High photosynthetic efficiency of a rice (Oryza sativa L.) xantha mutant

Comparative analysis revealed that a xantha rice mutant (cv. Huangyu B) had higher ratios of chlorophyll (Chl) a/b and carotenoids/Chl, and higher photosynthetic efficiency than its wild type parent (cv. II32 B). Unexpectedly, the mutant had higher net photosynthetic rate (P _N) than II32 B. This might have resulted from its lower non-photochemical quenching (q_N) but higher maximal photochemical efficiency (F_V/F_M), higher excitation energy capture efficiency of photosystem 2 (PS2) reaction centres (F_V′/F_M′), higher photochemical quenching (q_P), higher effective PS2 quantum yield (Φ_PS2), and higher non-cyclic electron transport rate (ETR). This is the first report of a chlorophyll mutant that has higher photosynthetic efficiency and main Chl fluorescence parameters than its wild type. This mutant could become a unique material both for the basic research on photosynthesis and for the development of high yielding rice cultivars.     

Physiological character and molecular mapping of leaf-color mutant wyv1 in rice (Oryza sativa L.)

The seed of an excellent indica restorer line Jinhui10 (Oryza sativa L. ssp. indica) was treated by ethyl methanesulfonate (EMS); a leaf-color mutant displaying distinct phenotype throughout development grown in paddy field was identified from the progeny. The mutant leaf showed white-yellow at seedling stage and then turned to yellow-green at tillering stage, after that, virescent color appeared until to maturity. The mutant was thus temporarily designed as wyv1. The chlorophyll contents decreased significantly and the changing was consistent with the chlorotic level of wyv1 leaves. Chlorophyll fluorescence kinetic parameters measured at the seedling stage showed that co-efficiency of photochemical quenching (qP), actual photosystem II efficiency (ΦPS II), electron transport rate (ETR) and initial chlorophyll fluorescence level (Fo), net photosynthetic rate (Pn) and maximum photochemical efficiency (Fv / Fm) significantly decreased in severe chlorotic leaf of the mutant compared with that of wild type. However, no significant differences were observed for Pn and Fv/Fm between virescent leaf and normal green leaf. Genetic analysis suggested that the mutant phenotype was controlled by a single recessive nuclear gene which was finally mapped between SSR marker Y7 and Y6 on rice chromosome 3 based on F2 population of Xinong1A / wyv1. Genetic distances were 0.06 cM and 0.03 cM respectively, and the physical distance was 84 kb according to the sequence of indica rice 9311. The results must facilitate map-based cloning and functional analysis of WYV1 gene.     

Genetic analysis and gene mapping of a rice few-tillering mutant in early backcross populations (Oryza sativa L.)

A rice mutant, G069, characteristic of few tiller numbers, was found in anther culture progeny from the F1 hybrid between an indica-japonica cross, Gui630×02428. The mutant has another two major features: delayed tillering development and yellowing apex and margin on the mature leaves. As a donor parent, G069 was further backcrossed with the recurrent parent, 02428, for two turns to develop a BC2F2 population. Genetic analysis in the BC2F2 population showed that the traits of few-tillering and yellowing apex and margin on the mature leaves were controlled by one recessive gene. A pool of equally mixed genomic DNA, from few-tillering individual plants in BC2F2, was constructed to screen polymorphism with simple sequence repeat (SSR) markers in comparison with the 02428 genome. One SSR marker and three restriction fragment length polymorphism (RFLP) markers were found possibly linked with the recessive gene. By using these markers, the gene of few-tillering was mapped on chromosome 2 between RFLP marker C     

Genetic mapping of hypervariable minisatellite sequences in rice (Oryza sativa L.)

