Rice genetic resources: history,conservation, investigative characterization and use in Japan

Rice has been grown in Japan for about 3000 years. Although both japonica and indica varieties have been grown in Japan, now japonica rices are grown. Japanese rice breeding has used an ecological breeding approach. While emphasis in rice breeding in the 1940's and 1950's focussed on yield in recent decades quality has been of major importance. Consumer preference and name recognition of high quality varieties, such as Koshihikari, has resulted in slow acceptance of new varieties.Rice germplasm was systematically collected throughout Japan between 1962 and 1963. Subsequent acquisition and collecting, in Japan and other countries, has resulted in 28,000 accessions being conserved in the National Genebank, based at the National institute of Agrobiological Resources (NIAR).Research on genetic diversity of rice using a range of techniques, for example esterase isozymes, has revealed clinal variation in rice radiating from the center of diversity of rice in and around southwest China. Newly found genes in traditional rice germplasm, such as genes for non-elongating mesocotyl, are now routinely identified on the rice genome. Pioneering studies on eco-genetic differentiation of species in the genus Oryza in Japan has revealed much about the complex genepool for which rice evolved.Pest and disease resistance sources, particularly to blast, bacterial blight and brown plant hopper, from many countries have been incorporated into Japanese varieties. Cold tolerance at the booting stage was found in the Indonesian variety Silewah. In the future in characterisation of rice germplasm and interaction between rice germplasm specialists and rice molecular scientists, both in Japan and internationally, will be corner stones to securing rice genetic diversity and rice improvement in the next century.     

Determination of heterotic groups for tropical Indica hybrid rice germplasm

Key message

Two heterotic groups and four heterotic patterns were identified for IRRI hybrid rice germplasm to develop hybrid rice in the tropics based on SSR molecular data and field trials.

Abstract

Information on heterotic groups and patterns is a fundamental prerequisite for hybrid crop breeding; however, no such clear information is available for tropical hybrid rice breeding after more than 30 years of hybrid rice commercialization. Based on a study of genetic diversity using molecular markers, 18 parents representing hybrid rice populations historically developed at the International Rice Research Institute (IRRI) were selected to form diallel crosses of hybrids and were evaluated in tropical environments. Yield, yield heterosis and combining ability were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. Results revealed that inter-group hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IRRI B- and R-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IRRI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IRRI hybrid rice parents.     

籼稻基因枪转化的研究

对国内外１７个籼稻品种进行了基因枪转化,研究了有利于籼稻愈伤组织诱导和生长的培养条件和筛选程序,１５个品种获得了潮霉素抗性愈伤组织,５个品种再生了植株,包括当前国际上推广的ＩＲ系统及国内的优良品种和恢复系,分子生物学证据证明潮霉素基因已经整合入籼稻的基因组。最高植株转化频率接近一般粳稻水平,多数低于粳稻水平。这为建立籼稻的转化系统打下了基础。     

国际水稻遗传评价圃资源在广东的试验和评价利用

2001-2005年广东省农业科学院植物保护研究所、水稻研究所参加6个国际水稻遗传评价试验圃（INGER）,包括国际褐稻虱圃、稻瘿蚊圃、稻瘟病圃、白叶枯病圃、灌溉稻观察圃和靓粒香稻圃,引进水稻种质资源1778份,经鉴定试验和田间评价试验,评选出一批适合广东的抗病虫或具丰产潜能的优质种质。这些种质资源在我省水稻抗病虫性研究和抗病虫育种中得到广泛应用,2001-2005年用4个INGER材料培育出9个优质丰产抗病虫品种,合计应用面积25万hm^2。这些品种组合控制了广东水稻病虫褐稻虱、稻瘟病、白叶枯病的灾害性发生,具有重要的经济效益和生态效应。目前,广东省农业科学院植物保护研究所和水稻研究所分别保留了200多份和5000多份可进一步利用的水稻种质材料。通过INGER试验引进的水稻种质资源对丰富广东水稻育种的遗传背景,提高广东省水稻抗病虫性研究和抗病虫育种水平以及种质研究利用水平具有重要意义。     

Genetic and genomic approaches to develop rice germplasm for problem soils

Soils that contain toxic amounts of minerals or are deficient in essential plant nutrients are widespread globally and seriously constrain rice production. New methods are necessary to incorporate the complex adaptive traits associated with tolerance of these abiotic stresses, while simultaneously retaining the high yield potential of rice varieties when conditions are favorable. Significant progress in the genetic characterization of stress response pathways and recent advances in genomics have provided powerful tools for in-depth dissection of tolerance mechanisms. Additionally, tolerance of most of these abiotic stresses in rice is controlled by a few QTLs with large effects despite the intricacy of the numerous traits involved. Genetic dissection of these QTLs and their incorporation into high-yielding varieties will significantly enhance and stabilize rice productivity in these problem soils. Current efforts at IRRI and in rice breeding programs worldwide are seeking to explore diverse germplasm collections and genetically dissect the causal mechanisms of tolerance to facilitate their use in breeding. This review focuses on salinity and P and Zn deficiency as the major problems encountered in rice soils, and examines current understanding of the mechanisms involved and efforts toward germplasm improvement.     

Super Hybrid Rice Breeding in China：Achievements and Prospects

Hybrid rice has contributed greatly to the self-sufficiency of food supply In China. To meet the future demand for rice production, a national program on super rice breeding was established In China In 1996. The corresponding targets, breeding strategies and most significant advances are reviewed In this paper. New plant type models have been modified to adjust to various rice growing regions. In recognition of the Importance of applying parents with Intermediate subspecies differentiation In Increasing F1 yield, medium type parental lines were selected from populations derived from Inter-subspecies crosses with the assistance of DNA markers for subspecies differentiation. Results also indicate that a substantial increase of blomass Is the basis for further enhancement of the grain yield potential, and amelioration of leaf characteristics Is helpful In Increasing the photosynthetic rate. Thirty-four super hybrid rice varieties have been released commercially, growing In a total area of 13.5 million hm2 and producing 6.7 thousand million kg more rice In 1998-2005. Although remarkable progress has been made In super hybrid rice breeding In China, selections on the root system and Integration of more blotechnologlcal tools remain a great challenge.     

Genetic variation and covariation in a population of tetraploid Dactylis L. accessions

Summary Efficient utilization of divergent germ plasm sources in breeding cultivated Dactylis glomerata L. ssp. glomerata Domin depends on knowledge of quantitative variation within and among accessions. This study was undertaken to quantify variation and covariation for forage yield, maturity, disease reaction, and ground cover within a population of tetraploid Dactylis accessions. Variation was observed among families within the population for each variable. Most genetic variation (73%–93% of the family sums of squares) was within country sources or within accessions. Thus, country boundaries, which are traditionally important factors used in defining limits of plant exploration expeditions, have limited expected use in targeting future exploration for specific sources of high yield, disease resistance, or ground cover. Maturity was the exception to this; late-maturing accessions were identified as originating exclusively from the USSR. Some relationships among traits, such as that for yield and disease reaction, differed for accessions and cultivars. Several accessions and families within accessions were identified to have performance superior to most or all cultivars included in this study. Existing germ plasm from several countries was identified to have potential in breeding orchardgrass, while that from other countries appeared to have little or no potential in supplying germ plasm for hay production in humid-temperate environments.     

抽穗开花期耐高温的爪哇稻资源筛选

通过人工气候室鉴定和分期播种试验,对来自于不同国家和地区的95份爪哇稻进行抽穗开花期耐高温特性评价。以综合结实率为指标,通过聚类分析将95份爪哇稻分为耐热能力不同的3类。综合考虑大田分期播种的结实率和人工气候室鉴定结果,筛选出耐高温品种IRAT109 (IRRI编号38563)、260（IRRI编号14888）和L 4-34（IRRI编号13403）,它们可用于水稻耐高温新品种的选育及耐热性遗传研究。     

闽北锥栗种质资源及其开发利用

通过对福建省建瓯市锥栗种质资源的调查和收集,分析19个锥栗品种的性状,为锥栗的遗传改良、新品种培育提供育种资源,并为锥粟种质资源的开发利用、良种选育提供繁殖材料。     

Recent Progress on Rice Genetics in China

Through thousands of years of evolution and cultivation, tremendously rich genetic diversity has been accumulated in rice （Oryza sativa L.）, developing a large germplasm pool from which people can select varieties with morphologies of Interest and other important agronomic traits. With the development of modern genetics, scientists have paid more attention to the genetic value of these elite varieties and germplasms, and such rich rice resources provide a good foundation for genetic research in China. Approximately 100 000 accessions of radiation-, chemical- or insertion-induced mutagenesis have been generated since the 1980s, and great progress has been made on rice molecular genetics. So far at least 16 variant/mutant genes Including MOC1, BC1, SKC1, and Rfgenes have been isolated and characterized in China. These achievements greatly promote the research on functional genomics, understanding the mechanism of plant development and molecular design breeding of rice in China. Here we review the progress of three aspects of rice genetics in China： moving forward at the molecular level, genetic research on elite varieties and germplasms, and new gene screening and genetic analysis using mutants. The prospects of rice genetics are also discussed.     

中国小麦生产上年种植面积超66.7万hm2的品种及其分析

中国在1950～2000年期间,小麦生产上年种植面积超66.7万hm2的品种共53个.对这53个品种的分析结果表明,有6个原产国外,本国的品种主要是河南、山东、四川、陕西、河北等省市的;除2个地方品种外,其它品种的亲本间都是地理远缘的或有地理远缘血统的;随年代的推移,品种的数量逐渐增多,而最大年种植面积和单个品种种植地区逐渐减少,这些变化是我国小麦育种水平提高的结果.     

Quantitative analysis of the effect of selection history on sugar yield adaptation of sugarcane clones

An objective of the CSR sugarcane breeding programme in Australia was to assess the scope for broadening the genetic base of the commercial sugarcane germ plasm through interspecific hybridization with Saccharum spontaneum clones. The contribution of both selection history and S. spontaneum to sugar yield and its components was investigated in the germ plasm pool assembled. The analysis was conducted on a data-set of 256 clones, consisting of parents and full-sib families generated from 32 biparental crosses, tested in six environments. The minimum number of generations back to S. spontaneum ancestor in the clone's pedigree was used as a germ plasm score. The geographical origin and selection history of each parent and their use in the biparental crosses were used to develop a selection history score for parents and offspring. The variation for seven attributes, cane yield, commercial cane sugar %, sugar yield, stalk number per stool, stalk weight, fibre % and ash % juice was partitioned according to the germ plasm and selection history scores. Significant (P<0.05) clone variation and clone x environment interaction for all attributes was present. The germ plasm scores accounted for a significant (P<0.05) component of the clone variation for all of the attributes except cane yield. There was an increase in sugar yield with an increase in the minimum number of generations back to a S. spontaneum clone. The selection history groups accounted for a high proportion of the variation among parental clones for all of the attributes except cane yield. This suggested that parents were the outcome of strong selection pressure for the commercial cane attributes. However, the selection history groups for the offspring produced by random mating of parents did not account for a high proportion of the variation for the attributes. Using the mixture method of classification we partitioned the 256 clones into five groups for patterns of performance for the seven attributes across the six environments. The five groups emphasized major differences in the patterns of performance for the seven attributes across environments. The distribution of germ plasm and selection history scores in each of the five groups indicated that their patterns of performance were associated with selection history and minimum generations to S. spontaneum. Therefore, both the analysis on selection history and germ plasm scores (extrinsic classification) and the analysis on the mixture method of classification (intrinsic classification) emphasized the influence of selection history on the sugar yield of sugarcane.     

Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs

Genetic analysis across a whole plant genome based on pedigree information offers considerable potential for enhancing genetic gain from plant breeding programs through quantitative trait loci (QTL) mapping and marker-assisted selection. Here, we report its application for graphically genotyping varieties used in Chinese japonica rice (Oryza sativa L.) pedigree breeding programs. We identified 34 important chromosomal regions from the founder parent that are under selection in the breeding programs, and by comparing donor genomic regions that are under selection with QTL locations of agronomic traits, we found that QTL clustered in important genomic regions, in accordance with association analyses of natural populations and other previous studies. The convergence of genomic regions under selection with QTL locations suggests that donor genomic regions harboring key genes/QTL for important agronomic traits have been selected by plant breeders since the 1950s from the founder rice plants. The results provide better understanding of the effects of selection in breeding programs on the traits of rice cultivars. They also provide potentially valuable information for enhancing rice breeding programs through screening candidate parents for targeted molecular markers, improving crop yield potential and identifying suitable genetic material for use in future breeding programs.     

秦岭黄果悬钩子野生种质资源与引种试验研究

对黄果悬钩子在秦岭山区的分布、习性、果实经济性状、营养成分、产量构成以及引种栽培条件下的物候期、根系特征、发枝习性,繁殖特点等内容的研究结果表明,黄果悬钧子植株矮小,具有较耐旱的根系组成特点;果大,质优、风味好,营养丰富;适应性较强,容易繁殖,是一种优良的栽培树萄果树引种驯化,矮化育种野生种质资源。     

一个新的水稻小粒矮秆基因的分子标记定位及效应分析

从水稻(Oryza safjva L．)半矮秆品种蜀恢I62中发现一份小粒矮秆突变体“I62d”。对I62d与4个半矮秆品种杂交F1和F2代的遗传分析表明,I62d的矮生性由一对隐性基因控制。以II-32B／162d F2代作定位群体,用分子标记将I62d突变基凶定位丁水稻第3染色体短臂,该基因与微卫星标记RM218和RMI57之间的遗传距离分别为3．5cM和10．0cM。同时,利用近等基因系分析了该基因的表型效应,结果表明它可使株高降为正常高度的1／4左右,籽粒降为正常大小的1／4左右,并使叶片显著缩短、加宽,结实率显著降低。我们认为162d突变基因是一个新的水稻小粒矮秆某因,暂命名为dI62(t）。     

Retrospective and perspective of rice breeding in China

Breeding is the art and science of selecting and changing crop traits for the benefit of human beings. For several decades, tremendous efforts have been made by Chinese scientists in rice breeding in improving grain yield, nutrition quality, and environmental performance, achieving substantial progress for global food security. Several generations of crop breeding technologies have been developed, for example, selection of better performance in the field among variants (conventional breeding), application of molecular markers for precise selection (molecular marker assisted breeding), and development of molecular design (molecular breeding by rational design). In this review, we briefly summarize the advances in conventional breeding, functional genomics for genes and networks in rice that regulate important agronomic traits, and molecular breeding in China with focuses on high yield, good quality, stress tolerance, and high nutrient-use efficiency. These findings have paved a new avenue for rational design of crops to develop ideal varieties with super performance and productivity.     

Heterosis breeding in rice (Oryza sativa L.)

Summary Studies conducted at the International Rice Research Institute (IRRI) during 1980 and 1981 have shown up to 73% heterosis, 59% heterobeltiosis and 34% standard heterosis for yield in rice. The latter was estimated in comparison to commercial varieties: IR36 and IR42 (yield 4–5 t/ha in wet season trials and 7–8 t/ha in dry season trials). Generally speaking, absolute yield was lower and extent of standard heterosis was higher in wet season than in dry season with some exception. Yields up to 5.9 t/ha (22% standard heterosis) in the wet season and 10.4 t/ha (34% standard heterosis) in the dry season were obtained. Most of the hybrids performed better in some season while some performed better in both seasons. Hybrids showed better lodging resistance although they were 5–10 cm taller. F₁ hybrids had significant positive correlations with the parental traits viz., yield (r = 0.446), tillering (r = 0.746), height (r = 0.810) and flowering (r = 0.843). Selection of parents among elite breeding lines on the basis of their per se yield performance, diverse origin and resistance to insects and diseases should give heterotic combination. Yield advantage of hybrids was due primarily to increase in number of spikelets per unit area even though tiller number was reduced. Grain weight was either the same or slightly higher. High yielding hybrids also showed significant heterosis and heterobeltiosis for total dry matter and harvest index. For commercial utilization of heterosis in rice, effective male sterility and fertility restoration systems are available and up to 45% natural outcrossing on male sterile lines has been observed. Consequently, F₁ rice hybrid have been successfully developed and used in China. Prospects of developing hybrid rice varieties elsewhere appear bright especially in countries that have organized seed production, certification and distribution programs and where hybrid seed can be produced at a reasonable cost.     

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture,Training Population Composition,Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite,Tropical Rice Breeding Lines

Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute''s (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.     

Evaluation of the genetic structure of Xylella fastidiosa populations from different Citrus sinensis varieties

Xylella fastidiosa was isolated from sweet orange plants (Citrus sinensis) grown in two orchards in the northwest region of the Brazilian state of S?o Paulo. One orchard was part of a germ plasm field plot used for studies of citrus variegated chlorosis resistance, while the other was an orchard of C. sinensis cv. Pêra clones. These two collections of strains were genotypically characterized by using random amplified polymorphic DNA (RAPD) and variable number of tandem repeat (VNTR) markers. The genetic diversity (H(T)) values of X. fastidiosa were similar for both sets of strains; however, H(T)(RAPD) values were substantially lower than H(T)(VNTR) values. The analysis of six strains per plant allowed us to identify up to three RAPD and five VNTR multilocus haplotypes colonizing one plant. Molecular analysis of variance was used to determine the extent to which population structure explained the genetic variation observed. The genetic variation observed in the X. fastidiosa strains was not related to or dependent on the different sweet orange varieties from which they had been obtained. A significant amount of the observed genetic variation could be explained by the variation between strains from different plants within the orchards and by the variation between strains within each plant. It appears, therefore, that the existence of different sweet orange varieties does not play a role in the population structure of X. fastidiosa. The consequences of these results for the management of sweet orange breeding strategies for citrus variegate chlorosis resistance are also discussed.     

Variety x line cross — A suggested breeding procedure for maize in developing countries

Summary Phra-Phutthabat No.5 (PB5), a widely grown local variety in Thailand, was crossed with open-pollinated varieties, S₃ and S₆ lines from different parts of the world. The resulting hybrids were tested in the dry season in Thailand, Laos and Israel with PB5 as the control. A number of hybrids were also tested in the wet season in Thailand and Laos. Hybrids giving significantly higher yields than PB5 were found in both the dry and the wet seasons. The variety x line crosses were superior to the variety x variety crosses at all locations. The hybrids with the South African germ plasm were intermediate, and those with the African and Asian germ plasm gave the lowest yields. The variety x line cross is suggested as a simple and rapid breeding procedure for the developing countries.In memory of the senior author, deceased November 2, 1972