Indica-japonica differentiation in Chinese rice landraces

Summary Ninety Chinese rice landraces were examined with special reference to the indica-japonica differentiation in terms of traditional criteria, isozyme analysis and PCR analysis of the chloroplast DNA (cpDNA). Cultivars were separated into indica and japonica defined by a discriminant function (Z) based on key characters, as well as by isozyme genotypes. Most indica landraces had chloroplast DNAs with a deletion at the Pst-12 fragment, while most japonica landraces had cpDNAs without the deletion. Two traditionally recognized varietal groups in China, keng and hsien, corresponded largely to the respective japonica and indica revealed in our study. The results obtained in this study showed good agreement for classification of indica and japonica types by the three methods: discriminant analysis by Z value, isozyme analysis, and PCR analysis for cpDNA.     

Genetic characterization of rainfed upland New Rice for Africa (NERICA) varieties

A total of 18 rainfed upland New Rice for Africa (NERICA) varieties were categorized as the heavy panicle and low tillering types and early heading, in compared with 32 different varieties. These chromosome components were clarified using 243 SSR markers which showed polymorphism among NERICA varieties and their parents, CG 14 (O. glaberrima Steud.) and one of the recurrent parents, WAB-56-104 (O. sativa L.). NERICA varieties were classified into three groups, which corresponded with these parents’ continuation including two exceptions, NERICAs 14 and 17, by a cluster analysis using polymorphism data of SSR markers and 14 differential markers among them were selected to classify NERICA varieties. However, three groups: NERICAs, 3 and 4, NERICAs, 8, 9 and 11 and NERICAs, 15 and 16 were not distinguishable. Association analysis was carried out for characterization of NERICA varieties by using SSR markers genotype and phenotype of agronomic traits. A total of 131 quantitative trait loci between SSR markers and 11 agronomic traits were detected. The characteristics of early maturity and heavy panicle of upland NERICA varieties were succeeded from Asian rice varieties and the characteristics of high dry matter production and late heading were introduced from CG 14 and the other varieties.     

Screening of Rice Varieties for Endosperm Storage Proteins

A total of 118 rice varieties/lines (Oryza sativa L.) from Bangladesh were analyzed for endosperm storage proteins on a single seed basis. The screening was done by observing the profiles of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) with standard japonica variety ‘Kinmaze’. Six groups were classified on the basis of the poly-peptide banding patterns. Two-dimensional gel electrophoresis was performed to ensure the SDS-PAGE results in selected varieties. The analysis of extracted protein fractions revealed that one variety had low prolamin and one variety had high glutelin content.     

Two novel QTLs regulate internode elongation in deepwater rice during the early vegetative stage

Deepwater rice possesses internode elongation ability to avoid drowning under deepwater conditions. Previous studies identified three QTLs regulating internode elongation ability on chromosomes 1, 3 and 12 using different populations. However, these QTLs only induce internode elongation in response to deepwater conditions from the 7-leaf stage and not during the early leaf stage. In this study, we detected two novel QTLs, qTIL2 and qTIL4 regulating deepwater response at the early leaf stage using an F₂ population derived from the cross between NIL1-3-12 carrying the three QTLs regulating deepwater response in T65 (O. sativa ssp. japonica) genetic background and C9285 (O. sativa ssp. indica, deepwater rice). Plants of the BC₂F₂ population derived from NIL1-3-12/C9285 and the RILs of T65/Bhadua (O. sativa ssp. indica, deepwater rice) possessing these QTLs as well as the three QTLs previously identified also showed internode elongation during the early leaf stage. These results indicate that qTIL2 and qTIL4 regulate early internode elongation and function in coordination with the three major QTLs under deepwater conditions. The results presented here would not only help define the mechanism of deepwater response in rice but also contribute in the breeding of deepwater tolerant rice that is adapted to various water depths.     

不同氮肥水平下中熟籼稻和粳稻产量、氮素吸收利用差异及相互关系

选用生育期相近的中熟中籼(138~143 d)和中熟中粳(136~145 d),于大田条件下探讨了4种氮肥水平即0、150、225、300 kg hm^-2纯氮对产量的影响及不同生育阶段氮素吸收利用的差异。结果表明,随着氮肥施用量的增加粳稻平均产量呈增加趋势,而籼稻平均产量中氮水平达最高,高氮水平有所降低。各处理下籼稻产量明显高于粳稻,籼稻有较高的穗粒数和千粒重,平均分别比粳稻高22.45%、7.51%。植株氮素阶段吸收量,拔节、抽穗和成熟期籼稻平均分别比粳稻高24.26%、3.14%和6.45%;植株氮素阶段吸收速率,移栽至拔节、拔节至抽穗和抽穗至成熟阶段籼稻平均分别比粳稻高38.07%、16.05%和23.22%。相关分析表明,籽粒产量与氮素阶段吸收量、阶段吸收速率和氮肥利用率呈显著或极显著正相关关系。说明生育期相近的中熟中籼产量高于中熟中粳与籼稻植株较强的氮素吸收特性有关。     

Variation in cooking and eating quality traits in Japanese rice germplasm accessions

The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan.     

Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L.

The wild relatives of rice (Oryza sativa L.) are useful sources of alleles that have evolved to adapt in diverse environments around the world. Oryza rufipogon, the known progenitor of the cultivated rice, harbors genes that have been lost in cultivated varieties through domestication or evolution. This makes O. rufipogon an ideal source of value-added traits that can be utilized to improve the existing rice cultivars. To explore the potential of the rice progenitor as a genetic resource for improving O. sativa, 33 chromosome segment substitution lines (CSSLs) of O. rufipogon (W0106) in the background of the elite japonica cultivar Koshihikari were developed and evaluated for several agronomic traits. Over 90% of the entire genome was introgressed from the donor parent into the CSSLs. A total of 99 putative QTLs were detected, of which 15 were identified as major effective QTLs that have significantly large effects on the traits examined. Among the 15 major effective QTLs, a QTL on chromosome 10 showed a remarkable positive effect on the number of grains per panicle. Comparison of the putative QTLs identified in this study and previous studies indicated a wide genetic diversity between O. rufipogon accessions.     

Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice

To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japonica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hd16 and Hd17 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hd16 and Hd17 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been detected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These results led us to propose a new selection strategy to improve agronomic performance in temperate japonica rice cultivars.     

Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP,ISSR and SSR markers

Molecular markers provide novel tools to differentiate between the various grades of Basmati rice, maintain fair-trade practices and to determine its relationship with other rice groups in Oryza sativa. We have evaluated the genetic diversity and patterns of relationships among the 18 rice genotypes representative of the traditional Basmati, cross-bred Basmati and non-Basmati (indica and japonica) rice varieties using AFLP, ISSR and SSR markers. All the three marker systems generated higher levels of polymorphism and could distinguish between all the 18 rice cultivars. The minimum number of assay-units per system needed to distinguish between all the cultivars was one for AFLP, two for ISSR and five for SSR. A total of 171 (110 polymorphic), 240 (188 polymorphic) and 160 (159 polymorphic) bands were detected using five primer combinations of AFLP, 25 UBC ISSR primers and 30 well distributed, mapped SSR markers, respectively. The salient features of AFLP, ISSR and SSR marker data analyzed using clustering algorithms, principal component analysis, Mantel test and AMOVA analysis are as given below: (i) the two traditional Basmati rice varieties were genetically distinct from indica and japonica rice varieties and invariably formed a separate cluster, (ii) the six Basmati varieties developed from various indica × Basmati rice crosses and backcrosses were grouped variably depending upon the marker system employed; CSR30 and Super being more closer to traditional Basmati followed by HKR228, Kasturi, Pusa Basmati 1 and Sabarmati, (iii) AFLP, ISSR and SSR marker data-sets showed moderate levels of positive correlation (Mantel test, r = 0.42–0.50), and (iv) the partitioning of the variance among and within rice groups (traditional Basmati, cross-bred Basmati, indica and japonica) using AMOVA showed greater variation among than within groups using SSR data-set, while reverse was true for both ISSR and AFLP data-sets. The study emphasizes the need for using a combination of different marker systems for a comprehensive genetic analysis of Basmati rice germplasm. The high-level polymorphism generated by SSR, ISSR and AFLP assays described in this study shall provide novel markers to differentiate between traditional Basmati rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.The first two authors have equal contribution     

SSR analysis of chromosome 8 regions associated with aroma and cooked kernel elongation in Basmati rice

Aroma and cooked kernel elongation (CKE) are the two most important quality traits, which differentiate the highly valued Basmati rice from other rice types. Previous studies on genetic analysis have shown that genes/QTLs for these two traits are linked and present on chromosome number 8. We have evaluated the genetic diversity in 33 rice genotypes representative of the traditional Basmati (TB), cross-bred Basmati derived from indica × Basmati rice crosses and non-Basmati (indica and japonica) rice varieties for chromosome number 8 using 26 SSR markers including a specific marker (SCU-SSR1) for RG28 locus; the results have been compared with whole genome based SSR allelic data. The 26 SSR markers (24 polymorphic and 2 monomorphic) amplified a total of 106 alleles; 21 of these alleles were detected to be unique, present in only one genotype. The number and size of the alleles, and polymorphism information content (PIC) values ranged between 1–8, 87–312 and 0–0.736 bp, respectively. SCU-SSR1 marker amplified a total of three alleles (128, 129 and 130 bp). All the TB varieties except Basmati 217 (129 bp) and 7/13 cross-bred Basmati varieties had the 130 bp allele. Alleles of 129 and 128 bp were present in majority of the indica and japonica varieties, respectively. The average pair-wise Jaccard similarity coefficients for TB, indica and japonica varieties were 0.512, 0.483 and 0.251, respectively. Average similarity coefficient between TB and japonica was higher (0.236) compared to that between TB and indicas (0.150). Genetic relationships as determined by Principal Component Analysis (PCA, NTSYS-pc), PowerMarker tree, and Structure analyses, clearly showed high-level differentiation between TB and indica rice varieties, which formed two distinct clusters. The cross-bred Basmati and japonica rice genotypes were placed between these two clusters. Basmati 217 and Ranbir Basmati were quite divergent from rest of the TB varieties. Some of cross-bred Basmati varieties including Super, CSR30 and kernel were closer to TB. Indica rice varieties, CSR10 (salt tolerant variety) and Pokkali (salt tolerant landrace) formed a separate distinct cluster. The Pritchard structure analysis divided the rice genotypes in four major sub-populations of TB, cross-bred Basmati, indica and japonica (including Ranbir Basmati and Basmati 217) rice varieties. Chromosome 8 data-set showed a positive correlation (Mantel test, r = 0.739) with the allelic data-set for 30 SSR markers well-distributed on 12 rice chromosomes indicating a higher level of similarity between the two. The study demonstrates the distinctness of TB from other rice types (indica and japonica) and also provides several novel markers for differentiation between TB rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.     

How Does the Variability in Aus Rice Yield Respond to Climate Variables in Bangladesh?

In this study, the impacts of climate variables on the mean and variability in Aus variety rice yield in Bangladesh are assessed. Using the theoretical framework of the Just–Pope production function, cross‐sectional time series data on Aus rice yield and maximum temperature, minimum temperature and rainfall at a district level over a period of 38 years are analysed for evidence of rice yield variability as a result of climate change. The findings reveal that minimum temperature and rainfall decrease Aus yield variability. However, maximum temperature appears to increase variability, which may reduce Aus rice production. Therefore, government should create an enabling environment to develop temperature‐tolerant rice varieties for Aus rice crop to ensure ongoing food security.     

Effect of panicle nitrogen on grain filling characteristics of high-yielding rice cultivars

The effects of four levels of panicle nitrogen fertilizer on the grain filling characteristics of three rice (Oryza sativa L.) varieties (super japonica rice Ningjing 3, three-line japonica hybrid rice Changyou 3 and three-line indica–japonica hybrid rice Yongyou 12) were analyzed. The results showed that difference in time of maximum filling rate (T_max) was the smallest between the superior and inferior spikelets of Ningjing 3, bigger between those of Changyou 3, the biggest between those of Yongyou 12. Ningjing 3 was of the synchronous grain-filling type, Yongyou 12 the asynchronous type, and the Changyou 3 the medium type. The grain filling rate, the initial filling power (R₀), the maximum filling rate (G_max), and the average filling rate (G) of the superior and inferior spikelets of the three varieties under the treatment of panicle N with the amount of 120 kg ha⁻¹ (middle panicle N, shortened as NM) treatment were higher than those of other treatments. NM treatment led to the highest increase in grain weight at the middle stage of filling for all the three varieties. The treatment shortened the early and late stages of grain filling, but extended the middle stage when the filling rate was the highest. However, the middle stage of grain filling of Changyou 3 and Yongyou 12 was much more extended than that of Ningjing 3, indicating a better effect of N on hybrid rice varieties.     

Influence of single-nucleotide polymorphisms in the gene encoding granule-bound starch synthase I on amylose content in Vietnamese rice cultivars

Amylose content is one of the most important factors influencing the physical and chemical properties of starch in rice. Analysis of 352 Vietnamese rice cultivars revealed a wide range of variation in apparent amylose content and the expression level of granule-bound starch synthase. On the basis of single-nucleotide polymorphisms (SNP) at the splicing donor site of the first intron and in the coding region of the granule-bound starch synthase I gene, Waxy gene, alleles can be classified into seven groups that reflect differences in apparent amylose content. The very low and low apparent amylose content levels were tightly associated with a G to T in the first intron whereas intermediate and high amylose was associated with a T genotype at SNP in exon 10. The correlation between the combination of T genotype at SNP in the first intron, C in exon 6, or C in exon 10 was predominant among low amylose rice varieties. Our analysis confirmed the existence of Wx^op allele in Vietnamese rice germplasm. The results of this study suggest that the low amylose properties of Vietnamese local rice germplasm are attributable to spontaneous mutations at exons, and not at the splicing donor site.     

Genetic mechanisms of postzygotic reproductive isolation: An epistatic network in rice

Products of interspecific crosses often show abnormal phenotypes such as sterility, weakness and inviability. These phenomena play an important role in speciation as mechanisms of postzygotic reproductive isolation (RI). During the past two decades, genetics studies in rice have characterized a number of gene loci responsible for postzygotic RI. I have identified 10 loci including three sets of epistatic networks in a single inter-subspecific cross (Oryza sativa ssp. indica × japonica). These results suggest that RI genes cause developmental dysfunction of vegetative and/or reproductive organs through a variety of molecular pathways. The latest molecular studies demonstrated that hybrid incompatibility is mainly due to deleterious interactions caused by species-specific mutations of two or more genes, mediated by proteins acting within the same molecular pathway. Because genetic interactions provide a perspective on gene function, epistatic networks are a key to the understanding of the molecular basis of postzygotic RI. In this review, I focus on recent progress in postzygotic RI studies in rice and discuss the evolutionary significance as well as implications for improving rice productivity.     

The indica-japonica classification of Asian rice ecotypes and Japanese lowland and upland rice (Oryza sativa L.)

Summary Rice cultivars (Oryza sativa L.) belonging to five ecotypes (aus, aman, boro, bulu and tjereh) and to two groups of Japanese rice (lowland and upland) are examined with respect to KClO₃ resistance, phenol reaction and apiculus hair length. These characters have been used as available criteria to classify rice into two types indica and japonica, for the last thirty years.The findings of this study are that the aman, boro and tjereh ecotypes should be classified as typical indica; and that the Japanese lowland rice cultivars are mainly typical japonica. Some of the aus, bulu and Japanese upland rice cultivars differ from typical indica and typical japonica, so the respective terms aus type, bulu type and J.u.r. type, are proposed. Aman, boro tjereh and Japanese lowland rice are cultivated in lowland. Some of the aus, bulu and Japanese upland rice cultivars have the characteristics of upland rice. In general, lowland rice cultivars can be clearly classified into indica or japonica, while upland cultivars cannot.Abbreviations Aph dominant gene for apiculus hair length > 0.7 mm - aph recessive gene for apiculus hair length < 0.7 mm - J.u.r. type Japanese upland rice type     

Rice tungro spherical virus resistance into photoperiod-insensitive japonica rice by marker-assisted selection

Rice tungro disease (RTD) is one of the destructive and prevalent diseases in the tropical region. RTD is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Cultivation of japonica rice (Oryza sativa L. ssp japonica) in tropical Asia has often been restricted because most japonica cultivars are sensitive to short photoperiod, which is characteristic of tropical conditions. Japonica1, a rice variety bred for tropical conditions, is photoperiod-insensitive, has a high yield potential, but is susceptible to RTD and has poor grain quality. To transfer RTD resistance into Japonica1, we made two backcrosses (BC) and 8 three-way crosses (3-WC) among Japonica1 and RTSV-resistant cultivars. Among 8,876 BC₁F₂ and 3-WCF₂ plants, 342 were selected for photoperiod-insensitivity and good grain quality. Photoperiod-insensitive progenies were evaluated for RTSV resistance by a bioassay and marker-assisted selection (MAS), and 22 BC₁F₇ and 3-WCF₇ lines were selected based on the results of an observational yield trial. The results demonstrated that conventional selection for photoperiod-insensitivity and MAS for RTSV resistance can greatly facilitate the development of japonica rice that is suitable for cultivation in tropical Asia.     

Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar ‘Koshihikari’ was performed to extract regions containing large indels (10–51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between ‘Koshihikari’ and other diverse cultivars, we subtracted the indel regions detected in ‘Koshihikari’ from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including ‘Khao Nam Jen’ as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.     

不同粒型稻米碾磨特性及蛋白质分布的比较

以3个具不同品质和粒形特点的典型水稻品种,比较研究了稻米碾磨特性及蛋白质含量与组分在籽粒内部的分布情况。碾磨程度和达到相应碾磨程度所需碾磨时间之间的非线性关系显示糠层由外到内硬度不断增加;淀粉胚乳层硬度保持不变,且高于糠层硬度。不同品种达到相同碾磨程度所需时间差异较大,说明淀粉等物质的沉积密度在品种中存在较大差异。蛋白质含量在籽粒不同部位不是均匀分布的,3个品种糙米中均约85%的蛋白质分布在胚乳层中,清芦占11的蛋白质含量以外层胚乳最高,苏御糯和扬辐粳4901蛋白质含量均以糠层最高。随碾磨程度的提高,籽粒蛋白质含量由表及里呈降低趋势,核心层胚乳只有糠层的1/2左右,但不同类型水稻品种的降低趋势不同。SDS-PAGE分析表明,不同种子贮藏蛋白组分在籽粒内部的分布是相对均匀的,说明不同蛋白质组分在积累过程中,其遗传表达相对同步。     

Mapping three new interspecific hybrid sterile loci between Oryza sativa and O. glaberrima

Hybrid sterility hinders the transfer of useful traits between Oryza sativa and O. glaberrima. In order to further understand the nature of interspecific hybrid sterility between these two species, a strategy of multi-donors was used to elucidate the range of interspecific hybrid sterility in this study. Fifty-nine accessions of O. glaberrima were used as female parents for hybridization with japonica cultivar Dianjingyou 1, after several backcrossings using Dianjingyou 1 as the recurrent parent and 135 BC₆F₁ sterile plants were selected for genotyping and deducing hybrid sterility QTLs. BC₆F₁ plants containing heterozygous target markers were selected and used to raise BC₇F₁ mapping populations for QTL confirmation and as a result, one locus for gamete elimination on chromosome 1 and two loci for pollen sterility on chromosome 4 and 12, which were distinguished from previous reports, were confirmed and designated as S37(t), S38(t) and S39(t), respectively. These results will be valuable for understanding the range of interspecific hybrid sterility, cloning these genes and improving rice breeding through gene introgression.