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
  Taikui Zhang, Weichen Huang, Lin Zhang, De-Zhu Li, Ji Qi, Hong Ma
  Nature Communications.2024;[Epub]     CrossRef
• Grain protein function prediction based on self-attention mechanism and bidirectional LSTM
  Jing Liu, Xinghua Tang, Xiao Guan
  Briefings in Bioinformatics.2023;[Epub]     CrossRef

Gelatinization temperature (GT) is an important component of eating and cooking quality (ECQ) of rice. While direct measurement of GT is cumbersome, the alkali spreading value (ASV) test is a robust method commonly used to rapidly identify different GT types. In this study, we employed a modified ASV assay to screen a population of chemically-induced rice (cv. Kitaake) mutants (n = 405). Two mutant families, KDS-1623B and KDS-1824B, with significantly lower ASV (higher GT type) than wild type Kitaake (low GT type) were isolated. A nonsynonymous homozygous mutation in the isoamylase-type starch debranching enzyme gene ISA1 was identified in KDS-1623B. The mutation (G2709T) is predicted to change a valine at position 354 to a leucine in the α-amylase catalytic domain of ISA1. This result is consistent with the shrunken endosperm exhibited by KDS-1623B grains and the replacement of starch with phytoglycogen in isa1 (sugary-1) mutants. The altered ASV trait in KDS-1824B appears to be controlled by a single recessive mutation; however, the causal genetic lesion remains to be determined. These mutants will be useful resources for elucidating the complex nature of starch metabolism and its influence on ECQ of rice.

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• Identification of a novel mutant allele of the LIKE EARLY STARVATION 1 gene in rice (Oryza sativa L.) using QTL-seq
  Kyu-Chan Shim, HyunJung Kim, Mi-Ra Yoon, Sung-Ho Na, Sa-Eun Park, Sang-Nag Ahn, Thomas H Tai, J Holland
  G3: Genes, Genomes, Genetics.2026;[Epub]     CrossRef
• Efficient identification of palatability-related genes using QTL mapping in rice breeding
  Yoon-Hee Jang, Jae-Ryoung Park, Eun-Gyeong Kim, Rahmatullah Jan, Saleem Asif, Muhammad Farooq, Dan-Dan Zhao, Kyung-Min Kim
  Molecular Breeding.2023;[Epub]     CrossRef

The
objective
of this study was to detect QTLs for rice seedling traits under normal water (control) and low water conditions (drought stress). Ninety-eight recombinant inbred lines (RILs) from a cross between closely-related japonica cultivars, M-203 and M-206 were grown under both low water and normal water conditions. QTLs for morphological traits were investigated at seedling stage using 5,164 single nucleotide polymorphisms via genotyping-by-sequencing. Twenty-three QTLs were associated with four seedling traits: shoot length (SL), root length (RL), shoot dry weight (SW) and root dry weight (RW), were detected and most QTLs were clustered on chromosome 1, 6, 7 and 11. Under normal water conditions, nine QTLs for seedling traits were detected and M-203 alleles increased all the values. The locations of most QTLs were consistent with genes that regulate or respond to auxin and gibberellin. For drought tolerance, fourteen QTLs were detected including seven for drought stress conditions and seven for relative performance (values from drought stress conditions/normal water conditions). Seven QTLs from drought stress conditions coincided with the loci of previously identified drought tolerance genes. Based on the shoot and root length under drought stress conditions, five lines exhibiting the highest values in common were selected as a drought tolerance group. Those lines exhibited better growth than the parents under drought stress conditions and had QTLs alleles for drought tolerance detected in this study. QTL information and selected lines may be used for improving seedling vigor and drought tolerance of rice in breeding programs.

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• Morpho-physiological and biochemical response of rice (Oryza sativa L.) to drought stress: A review
  Utsav Bhandari, Aakriti Gajurel, Bharat Khadka, Ishwor Thapa, Isha Chand, Dibya Bhatta, Anju Poudel, Meena Pandey, Suraj Shrestha, Jiban Shrestha
  Heliyon.2023; 9(3): e13744.     CrossRef
• Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions
  Bahman Khahani, Elahe Tavakol, Vahid Shariati, Laura Rossini
  Scientific Reports.2021;[Epub]     CrossRef

