A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions

Glutamate Signaling in Hepatic Stellate Cells Drives Alcoholic Steatosis

Activation of hepatocyte cannabinoid receptor-1 (CB₁R) by hepatic stellate cell (HSC)-derived 2-arachidonoylglycerol (2-AG) drives de novo lipogenesis in alcoholic liver disease (ALD). How alcohol stimulates 2-AG production in HSCs is unknown. Here, we report that chronic alcohol consumption induced hepatic cysteine deficiency and subsequent glutathione depletion by impaired transsulfuration pathway. A compensatory increase in hepatic cystine-glutamate anti-porter xCT boosted extracellular glutamate levels coupled to cystine uptake both in mice and in patients with ALD. Alcohol also induced the selective expression of metabotropic glutamate receptor-5 (mGluR5) in HSCs where mGluR5 activation stimulated 2-AG production. Consistently, genetic or pharmacologic inhibition of mGluR5 or xCT attenuated alcoholic steatosis in mice via the suppression of 2-AG production and subsequent CB₁R-mediated de novo lipogenesis. We conclude that a bidirectional signaling operates at a metabolic synapse between hepatocytes and HSCs through xCT-mediated glutamate-mGluR5 signaling to produce 2-AG, which induces CB₁R-mediated alcoholic steatosis.

Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome)

BACKGROUND

Inflorescence dichotomy in Musa species is a rare developmental event which leads to the production of multiple bunches on a single pseudostem at fruiting. In spite of its fascinating attraction and seductive appeal, little is known about the cytogenetic basis and molecular mechanisms that could be ascribed to this phenomenon. To bridge this gap in information, an integrative approach using cytological fingerprinting and DNA ploidy level profiling (based on chromosome counting and flow cytometry) were assayed on five inflorescence dichotomous plantain varieties and a single-bunching cultivar that served as control. This was done to assess the number and behaviour of chromosomes on the one hand and single nucleotide polymorphisms identified during analysis of nucleotide variations on the other.

RESULTS

Chromosomes stained with aceto-orcein were very tiny, compact, metacentric and acrocentric, and differed both in number and ploidy level between the inflorescence dichotomous and single-bunching cultivars. The dichotomous plantains were mainly diploid (2n = 2x = 22) while the single-bunching 'Agbagba' cultivar was consistently a triploid (2n = 3x = 33), as revealed by histological chromosome counting and flow cytometry, implying that there was a high incidence of genomic divergence on account of ploidy variations among the different Musa cultivars. Molecular genotyping using single nucleotide polymorphisms detected on the GTPase-protein binding gene of the leaf tissue gene complex provided further evidence indicating that differences in the number of bunches among the inflorescence dichotomous cultivars could be ascribed to nucleotide diversity that was elicited by changes in amino acid sequences in the genome of the crops. Non-synonymous nucleotide substitutions resulted mainly from transversion (from purine to pyramidine and vice versa), tacitly implying that these changes were crucial and promoted a cascade of reactions in the genome that were, probably, responsible for the non-persistence of the dichotomization event(s) or the reversals in the bunch phenotype detected among the inflorescence dichotomous cultivars.

CONCLUSIONS

This is the first report of cytogenetic fingerprints and nucleotide diversity detection among single- and multiple-bunching Musa cultivars. A clear distinction between the two groups was found that is indicative of variations both in ploidy level and nucleotide sequences. The pattern of single nucleotide polymorphisms provided profound clues suggesting that there was a high incidence of genomic divergence, due to random and unstable genetic events that were triggered by frequent spontaneous somatic mutations.

Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India

Background

Hill rices (Oryza sativa L.) are direct seeded rices grown on hill slopes of different gradients. These landraces have evolved under rainfed and harsh environmental conditions and may possess genes governing adaptation traits such as tolerance to cold and moisture stress. In this study, 64 hill rice landraces were collected from the state of Arunachal Pradesh of North-Eastern region of India, and assessed by agro-morphological variability and microsatellite markers polymorphism. Our aim was to use phenotypic and genetic diversity data to understand the basis of farmers’ classification of hill rice landraces into two groups: umte and tening. Another goal was to understand the genetic differentiation of hill rices into Indica or japonica subspecies.

