We conducted transcriptome profiling analysis of O. glaberrima root using RNA-Seq at the control (OCR) and 100 mM NaCl treatment (OTR) at two time points (6 and 24 hours after treatment) to detect genes induced by salt stress. RNA-Seq analysis generated 102,690,698 sequence reads representing 30,388 predicted transcripts including 6,189 unannotated in Rice Annotation Project database. A total of 539 and 424 of differentially expressed genes (DEGs) were detected between OCR_6hours vs OTR_6hours and between OCR_24hours vs OTR_24hours, respectively (P < 0.001, q < 0.05). Among these DEGs, 262 genes showed constant differential expression at both 6 hours and 24 hours, and these included a bHLH containing protein, WRKY transcription factor, serine/threonine kinase, R2R3 MYB protein, and amino acid transporters. Interestingly, an enhanced seedling salt tolerant introgression line IL55 from a cross between a salt sensitive indica cultivar “Milyang23” and O. glaberrima harbors one DEG, Os02g0787300 encoding a mitogen activated protein kinase kinase (MAPKK) on chromosome 2. Analysis of the salt tolerance of the F_2:3 lines from a cross between IL55 and Milyang23 indicated that the O. glaberrima segment on chromosome 2 containing the MAPKK gene was responsible for better shoot growth under salt stress at the seedling stage. The salt inducible genes will be evaluated in introgression lines (ILs) to understand whether the expression of these genes is associated with salt tolerance in ILs having the Milyang23 genetic background. Transcriptome sequence information in this study may be useful for developing DNA markers linked to salinity tolerance for MAS breeding.

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• Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages
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• Grain protein function prediction based on self-attention mechanism and bidirectional LSTM
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This study was initiated to identify quantitative trait loci (QTL) involved in root system development by measuring root length and weight of rice seedlings grown in hydroponic culture condition. Growth conditions for estimating the root elongation were set up to supply NH₄⁺ as a single nitrogen source. Four rice accessions and 40 introgression lines (ILs) derived from a cross between ‘Ilpumbyeo’, a temperate japonica variety, and ‘Moroberekan’, a tropical japonica accession, were used to detect QTL for two root traits of seedlings grown in 0, 250 and 500 μM NH₄⁺. Seven chromosomal regions were found to be involved in root elongation. The qRW6 QTL detected on the long-arm of chromosome 6 promoted root weight and the ‘Moroberekan’ allele at this QTL was associated with enhanced root weight at 250 μM NH₄⁺ concentration. The Moroberekan alleles were beneficial at all loci except for qRW4 at which the Ilpumbyeo allele increased root weight under 0, 250 and 500 μM NH₄⁺. A field trial was conducted for selected four ILs to know whether the introgressed Moroberekan segments harboring the beneficial QTL were associated with effects on other agronomic traits. No significant difference was detected between four ILs and Ilpumbyeo for days to heading and culm length. Two lines showed significant difference from Ilpumbyeo in spikelets per panicle and 1,000 grain weight, and the difference might be attributed to the Moroberekan segment on chromosome 6. Our QTL results indicate that the Moroberekan introgression on chromosome 6 flanked by RM162-RM3430 has the potential to enhance root traits and yield potential in the temperate japonica background.

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• Identification of shoot and root genomic regions in response to nitrogen deficiency tolerance in rice through the use of rice back cross recombinant inbred lines (BRILs)
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• Genome-wide association study and transcriptome analysis reveal new QTL and candidate genes for nitrogen‐deficiency tolerance in rice
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• Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach
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• Mapping of quantitative trait loci for root elongation in rice ( Oryza sativa L.) treated with various nitrogen sources and concentrations
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• Root Branching and Nutrient Efficiency: Status and Way Forward in Root and Tuber Crops
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• RDWN6XB, a major quantitative trait locus positively enhances root system architecture under nitrogen deficiency in rice
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  BMC Plant Biology.2019;[Epub]     CrossRef

