem 2 (PS2) maximal photochemical efficiency, actual quantum yield of PS2 (ФPS2), photochemical quenching of chlorophyll (_qp) and lower non‐photochemical quenching (NPQ) than early cultivars, but had significantly lower gas exchange rates, intercellular CO₂ concentration, ФPS2, _qp and NPQ in the DRY treatment. In the WET treatment, the grain yield of early cultivars was significantly lower (10 %) than intermediate cultivars, but was significantly higher (17 %) than intermediate cultivars in the DRY treatment. The modern and intermediate cultivars had more sensitive stomata to water shortage, but the decreased activity of the PS2 reaction centre helped avoid damage from photoinhibition in these cultivars.     

我国水稻主栽品种抽穗期多样性的遗传分析

抽穗期决定着水稻品种的地区和季节适应性,我国水稻品种抽穗期表现出丰富的多样性。设置长、短日照和高、低温4种环境,分析了来自我国各稻区的83份粳稻和51份籼稻共134份水稻主栽品种的抽穗期感光性、感温性及基本营养生长性。回归分析表明我国水稻主栽品种的抽穗期与其感光性、基本营养生长性呈显著线性相关。高纬度地区的水稻品种往往具有弱的感光性和基本营养生长性,低纬度地区的品种感光性和基本营养生长性较强。利用一套抽穗期近等基因系对这134份品种抽穗期基因型进行了分析。结果表明,感光基因E₁与基本营养生长Ef-1位点的不同基因型对我国水稻主栽品种抽穗期多样性起着重要的作用。大多数带有非感光等位基因e₁的品种感光性与基本营养生长性都相对较弱,抽穗期较短;而携带感光性等位基因E₁或E₁^t的品种的感光性与基本营养生长性都相对较强,抽穗期较长。在Ef-1位点,携带显性早熟等位基因Ef-1的品种,其基本营养生长性较弱,抽穗期较短;而携带早熟效应较弱的等位基因Ef-1^t或迟熟等位基因ef-1的品种,其基本营养生长性较强,抽穗期较长。同时,各主基因的不同基因型在我国各稻区或各种类型水稻中的分布频率也表现出不同的特点。这些结果将对我国水稻种质的合理利用及广适应性水稻新品种的选育具有重要的指导意义。     

A gene complex for annual habit in sugar beet (Beta vulgaris L.)

Annual habit in sugar beet has been shown to be controlled by a dominant gene, B, which induces bolting under long days without the cold requirement usually essential for biennial cultivars. The induction of bolting by B, however, is often influenced by both environmental and genetic factors. We studied the genetic basis for bolting suppression, caused by delayed planting, in lines derived from a cross between annual and biennial lines. The F₂ progeny of a late-bolting F₁ plant yielded an unexpected segregation ratio of annuality from monogenic inheritance when planted in late May, there being an excess of non-bolting biennials, although the expected segregation was observed in the late April sowing. Bolting suppression was caused by restricted daylengths due to delayed planting because the segregation was normal under artificially induced long days. The analysis with Idh1, an isozyme marker proximal to B, demonstrated that heterozygous B plants were more susceptible to bolting suppression due to delayed planting than homozygous B plants. The results suggest that bolting suppression was controlled by a number of genes responsible for long daylength requirement, one of which was closely linked to B and formed a gene complex for annuality. The annual habit was controlled singly by B under long days but modified by the genes for long daylength requirement under restricted daylengths. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genotypic Differences in Root Hair Deformation and Subsequent Nodulation for Red Clover under Different Additions of Starter N Fertilization

Red clover cultivars, including diploid and tetraploid, are commonly used in legume‐based pasture mixtures. However, information on nodulation under different starter N regimens is limited. We hypothesized that there is genetic variability among different red clover cultivars for nodulation. A root hair deformation assay was conducted using three diploid (AC Christie, Tapani and CRS15) and three tetraploid (Tempus, CRS18 and CRS39) red clover cultivars by inoculating them with Rhizobium leguminosarum biovar trifolii. Nodulation and morphological characteristics of two selected red clover cultivars, AC Christie and Tempus, were determined under five starter N concentrations (0, 0.2, 0.4, 0.8 and 1.6 mg per plant). Inoculation with rhizobia increased root hair deformation with significant interaction across cultivars. Nodulation was delayed under high starter N concentrations, and genotypic differences were evident for days‐to‐nodule initiation. There was a positive quadratic response to starter N for AC Christie and a negative quadratic response for Tempus for nodulation. Tempus had more active nodules (92 %) than AC Christie (73 %). The genetic variability of red clover cultivars should be considered in N fixation studies and their response to availability of initial N.     