Results

According to farmers’ classification, hill rices were categorized into two groups: umte (large-grained, late maturing) and tening (small-grained, early maturing). We did not find significant difference in days to 50 % flowering between the groups. Principal component analysis revealed that two groups can be distinguished on the basis of kernel length-to-width ration (KLW), kernel length (KL), grain length (GrL), grain length-to-width ration (GrLW) and plant height (Ht). Stepwise canonical discriminant analysis identified KL and Ht as the main discriminatory characters between the cultivar groups. Genetic diversity analysis with 35 SSR markers revealed considerable genetic diversity in the hill rice germplasm (gene diversity: 0.66; polymorphism information content: 0.62). Pair-wise allelic difference between umte and tening groups was not statistically significant. The model-based population structure analysis showed that the hill rices were clustered into two broad groups corresponding to Indica and Japonica. The geographic distribution and cultivars grouping of hill rices were not congruent in genetic clusters. Both distance- and model-based approaches indicated that the hill rices were predominantly japonica or admixture among the groups within the subspecies. These findings were further supported by combined analysis hill rices with 150 reference rice accessions representing major genetic groups of rice.

Conclusion

This study collected a valuable set of hill rice germplasm for rice breeding and for evolutionary studies. It also generated a new set of information on genetic and phenotypic diversity of hill rice landraces in North-Eastern region of India. The collected hill rices were mostly japonica or admixture among the subpopulations of Indica or Japonica. The findings are useful for utilization and conservation of hill rice germplasm.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0414-1) contains supplementary material, which is available to authorized users.

Molecular and Cytogenetic Characterization of Wild Musa Species

The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region provided further information about evolutionary relationships between individual accessions and suggested that some of analyzed accessions were interspecific hybrids and/or backcross progeny.

Genetic Diversity and Population Structure of Basmati Rice (Oryza sativa L.) Germplasm Collected from North Western Himalayas Using Trait Linked SSR Markers

One hundred forty one basmati rice genotypes collected from different geographic regions of North Western Himalayas were characterized using 40 traits linked microsatellite markers. Number of alleles detected by the abovementioned primers were 112 with a maximum and minimum frequency of 5 and 2 alleles, respectively. The maximum and minimum polymorphic information content values were found to be 0.63 and 0.17 for the primers RM206 and RM213, respectively. The genetic similarity coefficient for the most number of pairs ranged between of 0.2-0.9 with the average value of 0.60 for all possible combinations, indicating moderate genetic diversity among the chosen genotypes. Phylogenetic cluster analysis of the SSR data based on distance divided all genotypes into four groups (I, II, III and IV), whereas model based clustering method divided these genotypes into five groups (A, B, C, D and E). However, the result from both the analysis are in well agreement with each other for clustering on the basis of place of collection and geographic region, except the local basmati genotypes which clustered into three subpopulations in structure analysis comparison to two clusters in distance based clustering. The diverse genotypes and polymorphic trait linked microsatellites markers in the present study will be used for the identification of quantitative trait loci/genes for different economically important traits to be utilized in molecular breeding programme of rice in the future.

Mapping of the quantitative trait locus (QTL) conferring partial resistance to rice leaf blast disease

Malaysian rice, Pongsu Seribu 2, has wide-spectrum resistance against blast disease. Chromosomal locations conferring quantitative resistance were detected by linkage mapping with SSRs and quantitative trait locus (QTL) analysis. For the mapping population, 188 F3 families were derived from a cross between the susceptible cultivar, Mahsuri, and a resistant variety, Pongsu Seribu 2. Partial resistance to leaf blast in the mapping population was assessed. A linkage map covering ten chromosomes and consisting of 63 SSR markers was constructed. 13 QTLs, including 6 putative and 7 putative QTLs, were detected on chromosomes 1, 2, 3, 5, 6, 10, 11 and 12. The resulting phenotypic variation due to a single QTL ranged from 2 to 13 %. These QTLs accounted for approx. 80 % of the total phenotypic variation within the F3 population. Therefore, partial resistance to blast in Pongsu Seribu 2 is due to combined effects of multiple loci with major and minor effects.

Genetic structure of Thai rice and rice accessions obtained from the International Rice Research Institute

BACKGROUND

Although the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world's largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs.