Grain weight (GW) is one of the most important targets for grain yield in rice breeding. In previous studies, two quantitative trait loci (QTLs) for grain weight, tgw2 and gw8.1, were identified using progeny derived from crosses between the japonica cultivar Hwaseong and Oryza grandiglumis, and between Hwaseong and O. rufipogon (IRGC 105491), respectively. The wild alleles increased GW at two loci. An F₂ population (186 plants) was developed by crossing two near isogenic lines (NILs) harboring tgw2 and gw8.1 to test their interaction. Simple sequence repeat (SSR) markers tightly linked to the two QTLs were used to check the genotype of the F₂ population. Based on the genotype at the two loci, tgw2 and gw8.1, the F₂ plants were classified into 9 groups with a combination of three genotypes at each of the two loci. Two-way ANOVA revealed no interaction between the 2 QTLs in the F₂ population. The 1,000 grain weight (TGW) of homozygous plants with wild alleles at the two loci was significantly higher than that of plants with a single QTL in the F₂ and F₃ lines. These results indicate that two QTLs act additively, in distinct or complementary pathways, to control grain weight. Based on these results, it is desirable to pyramid the two QTLs into a single line, since the double-QTL line displayed further increase of TGW in the Hwaseong background.

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Although traditional rice varieties and wild rice species exhibit vast genetic diversity, the transfer of useful genes to modern varieties is often hampered by linkage drag. In this study, the previously identified blast resistance locus Pi45(t) from a cross between ‘Ilpumbyeo’ and ‘Moroberekan’ was linked to the spreading-type panicle caused by the SPR3 locus. Using InDel4 and RM17579 linked to the Pi45(t) and the SPR3, respectively, the distance between the two loci was estimated to be 6.9cM. This suggests a tight, yet incomplete linkage and provides the opportunity to utilize Pi45(t) in breeding programs without including SPR3. Two groups based on the genotype at the SPR3 locus were assembled; the CLosed Panicle (CLP) and SPReading panicle (SPR) groups, with lines which were homozygous for the Ilpumbyeo and Moroberekan alleles, respectively. A comparison between the traits of CLP and SPR groups revealed a decrease in 1000-grain weight and length and an increase in spikelets per panicle and secondary branches in the SPR group. This complicates selection against SPR3 as it is not clear whether these quantitative trait loci are linked to either SPR3 or Pi45(t). Re-evaluation of these traits using lines recombinant at the two loci would be necessary to clarify this issue.

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  Plant Science.2019; 288: 110211.     CrossRef

Low-temperature stress is an important factor controlling the growth and development of rice (Oryza sativa L.) in temperate region. In this study, a molecular linkage map consisting of 136 SSR markers was employed to identify QTL associated with cold tolerance at the seedling stage. 80 recombinant inbred lines (RILs) from an intersubspecific cross between Milyang23 (O. sativa ssp. Indica) and Hapcheonaengmi3, a japonica weedy rice and the parents were evaluated for leaf discoloration and SAPD value of seedlings. Rice plants were grown for 15 days in the low-temperature condition (13/20°C day/night) and the control condition (25/20°C day/night) in the growth chamber. The degree of leaf discoloration showed a highly significant correlation with the SPAD value in the low-temperature plot (r = −0.708, P < 0.0001). A total of four QTLs for SPAD were identified and the phenotypic variance explained by each QTL ranged from 5.4 to 16.0%. Two QTLs detected in the control condition were located on chromosomes 2 and 5, respectively. Two QTL on chromosomes 1 and 4 were detected at the low-temperature condition and Hapcheonaengmi3 alleles increased the SPAD values at these loci. Substitution mapping was conducted to delimit the position of qSPA-4 using introgression lines derived from the same cross. Results indicated that qSPA-4 was located in a 810-Kb region flanked by RM16333 and RM16368. The results indicated that Hapcheonaengmi3 contains QTL alleles that are likely to improve cold tolerance of Indica rice.

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