Response to Daylength in Oats: Pre-Anthesis Development and Set of Spikelets and Florets

Daylength ranges between 15 h and 22 h when oats are sown in Finland. This study evaluated the effect of 15-h, 18-h and 24-h daylengths on apical development, pre-anthesis growth, and spikelet and floret set in two oat cultivars ( Avena sativa L.) adapted to northern growing conditions. Experiments were done in a growth chamber at 18°C.
Increases in daylength shortened the period of apical development. The oat cultivars were especially responsive to increase in daylength from 15 h to 18 h. The increase in daylength resulted in a 45 % reduction in number of fertile florets and a slight increase in the proportion of incompletely development and stunted florets. Fertility of florets was most reduced on the lower primary and secondary branches of the panicle. Total number of leaves and phyllochron decreased as daylength increased. Moreover, the longer the day, the lower the number of green leaves per main stem until developmental stage 11. However, at pollination, oats exposed to 15-h days had the lowest number of green leaves. Results of study indicated that delayed sowing, when associated with longer days at pre-anthesis, hastened apical development and decreased yield potential in oats.     

Inheritance of temperature sensitivity of the photoperiod response in common bean (Phaseolus vulgaris L.)

Summary Photoperiod response of flowering in common bean (Phaseolus vulgaris L.) is thought to be controlled by the genes Ppd and Hr. However, cultivars also vary in the degree that cooler temperatures reduces their sensitivity to photoperiod. To examine the inheritance of this temperature sensitivity, crosses of cvs. Gordo x de Celaya and Flor de Mayo × Rojo 70 were evaluated at two sites differing in mean temperature and using 12.5-h natural photoperiod or 18-h artificially extended photoperiod. Under 18-h photoperiod at the warmer site, Palmira, no plants of the parents or of the F₂ populations flowered, confirming that the parents were sensitive to photoperiod. Under 12.5-h photoperiod at the cooler site, Popayan, the parents for each cross flowered at similar dates and no segregation for days to flower was observed. However, under 18-h photoperiod, de Celaya and Rojo 70 and the F₁ populations did not flower within 100 days after planting, while the F₂ and F₃ populations showed segregation that was consistent with single gene inheritance, late flowering being dominant. Late flowering at Popayan under 18-h photoperiod indicates a lack of temperature sensitivity, so temperature insensitivity of the photoperiod response was dominant to sensitivity. The name Tip, for temperature insensitivity of photoperiod response, is proposed for this gene, with the recessive form of this gene conditioning earlier flowering at cooler temperatures with long daylengths. It is recognized that the observed segregation patterns could represent the effect of multiple alleles at the Ppd or Hr loci, and studies are proposed to test this possibility with molecular markers and recombinant inbred lines.     

Habitat and management affect genetic structure of Festuca pratensis but not Lolium multiflorum ecotype populations

Genetic diversity present in permanent grassland may be valuable for broadening gene pools in breeding programmes and for conservation of genetic resources. However, little is known about the amount of genetic diversity present at specific habitats and about site‐related factors affecting it. To identify valuable habitats, genetic diversity of 12 ecotype populations and four reference cultivars of both Festuca pratensis Huds. and Lolium multiflorum Lam. was analysed using Simple sequence repeat markers (SSR). Analysis of molecular variance revealed a larger within population variation for L. multiflorum (97.1%) than for F. pratensis (92.6%). F. pratensis ecotype populations were clearly separated from cultivars and formed three distinct subclusters according to the geographic regions they were sampled from. Differences between L. multiflorum ecotype populations and cultivars were small and no grouping of populations was observed. Thus, only F. pratensis ecotype populations were structured and habitat as well as management had a slight influence on genetic structure. This information may allow the design of individual strategies for targeted utilization of genetic resources in plant breeding programmes.     

Estimation of quantitative genetic parameters for grain yield and quality in winter wheat under high and low nitrogen fertilization

The main question connected with developing wheat cultivars adapted to low nitrogen (N) is whether separate breeding programs for low and high input conditions are necessary. Nineteen wheat cultivars were grown over three years in Croatia in a total of eight environments at high N and low N in order to determine the effect of two N levels on means, variances and heritability of grain yield and bread-making quality and to assess the relative efficiency of indirect selection under high N in improving trait means under low N. Means of grain yield and grain protein content decreased under low N 10 and 13 %, respectively compared to the high N, whereas higher reductions of means due to lower fertilization were observed for grain N yield (21 %), wet gluten content (20 %), Zeleny sedimentation value (27 %) and for most rheological parameters, whose mean values were reduced from 20 % to as much as 57 %. Heritabilities for grain yield and grain N yield at high N were 0.82 and 0.76, respectively, and 0.77 and 0.43 at low N. Heritability for dough development time, stability and resistance also tended to be higher at high N than at low N due to a decrease in genetic variance and an increase in error variance at low N. The genetic correlation coefficients between high and low N were higher than 0.90 and the efficiency of indirect selection under high N for performance under low N was near 1.0 for grain yield and for most bread-making quality traits.     