Minisatellites, or DNA fingerprinting sequences, have been utilized in animal linkage studies for several years but have not been used as markers for plant genome mapping. In animal genome mapping they have resulted in limited success because they are evenly dispersed in some species but are often clustered near telomeric regions, as observed on human chromosomes. The purpose of the present study was to generate DNA fingerprints utilizing several rice-derived minisatellites containing different core sequences and numbers of repeat units, followed by assessing their potential for use as genetic markers when mapped to a rice recombinant inbred line (RIL) population. Sites of segregating minisatellite loci were mapped onto 11 of the 12 rice RIL linkage maps. The implications for the use of rice minisatellite core sequences as genetic markers on linkage maps in rice are discussed. Received: 1 March 1999 / Accepted: 22 June 1999     

Morphological and physiological characteristics of a root-hairless mutant in rice (Oryza sativa L.)

This paper reports morphological and physiological characteristics of a first root-hairless mutant (RH2) of rice (Oryza sativa L.), which can be useful in advancing knowledge on the role of root hairs in water and nutrient uptake, and genetics of root hairs. The mutant was selected among NaN₃ mutagenized progeny of the rice cultivar Oochikara. Microscopic observations showed absence of root hairs in RH2. At the seedling stage, RH2 showed shorter seedling height and shorter roots compared to the wild type variety Oochikara. Because of the differences in seedling growth, all comparisons between Oochikara and RH2 in uptake-related characters were made on the basis of values adjusted by the dry weight of either the shoot or the root. When grown at low water potential in soil, Oochikara and RH2 were similar in shoot water content and transpiration per unit shoot dry weight, and similarly, at low water potential in solution culture, there was no significant difference between Oochikara and RH2 in transpiration per unit shoot dry weight. These results suggest that at the seedling stage, root hairs do not significantly contribute to uptake of water. In solution culture, Oochikara and RH2 did not significantly differ in phosphate uptake per unit root dry weight. This result supports the previous work that root hairs do not contribute to phosphate uptake in solution culture. Regarding to response to plant hormones, RH2 showed a higher level of resistance to two synthetic auxins, 2,4-dichlorophenoxyacetic acid (2,4-D) and 1-naphthaleneacetic acid (NAA) than Oochikara. NAA treatment induced very short root hairs in RH2, suggesting that the absence of root hairs in RH2 may be due to a shortage of endogenous auxin. Genetic analysis showed that the root hairless character in RH2 is inherited as a single recessive gene.     

Arsenic toxicity to rice (Oryza sativa L.) in Bangladesh

Natural contamination of groundwater with arsenic (As) occurs around the world but is most widespread in the river basin deltas of South and Southeast Asia. Shallow groundwater is extensively used in the Bengal basin for irrigation of rice in the dry winter season, leading to the possibility of As accumulation in soils, toxicity to rice and increased levels of As in rice grain and straw. The impact of As contaminated irrigation water on soil-As content and rice productivity was studied over two winter-season rice crops in the command area of a single tubewell in Faridpur district, Bangladesh. After 16–17 years of use of the tubewell, a spatially variable build up of As and other chemical constituents of the water (Fe, Mn and P) was observed over the command area, with soil-As levels ranging from about 10 to 70 mg kg^?1. A simple mass balance calculation using the current water As level of 0.13 mg As L^?1 suggested that 96% of the added arsenic was retained in the soil. When BRRI dhan 29 rice was grown in two successive years across this soil-As gradient, yield declined progressively from 7–9 to 2–3 t ha^?1 with increasing soil-As concentration. The average yield loss over the 8 ha command area was estimated to be 16%. Rice-straw As content increased with increasing soil-As concentration; however, the toxicity of As to rice resulted in reduced grain-As concentrations in one of the 2 years. The likelihood of As-induced yield reductions and As accumulation in straw and grain has implications to agricultural sustainability, food quality and food security in As-affected regions throughout South and Southeast Asia.     

Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.)

Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers’ genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion.     

QTL mapping for the paste viscosity characteristics in rice (Oryza sativa L.)