RESULTS

From the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species.

CONCLUSIONS

Thai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.

Development of a genome-wide multiple duplex-SSR protocol and its applications for the identification of selfed progeny in switchgrass

Background

Switchgrass (Panicum virgatum) is a herbaceous crop for the cellulosic biofuel feedstock development in the USA and Europe. As switchgrass is a naturally outcrossing species, accurate identification of selfed progeny is important to producing inbreds, which can be used in the production of heterotic hybrids. Development of a technically reliable, time-saving and easily used marker system is needed to quantify and characterize breeding origin of progeny plants of targeted parents.

Results

Genome-wide screening of 915 mapped microsatellite (simple sequence repeat, SSR) markers was conducted, and 842 (92.0%) produced clear and scorable bands on a pooled DNA sample of eight switchgrass varieties. A total of 166 primer pairs were selected on the basis of their relatively even distribution in switchgrass genome and PCR amplification quality on 16 tetraploid genotypes. Mean polymorphic information content value for the 166 markers was 0.810 ranging from 0.116 to 0.959. From them, a core set of 48 loci, which had been mapped on 17 linkage groups, was further tested and optimized to develop 24 sets of duplex markers. Most of (up to 87.5%) targeted, but non-allelic amplicons within each duplex were separated by more than 10-bp. Using the established duplex PCR protocol, selfing ratio (i.e., selfed/all progeny x100%) was identified as 0% for a randomly selected open-pollinated ‘Kanlow’ genotype grown in the field, 15.4% for 22 field-grown plants of bagged inflorescences, and 77.3% for a selected plant grown in a growth chamber.

Conclusions

The study developed a duplex SSR-based PCR protocol consisting of 48 markers, providing ample choices of non-tightly-linked loci in switchgrass whole genome, and representing a powerful, time-saving and easily used method for the identification of selfed progeny in switchgrass. The protocol should be a valuable tool in switchgrass breeding efforts.

Development and application of a whole-genome simple sequence repeat panel for high-throughput genotyping in soybean

Among commonly applied molecular markers, simple sequence repeats (SSRs, or microsatellites) possess advantages such as a high level of polymorphism and codominant pattern of inheritance at individual loci. To facilitate systematic and rapid genetic mapping in soybean, we designed a genotyping panel comprised 304 SSR markers selected for allelic diversity and chromosomal location so as to provide wide coverage. Most primer pairs for the markers in the panel were redesigned to yield amplicons of 80-600 bp in multiplex polymerase chain reaction (PCR) and fluorescence-based sequencer analysis, and they were labelled with one of four different fluorescent dyes. Multiplex PCR with sets of six to eight primer pairs per reaction generated allelic data for 283 of the 304 SSR loci in three different mapping populations, with the loci mapping to the same positions as previously determined. Four SSRs on each chromosome were analysed for allelic diversity in 87 diverse soybean germplasms with four-plex PCR. These 80 loci showed an average allele number and polymorphic information content value of 14.8 and 0.78, respectively. The high level of polymorphism, ease of analysis, and high accuracy of the SSR genotyping panel should render it widely applicable to soybean genetics and breeding.

A platform for efficient genotyping in Musa using microsatellite markers

BACKGROUND AND AIMS

Bananas and plantains (Musa spp.) are one of the major fruit crops worldwide with acknowledged importance as a staple food for millions of people. The rich genetic diversity of this crop is, however, endangered by diseases, adverse environmental conditions and changed farming practices, and the need for its characterization and preservation is urgent. With the aim of providing a simple and robust approach for molecular characterization of Musa species, we developed an optimized genotyping platform using 19 published simple sequence repeat markers.

METHODOLOGY

The genotyping system is based on 19 microsatellite loci, which are scored using fluorescently labelled primers and high-throughput capillary electrophoresis separation with high resolution. This genotyping platform was tested and optimized on a set of 70 diploid and 38 triploid banana accessions.

PRINCIPAL RESULTS

The marker set used in this study provided enough polymorphism to discriminate between individual species, subspecies and subgroups of all accessions of Musa. Likewise, the capability of identifying duplicate samples was confirmed. Based on the results of a blind test, the genotyping system was confirmed to be suitable for characterization of unknown accessions.