Aerial surfaces of terrestrial plants are protected from the uncontrolled loss of water and gas by the cuticle, a membrane of fatty acid polymers on the outer surface of epidermal cells. Composed of cutin and waxes, the cuticle protects against a wide range of external stresses and has an important role in plant development and reproduction. Plants with reduced cuticular waxes often exhibit glossy, bright green leaves, which in rice are only observed in the presence of water adhesion. In this study, a wet leaf/glossy (wlg) mutant KDS-2249D was subjected to targeted exon capture and sequencing to identify candidate mutations. A single nonsynonymous, homozygous mutation was found in the KDS-2249D mutant. The mutation (G1080A) is predicted to change a tryptophan at position 360 to a stop codon in the Glossy1-like-1/wax crystal-sparse leaf 2 gene. This mutation completely co-segregated with the wlg phenotype in an F₂ mapping population (n = 435) and the KDS-2249D mutant exhibited a 40–50% decrease in total wax and significant increase in membrane permeability. This mutant will be useful for studies examining the role of cuticle waxes in protecting rice plants from environmental stresses.

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• Identification of a novel mutant allele of the LIKE EARLY STARVATION 1 gene in rice (Oryza sativa L.) using QTL-seq
  Kyu-Chan Shim, HyunJung Kim, Mi-Ra Yoon, Sung-Ho Na, Sa-Eun Park, Sang-Nag Ahn, Thomas H Tai, J Holland
  G3: Genes, Genomes, Genetics.2026;[Epub]     CrossRef
• Comparative Genomic Analysis and Functional Identification of CER1 and CER3 Homologs in Rice Wax Synthesis
  Nesma E. E. Youssif, Bowen Yang, Haodong Huang, Mohamed Hamdy Amar, Mohamed Ezzat, Mohammad Belal, Sanaa A. M. Zaghlool, Huayan Zhao, Dong Fu, Shiyou Lü
  Biology.2026; 15(2): 166.     CrossRef
• Identification and bioinformatic characterization of rare variants of Rhododendron canescens architecture genes
  Lav K. Yadav, H. Dayton Wilde
  Euphytica.2022;[Epub]     CrossRef
• Identification of Rice Mutants with Altered Grain Alkali Digestion Trait
  HyunJung Kim, Ralph Vin B. Imatong, Thomas H. Tai
  Plant Breeding and Biotechnology.2020; 8(1): 19.     CrossRef
• Deciphering the Novel Role of AtMIN7 in Cuticle Formation and Defense against the Bacterial Pathogen Infection
  Zhenzhen Zhao, Xianpeng Yang, Shiyou Lü, Jiangbo Fan, Stephen Opiyo, Piao Yang, Jack Mangold, David Mackey, Ye Xia
  International Journal of Molecular Sciences.2020; 21(15): 5547.     CrossRef

Low temperature germinability (LTG) is an important trait for stand establishment in the direct-seeding method of rice cultivation. In temperate growing regions, water temperature during sowing season is frequently below 15°C resulting in poor crop establishment. The
objective
of this study was to select enhanced rice germplasm for low temperature germinability. Association of the phenotype for LTG with the genotype for qLTG3-1, a major QTL for LTG, in japonica rice accessions (n = 180) from East Asia was conducted. A highly significant association was observed between qLTG3-1 alleles and tolerant (χ² = 56.617, P = 5.08E-13) or sensitive (χ² = 32.844, P = 7.38E-08) accessions. Association of genotype and phenotype suggested the germplasm panel used in this study were closely associated with cold environment at the germination stage. Genotypic data from 32 SNP markers derived from previously reported LTG QTLs showed a mean polymorphism information content (PIC) of 0.248 and an average gene diversity of 0.307. A neighbor-joining tree clustered 23 tolerant accessions into one group and the genotypic data for four of the markers revealed that all of these accessions had the alternative allele for the qLTG3-1 and qLTG2-6 markers and the reference allele at the qLTG11-1 marker. Sensitive accessions clustered into one group and harbored the reference allele at the qLTG4-3 marker. Finally, ten accessions were selected after phenotypic and genotypic evaluation for LTG and these temperate japonica cultivars or breeding lines may contribute to the breeding of rice varieties for direct-seeding systems.

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• Morphological and molecular evaluation for germinability in rice varieties under low-temperature and anaerobic conditions
  Do Yoon Hyun, MyeongWon Oh, Yu-Mi Choi, Sukyeung Lee, Myung-Chul Lee, Sejong Oh
  Journal of Crop Science and Biotechnology.2017; 20(1): 21.     CrossRef