In order to understand the genetic basis of the paste viscosity characteristics (RVA profile, which is tested on the Rapid Visco Analyser) of the rice grain, we mapped QTLs for RVA profile parameters using a DH population derived from a cross between an indica variety, Zai-Ye-Qing 8 (ZYQ8), and a japonica variety, Jing-Xi 17 (JX17). Evidence of genotype-by-environment interaction was found by comparing the mapped QTLs between two locations, Hainan (HN) and Hangzhou (HZ). A total of 20 QTLs for six parameters of the RVA profiles were identified at least one location. Only the waxy locus (wx) located on chromosome 6 was detected significantly at both environments for five traits, i.e. hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), consistency viscosity (CSV) and setback viscosity (SBV). This locus explained 19.5%–63.7% of the total variations at both environments, suggesting that the RVA profiles were mainly controlled by the wx gene. HPV, CPV, BDV, CSV and SBV were also controlled by other QTLs whose effects on the respective parameter were detected only in one environment, while for the peak viscosity (PKV), only 2 QTLs, 1 at HN,the other at HZ, were identified. These results indicate that RVA profiles are obviously affected by environment. Received: 18 July 1999 / Accepted: 27 August 1999     

Molecular mapping of genes conferring aluminum tolerance in rice (Oryza sativa L.)

Crop productivity on acid soil is restricted by multiple abiotic stress factors. Aluminum (Al) tolerance seems to be a key to productivity on soil with a pH below 5.0, but other factors such as Mn toxicity and the deficiency of P, Ca and Mg also play a role. The development of Al-tolerant genotypes of rice is an urgent necessity for improving crop productivity in developing countries. Inhibition of root growth is a primary and early symptom of Al toxicity. The present study was conducted to identify genetic factors controlling the aluminum tolerance of rice. Several parameters related to Al tolerance, most importantly the relative root growth under Al stress versus non-stress conditions, were scored in 188 F₃ selfed families from a cross between an Al-tolerant Vietnamese local variety, Chiembau, and an Al-susceptible improved variety, Omon269–65. The two varieties are both Oryza sativa ssp. indica, but showed a relatively high level of DNA polymorphism, permitting the assembly of an RFLP map consisting of 164 loci spanning 1,715.8 cM, and covering most of the rice genome. A total of nine different genomic regions on eight chromosomes have been implicated in the genetic control of root and shoot growth under aluminum stress. By far the greatest effects on aluminum tolerance were associated with the region near WG110 on chromosome 1. This region does not seem to correspond to most of the genes that have been mapped for aluminum tolerance in other species, nor do they correspond closely to one another. Most results, both from physiological studies and from molecular mapping studies, tend to suggest that aluminum tolerance is a complex multi-genic trait. The identification of DNA markers (such as WG110) that are diagnostic for aluminum tolerance in particular gene pools provides an important starting point for transferring and pyramiding genes that may contribute to the sustainable improvement of crop productivity in aluminum-rich soils. The isolation of genes responsible for aluminum tolerance is likely to be necessary to gain a comprehensive understanding of this complex trait. Received: 29 March 2000 / Accepted: 16 August 2000     

Characteristics of floral organs related to reliable self-pollination in rice (Oryza sativa L.)

In many varieties of rice, the length of basal pores on the thecae just after anthesis is strongly correlated both with the percentage of florets receiving adequate pollen and with the number of pollen grains deposited on the stigmata and its variation (coefficient of variation). Therefore, the size of the basal pores is considered to be an important factor for the reliable self-pollination of rice. We discuss how long basal pores may facilitate self- pollination.     

Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm.     

RFLP mapping of the genes controlling hybrid breakdown in rice (Oryza sativa L.)