CONCLUSIONS

Here we report on the first complex and standardized platform for molecular characterization of Musa germplasm that is ready to use for the wider Musa research and breeding community. We believe that this genotyping system offers a versatile tool that can accommodate all possible requirements for characterizing Musa diversity, and is economical for samples ranging from one to many accessions.

Functionally relevant microsatellites in sugarcane unigenes

BACKGROUND

Unigene sequences constitute a rich source of functionally relevant microsatellites. The present study was undertaken to mine the microsatellites in the available unigene sequences of sugarcane for understanding their constitution in the expressed genic component of its complex polyploid/aneuploid genome, assessing their functional significance in silico, determining the extent of allelic diversity at the microsatellite loci and for evaluating their utility in large-scale genotyping applications in sugarcane.

RESULTS

The average frequency of perfect microsatellite was 1/10.9 kb, while it was 1/44.3 kb for the long and hypervariable class I repeats. GC-rich trinucleotides coding for alanine and the GA-rich dinucleotides were the most abundant microsatellite classes. Out of 15,594 unigenes mined in the study, 767 contained microsatellite repeats and for 672 of these putative functions were determined in silico. The microsatellite repeats were found in the functional domains of proteins encoded by 364 unigenes. Its significance was assessed by establishing the structure-function relationship for the beta-amylase and protein kinase encoding unigenes having repeats in the catalytic domains. A total of 726 allelic variants (7.42 alleles per locus) with different repeat lengths were captured precisely for a set of 47 fluorescent dye labeled primers in 36 sugarcane genotypes and five cereal species using the automated fragment analysis system, which suggested the utility of designed primers for rapid, large-scale and high-throughput genotyping applications in sugarcane. Pair-wise similarity ranging from 0.33 to 0.84 with an average of 0.40 revealed a broad genetic base of the Indian varieties in respect of functionally relevant regions of the large and complex sugarcane genome.

CONCLUSION

Microsatellite repeats were present in 4.92% of sugarcane unigenes, for most (87.6%) of which functions were determined in silico. High level of allelic diversity in repeats including those present in the functional domains of proteins encoded by the unigenes demonstrated their use in assay of useful variation in the genic component of complex polyploid sugarcane genome.

Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach

BACKGROUND

Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size.

RESULTS

The thematic core collection obtained meets the minimum requirements for a core sample - maintenance of at least 80% of the allelic richness of the thematic collection, with, approximately, 15% of its size. The method was compared with other methodologies based on the M strategy, and also with a core collection generated by random sampling. Higher proportions of retained alleles (in a core collection of equal size) or similar proportions of retained alleles (in a core collection of smaller size) were detected in the two methods based on the M strategy compared to the proposed methodology. Core sub-collections constructed by different methods were compared regarding the increase or maintenance of phenotypic diversity. No change on phenotypic diversity was detected by measuring the trait "Weight of 100 Seeds", for the tested sampling methods. Effects on linkage disequilibrium between unlinked microsatellite loci, due to sampling, are discussed.

CONCLUSIONS

Building of a thematic core collection was here defined by prior selection of accessions which are diverse for the trait of interest, and then by pairwise genetic distances, estimated by DNA polymorphism analysis at molecular marker loci. The resulting thematic core collection potentially reflects the maximum allele richness with the smallest sample size from a larger thematic collection. As an example, we used the development of a thematic core collection for drought tolerance in rice. It is expected that such thematic collections increase the use of germplasm by breeding programs and facilitate the study of the traits under consideration. The definition of a core collection to study drought resistance is a valuable contribution towards the understanding of the genetic control and the physiological mechanisms involved in water use efficiency in plants.

Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups

Background

Completely sequenced plant genomes provide scope for designing a large number of microsatellite markers, which are useful in various aspects of crop breeding and genetic analysis. With the objective of developing genic but non-coding microsatellite (GNMS) markers for the rice (Oryza sativa L.) genome, we characterized the frequency and relative distribution of microsatellite repeat-motifs in 18,935 predicted protein coding genes including 14,308 putative promoter sequences.

