Starch RVA profile parameters of rice are mainly controlled byWx gene

Quantitative trait locus (QTLs) mapping for rapid visco analyser (RVA) profile parameters has been carried out by using a double haploid (DH) population derhred from a cross betweenindica variety Zhai-Ye-Qing 8 andjaponica variety Jing-Xi 17 and its genetic linkage map. The results indicate that the segregation of the RVA profiles is continually distributed among the DH lines, and some DH lines show transgressive segregation for all the parameters. A major QTL,Waxy (Wx) gene on chromosome 6 which controls the amylose synthesis, has been detected significantly for 5 traits: hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), consistency viscoslty (CSV) and setback viscoslty (SBV). Therefore, the RVA profile parameters are mainly controlled byWx gene. Other 3 and 2 QTLs have also been identified for BDV and SBV, respectively, and two of them share the same region on chromosomes 1 and 5. However, the peak viscosity (PKV) is controlled by a minor QTL on chromosome 12, qPKV-12.     

Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research

An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the polymorphisms of insertion/deletion (InDel) DNA fragments obtained from the basic local alignment search tool (BLAST) to the entire genomic sequences of indica (93-11) and japonica rice (Nipponbare). The 45 InDel loci were validated experimentally by the polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE) in 44 typical indica and japonica rice varieties, including 93-11 and Nipponbare. A neutrality test of the data matrix generated from electrophoretic banding patterns of various InDel loci indicated that 34 InDel loci were strongly associated with the differentiation of indica and japonica rice. More extensive analyses involving cultivated rice varieties from 11 Asian countries, and 12 wild Oryza species with various origins confirmed that indica and japonica characteristics could accurately be determined via calculating the average frequency of indica- or japonica-specific alleles on different InDel loci across the rice genome. This method was named as the “InDel molecular index” that combines molecular and statistical methods in determining the indica and japonica characteristics of rice varieties. Compared with the traditional methods based essentially on morphology, the InDel molecular index provides a very accurate, rapid, simple, and efficient method for identifying indica and japonica rice. In addition, the InDel index can be used to determine indica or japonica characteristics of wild Oryza species, which largely extends the utility of this method. The InDel molecular index provides a new tool for the effective selection of appropriate indica or japonica rice germplasm in rice breeding. It also offers a novel model for the study of the origin, evolution, and genetic differentiation of indica and japonica rice adapted to various environmental changes.     

QTL analysis of rice low temperature germinability

A double haploid population, derived from anther culture of F1 hybrid between a typical indica and a japonica (ZYQ8/JX17), has been used to investigate the low temperature germinability (LTG) at 15 ℃. The low temperature germinability of two parents was significantly different. In 6-11 d, the germination percentage of ZYQ8 was higher than that of JX17. In 12-16 d, the germination percentage of JX17 was higher than that of ZYQ8. The quantitative trait loci (QTLs) of every day for low temperature germinabilityhave been mapped based on a molecular linkage map constructed from this population. In 8-11 d, qLTG-9 was identified in C397B-RZ617B on chromosome 9, the additive effect was positive, showing that, the allele from JX17 could increase low temperature germinability. In 12-16 d, qLTG-4 was mapped between RG908 and CT563 on chromosome 4, the additive effect was negative, showing that the allele from ZYQ8 could increase low temperature germinability. These two QTLs were detected at different stages, showing the complexity of the mechanism of low temperature germinability.     

Transformation of japonica rice with<Emphasis Type="Italic">RHL</Emphasis> gene and salt tolerance of the transgenic rice plant

Overexpression of the yeastHAL2 gene increases salt tolerance of yeast and plant. RiceHAL2-like (RHL) gene was introduced into ajaponica rice cultivar HJ19 withAgrobacterium tumefaciens-mediated transformation. Transgenic plants in R₀ generation were selected on the principle of GUS-positive,RHL gene PCR-positive and normal growth. Hygromycin-resistant plants of some transgenic lines in R₁ generation increased salt tolerance during the seedling and booting stage, being less damaged in the cytomembrane and stronger in leaf tissue viability under salt stress during booting period. Southern analysis of transgenic lines tolerant to salt in R₁ generation showed that theRHL gene expression cassette had been successfully integrated into rice genome. Moreover, gene engineering breeding methodology and really salt-tolerant rice cultivar were discussed.     

