Genetic Diversity and Structure of New Inbred Rice Cultivars in China

A total of 408 inbred rice cultivars bred in the last decade were analyzed for 24 SSR markers. The results showed the genetic diversity of indica cultivars was higher than that of japonica cultivars, and the genetic diversity of new cultivars raised in recent years was lower. Among the six rice cropping regions （RCRs） in China, genetic diversity was the highest in the central rice region （RCR-II） and the southwest rice region （RCR-III）. Genetic differences among subpopulations of japonica were more complex than those in indica. Differentiation among seasonal ecotypes and RCRs in indica populations was unclear, but differentiation between RCR-II and northeast rice region （RCR-V） was more distinct for japonica cultivars. Considering the North rice region （RCR-IV） has very low genetic diversity among the tested cultivars, it is important to broaden the genetic background for future cultivars in rice breeding programs.

Genetic Analysis and Primary Mapping of pms4, a Photoperiod-Sensitive Genic Male Sterility Gene in Rice (Oryza sativa)

To understand the genetic characteristics of a new photoperiod-sensitive genic male sterile line Mian 9S, some reciprocal crosses were made between Mian 9S and six indica rice materials, Yangdao 6, Luhui 602, Shuihui 527, Mianhui 725, Fuhui 838 and Yixiang 1B. Genetic analysis results suggested that the photoperiod-sensitive genic male sterility （PGMS） of Mian 9S was controlled by a single recessive nuclear gene. Thus, the F2 population derived from the cross of Yangdao 6/Mian 9S was used to map the PGMS gene in Mian 9S. By using SSR markers, the PGMS gene of Mian 9S was mapped on one side of the markers, RM6659 and RM1305, on rice chromosome 4, with the genetic distances of 3.0 cM and 3.5 cM, respectively. The gene was a novel PGMS gene and designated tentatively as pms4. In addition, the application of the pms4 gene was discussed.

Subcellular Cd accumulation characteristic in root cell wall of rice cultivars with different sensitivities to Cd stress in soil

The variations of grain cadmiun（Cd） concentrations, translocation factors（TFs） of Cd from roots to shoots/grains of six rice cultivars, characterized with different Cd-sensitivities in polluted soil were studied, the selected rice cultivars were Xiangzao 17（R1）, Jiayu 211（R2）, Xiangzao 42（R3）, Zhuliangyou 312（R4）, Zhuliangyou 611（R5）, and Jinyou 463（R6）, respectively. The Cd subcellular distribution and Cd binding characteristics on subcellular fractions of rice root cell wall（CW） were further investigated. The results showed that the rice grain Cd contents varied significantly, with a maximum variation of 47.0% among the cultivars, the largest grain Cd content was observed with cultivar R1（Cd-sensitivity cultivar） and the smallest with R5（Cd-tolerance cultivar）. The translocation factors of Cd from roots to shoots（TF_（shoot）） and roots to grains（TF_（grain）） varied greatly among the cultivars. In general, the TFgrain of the cultivars followed the order of R1〉R2〉R3〉R4〉 R6-R5. The Cd concentration（mg kg^（–1） FW） in the fraction of root CW, the fraction of cell wall removing pectin（CW-P） and the fraction of cell wall removing pectin and hemicellulose（CW-P-HC） of the cultivars generally followed the order of CW-P〉CW〉CWP-HC; the ratios of Cd concentration（mg kg–1 FW） in the fraction of CW-P to that of CW were mostly more than 1.10, while the ratios of Cd concentration in the fraction of CW-P-HC to that of CW were mostly less than 0.60, indicating that Cd was mainly stored in the hemicellulose of the root CW. The ratios of Cd of CW-P-HC to CW generally followed the descending order of R1~R2〉R3〉R4〉R5~R6 for the cultivars, which implied that hemicellulose is probably the main subcellular pool for transferring Cd into rice grain, and it restrains the translocation of Cd from shoot to the grain, especially for the Cd-tolerance cultivars（R5 and R6）, the compartmentation of more Cd in hemicellulose in root CW is probably one of the main mechanisms for Cd tolerance of rice cultivars.

Comparison and analysis of QTLs for grain and hull thickness related traits in two recombinant inbred line(RIL) populations in rice(Oryza sativa L.)