 Complementary recessive genes hwd1 and hwd2 controlling hybrid breakdown (weakness of F₂ and later generations) were mapped in rice using RFLP markers. These genes produce a plant that is shorter and has fewer tillers than normal plants when the two loci have only one or no dominant allele at both loci. A cultivar with two dominant alleles at the hwd1 locus and a cultivar with two dominant alleles at the hwd2 locus were crossed with a double recessive tester line. Linkage analysis was carried out for each gene independently in two F₂ populations derived from these crosses. hwd1 was mapped on the distal region of rice genetic linkage map for chromosome 10, flanked by RFLP markers C701 and R2309 at a distance of 0.9 centiMorgans (cM) and 0.6 cM, respectively. hwd2 was mapped in the central region of rice genetic linkage map for chromosome 7, tightly linked with 4 RFLP markers without detectable recombination. The usefulness of RFLP mapping and map information for the genes controlling reproductive barriers are discussed in the context of breeding using diverse rice germplasm, especially gene introduction by marker-aided selection.     

Epigenetic responses to drought stress in rice (Oryza sativa L.)

Cytosine methylation polymorphism plays a key role in gene regulation, mainly in expression of genes in crop plants. The differential expression of cytosine methylation over drought stress response was analyzed in rice using drought susceptible but agronomically superior lines IR 20 and CO 43, and drought tolerant genotypes PL and PMK 3 and their F₁ hybrids. The parents and hybrids were subjected to two moisture regimes viz., one under drought condition and another under control condition. The cytosine methylation polymorphism in genomic DNA was quantified under both the conditions at the reproductive stage of the plant using the Methylation Sensitive Amplified Polymorphism (MSAP) technique devised by Xiong et al. (261:439–446, 1999). The results depicted that under drought condition, hyper-methylation was predominant in the drought susceptible genotypes while drought tolerant genotypes presented hypo-methylation behavior. While imposing drought, spikelet sterility per cent was positively correlated to percentage of methylation whereas, panicle length, number of seed per panicle, panicle weight, 100 seed weight, and yield/plant were negatively correlated indicating the role of epigenetic regulation in yield attributing traits in response to drought. Thus, methylation can be considered as an important epigenetic regulatory mechanism in rice plants to adapt drought situation. From this study, we speculate that the hyper- methylation may be an indicator of drought susceptibility and the hypo-methylation for drought tolerance and this methylation polymorphism can be effectively used in drought screening program.     

Time-related mapping of quantitative trait loci controlling grain-filling in rice (Oryza sativa L.)

Grain-filling is a crucial process that determines final grain yield in rice (Oryza sativa L.). To understand the genetic basis of dynamics of grain-filling, quantitative trait locus (QTL) analysis was conducted using time-related phenotypic data on grain-filling collected from a population of 155 recombinant inbred lines (F12), derived from a cross between Milyang 23 and Akihikari. Two QTLs detected on chromosomes 8 and 12 were strongly associated with increased filling percentage per panicle. These QTLs were not linked with those controlling spikelet numbers per panicle. This result confers the possibility of improving grain-filling together with an enlargement of sink size. The QTL for filling percentage per panicle on chromosome 8 exactly overlapped that for non-structural carbohydrate (NSC) content in the culm and leaf sheaths during grain-filling, and the Milyang 23 allele associated with increased grain-filling percentage per panicle was associated with decreased NSC content. Therefore, this QTL may be directly involved in NSC translocation from the culm and leaf sheaths to panicle. In addition, the Milyang 23 alleles of QTLs associated with greater spikelet number per panicle on chromosomes 1 and 6 were also related with a reduction in NSC content in the culm and leaf sheaths during grain-filling. These results indicate that NSC dynamics during grain-filling is partly dependent on sink size. NSC accumulation in the culm and leaf sheaths at the heading stage was mainly controlled by different genetic regulations from NSC dynamics during grain-filling. Nitrogen dynamics during grain-filling may also be involved in carbohydrate dynamics.     

Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.)

Key message

Twenty-seven QTLs were identified for rice seed vigor, in which 16 were novel QTLs. Fifteen elite parental combinations were designed for improving seed vigor in rice.

Abstract

Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker–trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.