Nuclear Mutations Affecting Chloroplastic Pigments of Photoperiod-insensitive Barley

Three photoperiod-sensitive spring barley cultivars (Hordeum vulgare L.) and three independently derived, single-gene, nuclear mutants expressing photoperiod insensitivity and extremely early heading time under short daylengths were investigated for chloroplastic pigment variation in three environments using reverse-phase high-performance liquid chromatography (HPLC) to account for differences in laminae colour. In a greenhouse, non-stress environment and in a full sunlight, high-temperature stress environment, no systematic differences were observed among pigments of the mutant-parent pairs. However, under 12 h of daily light (600 μE m ²sec^?1) and stress temperatures (20/10°C, night/day) in a growth chamber, the three mutants appeared similar to each other in chlorotic appearance and laminae pigment contents, but differed from the three non -chlorotic parents, which were similar to each other. The mutants had less chlorophyll a and b, β-carotene, lutein, taraxanthin, violaxanthin, and neoxanthin but more zeaxanthin than their parents. When shaded, the mutants became less chlorotic. How phenotypic differences for heading time and perception of day-length might be related to altered chloroplast contents remains unclear. The single-gene mutants conferring photopenod insensitivity were more sensitive to photothermal stress than their photoperiod-sensitive counterparts and as a result, their zeaxanthin content increased but the level of other pigments decreased.     

Distribution of photoperiod-insensitive alleles Ppd-B1a and Ppd-D1a and their effect on heading time in Japanese wheat cultivars

The genotypes of photoperiod response genes Ppd-B1 and Ppd-D1 in Japanese wheat cultivars were determined by a PCR-based method, and heading times were compared among genotypes. Most of the Japanese wheat cultivars, except those from the Hokkaido region, carried the photoperiod-insensitive allele Ppd-D1a, and heading was accelerated 10.3 days compared with the Ppd-D1b genotype. Early cultivars with Ppd-D1a may have been selected to avoid damage from preharvest rain. In the Hokkaido region, Ppd-D1a frequency was lower and heading date was late regardless of Ppd-D1 genotype, suggesting another genetic mechanism for late heading in Hokkaido cultivars. In this study, only 11 cultivars proved to carry Ppd-B1a, and all of them carried another photoperiod-insensitive allele, Ppd-D1a. The Ppd-B1a/Ppd-D1a genotype headed 6.7 days earlier than the Ppd-B1b/Ppd-D1a genotype, indicating a significant effect of Ppd-B1a in the genetic background with Ppd-D1a. Early-maturity breeding in Japan is believed to be accelerated by the introduction of the Ppd-B1a allele into medium-heading cultivars carrying Ppd-D1a. Pedigree analysis showed that Ppd-B1a in three extra-early commercial cultivars was inherited from ‘Shiroboro 21’ by early-heading Chugoku lines bred at the Chugoku Agriculture Experimental Station.     

QTL mapping for seedling traits associated with low‐nitrogen tolerance using a set of advanced backcross introgression lines of rice

Nitrogen (N) deficiency is a major yield‐limiting factor in rice production. The objective of this study was to identify putative QTLs for low‐N stress tolerance of rice, using an advanced backcross population derived from crosses between an indica cultivar ‘93‐11’ and a japonica cultivar ‘Nipponbare’ and genotyped at 250 marker loci. Plant height, maximum root length, root dry weight, shoot dry weight and plant dry weight under two N conditions and their relative traits were used to evaluate low‐N tolerance at the seedling stage. A total of 44 QTLs were identified on chromosomes 1, 2, 3, 4, 5, 6, 8 and 9. Eight intervals on five chromosomes were identified to harbour multiple QTLs, suggesting pleiotropism or multigenic effects according to the contributor of alleles. Some QTL clusters were found in the nearby regions of genes associated with N recycling in rice, indicating that the key N metabolism genes might have effects on the expression of QTLs. Several unique QTLs for relative traits were detected, which suggested the specific genetic basis of relative performance.     

Distribution of photoperiod-insensitive allele Ppd-A1a and its effect on heading time in Japanese wheat cultivars

The Ppd-A1 genotype of 240 Japanese wheat cultivars and 40 foreign cultivars was determined using a PCR-based method. Among Japanese cultivars, only 12 cultivars, all of which were Hokkaido winter wheat, carried the Ppd-A1a allele, while this allele was not found in Hokkaido spring wheat cultivars or Tohoku-Kyushu cultivars. Cultivars with a photoperiod-insensitive allele headed 6.9–9.8 days earlier in Kanto and 2.5 days earlier in Hokkaido than photoperiod-sensitive cultivars. The lower effect of photoperiod-insensitive alleles observed in Hokkaido could be due to the longer day-length at the spike formation stage compared with that in Kanto. Pedigree analysis showed that ‘Purple Straw’ and ‘Tohoku 118’ were donors of Ppd-A1a and Ppd-D1a in Hokkaido wheat cultivars, respectively. Wheat cultivars recently developed in Hokkaido carry photoperiod-insensitive alleles at a high frequency. For efficient utilization of Ppd-1 alleles in the Hokkaido wheat-breeding program, the effect of Ppd-1 on growth pattern and grain yield should be investigated. Ppd-A1a may be useful as a unique gene source for fine tuning the heading time in the Tohoku-Kyushu region since the effect of Ppd-A1a on photoperiod insensitivity appears to differ from the effect of Ppd-B1a and Ppd-D1a.