Introduction of antisensewaxy gene into main parent lines ofindica hybrid rice

Amylose content in rice endosperm is one of the key determinants of rice eating and cooking quality, and the poor quality ofindica hybrid rice is closely related to the high amylose level in rice grains. In order to improve the grain quality of theindica hybrid rice by genetic engineering, an antisense fragment of ricewaxy gene, driven by the 5′-franking sequences of the ricewaxy gene, was successfully introduced into three major parent lines ofindica hybrid rice, all contain a high amylose level in the grains, viaAgrobacterium, and more than 100 hygromycinresistant plants were regenerated. The analysis of PCR amplification and Southern blots indicated that the T-DNA containing the antisensewaxy gene had been integrated into the genome of transgenic rice plants. Most of the primary transgenic rice plants grew normally, and the mature seeds from these transgenic plants were performed for analysis of the amylose content. The results showed that the amylose content in the endosperm of some grains was reduced and the lowest reached 7.02% in one homozygous transgenic line, 72.4% lower than that of the wild type. The influence of the altered amylose content on the gelatinization temperature and gel consistency was also observed in several homozygous transgenic rice plants. The two authors contributed equally to this work.     

Detecting quantitative trait loci for water use efficiency in rice using a recombinant inbred line population

Breeding rice with high water use efficiency (WUE) can ameliorate water shortage through water-saving irrigation.However,WUE is a complex quantitative trait and very few studies have been conducted to measure WUE directly.In this study,a recombined inbred line population derived from a cross between an indica lowland rice and upland japonica rice was used to dissect the genetic control of WUE by fine-monitored water supply experiments.Quantitative trait loci (QTL) were scanned for 10 traits including heading date (HD),water-consumption per day (water/d),shoot weight gain per day (shootw/d),root weight gain per day (rootw/d),kernel weight gain per day (kernelw/d),average WUE at whole plant level (WUEwhole/d),average WUE for up-ground biomass (WUEup/d),average WUE for grain yield (WUEyield/d),average economic index (econindex/d),and average root/shoot ratio per day (ratio/d).The results show that most of the traits were significantly correlated to each other.Twenty-four QTL (LOD ≥ 2.0) were detected for econindex,econindex/d,WUEyield,WUEyield/d,WUEup,WUEup/d,WUEwhole,WUEwhole/d,kernelw,kernelw/d,rootw,and water/d by composite interval mapping.These QTLs are located on chromosomes 1,2,4,6,7,8,and 12.Individual QTLs accounted for 4.97%-10.78% of the phenotypic variation explained.Some of these QTLs overlapped with previously reported drought resistance QTLs detected in this population.These results provide useful information for further dissection of the genetic basis and marker-assisted selection of WUE in rice.     

Identification of quantitative trait loci affecting tolerance to low phosphorus in rice (Oryza Sativa L.)

Phosphorus (P)-deficiency in rice (Oryza. Sativa. L) may cause yield reductions. This research has been conducted to map quantitative trait loci (QTLs) for tolerance to low phosphorus stress in a doubled haploid (DH) population. By using the linkage map of this population, the QTLs for relative dry weight, relative P content and relative P utilization efficiency have been located. The results indicate that one RFLP marker located on chromosome 6 is closely associated with relative root dry weight, relative shoot dry weight and relative total dry weight, which explain 24.9%, 20.5% and 25.2% of the total phenotypic variations, respectively. Two QTLs affect relative P uptake content, which account for 20.7% of the total phenotypic variations. One micro-effect QTL has been found to be associated with relative P utilization efficiency. It is suggested that the P uptake efficiency is more associated with P efficiency. Among the secondary physiological indices of P uptake efficiency, the root dry weight is more important than others.     

Advances in the understanding of inter-subspecific hybrid sterility and wide-compatibility in rice

Hybrid sterility is a major form of postzygotic reproductive isolation and frequently occurs in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice （Oryza sativa L.）. It has been a major barrier for utilization of the strong heterosis expressed in hybrids between indica and japonica. A large number of loci for rice inter-subspecific hybrid sterility have been identified by genetic analysis. Cytological studies revealed that male and female gamete abortions and reduced affinity between the uniting gametes all occurred in indica-japonica hybrids, suggesting the complexity of the causes for inter-subspecific hybrid sterility. Two genes conditioning embryo-sac and pollen sterility respectively in indica-japonica hybrids have been cloned recently, providing opportunities for molecular characterization of the indica-japonica hybrid sterility and wide-compatibility. Future studies should aim at cloning more genes for indica-japonica hybrid sterility, characterizing the underlying molecular mechanism, and utilization of the findings for the development of inter-subspecific hybrids to increase rice productivity.     