Results

We identified 19,555 perfect GNMS repeats with densities ranging from 306.7/Mb in chromosome 1 to 450/Mb in chromosome 12 with an average of 357.5 GNMS per Mb. The average microsatellite density was maximum in the 5' untranslated regions (UTRs) followed by those in introns, promoters, 3'UTRs and minimum in the coding sequences (CDS). Primers were designed for 17,966 (92%) GNMS repeats, including 4,288 (94%) hypervariable class I types, which were bin-mapped on the rice genome. The GNMS markers were most polymorphic in the intronic region (73.3%) followed by markers in the promoter region (53.3%) and least in the CDS (26.6%). The robust polymerase chain reaction (PCR) amplification efficiency and high polymorphic potential of GNMS markers over genic coding and random genomic microsatellite markers suggest their immediate use in efficient genotyping applications in rice. A set of these markers could assess genetic diversity and establish phylogenetic relationships among domesticated rice cultivar groups. We also demonstrated the usefulness of orthologous and paralogous conserved non-coding microsatellite (CNMS) markers, identified in the putative rice promoter sequences, for comparative physical mapping and understanding of evolutionary and gene regulatory complexities among rice and other members of the grass family. The divergence between long-grained aromatics and subspecies japonica was estimated to be more recent (0.004 Mya) compared to short-grained aromatics from japonica (0.006 Mya) and long-grained aromatics from subspecies indica (0.014 Mya).

Conclusion

Our analyses showed that GNMS markers with their high polymorphic potential would be preferred candidate functional markers in various marker-based applications in rice genetics, genomics and breeding. The CNMS markers provided encouraging implications for their use in comparative genome mapping and understanding of evolutionary complexities in rice and other members of grass family.

Identification of drought-responsive genes in roots of upland rice (Oryza sativa L)

Background

Rice (Oryza sativa L.) germplasm represents an extraordinary source of genes that control traits of agronomic importance such as drought tolerance. This diversity is the basis for the development of new cultivars better adapted to water restriction conditions, in particular for upland rice, which is grown under rainfall. The analyses of subtractive cDNA libraries and differential protein expression of drought tolerant and susceptible genotypes can contribute to the understanding of the genetic control of water use efficiency in rice.

Results

Two subtractive libraries were constructed using cDNA of drought susceptible and tolerant genotypes submitted to stress against cDNA of well-watered plants. In silico analysis revealed 463 reads, which were grouped into 282 clusters. Several genes expressed exclusively in the tolerant or susceptible genotypes were identified. Additionally, proteome analysis of roots from stressed plants was performed and 22 proteins putatively associated to drought tolerance were identified by mass spectrometry.

Conclusion

Several genes and proteins involved in drought-response, as well as genes with no described homologs were identified. Genes exclusively expressed in the tolerant genotype were, in general, related to maintenance of turgor and cell integrity. In contrast, in the susceptible genotype, expression of genes involved in protection against cell damage was not detected. Several protein families identified in the proteomic analysis were not detected in the cDNA analysis. There is an indication that the mechanisms of susceptibility to drought in upland rice are similar to those of lowland varieties.

Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference

Background

Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism Neurospora crassa is an excellent system to study evolution and biological function of SSRs.

Results

We identified and characterized 2749 SSRs of 963 SSR types in the genome of N. crassa. The distribution of tri-nucleotide (nt) SSRs, the most common SSRs in N. crassa, was significantly biased in exons. We further characterized the distribution of 19 abundant SSR types (AST), which account for 71% of total SSRs in the N. crassa genome, using a Poisson log-linear model. We also characterized the size variation of SSRs among natural accessions using Polymorphic Index Content (PIC) and ANOVA analyses and found that there are genome-wide, chromosome-dependent and local-specific variations. Using polymorphic SSRs, we have built linkage maps from three line-cross populations.

Conclusion

Taking our computational, statistical and experimental data together, we conclude that 1) the distributions of the SSRs in the sequenced N. crassa genome differ systematically between chromosomes as well as between SSR types, 2) the size variation of tri-nt SSRs in exons might be an important mechanism in generating functional variation of proteins in N. crassa, 3) there are different levels of evolutionary forces in variation of amino acid repeats, and 4) SSRs are stable molecular markers for genetic studies in N. crassa.

Rice molecular breeding laboratories in the genomics era: Current status and future considerations

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information-coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools-provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to "bridge the application gap" between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs.