Publications by authors named "Endang M Septiningsih"

29 Publications

  • Page 1 of 1

Non-Invasive Identification of Nutrient Components in Grain.

Molecules 2021 May 24;26(11). Epub 2021 May 24.

Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.

Digital farming is a modern agricultural concept that aims to maximize the crop yield while simultaneously minimizing the environmental impact of farming. Successful implementation of digital farming requires development of sensors to detect and identify diseases and abiotic stresses in plants, as well as to probe the nutrient content of seeds and identify plant varieties. Experimental evidence of the suitability of Raman spectroscopy (RS) for confirmatory diagnostics of plant diseases was previously provided by our team and other research groups. In this study, we investigate the potential use of RS as a label-free, non-invasive and non-destructive analytical technique for the fast and accurate identification of nutrient components in the grains from 15 different rice genotypes. We demonstrate that spectroscopic analysis of intact rice seeds provides the accurate rice variety identification in ~86% of samples. These results suggest that RS can be used for fully automated, fast and accurate identification of seeds nutrient components.
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http://dx.doi.org/10.3390/molecules26113124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8197263PMC
May 2021

OsCOP1 regulates embryo development and flavonoid biosynthesis in rice (Oryza sativa L.).

Theor Appl Genet 2021 May 5. Epub 2021 May 5.

Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.

Key Message: Novel mutations of OsCOP1 were identified to be responsible for yellowish pericarp and embryo lethal phenotype, which revealed that OsCOP1 plays a crucial role in flavonoid biosynthesis and embryogenesis in rice seed. Successful production of viable seeds is a major component of plant life cycles, and seed development is a complex, highly regulated process that affects characteristics such as seed viability and color. In this study, three yellowish-pericarp embryo lethal (yel) mutants, yel-hc, yel-sk, and yel-cc, were produced from three different japonica cultivars of rice (Oryza sativa L). Mutant seeds had yellowish pericarps and exhibited embryonic lethality, with significantly reduced grain size and weight. Morphological aberrations were apparent by 5 days after pollination, with abnormal embryo development and increased flavonoid accumulation observed in the yel mutants. Genetic analysis and mapping revealed that the phenotype of the three yel mutants was controlled by a single recessive gene, LOC_Os02g53140, an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). The yel-hc, yel-sk, and yel-cc mutants carried mutations in the RING finger, coiled-coil, and WD40 repeat domains, respectively, of OsCOP1. CRISPR/Cas9-targeted mutagenesis was used to knock out OsCOP1 by targeting its functional domains, and transgenic seed displayed the yel mutant phenotype. Overexpression of OsCOP1 in a homozygous yel-hc mutant background restored pericarp color, and the aberrant flavonoid accumulation observed in yel-hc mutant was significantly reduced in the embryo and endosperm. These results demonstrate that OsCOP1 is associated with embryo development and flavonoid biosynthesis in rice grains. This study will facilitate a better understanding of the functional roles of OsCOP1 involved in early embryogenesis and flavonoid biosynthesis in rice seeds.
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http://dx.doi.org/10.1007/s00122-021-03844-9DOI Listing
May 2021

Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice.

Int J Mol Sci 2021 Apr 24;22(9). Epub 2021 Apr 24.

Southern Cross Plant Sciences, Southern Cross University, 1 Military Road, Lismore 2480, Australia.

Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize (), a major centromere-spanning AG tolerance QTL, derived from the indica variety Ma-Zhan Red, have failed. Here, a novel approach of "enriched haplotype" genome-wide association study based on the Ma-Zhan Red haplotype in the region was successfully used to narrow down from more than 7 Mb to less than 0.7 Mb. The peak region contained 27 genes, including the gene, responsible for red pericarp development in pigmented rice. Through comparative variant and transcriptome analysis between AG tolerant donors and susceptible accessions several candidate genes potentially controlling were identified, among them several regulatory genes. Genome-wide comparative transcriptome analysis suggested differential regulation of sugar metabolism, particularly trehalose metabolism, as well as differential regulation of cell wall modification and chloroplast development to be implicated in AG tolerance mechanisms.
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http://dx.doi.org/10.3390/ijms22094445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8123023PMC
April 2021

Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice.

Plants (Basel) 2021 Apr 6;10(4). Epub 2021 Apr 6.

International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines.

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, and , with LOD scores of 7.1 and 15.0 and R values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.
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http://dx.doi.org/10.3390/plants10040705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067528PMC
April 2021

Raman Spectroscopy Enables Non-invasive and Confirmatory Diagnostics of Salinity Stresses, Nitrogen, Phosphorus, and Potassium Deficiencies in Rice.

Front Plant Sci 2020 22;11:573321. Epub 2020 Oct 22.

Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States.

Proper management of nutrients in agricultural systems is critically important for maximizing crop yields while simultaneously minimizing the health and environmental impacts of pollution from fertilizers. These goals can be achieved by timely confirmatory diagnostics of nutrient deficiencies in plants, which enable precise administration of fertilizers and other supplementation in fields. Traditionally, nutrient diagnostics are performed by wet-laboratory analyses, which are both time- and labor-consuming. Unmanned aerial vehicle (UAV) and satellite imaging have offered a non-invasive alternative. However, these imaging approaches do not have sufficient specificity, and they are only capable of detecting symptomatic stages of nutrient deficiencies. Raman spectroscopy (RS) is a non-invasive and non-destructive technique that can be used for confirmatory detection and identification of both biotic and abiotic stresses on plants. Herein, we show the use of a hand-held Raman spectrometer for highly accurate pre-symptomatic diagnostics of nitrogen, phosphorus, and potassium deficiencies in rice (). Moreover, we demonstrate that RS can also be used for pre symptomatic diagnostics of medium and high salinity stresses. A Raman-based analysis is fast (1 s required for spectral acquisition), portable (measurements can be taken directly in the field), and label-free (no chemicals are needed). These advantages will allow RS to transform agricultural practices, enabling precision agriculture in the near future.
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http://dx.doi.org/10.3389/fpls.2020.573321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642205PMC
October 2020

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in L.

Int J Mol Sci 2020 Oct 31;21(21). Epub 2020 Oct 31.

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.

The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.
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http://dx.doi.org/10.3390/ijms21218148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7663775PMC
October 2020

Flood resilience loci and interact in seedlings established underwater.

Plant Direct 2020 Jul 21;4(7):e00240. Epub 2020 Jul 21.

Department of Botany and Plant Sciences Center for Plant Cell Biology University of California Riverside Riverside CA USA.

Crops with resilience to multiple climatic stresses are essential for increased yield stability. Here, we evaluate the interaction between two loci associated with flooding survival in rice ( L.). (), encoding 7 (), promotes mobilization of endosperm reserves to enhance the elongation of a hollow coleoptile in seeds that are seeded directly into shallow paddies. (), encoding the ethylene-responsive transcription factor , confers tolerance to complete submergence by dampening carbohydrate catabolism, to enhance recovery upon desubmergence. Interactions between and were investigated under three flooding scenarios using four near-isogenic lines by surveying growth and survival. Pyramiding of the two loci does not negatively affect anaerobic germination or vegetative-stage submergence tolerance. However, the pyramided genotype displays reduced survival when seeds are planted underwater and maintained under submergence for 16 d. To better understand the roles of and and their interaction, temporal changes in carbohydrates and shoot transcriptomes were monitored in the four genotypes varying at the two loci at four developmental timeponts, from day 2 after seeding through day 14 of complete submergence. enhances early coleoptile elongation, whereas promotes precocious photoautotrophy and then restricts underwater elongation. By contrast, pyramiding of the and slows elongation growth, the transition to photoautotrophy, and survival. mRNA-sequencing highlights time-dependent and genotype-specific regulation of mRNAs associated with DNA repair, cell cycle, chromatin modification, plastid biogenesis, carbohydrate catabolism and transport, elongation growth, and other processes. These results suggest that interactions between and could impact seedling establishment if paddy depth is not effectively managed after direct seeding.
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http://dx.doi.org/10.1002/pld3.240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7403837PMC
July 2020

Responses of AG1 and AG2 QTL introgression lines and seed pre-treatment on growth and physiological processes during anaerobic germination of rice under flooding.

Sci Rep 2020 06 23;10(1):10214. Epub 2020 Jun 23.

International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.

Rice seeds germinating in flooded soils encounter hypoxia or even anoxia leading to poor seed germination and crop establishment. Introgression of AG1 and AG2 QTLs associated with tolerance of flooding during germination, together with seed pre-treatment via hydro-priming or presoaking can enhance germination and seedling growth in anaerobic soils. This study assessed the performance of elite lines incorporating AG1, AG2 and their combination when directly seeded in flooded soils using dry seeds. The QTLs were in the background of two popular varieties PSB Rc82 and Ciherang-Sub1, evaluated along with the donors Kho Hlan On (AG1) and Ma-Zhan Red (AG2) and recipient parents PSB Rc82 and Ciherang-Sub1. In one set of experiments conducted in the greenhouse, seedling emergence, growth, and carbohydrate mobilization from seeds were assessed. Metabolites associated with reactive oxygen species (ROS) scavenging including malondialdehyde (MDA) as a measure of lipid peroxidation, ascorbate, total phenolic concentration (TPC), and activities of ROS scavenging enzymes were quantified in seeds germinating under control (saturated) and flooded (10 cm) soils. In another set of experiments conducted in a natural field with 3-5 cm flooding depths, control and pretreated seeds of Ciherang-Sub1 introgression lines and checks were used. Flooding reduced seedling emergence of all genotypes, though emergence of AG1 + AG2 introgression lines was greater than the other AG lines. Soluble sugars increased, while starch concentration decreased gradually under flooding especially in the tolerant checks and in AG1 + AG2 introgression lines. Less lipid peroxidation and higher α-amylase activity, higher ascorbate (RAsA) and TPC were observed in the tolerant checks and in the AG1 + AG2 introgression lines. Lipid peroxidation correlated negatively with ascorbate, TPC, and with ROS scavengers. Seed hydro-priming or pre-soaking increased emergence by 7-10% over that of dry seeds. Introgression of AG2 and AG1 + AG2 QTLs with seed pretreatment showed 101-153% higher emergence over dry seeds of intolerant genotypes in the field. Lines carrying AG1 + AG2 QTLs showed higher α-amylase activity, leading to rapid starch degradation and increase in soluble sugars, ascorbate, and TPC, together leading to higher germination and seedling growth in flooded soils. Seed hydro-priming or pre-soaking for 24 h also improved traits associated with flooding tolerance. Combining tolerance with seed management could therefore, improve crop establishment in flooded soils and encourage large-scale adoption of direct seeded rice system.
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http://dx.doi.org/10.1038/s41598-020-67240-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311552PMC
June 2020

Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance.

Sci Rep 2020 05 25;10(1):8621. Epub 2020 May 25.

ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India.

Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety FR13A. Therefore, we analysed the allelic sequence variation in three Sub1 genes in a panel of 179 rice genotypes and its association with submergence tolerance. Population structure and diversity analysis based on a 36-plex genome wide genic-SNP assay grouped these genotypes into two major categories representing Indica and Japonica cultivar groups with further sub-groupings into Indica, Aus, Deepwater and Aromatic-Japonica cultivars. Targetted re-sequencing of the Sub1A, Sub1B and Sub1C genes identfied 7, 7 and 38 SNPs making 8, 9 and 67 SNP haplotypes, respectively. Haplotype networks and phylogenic analysis revealed evolution of Sub1B and Sub1A genes by tandem duplication and divergence of the ancestral Sub1C gene in that order. The alleles of Sub1 genes in tolerant reference variety FR13A seem to have evolved most recently. However, no consistent association could be found between the Sub1 allelic variation and submergence tolerance probably due to low minor allele frequencies and presence of exceptions to the known Sub1A-1 association in the genotype panel. We identified 18 cultivars with non-Sub1A-1 source of submergence tolerance which after further mapping and validation in bi-parental populations will be useful for development of superior flood tolerant rice cultivars.
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http://dx.doi.org/10.1038/s41598-020-65588-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7248102PMC
May 2020

An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies.

PLoS One 2020 14;15(5):e0232479. Epub 2020 May 14.

Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America.

Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232479PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224494PMC
July 2020

Genome-Wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery During Germination in Rice.

Front Genet 2020 21;11:22. Epub 2020 Feb 21.

Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States.

Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of < 0.001, a total of 20 QTLs were identified in the subset of accessions, while 9 QTLs were identified in the subset of accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the subset, and 7 distinct QTL regions in the subset. Among these QTL regions, three regions were common between the whole panel and , three regions were common between the whole panel and , and one region was common between and . A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the subset, 4 from the subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the subset, and 1 from the subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments.
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http://dx.doi.org/10.3389/fgene.2020.00022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7047875PMC
February 2020

Trait-based mapping to identify the genetic factors underlying anaerobic germination of rice: Phenotyping, GXE, and QTL mapping.

BMC Genet 2020 01 17;21(1). Epub 2020 Jan 17.

International Rice Research Institute, Los Baños, Laguna, Philippines.

Background: Anaerobic germination is one of the most important traits for rice under direct-seeded conditions. The trait reduces risk of crop failure due to waterlogged conditions after seeding and allows water to be used as a means of weed control. The identification of QTLs and causal genes for anaerobic germination will facilitate breeding for improved direct-seeded rice varieties. In this study, we explored a BCF population developed from a cross between BJ1, an indica landrace, and NSIC Rc222, a high-yielding recurrent parent. The population was phenotyped under different screening methods (anaerobic screenhouse, anaerobic tray, and aerobic screenhouse) to establish the relationship among the methods and to identify the most suitable screening method, followed by bulk segregant analysis (BSA) to identify large-effect QTLs.

Results: The study showed high heritability for survival (SUR) under all three phenotyping conditions. Although high correlation was observed within screening environments between survival at 14 and 21 days after seeding, the correlation across environments was low. Germination under aerobic and anaerobic conditions showed very low correlation, indicating the independence of their genetic control. The results were further confirmed through AMMI analysis. Four significant markers with an effect on anaerobic germination were identified through BSA. CIM analysis revealed qAG1-2, qAG6-2, qAG7-4, and qAG10-1 having significant effects on the trait. qAG6-2 and qAG10-1 were consistent across screening conditions and seedling age while qAG1-2 and qAG7-4 were specific to screening methods. All QTLs showed an effect when survival across all screening methods was analyzed. Together, the QTLs explained 39 to 55% of the phenotypic variation for survival under anaerobic conditions. No QTL effects were observed under aerobic conditions.

Conclusions: The study helped us understand the effect of phenotyping method on anaerobic germination, which will lead to better phenotyping for this trait in future studies. The QTLs identified through this study will allow the improvement of breeding lines for the trait through marker-assisted selection or through forward breeding approaches such as genomic selection. The high frequency of the BJ1 allele of these QTLs will enhance the robustness of germination under anaerobic conditions in inbred and hybrid rice varieties.
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http://dx.doi.org/10.1186/s12863-020-0808-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6969419PMC
January 2020

QTL mapping for tolerance to anaerobic germination in rice from IR64 and the landrace Kharsu 80A.

Breed Sci 2019 Jun 9;69(2):227-233. Epub 2019 Apr 9.

Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483, USA.

Direct seeding of rice often results in poor crop establishment due to unlevelled fields, unpredicted heavy rains after sowing, and weed and pest invasion. Thus, it is important to develop varieties able to tolerate flooding during germination, also known as anaerobic germination (AG), to address these constraints. A study was conducted to identify QTLs associated with AG tolerance from an IR64/Kharsu 80A F mapping population using 190 lines phenotyped for seedling survival under the stress. Genotyping was performed using a genomewide 384-plex Indica/Indica SNP set. Four QTLs derived from Kharsu 80A providing increased tolerance to anaerobic germination were identified: three on chromosome 7 (, and ) and one on chromosome 3 (), with LOD values ranging from 5.7 to 7.7, and phenotypic variance explained (R) from 8.1% to 12.6%. The QTLs identified in this study can be further investigated to better understand the genetic bases of AG tolerance in rice, and used for marker-assisted selection to develop more robust direct-seeded rice varieties.
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http://dx.doi.org/10.1270/jsbbs.18159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711729PMC
June 2019

Deciphering Genetics Underlying Stable Anaerobic Germination in Rice: Phenotyping, QTL Identification, and Interaction Analysis.

Rice (N Y) 2019 Jul 15;12(1):50. Epub 2019 Jul 15.

International Rice Research Institute, Los Baños, Laguna, Philippines.

Anaerobic germination (AG) is an important trait for direct-seeded rice (DSR) to be successful. Rice usually has low germination under anaerobic conditions, which leads to a poor crop stand in DSR when rain occurs after seeding. The ability of rice to germinate under water reduces the risk of poor crop stand. Further, this allows the use of water as a method of weed control. The identification of the genetic factors leading to high anaerobic germination is required to develop improved DSR varieties. In the present study, two BCF mapping families involving a common parent with anaerobic germination potential, Kalarata, an indica landrace, and two recurrent parents, NSIC Rc222 and NSIC Rc238, were used. Phenotyping was done under two environmental conditions and genotyping was carried out through the KASP SNP genotyping platform. A total of 185 and 189 individuals genotyped with 170 and 179 polymorphic SNPs were used for QTL analysis for the two populations, Kalarata/NSIC Rc238 and Kalarata/NSIC Rc222, respectively. A total of five QTLs on chromosomes 3, 5, 6, 7, and 8 for survival (SUR) and four QTLs on chromosomes 1, 3 (two locations), and 7 for the trait seedling height (SH) across the populations and over the screening conditions were identified. Except for the QTLs on chromosomes 5 and 8, the parent with AG potential, Kalarata, contributed all the other QTLs. Among the five QTLs for SUR, the second-largest QTL (qSUR6-1) was novel for AG potential in rice, showing a stable expression in terms of genetic background and screening conditions explaining 11.96% to 16.01% of the phenotypic variation. The QTL for SH (qSH1-1) was also novel. Considering different genetic backgrounds and different screening conditions, the QTLs identified for the trait SUR explained phenotypic variation in the range of 57.60% to 73.09% while that for the trait SH ranged from 13.53% to 34.30%.
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http://dx.doi.org/10.1186/s12284-019-0305-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629739PMC
July 2019

Increasing flooding tolerance in rice: combining tolerance of submergence and of stagnant flooding.

Ann Bot 2020 01;124(7):1199-1210

International Rice Research Institute, Metro Manila, Philippines.

Background And Aims: Rice ecosystems in the tropical coastal areas are subject to two types of flooding stress: transient complete submergence and long-term water stagnation (stagnant flooding). Here, we aimed to dissect the mechanisms for stagnant flooding tolerance of rice genotypes carrying SUB1, a quantitative trait locus for submergence tolerance.

Methods: We screened 80 elite genotypes under stagnant flooding stress in the lowland rice fields in the wet and dry seasons, and examined the tolerance mechanisms of promising genotypes for the two following seasons.

Key Results: Yield reduction under stagnant flooding averaged 48 % in the dry season and 89 % in the wet season. Elite genotypes carrying SUB1 showed 49 % lower yield than those without SUB1 under stagnant flooding, with no differences under shallow water conditions. However, we identified a few high-yielding Sub1 genotypes that were as tolerant of stagnant flooding as a reference genotype that lacked SUB1. These genotypes had intermediate stature with more shoot elongation in response to rising water than a moderately tolerant Sub1 reference variety, resulting in greater canopy expansion and higher yield. It was important to increase lodging resistance, since plant height >140 cm increased lodging under stagnant flooding. The culm diameter was closely associated with culm strength; reduced aerenchyma formation and increased lignin accumulation in the culm should increase lodging resistance.

Conclusions: The study demonstrated a successful combination of submergence and stagnant flooding tolerance in a rice breeding programme, and identified elite Sub1 genotypes that also tolerate stagnant flooding. Our results will support genetic improvement of Sub1 varieties for stagnant flooding tolerance.
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http://dx.doi.org/10.1093/aob/mcz118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944782PMC
January 2020

Optimizing Sowing and Flooding Depth for Anaerobic Germination-Tolerant Genotypes to Enhance Crop Establishment, Early Growth, and Weed Management in Dry-Seeded Rice ( L.).

Front Plant Sci 2018 23;9:1654. Epub 2018 Nov 23.

The Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Gatton, QLD, Australia.

Poor crop establishment, high weed infestation, and consequent yield loss are major concerns for dry-seeded rice (DSR). Flooding after seeding helps in managing weeds but reduces seed germination and crop stand. Anaerobic germination (AG)-tolerant rice genotypes could overcome these problems in DSR. Screenhouse experiments were established to evaluate the effect of seed sowing depth (SD) (0.5 cm, 1 cm, and 2 cm) and flooding depth (FD) (saturated, 2 cm, and 5 cm) on crop establishment, early growth, and weed competitiveness in DSR using AG-tolerant genotypes (Khao Hlan On, Ma-Zhan Red, IR64+AG1, and IR64). , , and were used in the weedy treatment. Rice plants reached maximum emergence 9-13 days later under flooding compared with saturated conditions. Crop emergence decreased by 12-22% at 0.5 and 1 cm SD and by 48-60% at 2 cm SD, when combined with 2 or 5 cm FD compared with saturated conditions. The 2 cm SD reduced seedling emergence by 23-42% in Khao Hlan On and Ma-Zhan Red, by 62-70% in IR64+AG1, and by 90-92% in IR64 under flooding. Initial growth in rice plant height was slow under flooding but increased progressively after the seedlings emerged from water and the final height was not affected by FD. Leaf area, total shoot biomass, tiller density, and leaf number per pot of rice were higher at 1 cm SD (< 0.05), but decreased drastically at 2 cm SD under flooding. The emergence of and decreased by 53-65% and 89-95%, respectively, but increased by 49-68% in under 2 and 5 cm FD, respectively, compared with saturated conditions. The shoot biomass of the weeds followed the same trend. Khao Hlan On showed the highest weed-competitive ability under all FD while the biomass of IR64+AG1 and IR64 decreased by 10-14% due to weed competition under 2 cm FD. The 1 cm SD showed better growth for all genotypes under different FD. The 2 cm FD is sufficient to have a significant control of problematic weed species. The tolerance of AG of rice genotypes should be further enhanced to increase their weed-competitive ability.
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http://dx.doi.org/10.3389/fpls.2018.01654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265439PMC
November 2018

Identification of QTLs for yield and agronomic traits in rice under stagnant flooding conditions.

Rice (N Y) 2017 Dec 20;10(1):15. Epub 2017 Apr 20.

Present address: Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.

Background: Stagnant flooding, where water of 25-50 cm remains until harvest time, is a major problem in rainfed lowland areas. Most of the Sub1 varieties, which can withstand around 2 weeks of complete submergence, perform poorly in these conditions. Hence, varieties tolerant of stagnant flooding are essential.

Results: This paper presents the first study to map QTLs associated with tolerance to stagnant flooding, along with a parallel study under normal irrigation, using an F mapping population consisting of 148 RILs derived from a cross of Ciherang-Sub1 and the stagnant-flooding tolerant line IR10F365. Phenotypic data was collected for 15 key traits under both environments. Additionally, survival rate was measured under stress conditions. Genotyping was performed using the Illumina Infinium genotyping platform with a 6 K SNP chip, resulting in 469 polymorphic SNPs. Under stress and irrigated conditions, 38 and 46 QTLs were identified, respectively. Clusters of QTLs were detected in both stress and normal conditions, especially on chromosomes 3 and 5.

Conclusions: Unique and common QTLs were identified and their physiological consequences are discussed. These beneficial QTLs can be used as targets for molecular breeding and can be further investigated to understand the underlying molecular mechanisms involved in stagnant flooding tolerance in rice.
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http://dx.doi.org/10.1186/s12284-017-0154-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398972PMC
December 2017

Genetics, Physiological Mechanisms and Breeding of Flood-Tolerant Rice (Oryza sativa L.).

Plant Cell Physiol 2017 02;58(2):185-197

National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.

Flooding of rice fields is a serious problem in the river basins of South and South-East Asia where about 15 Mha of lowland rice cultivation is regularly affected. Flooding creates hypoxic conditions resulting in poor germination and seedling establishment. Flash flooding, where rice plants are completely submerged for 10-15 d during their vegetative stage, causes huge losses. Water stagnation for weeks to months also leads to substantial yield losses when large parts of rice aerial tissues are inundated. The low-yielding traditional varieties and landraces of rice adapted to these flooding conditions have been replaced by flood-sensitive high-yielding rice varieties. The 'FR13A' rice variety and the Submergence 1A (SUB1A) gene were identified for flash flooding and subsequently introgressed to high-yielding rice varieties. The challenge is to find superior alleles of the SUB1A gene, or even new genes that may confer greater tolerance to submergence. Similarly, genes have been identified in tolerant landraces of rice for their ability to survive by rapid stem elongation (SNORKEL1 and SNORKEL2) during deep-water flooding, and for anaerobic germination ability (TPP7). Research on rice genotypes and novel genes that are tolerant to prolonged water stagnation is in progress. These studies will greatly assist in devising more efficient and precise molecular breeding strategies for developing climate-resilient high-yielding rice varieties for flood-prone regions. Here we review the state of our knowledge of flooding tolerance in rice and its application in varietal improvement.
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http://dx.doi.org/10.1093/pcp/pcw206DOI Listing
February 2017

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments.

Plant Cell 2016 10 21;28(10):2365-2384. Epub 2016 Sep 21.

Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 11225

Environmental gene regulatory influence networks (EGRINs) coordinate the timing and rate of gene expression in response to environmental signals. EGRINs encompass many layers of regulation, which culminate in changes in accumulated transcript levels. Here, we inferred EGRINs for the response of five tropical Asian rice (Oryza sativa) cultivars to high temperatures, water deficit, and agricultural field conditions by systematically integrating time-series transcriptome data, patterns of nucleosome-free chromatin, and the occurrence of known cis-regulatory elements. First, we identified 5447 putative target genes for 445 transcription factors (TFs) by connecting TFs with genes harboring known cis-regulatory motifs in nucleosome-free regions proximal to their transcriptional start sites. We then used network component analysis to estimate the regulatory activity for each TF based on the expression of its putative target genes. Finally, we inferred an EGRIN using the estimated transcription factor activity (TFA) as the regulator. The EGRINs include regulatory interactions between 4052 target genes regulated by 113 TFs. We resolved distinct regulatory roles for members of the heat shock factor family, including a putative regulatory connection between abiotic stress and the circadian clock. TFA estimation using network component analysis is an effective way of incorporating multiple genome-scale measurements into network inference.
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http://dx.doi.org/10.1105/tpc.16.00158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134975PMC
October 2016

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions.

Elife 2015 Nov 26;4. Epub 2015 Nov 26.

Department of Biology, New York University, New York, United States.

Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for broad-based predictive modeling of plant gene expression in the field.
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http://dx.doi.org/10.7554/eLife.08411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718725PMC
November 2015

A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice.

Nat Plants 2015 Aug 24;1:15124. Epub 2015 Aug 24.

International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.

Global socioeconomic developments create strong incentives for farmers to shift from transplanted to direct-seeded rice (DSR) as a means of intensification and economization(1). Rice production must increase to ensure food security(2) and the bulk of this increase will have to be achieved through intensification of cultivation, because expansion of cultivated areas is reaching sustainable limits(3). Anaerobic germination tolerance, which enables uniform germination and seedling establishment under submergence(4), is a key trait for the development of tropical DSR varieties(5,6). Here, we identify a trehalose-6-phosphate phosphatase gene, OsTPP7, as the genetic determinant in qAG-9-2, a major quantitative trait locus (QTL) for anaerobic germination tolerance(7). OsTPP7 is involved in trehalose-6-phosphate (T6P) metabolism, central to an energy sensor that determines anabolism or catabolism depending on local sucrose availability(8,9). OsTPP7 activity may increase sink strength in proliferating heterotrophic tissues by indicating low sugar availability through increased T6P turnover, thus enhancing starch mobilization to drive growth kinetics of the germinating embryo and elongating coleoptile, which consequently enhances anaerobic germination tolerance.
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http://dx.doi.org/10.1038/nplants.2015.124DOI Listing
August 2015

Physiological analyses of traits associated with tolerance of long-term partial submergence in rice.

AoB Plants 2014 Sep 30;6. Epub 2014 Sep 30.

International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

Floods are major constraints to crop production worldwide. In low-lying, flood-prone areas of the tropics, longer-term partial submergence (stagnant flooding [SF]) greatly reduces rice yield. This study assesses shoot growth and several physiological mechanisms associated with SF tolerance in rice. Five rice genotypes with contrasting responses to SF were evaluated in field ponds. Following transplanting, floodwater was gradually increased at a rate of ∼2 cm day(-1) to reach a final depth of 50 cm and then maintained until maturity. Although plants were not fully submerged, the yield was reduced by 47 % across genotypes compared with those grown under control conditions (6.1 vs. 3.3 t ha(-1)). This reduction was mainly attributed to the reduction in biomass caused by reduced light interception and leaf growth above the water. Stagnant flooding also reduced panicle number per unit area by 52 % because of reduced tillering. Shoot elongation rate kept pace with rising floodwater and correlated positively with leaf growth and biomass production. Conversely, stem non-structural carbohydrate (NSC) concentration correlated negatively with shoot elongation rate, suggesting that fast-elongating genotypes actively consume NSCs to avoid complete submergence. Moderate shoot elongation rate strongly and positively correlated with grain yield under SF; however, elongation at rates >2.0 cm day(-1) was associated with reduced harvest index due to a smaller panicle size and increased lodging. Tolerant varieties were found to be either inherently tall or elongate moderately with rising floodwater. Our studies suggest that to improve tolerance of SF an appropriate phenotype should combine both of these traits. Fine-tuning for optimum shoot elongation with rising floodwater is, therefore, a priority for future work.
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http://dx.doi.org/10.1093/aobpla/plu058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216431PMC
September 2014

QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red.

Theor Appl Genet 2013 May 16;126(5):1357-66. Epub 2013 Feb 16.

International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.

Wide adoption of direct-seeded rice practices has been hindered by poorly leveled fields, heavy rainfall and poor drainage, which cause accumulation of water in the fields shortly after sowing, leading to poor crop establishment. This is due to the inability of most rice varieties to germinate and reach the water surface under complete submergence. Hence, tolerance of anaerobic conditions during germination is an essential trait for direct-seeded rice cultivation in both rainfed and irrigated ecosystems. A QTL study was conducted to unravel the genetic basis of tolerance of anaerobic conditions during germination using a population derived from a cross between IR42, a susceptible variety, and Ma-Zhan Red, a tolerant landrace from China. Phenotypic data was collected based on the survival rates of the seedlings at 21 days after sowing of dry seeds under 10 cm of water. QTL analysis of the mapping population consisting of 175 F2:3 families genotyped with 118 SSR markers identified six significant QTLs on chromosomes 2, 5, 6, and 7, and in all cases the tolerant alleles were contributed by Ma-Zhan Red. The largest QTL on chromosome 7, having a LOD score of 14.5 and an R (2) of 31.7 %, was confirmed using a BC2F3 population. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to rapidly develop varieties with improved tolerance to anaerobic condition during germination. Ultimately, this trait can be combined with other abiotic stress tolerance QTLs to provide resilient varieties for direct-seeded systems.
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http://dx.doi.org/10.1007/s00122-013-2057-1DOI Listing
May 2013

Comparison of phenotypic versus marker-assisted background selection for the SUB1 QTL during backcrossing in rice.

Breed Sci 2012 Sep 1;62(3):216-22. Epub 2012 Nov 1.

Bangladesh Rice Research Institute , Gazipur-1701, Bangladesh.

Marker assisted backcrossing has been used effectively to transfer the submergence tolerance gene SUB1 into popular rice varieties, but the approach can be costly. The selection strategy comprising foreground marker and phenotypic selection was investigated as an alternative. The non-significant correlation coefficients between ranking of phenotypic selection and ranking of background marker selection in BC(2)F(1), BC(3)F(1) and BC(3)F(2) generations indicated inefficiency of phenotypic selection compared to marker-assisted background selection with respect to recovery of the recipient genome. In addition, the introgression size of the chromosome fragment containing SUB1 was approximately 17 Mb, showing the effects of linkage drag. The significant correlation coefficient between rankings of phenotypic selection with the percentage of recipient alleles in the BC(1)F(1) generation suggested that background selection could be avoided in this generation to minimize the genotyping cost. The phenotypically selected best plant of the BC(3)F(1) generation was selfed and backcross recombinant lines were selected in the resulting BC(3)F(4) generation. The selection strategy could be appropriate for the introgression of SUB1 QTL in countries that lack access to high-throughput genotyping facilities.
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http://dx.doi.org/10.1270/jsbbs.62.216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501938PMC
September 2012

Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru.

Theor Appl Genet 2012 Mar 15;124(5):867-74. Epub 2011 Nov 15.

International Rice Research Institute, Metro Manila, Philippines.

Short-term submergence is a recurring problem in many rice production areas. The SUB1 gene, derived from the tolerant variety FR13A, has been transferred to a number of widely grown varieties, allowing them to withstand complete submergence for up to 2 weeks. However, in areas where longer-term submergence occurs, improved varieties having higher tolerance levels are needed. To search for novel quantitative trait loci (QTLs) from other donors, an F(2:3) population between IR72 and Madabaru, both moderately tolerant varieties, was investigated. After a repeated phenotyping of 466 families under submergence stress, a subset of 80 families selected from the two extreme phenotypic tails was used for the QTL analysis. Phenotypic data showed transgressive segregation, with several families having an even higher survival rate than the FR13A-derived tolerant check (IR40931). Four QTLs were identified on chromosomes 1, 2, 9, and 12; the largest QTL on chromosome 1 had a LOD score of 11.2 and R (2) of 52.3%. A QTL mapping to the SUB1 region on chromosome 9, with a LOD score of 3.6 and R (2) of 18.6%, had the tolerant allele from Madabaru, while the other three QTLs had tolerant alleles from IR72. The identification of three non-SUB1 QTLs from IR72 suggests that an alternative pathway may be present in this variety that is independent of the ethylene-dependent pathway mediated by the SUB1A gene. These novel QTLs can be combined with SUB1 using marker assisted backcrossing in an effort to enhance the level of submergence tolerance for flood-prone areas.
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http://dx.doi.org/10.1007/s00122-011-1751-0DOI Listing
March 2012

Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A.

Theor Appl Genet 2010 Nov 22;121(8):1441-53. Epub 2010 Jul 22.

Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.

The major rice quantitative-trait locus Submergence 1 (Sub1) confers tolerance of submergence for about 2 weeks. To identify novel sources of tolerance, we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C, two of the three transcription-factor genes within the Sub1 locus. The objective was to identify tolerant genotypes without the SUB1A gene or with the intolerant SUB1A-2 allele. The survey revealed that all tolerant genotypes possessed the tolerant Sub1 haplotype (SUB1A-1/SUB1C-1), whereas all accessions without the SUB1A gene were intolerant. Only the variety James Wee with the SUB1A-2 allele was moderately tolerant. However, some intolerant genotypes with the SUB1A-1 allele were identified and RT-PCR analyses were conducted to compare gene expression in tolerant and intolerant accessions. Initial analyses of leaf samples failed to reveal a clear association of SUB1A transcript abundance and tolerance. Temporal and spatial gene expression analyses subsequently showed that SUB1A expression in nodes and internodes associated best with tolerance across representative genotypes. In James Wee, transcript abundance was high in all tissues, suggesting that some level of tolerance might be conferred by high expression of the SUB1A-2 allele. To further assess tissue-specific expression, we have expressed the GUS reporter gene under the control of the SUB1A-1 promoter. The data revealed highly specific GUS expression at the base of the leaf sheath and in the leaf collar region. Specific expression in the growing part of rice leaves is well in agreement with the role of SUB1A in suppressing leaf elongation under submergence.
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http://dx.doi.org/10.1007/s00122-010-1400-zDOI Listing
November 2010

Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond.

Ann Bot 2009 Jan 30;103(2):151-60. Epub 2008 Oct 30.

International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.

Background And Aims: Submergence is a recurring problem in the rice-producing rainfed lowlands of south and south-east Asia. Developing rice cultivars with tolerance of submergence and with agronomic and quality traits acceptable to farmers is a feasible approach to address this problem. The objectives of this study were to (a) develop mega varieties with Sub1 introgression that are submergence tolerant, (b) assess the performance of Sub1 in different genetic backgrounds, (c) determine the roles of the Sub1A and Sub1C genes in conferring tolerance, and (d) assess the level of tolerance in F(1) hybrids heterozygous for the Sub1A-1-tolerant allele.

Methods: Tolerant varieties were developed by marker-assisted backcrossing through two or three backcrosses, and their performance was evaluated to determine the effect of Sub1 in different genetic backgrounds. The roles of Sub1A and Sub1C in conferring the tolerant phenotype were further investigated using recombinants identified within the Sub1 gene cluster based on survival and gene expression data.

Key Results: All mega varieties with Sub1 introgression had a significantly higher survival rate than the original parents. An intolerant Sub1C allele combined with the tolerant Sub1A-1 allele did not significantly reduce the level of tolerance, and the Sub1C-1 expression appeared to be independent of the Sub1A allele; however, even when Sub1C-1 expression is completely turned off in the presence of Sub1A-2, plants remained intolerant. Survival rates and Sub1A expression were significantly lower in heterozygotes compared with the homozygous tolerant parent.

Conclusions: Sub1 provided a substantial enhancement in the level of tolerance of all the sensitive mega varieties. Sub1A is confirmed as the primary contributor to tolerance, while Sub1C alleles do not seem important. Lack of dominance of Sub1 suggests that the Sub1A-1 allele should be carried by both parents for developing tolerant rice hybrids.
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http://dx.doi.org/10.1093/aob/mcn206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2707316PMC
January 2009

Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers.

Theor Appl Genet 2007 Feb 29;114(3):559-68. Epub 2006 Nov 29.

Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Jl. Tentara Pelajar 3A, Bogor, 16111, Indonesia.

The archipelago of Indonesia has a long history of rice production across a broad range of rice-growing environments resulting in a diverse array of local Indonesian rice varieties. Although some have been incorporated into modern breeding programs, the vast majority of these landraces remain untapped. To better understand this rich source of genetic diversity we have characterized 330 rice accessions, including 246 Indonesian landraces and 63 Indonesian improved cultivars, using 30 fluorescently-labeled microsatellite markers. The landraces were selected across 21 provinces and include representatives of the classical subpopulations of cere, bulu, and gundil rices. A total of 394 alleles were detected at the 30 simple sequence repeat loci, with an average number of 13 alleles per locus across all accessions, and an average polymorphism information content value of 0.66. Genetic diversity analysis characterized the Indonesian landraces as 68% indica and 32% tropical japonica, with an indica gene diversity of 0.53 and a tropical japonica gene diversity of 0.56, and a Fst of 0.38 between the two groups. All of the improved varieties sampled were indica, and had an average gene diversity of 0.46. A set of high quality Indonesian varieties, including Rojolele, formed a separate cluster within the tropical japonicas. This germplasm presents a valuable source of diversity for future breeding and association mapping efforts.
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http://dx.doi.org/10.1007/s00122-006-0457-1DOI Listing
February 2007

Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL.

Genetics 2006 Apr 1;172(4):2501-14. Epub 2006 Feb 1.

Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA.

A quantitative trait locus (QTL), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the Oryza sativa variety Jefferson and an accession of the wild rice relative Oryza rufipogon. A series of near-isogenic lines (NILs) containing different O. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. In contrast to the late-flowering O. rufipogon parent, O. rufipogon alleles in the substitution lines caused early flowering under both short- and long-day lengths and provided evidence for at least two distinct sub-QTL: dth1.1a and dth1.1b. Potential candidate genes underlying these sub-QTL include genes with sequence similarity to Arabidopsis GI, FT, SOC1, and EMF1, and Pharbitis nil PNZIP. Evidence from families with nontarget O. rufipogon introgressions in combination with dth1.1 alleles also detected an early flowering QTL on chromosome 4 and a late-flowering QTL on chromosome 6 and provided evidence for additional sub-QTL in the dth1.1 region. The availability of a series of near-isogenic lines with alleles introgressed from a wild relative of rice provides an opportunity to better understand the molecular basis of transgressive variation in a quantitative trait.
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http://dx.doi.org/10.1534/genetics.105.050500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456415PMC
April 2006