Comparative mapping of rice root traits in seedlings grown in nutrient or non-nutrient solution

The component and amount of nutrient in the growth medium are the major factors affecting root growth.For the systematic dissection of root gene expression,evaluation of nutrient and non-nutrient solutions was conducted for their effect on root traits and quantitative trait loci(QTL)mapping.Three rice root parameters,maximum root length(MRL),root dry weight(RDW),and root/ shoot ratio of dry weight(RSR),were characterized within a double haploid(DH)population from a cross of ZYQ8(indica)and JX17(japonica).The value of the three root traits in two parents all decreased under the nutrient condition compared to those under the nonnutrient condition,of which RSR decreased up to 2.6-fold on average.In the DH population,more than 70 % lines in MRL,94 % lines in RDW,and all the lines in RSR were scored lower.In total,eight QTLs were identified in nutrient system(5 from JX17 alleles and 3 from ZYQ8 alleles)while five QTLs were detected in non-nutrient system(4 from JX17 alleles and 1 from ZYQ8 alleles).Of them,one QTL for RSR was shared by both culturing systems,seven QTLs were specific in nutrient system and the other four QTLs were specific in non-nutrient system.All 13 QTLs were distributed over 7 rice chromosomes-2,3,4,5,6,9 and 10,respectively.     

Relationships between D1 protein, xanthophyll cycle and photodamage-resistant capacity in rice (Orysa sativa L.)

Relationships between D1 protein, xanthophyll cycle and subspecific difference of photodamage-resistant capacity have been studied inO. japonica rice varieties 02428 and 029 (photoinhibition-tolerance) andO. indica rice varieties 3037 and Palghar (photoinhibition-sensitivity) and their reciprocal cross F₁ hybrids after photoinhibitory treatment. It was shown that PS II photochemical efficiency (F _v /F _m) decreased, and xanthophyll cycle from violaxanthin (V), via anaxanthin (A), to zeaxanthin (Z) was enhanced and non-photochemical quenching (qN) increased accordingly in SM-pretreated leaves of rice when the synthesis of D1 protein was inhibited, and that there was a decrease inqN and, as a result, more loss of D1 protein and a big decrease inF _v/F _m in DTT-pretreated leaves when xanthophyll cycle was inhibited.O. japonica subspecies had a higher maintaining capacity of D1 protein and a decrease ofF _v/F _m in a more narrow range, and exhibited more resistance against photodamage, as compared withO. indica subspecies. The above physiological indexes in reciprocal cross F₁ hybrids, though between the values of their parents, were closer to maternal lines than to paternal lines. Experimental results support the concept that the turnover capacity for D1 protein is an important physiological basis of photoinhibition-tolerance, and will provide the physiological basis for selection of the photoinhibition-tolerant parents and develop a new approach to breed hybrids with high photosynthetic efficiency.     

转录因子OsNAC2对逆境下水稻产量性状的影响

以水稻OsNAC2过表达、RNAi转基因株系和野生型（日本晴）为材料,分别在苗期和生殖期进行干旱和盐胁迫处理,探索逆境条件下OsNAC2对水稻产量性状的影响。结果表明,不论是在苗期还是生殖期,OsNAC2-RNAi株系的叶相对含水量均比野生型更高,对干旱胁迫具有更强的适应能力;而OsNAC2过表达株系则相反。虽然苗期和生殖期遭遇盐胁迫的OsNAC2-RNAi株系相比野生型具有更高的叶相对含水量,但是OsNAC2的过量表达与RNAi株系的产量性状跟野生型相比并没有明显不同。生殖期干旱和盐胁迫下转基因株系的产量性状分析显示：干旱胁迫下,OsNAC2-RNAi株系的结实率与野生型相比显著提高了20.8%~29.2%,千粒重则无明显差异;而OsNAC2过表达株系每株粒数和千粒重相比野生型株系均显著降低。虽然盐胁迫下OsNAC2-RNAi株系的分蘖数和有效穗数明显比野生型高,但单株粒数和千粒重则无明显差异。上述结果表明,OsNAC2-RNAi株系具有更强的耐旱性,对于干旱胁迫下水稻的产量有显著的提高作用。     

Experimental validation of inter-subspecific genetic diversity in rice represented by the differences between the DNA sequences of ＇Nipponbare＇ and ＇93-11＇

The pedigrees of three sequenced rice cultivars were analyzed to show that a majority of the genetic composition of ＇Nipponbare＇ originates from japonica cultivars while the minority originates from indica cultivars. In contrast, ＇93-11＇ is derived mainly from indica cultivars with a smaller contribution from japonica cultivars. All ancestors of ＇Guang lu ai 4＇ appeared to be indica lines. A set of molecular markers （46 InDels and 53 SSRs） polymorphic between ＇Nipponbare＇ and ＇93-11＇ were examined in 46 typical indica and 47 typical japonica cultivars selected from 443 accessions according to Cheng＇s index. All cultivars were divided into indica and japonica groups without overlapping when clustered by Cheng＇s index, InDels and SSRs. Much higher InDel and SSR diversity between groups than within groups implies that the marker polymorphisms between ＇Nipponbare＇ and ＇93-11＇ represent a large proportion of inter-subspecific diversity. About 85% of indica cultivars and more than 90% of japonica cultivars were confirmed to have the same PCR banding patterns as ＇93-11＇ and ＇Nipponbare＇, respectively. Some polymorphic loci between ＇Nipponbare＇ and ＇93-11＇ cannot be validated in other indica and japonica cultivars, either as subspecies-specific but not predominant alleles, or alleles not specific between the two groups. It was concluded that molecular markers developed from sequence polymorphism between ＇Nipponbare＇ and ＇93-11＇ often represent inter-subspecific diversity, although some exceptions were sensitive to either particular marker loci or particular cultivars.     

Genetic analysis and mapping of rice （Oryza sativa L.） male-sterile （OsMS-L） mutant

A rice male-sterile mutant OsMS-L of japonica cultivar 9522 background, was obtained in M4 population treated with ^60Co γ-Ray. Genetic analysis indicated that the male.sterile phenotype was controlled by a single recessive gene. Results of tissue section showed that at microspore stage, OsMS-L tapetum was retarded. Then tapetal calls expanded and microspores degenerated. No matured pollens were observed in OsMS-L anther locus. To map OsMS-L locus, an F2 population was constructed from the cross between the OsMS-L (japonica) and LongTeFu B(indica). Firstly, the OsMS-L locus was roughly mapped between two SSR markers, RM109 and RM7562 on chromosome 2. And then eleven polymorphic markers were developed for further fine fine-mapping. At last the OsMS-L locus was mapped between the two lnDel markers, Lhsl0 and Lhs6 with genetic distance of 0.4 cM, respectively. The region was delimited to 133 kb. All these results were useful for further cloning and functional analysis of OsMS-L.     

Study on heterosis of intersubspecies between indica and japonica rice （Oryza sativa L.） using chromosome segment substitution lines

Great heterosis exists in the inter-subspecific crossesbetween indica and japonica rice cultivars[1,2] and the ex-ploitation of this heterosis has long been considered as apromising method to further increase rice yield potential[3].Previous studies indicated that there were large differencesbetween the two subspecies with respect to morphology,isozyme, polymorphism of molecular markers and DNAstructure due to long time genetic differentiation[4,5]. Thosedifferences were identified to be clos…     

Identification and classification of subspecies of Asian cultivated rice and their hybrids

Having reviewed the major classification systems proposed by various scholars across the world, it is found thatindica andjaponica underO. sativa L. are two major directions thoroughly differentiated from the Asian cultivated rice, forming the framework of the classification structure. A system withindica andjaponica as the only two subspecies is therefore reiterated. There are various ways to determine the indica-japonica identity of hybrid rice, but the “combined morphological trait index” (CMT index) method is more efficient and easier to handle, although the isozyme analysis, molecular marker analysis and grain quality assay methods are also feasible.     

Identification of quantitative trait loci affecting tolerance to low phosphorus in rice (Oryza Sativa L.)

Phosphorus (P)-deficiency in rice (Oryza.Sativa.L) may cause yield reductions.This research has been conducted to map quantitative trait loci (QTLs) for tolerance to low phosphorus stress in a doubled haploid (DH) population.By using the linkage map of this population,the QTLs for relative dry weight,relative P content and relative P utilization efficiency have been located.The results indicate that one RFLP marker located on chromosome 6 is closely associated with relative root dry weight,relative shoot dry weight and relative total dry weight,which explain 24.9%,20.5% and 25.2% of the total phenotypic variations,respectively.Two QTLs affect relative P uptake content,which account for 20.7% of the total phenotypic variations.One micro-effect QTL has been found to be associated with relative P utilization efficiency.It is suggested that the P uptake efficiency is more associated with P efficiency.Among the secondary physiological indices of P uptake efficiency,the root dry weight is more important than others.     

