Temperate Japonica Rice Cultivars Research Articles

The origin of the A/G single nucleotide polymorphism of starch synthase IIa in rice and its relation to gelatinization temperature

AbstractBackground and objectivesThe domestication of cultivated rice (Oryza sativa L.) has long been studied, and many agronomically relevant genes have undergone artificial selection. Among them, the selection history of the starch synthase IIa (SSIIa) has not been fully discovered. The SSIIa is a genetic factor that controls the gelatinization temperature (GT) of rice starch, an important parameter for rice cooking quality.FindingsThe A/GC haplotype in SSIIa only presented in the japonica subspecies. GT was found to be strongly associated with SNPs in SSIIa, that is, G/GC haplotype rice had high or intermediate GT, while G/TT or A/GC haplotype rice had low GT. The nucleotide diversity (π) in japonica was much lower than that of indica and wild rice, indicating that a population bottleneck was experienced during japonica rice domestication. A possible positive selection on the A SNP of SSIIa in temperate japonica rice favoring low GT starch synthesis was proposed.ConclusionsThe evolution of SSIIa in the japonica rice was possibly under positive selection favoring low GT rice, which requires low energy input for cooking. The A SNP of SSIIa is only present in the japonica rice, which might be derived from a recent mutation. There are two ways, A/GC and G/TT, to make japonica rice with low GT, explaining why all the temperate japonica rice cultivars have low GT.Significance and noveltyFindings of this study provide an understanding of why all the temperate japonica rice have low GT starch, because there are two ways to make it GT low.

Evaluation of Rice Responses to the Blast Fungus Magnaporthe oryzae at Different Growth Stages.

Rice blast, caused by the fungus Magnaporthe oryzae, is the most damaging disease for rice worldwide. However, the reactions of rice to M. oryzae at different growth stages are largely unknown. In the present study, two temperate japonica rice cultivars, M-202 and Nipponbare, were inoculated synchronously at different vegetative growth stages, V1 to V10. Plants of M-202 at each stage from V1 to reproductive stage R8 were inoculated with M. oryzae race (isolate) IB-49 (ZN61) under controlled conditions. Disease reactions were recorded 7 days postinoculation by measuring the percentage of diseased area of all leaves, excluding the youngest leaf. The results showed that the plants were significantly susceptible at the V1 to V4 stages with a disease severity of 26.7 to 46.8% and disease index of 18.62 to 37.76 for M-202. At the V1 to V2 stages, the plants were significantly susceptible with a disease a severity of 28.6 to 39.3% and disease index of 23.65 to 29.82 for Nipponbare. Similar results were observed when plants of M-202 were inoculated at each growth stage with a disease severity of 29.7 to 60.6% and disease index of 21.93 to 59.25 from V1 to V4. Susceptibility decreased after the V5 stage (severity 4.6% and index 2.17) and became completely resistant at the V9 to V10 stages and after the reproductive stages, suggesting that plants have enhanced disease resistance at later growth stages. These findings are useful for managing rice blast disease in commercial rice production worldwide.

A differential tolerance to mild salt stress conditions among six Italian rice genotypes does not rely on Na+ exclusion from shoots

Rice is very sensitive to salt stress at the seedling level, with consequent poor crop establishment. A natural variability in susceptibility to moderate saline environments was found in a group of six Italian temperate japonica rice cultivars, and the physiological determinants for salt tolerance were investigated. Cation (Na+, K+ and Mg++) levels were determined in shoots from individual rice plantlets grown in the absence or in the presence of inhibitory, yet sublethal salt levels, and at increasing time after salt treatments. Significant variations were found among genotypes, but these were unrelated to the relative tolerance, which seems to result from neither mechanism(s) for reduced Na+ translocation to the aerial part, nor its increased retrieval from the xylem mediating Na+ exclusion from leaves. Accordingly, thiobarbituric acid reactive substance levels raised in leaf tissues of salt-treated seedlings, and osmo-induced proline accumulation was found in all genotypes. Data suggest that the difference in salt tolerance most likely depends on mechanisms for osmotic adjustment and/or antioxidative defence.

Genetic dissection of agronomically important traits in closely related temperate japonica rice cultivars.

Many quantitative trait loci (QTLs) for agronomically important traits such as grain yield, disease resistance, and stress tolerance of rice (Oryza sativa L.) have been detected by using segregating populations derived from crosses between indica and japonica subspecies or with wild relatives. However, the QTLs involved in the control of natural variation in agronomic traits among closely related cultivars are still unclear. Decoding the whole genome sequences of Nipponbare and other temperate japonica rice cultivars has accelerated the collection of a huge number of single nucleotide polymorphisms (SNPs). These SNPs are good resource for developing polymorphic DNA markers and for detecting QTLs distributed across all rice chromosomes. The temperate japonica rice cultivar Koshihikari has remained the top cultivar for about 40 years since 1979 in Japan. Unraveling the genetic factors in Koshihikari will provide important insights into improving agronomic traits in temperate japonica rice cultivars. Here we describe recent progress in our studies as an example of genetic analysis in closely related cultivars.

Evaluation of a M-202 × Oryza nivara advanced backcross mapping population for seedling vigor, yield components and quality

Oryza nivara, the ancestral species of cultivated rice (O. sativa), has been the source of novel alleles for resistance to biotic and abiotic stress lost during domestication. Interspecific advanced backcross (ABC) populations permit the introgression of desirable alleles from the wild species into O. sativa and allow traits to be mapped to chromosomal regions by QTL mapping. An ABC population was developed by crossing M-202, a California medium grain, temperate japonica cultivar with O. nivara (IRGC100195). The population has 177 BC2F2:5 progeny lines and was evaluated for 17 traits including seedling vigor under cool temperature (mesocotyl, coleoptile, shoot and root lengths), agronomic (days to heading, plant height, culm angle, panicle type), yield components (panicles per plant, panicle length, florets and seeds per panicle, 100-seed weight) and quality [kernel length and width, apparent amylose content (AAC), alkali spreading value (ASV)]. Most exciting was that the O. nivara parent improved seedling vigor by increasing both the coleoptile and shoot lengths. Wild donor alleles increased the panicles per plant and seed weight, but M-202 alleles improved fertility. For one locus, the O. nivara alleles accounted for increased kernel length even though this parent had smaller seeds than M-202. The AAC mapped to the WAXY locus and ASV to the ALK locus, with most progeny being similar to M-202 for these quality traits. Select progeny lines could be useful for improving seedling vigor. This interspecific population is the first in the background of a U.S. temperate japonica rice cultivar.

Genetic analysis of durable resistance to Magnaporthe oryzae in the rice accession Gigante Vercelli identified two blast resistance loci.

Rice cultivars exhibiting durable resistance to blast, the most important rice fungal disease provoking up to 30% of rice losses, are very rare and searching for sources of such a resistance represents a priority for rice-breeding programs. To this aim we analyzed Gigante Vercelli (GV) and Vialone Nano (VN), two temperate japonica rice cultivars in Italy displaying contrasting response to blast, with GV showing a durable and broad-spectrum resistance, whereas VN being highly susceptible. An SSR-based genetic map developed using a GV × VN population segregating for blast resistance identified two blast resistance loci, localized to the long arm of chromosomes 1 and 4 explaining more than 78% of the observed phenotypic variation for blast resistance. The pyramiding of two blast resistance QTLs was therefore involved in the observed durable resistance in GV. Mapping data were integrated with information obtained from RNA-seq expression profiling of all classes of resistance protein genes (resistance gene analogs, RGAs) and with the map position of known cloned or mapped blast resistance genes to search candidates for the GV resistant response. A co-localization of RGAs with the LOD peak or the marker interval of the chromosome 1 QTL was highlighted and a valuable tool for selecting the resistance gene during breeding programs was developed. Comparative analysis with known blast resistance genes revealed co-positional relationships between the chromosome 1 QTL with the Pi35/Pish blast resistance alleles and showed that the chromosome 4 QTL represents a newly identified blast resistance gene. The present genetic analysis has therefore allowed the identification of two blast resistance loci in the durable blast-resistant rice cultivar GV and tools for molecular selection of these resistance genes.

A BAC physical map of aus rice cultivar ‘Kasalath’, and the map‐based genomic sequence of ‘Kasalath’ chromosome 1

Comparative analysis using available genomic resources within closely related species is an effective way to investigate genomic sequence and structural diversity. Rice (Oryza sativa L.) has undergone significant physiological and morphological changes during its domestication and local adaptation. We present a complete bacterial artificial chromosome (BAC) physical map for the aus rice cultivar 'Kasalath', which covers 90% of the sequence of temperate japonica rice cultivar 'Nipponbare'. Examination of physical distances between computational and experimental measurements of 'Kasalath' BAC insert size revealed the presence of more than 500 genomic regions that appear to have significant chromosome structural changes between the two cultivars. In particular, a genomic region on the long arm of 'Kasalath' chromosome 11 carrying a disease-resistance gene cluster was greatly expanded relative to the 'Nipponbare' genome. We also decoded 41.37 Mb of high-quality genomic sequence from 'Kasalath' chromosome 1. Extensive comparisons of chromosome 1 between 'Kasalath' and 'Nipponbare' led to the discovery of 317,843 single-nucleotide polymorphisms (SNPs) and 66,331 insertion/deletion (indel) sites. Nearly two-thirds of the expressed genes on rice chromosome 1 carried natural variations involving SNPs and/or indels that resulted in substitutions, insertions or deletions of amino acids in one cultivar relative to the other. We also observed gain and loss of genes caused by large indels. This study provides an important framework and an invaluable dataset for further understanding of the molecular mechanisms underlying the evolution and functions of the rice genome.

A Mediterranean japonica rice (Oryza sativa) cultivar improvement through anther culture

Certified seed producers systematically select and propagate registered varieties year after year in order to maintain their uniformity and the original registered cultivar traits. However, natural mutations, spontaneous breeding between varieties and alien grain contamination can introduce undesirable variability. NRVC 980385 is a temperate japonica rice cultivar (Oryza sativa ssp. japonica) first registered in Spain in 2002. In 2005 certification tests detected a plot differing from the original traits in terms of uniformity and height suggesting the presence of a certain heterozygosis. This material was therefore seen as an opportunity to obtain newly stabilized doubled haploid (DH) lines which could compete in the Spanish short grain seed market. In this study, an in vitro anther culture protocol is defined which also covers the field tests selection to obtain four new, improved and stabilized DH derived lines ready to be registered for commercial proposes. This took just 4 years from the initial anther collection until new lines were grown in large scale field trials. Consequently, this protocol reduces the time for obtaining field assessed DH lines thereby having considerable advantages over other techniques by both maintaining the original registered cultivars and/or generating new derived varieties.

Identification of SNPs in Closely Related Temperate Japonica Rice Cultivars Using Restriction Enzyme-Phased Sequencing

Very low polymorphism in the germplasm typically used by breeding programs poses a significant bottleneck with regards to molecular breeding and the exploitation of breeding materials for quantitative trait analyses. California rice cultivars, derived from a very small base of temperate japonica germplasm and having a relatively brief breeding history, are a good example. In this study, we employed a reduced representation sequencing approach called Restriction Enzyme Site Comparative Analysis (RESCAN) to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in forty-five rice cultivars representing the majority of the 100 year-old breeding history in California. Over 20,000 putative SNPs were detected relative to the Nipponbare reference genome which enabled the identification and analysis of inheritance of pedigree haplotypes. Haplotype blocks distinguishing modern California cultivars from each other and from the ancestral short grain temperate japonica cultivars were easily identified. Reduced representation sequencing methods such as RESCAN are a valuable alternative to SNP chip genotyping and low coverage whole genome sequencing.

Validation of QTLs for Eating Quality of Japonica Rice ‘Koshihikari’ Using Backcross Inbred Lines

Using backcross inbred lines (BILs) derived from a cross between temperate japonica rice cultivars, Moritawase and Koshihikari, we validated the major quantitative trait loci (QTL) for eating quality and textural characteristics on chromosomes (Chr) 1, 2, 3, 6, 7, 10, and 12. Significant genetic differences in eating quality among BILs were detected at the QTL on Chr 3 and corresponded to the differences between the parents. Although differences in eating quality on the other chromosomes were not significant by t-test, cluster analysis and principal component analysis clearly showed that the genetic effects of the QTLs on Chr 6, 7, and 10 were similar to that on Chr 3, but the genetic effects of QTLs on Chr 1, 2, and 12 were entirely different from that on Chr 3. We previously identified that textural characteristics were highly correlated with eating quality. In this study, genetic differences in textural characteristics were similar to the genetic differences in eating quality among BILs. These results reveal major QTLs for eating quality of Koshihikari on Chr 3, 6, 7, and 10. The QTL on Chr 3 contributed most to the improvement of eating quality and textural characteristics.

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.

Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice

The temperate japonica rice cultivar M202 is the predominant variety grown in California due to its tolerance to low temperature stress, good grain quality and high yield. Earlier analysis of a recombinant inbred line mapping population derived from a cross between M202 and IR50, an indica cultivar that is highly sensitive to cold stress, resulted in the identification of a number of QTL conferring tolerance to cold-induced wilting and necrosis. A major QTL, qCTS12, located on the short arm of chromosome 12, contributes over 40% of the phenotypic variance. To identify the gene(s) underlying qCTS12, we have undertaken the fine mapping of this locus. Saturating the short arm of chromosome 12 with microsatellite markers revealed that qCTS12 is closest to RM7003. Using RM5746 and RM3103, which are immediately outside of RM7003, we screened 1,954 F(5)-F(10) lines to find recombinants in the qCTS12 region. Additional microsatellite markers were identified from publicly available genomic sequence and used to fine map qCTS12 to a region of approximately 87 kb located on the BAC clone OSJNBb0071I17. This region contains ten open reading frames (ORFs) consisting of five hypothetical and expressed proteins of unknown function, a transposon protein, a putative NBS-LRR disease resistance protein, two zeta class glutathione S-transferases (OsGSTZ1 and OsGSTZ2), and a DAHP synthetase. Further fine mapping with markers developed from the ORFs delimited the QTL to a region of about 55 kb. The most likely candidates for the gene(s) underlying qCTS12 are OsGSTZ1 and OsGSTZ2.

Fingerprinting temperate japonica and tropical indica rice genotypes by comparative analysis of DNA markers

This paper describes the relative efficiency of three marker systems, RAPD, ISSR, and AFLP, in terms of fingerprinting 14 rice genotypes consisting of seven temperatejaponica rice cultivars, three indica near-isogenic lines, three indica introgression lines, and one breeding line of japonica type adapted to high-altitude areas of the tropics with cold tolerance genes. Fourteen RAPD, 21 ISSR, and 8 AFLP primers could produce 970 loci, with the highest average number of loci (92.5) generated by AFLP. Although polymorphic bands in the genotypes were detected by all marker assays, the AFLP assay discriminated the genotypes effectively with a robust discriminating power (0.99), followed by ISSR (0.76) and RAPD (0.61). While significant polymorphism was detected among the genotypes of japonica and indica through analysis of molecular variance (AMOVA), relatively low polymorphism was detected within the genotypes of japonica rice cultivars. The correlation coefficients of similarity were significant for the three marker systems used, but only the AFLP assay effectively differentiated all tested rice lines. Fingerprinting of backcross-derived resistant progenies using ISSR and AFLP markers easily detected progenies having a maximum rate of recovery for the recurrent parent genome and suggested that our fingerprinting approach adopting the ‘undefined-element-amplifying’ DNA marker system is suitable for incorporating useful alleles from the indica donor genome into the genome of temperate japonica rice cultivars with the least impact of deleterious linkage drag.

The OsLti6 genes encoding low-molecular-weight membrane proteins are differentially expressed in rice cultivars with contrasting sensitivity to low temperature

Rice ( Oryza sativa L.) is sensitive to chilling particularly at early stages of seedling establishment. Two closely related genes ( OsLti6a, OsLti6b), which are induced by low temperature during seedling emergence were isolated from a cold tolerant temperate japonica rice cultivar. These genes are closely related to the Arabidopsis rare cold-inducible ( RCI2) and barley low-temperature-inducible ( BLT101) genes. Based on direct biochemical and indirect physiological evidence and similarity with a conserved protein domain in the Cluster of Orthologous Groups (COG) database (e.g., yeast PMP3), the rice genes belong to a class of low-molecular-weight hydrophobic proteins involved in maintaining the integrity of the plasma membrane during cold, dehydration and salt stress conditions. Both genes exhibit a genotype-specific expression signature characterized by early and late stress-inducible expression in tolerant and intolerant genotypes, respectively. The differences in temporal expression profiles are consistent with cultivar differences in cold-induced membrane leakiness and seedling vigor. The presence of CRT/DRE promoter cis-elements is consistent with the synchronized expression of OsLti6 genes with the C-repeat binding factor/drought responsive element-binding protein ( CBF/DREB) transcriptional activator. The present results indicate that the Oslti6 genes are part of a battery of cold stress defense-related genes regulated by a common switch.

QTL analysis for panicle characteristics in temperate japonica rice

To understand the genetic background of panicle characteristics in temperate japonica rice (Oryza sativa L.), we genetically analyzed DH lines derived from a cross between two temperate japonica rice cultivars, ‘Akihikari’ and ‘Koshihikari’,in 1996 and 1997. Four traits of panicle characteristics, number of primary branches per panicle (NPB), number of secondary branches per panicle (NSB), average number of spikelets on one primary branch (NSP)and average number of spikelets on one secondary branch (NSS), in 212 DH lines were measured, and the interval mapping of QTLs for these traits was carried out using169 DNA markers with an LOD threshold of2.5. Five, three and one putative QTLs for NPB, NSB and NSS were identified,respectively, and no QTLs relating to NSP appeared. The percentages in total phenotypic variation explained by all putative QTLs for NPB were 35.5%: and43.8% in 1996 and 1997, respectively. All putative QTLs for NSB accounted for 35.5%and 27.5% of total phenotypic variation in1996 and 1997, respectively. The QTLs identified in this study will be useful intemperate japonica rice breeding for improved spikelet yield.