Grain traits are major constraints in rice production, which are key factors in determining grain yield and market values. This study used two recombinant inbred line（RIL） populations, RIL-JJ（japonica/japonica） and RIL-IJ（indica/japonica） derived from the two crosses Shennong 265/Lijiangxintuanheigu（SN265/LTH） and Shennong 265/Luhui 99（SN265/LH99）. Sixty-eight quantitative trait loci（QTLs） associated with 10 grain traits were consistently detected on the 12 chromosomes across different populations and two environments. Although 61.75% of the QTLs clustered together across two populations, only 16.17% could be detected across two populations. Eight major QTLs were detected on the 9, 10 and 12 chromosomes in RIL-JJ under two environments, a novel QTL clustered on the 10 chromosome, q GT10, q BT10 and q TGW10, have a higher percentage of explained phenotypic variation（PVE） and additive effect; 15 major QTLs were detected on the 5, 8, 9, and 11 chromosomes in RIL-IJ under two environments, a novel clustered QTL, q GT8 and q TGW8, on the 8 chromosome have a higher additive effect. Finally, the analysis of major QTL-BSA mapping narrowed the q TGW10 to a 1.47-Mb region flanked by simple sequence repeat markers RM467 and RM6368 on chromosome 10. A comparison of QTLs for grain traits in two different genetic backgrounds recombinant inbred line populations confirmed that genetic background had a significant impact on grain traits. The identified QTLs were stable across different populations and various environments, and 29.42% of QTLs controlling grain traits were reliably detected in different environments. Fewer QTLs were detected for brown rice traits than for paddy rice traits, 7 and 17 QTLs for brown rice out of 25 and 43 QTLs under RIL-JJ and RILIJ populations, respectively. The identification of genes constituting the QTLs will help to further our understanding of the molecular mechanisms underlying grain shape.

Genetic expression and effects of the rolled leaf gene Rl(t) in hybrid rice (Oryza sativa L.)

We constructed a nearisogenic line of rolled leaf gene Rl(t), which ex-pressed incompletely dondnance for the character of rolled leaf(RL), with ge-netic background of Zhenshan 97B. Using RL Zhenshan 97B and the originalZhenshan 97B as the female parents, and Minghui 63 and Yanhui 559 as themale parents, crosses of RL Shanyu 63 (RS63) and Shanyu 63(S63), RLShanyou 559 (RS559) and Shanyou 559 (S559) were made. Inheritance andeffects of Rl(t) in hybrid rice were studied at the flowering and at the 20 d afterflowering, respectively. Results were as follow:

Genetic analysis of fertility restoration of Maxie cytoplasmic male sterility in rice(Oryza sativa L.)

The genetic behavior of fertility restorationgenes of the cytoplasmic male sterile line Max-ie A was studied to facilitate the use ofMaweizhan male sterile cytoplasm.The F,F,and Fof Maxie A/Minhui 63 were grownin paddy field,1993-1995.Meanwhile,someof the Fplants were testcrossed with themaintainer of Maxie A.The fertilities were

Genetic diversity of rice cultivars (Oryza sativa L.) in China and the temporal trends in recent fifty years

To understand geographical distribution of the genetic diversity of rice cultivars {Oryza sativa L.) and its trends in recent fifty years in China, 453 ’ accessions were analyzed by 36 microsatellites loci and 42 phenotypic traits. Results revealed that the genetic diversity by SSRs is highly consistent with that by phenotypic traits and the genetic diversity of indica cultivars was higher than that of japonica cultivars; the genetic diversity of cultivars declined from 1950s to 1980s and then increased greatly; among the six rice ecological zones (REZs), genetic diversity of REZTl was the highest and those of REZV and REZVT were the lowest at both DNA and phenotypic level. Jiangsu and Jiangxi provinces in the middle and lower reaches of Yangtze River and Sichuan province in southwest of China were the areas with the highest genetic diversity. Breeders in REZV which is an important japonica rice area but with very low genetic diversity should explore more gene resources to widen the genetic backgrounds of cultivars.

The arms race between Magnaporthe oryzae and rice: Diversity and interaction of Avr and R genes

Rice blast disease, caused by Magnaporthe oryzae, threatens global food security. The rice blast pathosystem is a longstanding model system for understanding plant-microbe interactions. In order to elucidate the coevolution of the host and pathogen, and provide the appropriate methods for preventing or controlling rice blast disease, researchers have focused on the evolution of virulence factors and resistance genes. Thus far, more than 30 rice blast resistance（R） genes and 12 avirulence（Avr） genes have been cloned. This review summarizes the cloned rice blast R genes, cloned Avr genes of M. oryzae and the interaction between them. This discussion also considers some of the major unanswered questions concerning this pathosystem and the opportunities for future investigations.

How rice organs are colored: The genetic basis of anthocyanin biosynthesis in rice

Anthocyanins are a major subclass of flavonoids that have diverse biological functions and benefit human health.In rice(Oryza sativa),the various colors shown by organs are due mainly to the accumulation of anthocyanins and are traits associated with domestication.Elucidating the genetic basis of anthocyanin biosynthesis in rice would support the engineering of anthocyanins as well as shedding light on the evolutionary history of O.sativa.We summarize recent progress in rice anthocyanin biosynthesis research,including gene cloning,biosynthetic pathway discovery,and study of the domestication process.We discuss the application of anthocyanin biosynthesis genes in rice breeding.Our object is to broaden knowledge of the genetic basis of anthocyanin biosynthesis in rice and support the breeding of novel rice cultivars.

A Comparative Study of SSR Diversity in Chinese Major Rice Varieties Planted in 1950s and in the Recent Ten Years(1995-2004)

Forty pairs of SSR markers were used to compare the genetic diversity changes in 151 Chinese major rice varieties planted in 1950s and in the recent ten years. Of 40 SSR loci, 39 were found to be polymorphic while one locus （RM479） monomorphic. A total of 213 alleles were identified from the 39 polymorphic loci. The average number of alleles per locus （Na） was of 5.5, ranging from 2 to 11. Nei＇s gene diversity index （He） varied drastically among loci from 0.309 at RM174 to 0.869 at RM418, with an average value of 0.649. There existed significant difference in SSR allelic diversity between indica and japonica subspecies, and indica had more variation than japonica both in Na and He. By comparison with the genetic changes in Na and He, it was revealed that the varieties planted in 1950s had more alleles and higher He than those in the recent ten years both for indica and japonica rices. The difference between two subspecies for Na was significant in a tendency over time （indica： z = 2.677, P = 0.007; japonica： z = 3.441, P = 0.001）, but not significant for He （indica： z = 1.471, P = 0.141; japonica： z = 1.932, P = 0.053）. Analysis of molecular variance （AMOVA） indicated that there existed significant difference （P 〈 0.05） in genetic variation between the two periods, of which more genetic variation was contributed by indica （Fst= 0.050） and japonica （Fst= 0.082） subsets. Using locus-by-locus AMOVA procedure, significant genetic differentiations were observed in 13 loci （RM21, RM128, RM147, RM169, RM190, RM221, RM231, RM251, RM253, RM317, RM341, RM418, and RM478） for indica varieties and 11 loci （RM101, RM135, RM152, RM159, RM169, RM190, RM251, RM253, RM311, RM418, and RM478） for japonica ones between the two periods. It was found some alleles had been lost in current major rice varieties as comparing with those in 1950s. Therefore, it should be necessary to exploit more alien elite genetic resources for extension of genetic background in current rice breeding program.

Morphogenesis,Anatomical Observation and Primary Genetic Analysis of a Multi-glume Floral Organ Mutant in Rice

A multi-glume （mg） mutant was obtained by screening the T-DNA inserted mutant pool. Anatomical observation revealed that the florets of the mutant showed elongated leafy paleas/lemmas and palea/lemma-like structures, just like multi-glumes. Among the 215 observed florets of the mutant, 14.27% were failed to produce pistil and stamens, 23.72% showed extra floret generated on the same rachilla, while 62.01% consisted of one to nine stamens and one to three pistils in a single floret. On the other hand, in some cases the transparent bulged vesile-like tissue could be observed at the basis of filament. The mutant showed glumaceous Iodicules, which prevented the florets from opening in natural conditions, while the absolute male and female sterility was an obvious character of the current mutant. Observation on the process of floral organ morphogenesis by a scanning electron microscopy （SEM） indicated that no phenotype difference in floret primordia was found between the wild-type and the mutant. Meanwhile, for the mutant, the beginning of stamen and pistil primordial differentiation was later than the wild type and the palea/lemma-like structure continued to differentiate after the formation of normal palea and lemma. Furthermore, in the mutant the asymmetrical division of floral primordial caused variation in the number of stamens and pistils. Therefore, the genetic analyses indicated that the mutation phenotype was a recessive trait controlled by a single gene and co-segregated with the T-DNA. Based on the phenotypic characteristics, it could be deduced that the mutant was the result of homeotic conversion from the function of the class E genes in ABCD model.

Oryza pan-genomics: A new foundation for future rice research and improvement

The wild rice species in the genus Oryza harbor a large amount of genetic diversity that has been untapped for rice improvement.Pan-genomics has revolutionized genomic research in plants.However,rice pan-genomic studies so far have been limited mostly to cultivated accessions,with only a few close wild relatives.Advances in sequencing technologies have permitted the assembly of highquality rice genome sequences at low cost,making it possible to construct genus-level pan-genomes across all species.In this review,we summarize progress in current research on genetic and genomic resources in Oryza,and in sequencing and computational technologies used for rice genome and pangenome construction.For future work,we discuss the approaches and challenges in the construction of,and data access to,Oryza pan-genomes based on representative high-quality genome assemblies.The Oryza pan-genomes will provide a basis for the exploration and use of the extensive genetic diversity present in both cultivated and wild rice populations.

Research progress on the divergence and genetic basis of agronomic traits in xian and geng rice

The Asian cultivated rice Oryza sativa can be classified into two major subspecies:japonica/geng and indica/xian.There are large physiological and phenotypic differences between the two subspecies,with each having its advantages and disadvantages.Understanding the differences between xian and geng could provide a foundation for cultivar improvement based on hybridization between subspecies in order to synthesize favorable traits.We review the origin and domestication of xian and geng rice,compare their differences in terms of physiological and phenotypical traits,and describe the molecular mechanism differences between the subspecies.Based on this knowledge,we propose an ideal plant architecture of geng rice varieties for northern regions.

Effects of Continuous Plastic Film Mulching on Soil Bacterial Diversity, Organic Matter and Rice Water Use Efficiency

Two field experiments were conducted to study the effects of 6-year plastic film mulching on bacterial diversity, organic matter of paddy soil and water use efficiency on different soils with great environmental variabilities in Zhejiang Province, China, under non-flooding condition. The experiment started in 2001 at two sites with one rice crop annually. Three treatments included plastic film mulching with no flooding (PM), no plastic film mulching and no flooding (UM), and traditional flooding management (TF). Soil samples were collected and analyzed for bacterial diversity by DGGE and organic matter content, and water use efficiency (WUE) was calculated. The results showed that PM treatment favored the development of a more total bacterial community compared with TF management, the total number of bands was 33.3, 31.7 at tiller stage and heading stage (p < 0.05*). Hence, organic matter content was decreased by 36.7% and 51.4% under PM at two sites. PM also produced similar rice grain yield as TF at Duntou site and Dingqiao site, the average was 7924 kg?ha?1 and 7015 kg?ha?1 for PM and 8150 kg?ha?1 and 6990 kg?ha?1 for TF, respectively. Compared to TF, WUE and irrigation water use efficiency were increased significantly by 70.2% - 80.4% and 273.7% - 1300.0% for PM. It is essential to develop the water-saving agriculture.

Temporal changes in SSR allelic diversity of major rice cultivars in China

Forty simple sequence repeats （SSRs） were used to assess the changes of diversity in 310 major Chinese rice cultivars grown during the 1950s-1990s. Of the 40 SSR loci, 39 were polymorphic. A total of 221 alleles were detected with an average of 5.7 alleles per locus （Na）. The Nei＇s genetic diversity index （He） varied drastically among the loci （0.207 to 0.874, mean 0.625）. Comparing the temporal changes in Na and He, the cultivars from the 1950s had more alleles and higher He scores than the cultivars from the other four decades. Analysis of molecular variance （AMOVA） indicated that the genetic differentiation among the five decades was not significant in the whole set, but significant within indica and japonica. More changes among the decades were revealed in indica cultivars than in japonica cultivars. Some alleles had been lost in current rice cultivars in the 1990s, occurring more frequently in indica. These results suggest that more elite alien genetic resources should be explored to widen the genetic backgrounds of rice cultivars currently grown in China.

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.

Prospect of the QTL-qSB-9^(Tq) utilized in molecular breeding program of japonica rice against sheath blight

The major QTL-qSB-9^Tq conferring partial resistance to rice （Oryza sativa L.） sheath blight （Rhizoctonia solani Kvhn） has been verified on chromosome 9 of the indica rice cultivar, Teqing. In this study, the prospect of this QTL utilized in molecular breeding program of japonica rice for sheath blight resistance was investigated. Most of the japonica rice cultivars showed lower level of sheath blight resistance than the indica rice cultivars. At the corresponding site of qSB-9^Tq, nine typical japonica rice cultivars from different ecological regions or countries proved to possess the susceptible allele（s）. Introgression of qSB-9^Tq into these cultivars enhanced their resistance level by decreasing sheath blight score of 1.0 （0.5-1.3）, which indicated that qSB-9^Tq had a large potential in strengthening the resistance of japonica rice to sheath blight. The use of the three molecular markers, which were polymorphic between Teqing and many japonica rice cultivars, promotes the application of qSB-9^Tq in a concrete molecular breeding program.

Why are There Indica Type and Japonica Type in Rice?——History of the Studies and a View for Origin of Two Types

On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps under a climate with freezing winter cold. These findings lead us to-examine the past ideas about domestication and differentiation of rice. Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Soon after that, the two types were classified by the associations of a number of genetically independent traits. The characteristic associations of traits have been explained by the hybrid sterility or reproductive barriers which were assumed to comprise a set of duplicate recessive lethal genes and to be an inner genetic mechanism to lead to the varietal differentiations In 1980s, the hybrid sterility between Indica and Japonica types was analyzed, and Indica, Japonica, and wide-compatibility type which gives fertile hybrids when cross to Indica and Japonica types, are proved to contain an allele, S5＇, S5＇ and S5^n, respectively at a locus on chromosome 6. And those gametes having Sj allele are found to be partially aborted in the hybrid genotypes of S5＇/S5＇ while no gamete abortion occurs in S5＇/S5^n and S5＇/S5^n genotypes. Since then, the gene S5^n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between subspecies, and the long-disputed problem of hybrid sterility has been solved. Also in such studies the characteristic association of traits found in each of vadetal groups is better explained by founder effects. On the other hand, a large number of native cultivars of rice were surveyed with enzyme polymorphism in 1980s and later with molecular markers. As a result, profound genetic diversity is found in cultivated rice as well as in wild rice. These findings seem to lead us to the idea of multiple independent domestications of rice. However, before reaching such a conclusion, at least two factors, i.e., long-distance-dissemination of some genotypes and the possibilities of introgression by local wild rice to primitive cultivars need to be examined. Taking the two factors as well as the historical events into consideration, it is considered here that the perennial japonica cultivars which are close to wild rice in the Changjiang River basin were disseminated to East India through Assam or along the Bengal Bay, where they were transformed under the introgressions of local wild rice and formed a secondary center, from which some genotypes seem to be disseminated to colonies in Southeast Asia under the influence of Hinduism. Later some of the genotypes were introduced into China and constituted so called Indica type. This may be a reasonable picture for the varietal differentiation.

Mapping a Rice Glabrous Gene Using Simple Sequence Repeat Markers

Inheritance analysis and gene mapping of the glabrous trait were conducted using the crosses between a pubescent rice material Chuanxiang 29B （an aromatic elite maintainer line of hybrid rice）, and two glabrous rice materials, Lemont and R2 （R2 is a new restorer line of hybrid rice）. All F1 plants from the two crosses had pubescent leaves, confirming that the pubescence trait in Chuanxiang 29B is dominant over the glabrous trait. In F2 individuals, the segregation ratio of three pubescent to one glabrous plant suggests that a single glabrous gene was present in Lemont and R2. Using the bulked segregant analysis, the linkage analysis of the simple sequence repeat markers showed that the glabrous gene, gl-1, was flanked by GL311 and GL8 with the genetic distances of 0.19 and 0.92 cM on chromosome 5, respectively.