QTL mapping of the root traits and their correlation analysis with drought resistance using DH lines from paddy and upland rice cross

A Double Haploid (DH) population, 116 plants, derived from the cross between Japonica upland rice IRAT109 and paddy rice Yuefu, planted in PVC pipe under upland ecosystem in 2001 and 2002, was used in this study. Seven root traits, including basal root thickness (BRT), total root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), ratio of root fresh weight to shoot fresh weight (RFW/SFW) and ratio of root dry weight to shoot dry weight (RDW/SDW), were studied. Using index of drought resistance (IDR), the ratio of yield under upland ecosystem to yield under lowland ecosystem of DH lines, as the criteria of drought resistance, and correla-tion analysis between root traits and IDR, showed that BRT, MRL and RN were significantly correlated with IDR. High IDR lines had thicker BRT, longer MRL and less RN than low IDR lines. A molecular linkage map with 94 RFLP markers and 71 SSR markers covering 1535.1 cM was pro-duced. QTLs and G譋 interactions for BRT, RN, MRL, RFW, RDW, RFW/SFW and RDW/SDW were obtained based on the constructed molecular linkage map and soft-ware QTLmapper version 1.0. A total of 18 additive QTLs and 18 pairs of epistatic QTLs associated with root traits were detected. There were nine additive QTLs and two pairs of epistatic QTLs performed significant interactions with environment. Some QTLs with high general contribution and no G譋 interaction were obtained. Two pairs of epistatic QTLs mrl3 and mrl8, brt3 and brt11a controlling MRL and BRT had high general contributions of 21.51% and 13.03% respectively. An additive QTL and a pair of epistatic QTLs controlling RFW and RDW had high general contributions of 13.50% and 25.64% respectively. Marker assisted selec-tion (MAS) for rice drought resistance based on QTL with high general contribution, low G譋 interaction and tightly linkage with IDR were also discussed.     

Analysis of rice blast resistance genes by QTL mapping

Resistance to rice blast pathogen mostly shows a quantitative trait controlled by several minor genes. Its complexity and the mutable characteristic of rice blast isolates both hinder the development of the blast resistance research. The article here tried to explore the resistance gene distribution on rice chromosomes and the way of function. Totally 124 QTLs have been identified against 20 isolates using Cartographer software with a ZYQ8/JX17 DH population, which separately are at 100 loci of 72 marker intervals on 12 rice chromosomes. Of them, 16 QTLs were determined by the isolate HB-97-36-1. 82 QTLs (66.13%) are from the resistant parent alleles, ZYQ8, while 42 QTLs (33.87%) are from the susceptible parent alleles, JX17. In comparison of their positions on chromosome, most QTLs are clustered together and distributed nearby the major genes especially the regions on chromosomes 1, 2, 8, 10 and 12. Each QTL could account for the resistance variation between 3~2%-68.64%. And, a positional QTL might display the resistance to several different isolates with different contributions.     

Expression analysis ofgdcsP promoter from C3-C4 intermediate plantFlaveria anomala in transgenic rice

ThegdcsP promoter isolated from C₃-C₄ intermediate plantFlaveria anomala was fused to the β-glucuronidase (GUS) gene. The chimeric gene was inserted into the binary vector pBin19 and introduced into the rice (Oryza sativa L.) cv. 8706 byAgrobacteriummediated gene transfer. GUS activity can be detected in leaf, leaf sheath, stem and root tissues via fluorometric GUS assay. However, no GUS activity was found in mature endosperm. Histochemical localization revealed that GUS expression was exclusively restricted to vascular tissues in transgenic plants. This promoter also showed spatial-temporal expression patterns that GUS expression declined significantly with the maturity of plants. These expression patterns make thegdcsP promoter extremely valuable in the applied biotechnology that needs target gene expression restricted to vascular tissues.     

Construction of a genetic map and location of quantitative trait loci for dwarf trait in maize by RFLP markers

Using F₂ population derived from the cross of tall inbred 7922 by dwarf inbred 5003, an RFLP linkage map of maize has been constructed, on which 85 markers are distributed among 10 linkage groups and span maize genome about 1827.8 cM with an average distance (24.4 cM) between markers. 106 F_2:3 lines of the population were grown in a 10 × 11 simple rectangular lattice design of one-raw plots with two replications and evaluated for plant height (PH). With interval mapping procedure, 5 QTLs controlling plant height have been identified and their genetic effects and gene action determined. 2 major QTLs with opposite effect have been discovered. One for increasing plant height isph1 which is located at chromosome 2 and accounts for 51.8% of the total phenotypic variation; the other for decreasing plant height isph3 which is located at chromosome 5 and accounts for 38.6% of the total phenotypic variation. The chromosomal location ofph3 might be the same as or close to the position ofbv1, a dwarf mutant of maize.