Tomato (Solanum lycopersicum) is a premier global crop, celebrated not only for its economic importance but also as a fundamental “well-being food” that provides essential vitamins, minerals, and potent antioxidants. This review highlights the transformative impact of CRISPR/Cas9 and next-generation precision tools, such as base and prime editing, on modern tomato breeding. Beyond functional genomics, we focus on the strategic engineering of tomato to maximize productivity through fruit size optimization and the biofortification of high-value metabolites (e.g., GABA, lycopene, and vitamins). Furthermore, we examine recent advances in developing multi-stress resilience against both biotic and abiotic challenges. A significant emphasis is placed on re-designing plant architecture and developmental traits to tailor tomato varieties for future agricultural systems, particularly indoor and vertical farming. By advanced delivery methods, CRISPR technologies offer unprecedented potential to accelerate the development of “smart” tomato, ensuring sustainable agriculture and global food security in a changing climate.

Mungbean is one of the prominent pulse crops in Indonesia since the mungbean seeds are highly nutritious and has become an important part of the diet for the community. The black-seeded mungbean highly nutritious as it contains high anthocyanin content. We have developed a black-seeded mungbean lines that need to be evaluated for drought tolerance. Drought tolerance is important as mungbean is usually cultivated during the drought-prone dry season that leads to total loss. This study aimed to (1) determine the effectiveness of drought tolerance indices to select drought tolerance in black-seeded mungbean, (2) reveal the drought indices most suitable to select drought-tolerant, high- yielding black-seeded mungbean lines. This study was conducted during dry season in the Field Laboratory of Universitas Nusa Cendana. A Split-Plot design was employed, consisting of irrigation frequencies as the main plot and mungbean genotype as the sub- plot treatments. The main plot consisted of three levels, i.e. irrigation every day (I₁), every four days (I₂), and every seven days (I₃), and the subplot consisted of 23 mungbean genotypes. Seed yields under non-stress and stress conditions were used to calculate the drought indices. The data were subjected to ANOVA, PCA and correlation analysis. There were significant variations in seed yields among genotypes under different drought indices. The indices MP, GMP, STI, HARM, MRP, SSI, YSI, MSTIK1, and MSTIK2 are suitable for selection of drought-tolerant, high-yielding mungbean lines. V9.HT, V10.HT, V11.HT, V16.HT, V18.HT, V19.HT, V20.HT, V22.HT were potential for further evaluation as promising drought tolerant, high yielding varieties.

Submergence damage to rice was reported as one of the major problems in rainfed lowland areas where the water remains. This study assessed the submergence tolerance of core collection during the seedling stage of the rice using dry seeds. Also, genome-wide association study (GWAS) combined with principal component analysis (PCA) and kinship matrix analysis was performed to identify quantitative trait loci (QTL) for submergence tolerance. Through this GWAS analysis, nine lead SNPs were confirmed to be associated with submergence tolerance, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Nine QTL were detected, on chromosomes 3 (qSUB3), 4 (qSUB4), 6 (qSUB6-1 and qSUB6-2), 11 (qSUB11-1, qSUB11-2 and qSUB11-3), and 12 (qSUB12-1 and qSUB12-2). Two candidate genes (Os03g0679300 and Os11g0517800) in the two QTL regions associated with submergence tolerance were detected. The results of this study provide associated SNPs in candidate genes for submergence condition and strategies for developing submergence condition in breeding programs.

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• Comprehensive Evaluation of Cold and Anaerobic Tolerance in Rice Oryza sativa L. and Screening of Multistress‐Resistant Germplasm
  Jianghui Yu, Shaoran Suo, Cheng Zheng, Ling Liu, Yunpeng Peng, Huang Zhou, Zhijun Wang, Huan Cao, Yongkang Liu, Xiwen Shi, Dingyang Yuan, Meijuan Duan
  Plant Breeding.2026; 145(3): 425.     CrossRef
• Identification of Candidate Genes for Hypoxia Tolerance in Rice by Genome-Wide Association Analysis and Transcriptome Sequencing
  Chenghang Tang, Di Bai, Xingmeng Wang, Guohui Dou, Jiaqi Lv, Yaling Bao, Nansheng Wang, Linjun Yu, You Zhou, Jinguo Zhang, Dezhuang Meng, Jun Zhu, Yingyao Shi
  Rice.2025;[Epub]     CrossRef
• Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1
  Md Ibrahim Khalil, Md Mahmudul Hassan, Swadesh Chandra Samanta, Abul Kashem Chowdhury, Md Zahid Hassan, Nasar Uddin Ahmed, Uzzal Somaddar, Sharmistha Ghosal, Arif Hasan Khan Robin, Ujjal Kumar Nath, Mohammad Golam Mostofa, David J. Burritt, Chien Van Ha,
  Plant Physiology and Biochemistry.2024; 206: 108224.     CrossRef
• Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)
  Sushma Naithani, Bijayalaxmi Mohanty, Justin Elser, Peter D’Eustachio, Pankaj Jaiswal
  Plants.2023; 12(11): 2146.     CrossRef

Cold stress is one of the serious abiotic stresses for stable rice production especially in high-latitude temperate region and high-altitude tropical area. Improving cold tolerance at seedling stage led stable seedling growth with yield stability. In this study, QTLs for cold tolerance at seedling stage were identified using the 96 introgression lines (ILs) derived from an inter-specific cross between Hwaseong (Oryza sativa) and Oryza rufipogon. Three QTLs were detected and the O. rufipogon alleles at two QTL (qCTS1 and qCTS12) improved cold tolerance in the Hwaseong genetic background whereas the O. rufipogon allele at qCTS10 on chromosome 10 decreased cold tolerance. Among these three QTLs, a major QTL qCTS12 explained 27.5% of phenotypic variation. Fine-mapping indicated that qCTS12 was different from those QTL reported in previous studies based on the map location suggesting that qCTS12 might be a new allele and is not associated with deleterious genes such fertility reduction. Among the 96 introgression lines, two lines, CR60 and CR61 were selected based on enhanced cold tolerance at seedling stage. qCTS12, therefore, provides a valuable allele for breeding rice with improved cold tolerance.

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• Stage-specific screening reveals differential resilience response to cold stress in rice
  Fahamida Akter, Partha S. Biswas, Abul Kalam Mohammad Aminul Islam, Mohammad Sharif Raihan, Md. Mizanur Rahman, Khandakar Md. Iftekharuddaula, Mohammad Rafiqul Islam, John Damien Platten, Md Ashrafuzzaman
  PLOS One.2026; 21(4): e0338290.     CrossRef
• Genome-wide Association Study for Cold Tolerance at Seedling Stage Using a Core Collection of Korean Rice
  Sa-Eun Park, Ngoc Ha Luong, Sang-Nag Ahn, Kyu-Chan Shim
  Journal of Agriculture & Life Science.2025; 59(2): 13.     CrossRef
• Identification of QTLs Related to Plant Growth at Low Temperatures in the Seedling Stage of Tongil Type Rice after Transplanting
  Seong-Gyu Jang, Ji-Yoon Lee, Ju-Won Kang, Youngho Kwon, So-Myeong Lee, Sais-Beul Lee, Jun-Hyeon Cho, Dong-Soo Park, Jong-Hee Lee, Soon-Wook Kwon, Sumin Jo
  Korean Journal of Breeding Science.2024; 56(3): 225.     CrossRef

Drought tolerance is derived from complex quantitative traits that are associated with different shoot and root morphological characters. This study assessed the genetic and phenotypic variation of 12 maize inbred lines and performed association analysis of 11 drought-related traits using 360 simple sequence repeats (SSRs), detecting 1,604 alleles, with an average of 4.4 alleles per locus. The average values of gene diversity (GD) and polymorphism information content (PIC) were 0.648 and 0.598, respectively. In principal component analysis (PCA), shoot fresh weight (SFW), shoot dry weight (SDW), stem weight (SW), leaf weight (LW), root fresh weight (RFW), root dry weight (RDW), and leaf area (LA) traits contributed greatly to the PCA. Association analysis was performed using a general linear model with a Q-matrix (Q GLM) and a mixed linear model with Q and K-matrices (Q + K MLM). Twelve SSR markers for drought tolerance trait were detected by Q GLM, and all maize inbred lines were clearly divided into two groups in accordance with their drought tolerance. Duplicated significant marker-trait associations (SMTAs) between Q GLM and Q + K MLM identified eight marker-trait associations involving four SSR markers that were associated with the traits of SW, SFW, RFW, and RDW with a significant level of P < 0.05. The umc1175 and umc2092 were associated with SW and SFW; umc1503 was associated with RFW, SFW, and SW; and umc2341 was associated with RDW. The detection of loci associated with drought-related traits in this study may provide better opportunities to improve maize drought tolerance by marker-assisted selection (MAS).

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• Using Flint Maize for Developing New Hybrids: A Case Study in Romania
  Roxana Elena Călugăr, Andrei Varga, Carmen Daniela Vana, Loredana Ancuța Ceclan, Felicia Chețan, Andras Fodor, Nicolae Tritean
  Agronomy.2025; 15(9): 2215.     CrossRef
• Leveraging Multiomics Insights and Exploiting Wild Relatives’ Potential for Drought and Heat Tolerance in Maize
  Shakra Jamil, Shakeel Ahmad, Rahil Shahzad, Noroza Umer, Shamsa Kanwal, Hafiz Mamoon Rehman, Iqrar Ahmad Rana, Rana Muhammad Atif
  Journal of Agricultural and Food Chemistry.2024; 72(29): 16048.     CrossRef
• Association Mapping for Evaluation of Population Structure, Genetic Diversity, and Physiochemical Traits in Drought-Stressed Maize Germplasm Using SSR Markers
  Muhammad Zahaib Ilyas, Hyeon Park, So Jung Jang, Jungeun Cho, Kyu Jin Sa, Ju Kyong Lee
  Plants.2023; 12(24): 4092.     CrossRef
• Uncovering microsatellite markers associated with agronomic traits of South Sudan landrace maize
  Emmanuel Andrea Mathiang, Hyeon Park, So Jung Jang, Jungeun Cho, Tae Hyeon Heo, Ju Kyong Lee
  Genes & Genomics.2023; 45(12): 1587.     CrossRef

Sorghum is the fifth most important grain crop worldwide. It is not only used as food and feed, but also as a resource for biofuel production. In addition, it has potential uses as a model plant for research on adaptation to environmental stress. In this study, mutant sorghum lines were generated by gammy ray irradiation. Ten of the M₆ sorghum mutant lines were selected from 28 mutant lines on the basis of agronomic characteristics. These 10 lines, along with their original accessions/cultivar, were evaluated to determine the germination rate and the shoot and root length under salt treatment. Compared with their original accessions, three mutant lines (B5, SY6, and SY7) showed significant differentiation under saline conditions (150 mM NaCl), with increased shoot length (by 1.3-2.2 times) and root length (by 1.5-2.5 times). We determined the transcript levels of 20 abiotic stress-responsive genes in B5 (the most salt-tolerant mutant) and its original accession. These genes included those encoding heat shock proteins, aquaporins, ROS scavenging system, and transcription factors. In the B5 mutant, 15 genes showed differences in transcript levels between the control and the salt treatment. Salt treatment resulted in significant up-regulation of Sb03g045840 and down-regulation of Sb3g030750 in the B5 mutant. Here, we reported a simple method to identify genes related to salt tolerance in a sorghum mutant.

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• Alteration of gene expression profiles in the mutant line of Sorghum bicolor
  Sehyun Choi, Ji-Su Seo, Joon-Woo Ahn, Soon-Jae Kwon, Donghyun Jeon, Changsoo Kim
  Journal of Crop Science and Biotechnology.2023; 26(5): 537.     CrossRef
• Deciphering the Genetic Mechanisms of Salt Tolerance in Sorghum bicolor L.: Key Genes and SNP Associations from Comparative Transcriptomic Analyses
  Donghyun Jeon, Jin-Baek Kim, Beum-Chang Kang, Changsoo Kim
  Plants.2023; 12(14): 2639.     CrossRef

Development of salt tolerance in rice through breeding program is mainly depends on the salinity responses of the potential rice germplasms. Coastal rice landraces of Bangladesh possess diverse morphological and physiological responses to salinity. Hence, our target is to identify candidate salt-tolerant coastal rice genotypes as a new source of salt tolerance (12 dS/m). Here, we annotated 20 Bangladeshi coastal Aus landrace rice regarding their phenotypic and genetic relatedness to salinity tolerance through multivariate analyses of five morpho-physiological traits namely, salt injury score (SIS), ion-leakage, chlorophyll concentration, root-shoot reduction percentage and profiling of DNA using simple sequence repeat (SSR). Based on the standard evaluation score (SES) the salt-induced coastal rice landraces were grouped into highly susceptible (HS), susceptible (S), moderately tolerant (MT), tolerant (T) and highly tolerant (HT). Besides, a canonical discrimination analysis of the mean trait values of five morpho-physiological parameters confirmed the above mentioned five categories of salinity tolerance. Based on all morpho-physiological parameters one genotype (Kalihytta) as highly tolerant (HT), two genotypes (Manikmuri and Monsur IRRI) as tolerant (T) and five genotypes (Nara, Iratom 27, Matichak, Abdul high IRRI and Parija) were identified as moderately tolerant (MT) against salinity. Finally, the molecular characterization using two SSR markers (RM493 and RM3412) revealed Kalihytta, Nara, Iratom 27, Parija, Lal jamaibabu and Fullbadam, as tolerant against salt stress. Our candidate salt tolerant Aus rice genotypes could be useful as novel sources of salt tolerance for thriving salt-tolerant high yielding varieties in the coastal ecosystem of Bangladesh.

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• Marker-assisted breeding accelerates the development of multiple-stress-tolerant rice genotypes adapted to wider environments
  Vignesh Mohanavel, Valarmathi Muthu, Rohit Kambale, Rakshana Palaniswamy, Prisca Seeli, Bharathi Ayyenar, Veeraranjani Rajagopalan, Sudha Manickam, Raghu Rajasekaran, Hifzur Rahman, Jagadeeshselvam Nallathambi, Manonmani Swaminathan, Gopalakrishnan Chella
  Frontiers in Plant Science.2024;[Epub]     CrossRef

Pumpkin (Cucurbita moschata) has been increasingly used as bloomless rootstock for cucumber (Cucumis sativus), but it is sensitive to low-temperature, which is the major bottleneck for winter cultivation. Hence, to develop low-temperature tolerant rootstock varieties, it is needed to identify tolerant germplasm from a wide range of genetic resources. For this, we developed a selection criterion for a quick assessment of low-temperature tolerance in pumpkin germplasms from different geographical origins. We considered various indexes for the fast evaluation of low-temperature tolerance, including seedling developmental stage, type of seedling (excised or non-excised), growth space, etc. Under the testing condition (17℃/7℃, 8 hours light/16 hours dark, 150 μmol m^-2s^-1 light intensity), we found a correlation (r=0.71*) in root growth between 3 weeks-cultured excised seedlings and 6 weeks-cultured non-excised seedlings. Therefore, we extrapolate that excised cotyledonary stage seedling treated for 3 weeks is sufficient to differentiate the tolerant germplasms. Using this screening method, we identified the “S81015” could prevail low-temperature stress. Further, we tested grafting compatibility and growth of grafted cucumbers under the low-temperature condition to assess the effect of rootstock and identify low-temperature tolerant and grafting-compatible rootstock germplasm. Upon grafting, we found a high correlation (r=0.97**) between the root fresh weight of 6 weeks-cultured non-excised seedlings and the shoot fresh weight of the grafted cucumbers. In summary, we could identify the low-temperature tolerant pumpkin germplasms by screening at the early developmental stage. Further, as a rootstock, the tolerant pumpkins also fortified the low-temperature tolerance of grafted cucumbers.

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• Identification of a Novel Candidate Gene for Chilling Tolerance in Pumpkin (Cucurbita moschata) Using Whole-Genome Resequencing
  Hemasundar Alavilli, Jeong-Jin Lee, Chae-Rin You, Sang-Choon Lee, Kihwan Song
  Journal of Plant Biology.2023; 66(4): 317.     CrossRef

Peanut (Arachis hypogaea L.) is an important oilseed, cash crop grown worldwide mainly in a tropical and subtropical climate. Drought stress (DS) is one of the serious abiotic stresses that alter the morphological, physiological, biochemical and molecular responses of plants and causes huge production loss across the globe. The aim of this study, to investigate the twenty widely grown Korean genotypes at the seedling stage under the control and drought stress conditions, to identify tolerant lines as well as related traits. In addition, the influence of DS and rehydration or recovery after stress on peanut genotypes was also studied. Initial screening showed that given genotypes had a differential response to DS, demonstrating a wide range of variation in tested peanut genotypes during the seedling stage towards the DS. Further, based on investigation of the different growth attributes and biochemical assessment six genotypes (Palkwang, Milkwang, and Daekwang) and (Daekwang, Haeol, and Heukhwaseang) were observed as drought-tolerant and drought-sensitive lines respectively. The findings of this study will aid in the selection of peanut genotypes in future breeding efforts aimed at improving drought tolerance and minimizing peanut production loss.

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• Mitigating the negative impact of irrigation water deficit in oat (Avena sativa L.) with glutamic acid foliar application
  M. M. Tawfik, Gehan A. Amin, Mervat S. Sadak, Gehan Sh. Bakhoum
  Vegetos.2026; 39(2): 534.     CrossRef
• Within-plant variability in pod maturity and preharvest sprouting in peanut (Arachis hypogaea L.): Physiological drivers, agronomic impacts, and integrated mitigation strategies
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  Oil Crop Science.2026; 11(1): 92.     CrossRef
• State-of-the-art AI-enabled mobile device for real-time water stress detection of field crops
  Narendra Singh Chandel, Subir Kumar Chakraborty, Abhilash K. Chandel, Kumkum Dubey, Subeesh A, Dilip Jat, Yogesh A. Rajwade
  Engineering Applications of Artificial Intelligence.2024; 131: 107863.     CrossRef
• Optimizing Peanut (Arachis hypogaea L.) Production: Genetic Insights, Climate Adaptation, and Efficient Management Practices: Systematic Review
  Yohannes Gelaye, Huaiyong Luo
  Plants.2024; 13(21): 2988.     CrossRef
• Phenotyping Peanut Drought Stress with Aerial Remote-Sensing and Crop Index Data
  Maria Balota, Sayantan Sarkar, Rebecca S. Bennett, Mark D. Burow
  Agriculture.2024; 14(4): 565.     CrossRef
• Induction of Tolerance in Groundnut Plants Against Drought Stress and Cercospora Leaf Spot Disease with Exogenous Application of Arginine and Sodium Nitroprusside Under Field Conditions
  Gehan Sh. Bakhoum, Mervat Sh. Sadak, Marian S. Thabet
  Journal of Soil Science and Plant Nutrition.2023; 23(4): 6612.     CrossRef

Six durum and twelve bread wheat genotypes were evaluated under favorable and drought-stressed field conditions, and screened with thirty simple sequence repeats (SSR) markers. The traits studied were stomata frequency (STF), relative water content (RWC), flag leaf area (FLA), flag leaf weight (FLW), flag leaf dry matter content (FLD), chlorophyll a content (Chl.a), chlorophyll b content (Chl.b), grain yield/plant (GYP) and 1000-kerenl weight (TKW). Highly significant differences were observed among wheat genotypes for all the traits, indicating considerable genetic variation. Moderate to high broad-sense heritability estimates were observed for the studied traits. Under drought stress, GYP was positively correlated with RWC, FLA, FLW and TKW, whereas negatively correlated with STF. G3 (Svevo) and G6 (WK-12-1) were the most drought-tolerant durum wheat, whereas G11 (L.S-15) and G16 (SIDS-1) were the most drought-tolerant bread wheat genotypes. SSR markers analysis indicated considerable genetic variation between and within durum and bread wheat genotypes. The percentage of polymorphism ranged from 14.3% (Xgwm174-5D) to 100% (Xgwm294-2A and Xgwm573-7B), with an average of 61.4%. The polymorphism information content (PIC) ranged from 0.20 (Xwmc596-7A) to 0.48 (Xgwm294-2A), with an average of 0.33.The highest polymorphism (77.1%) was observed in the B genome followed by A (57.8%) and D (50.0%) genomes. Cluster analysis based on phenotypic data distinguished the most drought-tolerant genotypes (G6 and G11) from the remaining genotypes. Cluster analysis based on SSR markers distinguished durum from bread wheat genotypes. The study indicated that phenotypic data and SSR markers were effective in assessing the genetic diversity in the studied genotypes.

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• Revealing Genetic Diversity and Drought Tolerance in Durum Wheat through Agro-Physiological and Molecular Approaches
  Ferhat Kızılgeçi, Aras Türkoğlu, Kamil Haliloğlu, Seval Eliş, Büşra Polat, Gaye Akçelik, Mehmet Yıldırım, Fatih Demirel, Jan Bocianowski
  Turkish Journal Of Field Crops.2026;[Epub]     CrossRef
• Gene markers generating polygenic resistance in wheat - Bipolaris sorokiniana interaction pathosystem
  Fatemeh Qalavand, Mehdi Nasr Esfahani, Davood Amin Azarm, Maryam Monazzah, Marzie Motamedi, Niloufar Abbasi, Arman Nasr Esfahani, Mojtaba Mohammadi
  South African Journal of Botany.2025; 185: 182.     CrossRef
• Molecular marker based analysis of allelic variation in the spring wheat genome
  Hafiz Ghulam Muhu Din Ahmed, Tao Yang, Muhammad Irfan Akram, Rashid Iqbal, Abdullah Ahmed Al-Ghamdi, Dunia A. Al Farraj
  Genetic Resources and Crop Evolution.2025; 72(5): 5393.     CrossRef
• Genetic diversity of some bread wheat genotypes under water stress using morphological traits and SSR markers
  S.E Abd.Salam, E.E. Hassn, A.A. Hassan, Mohamed Abdelghany
  South African Journal of Botany.2025; 178: 360.     CrossRef
• Genetic diversity analysis of Azerbaijani bread wheat (Triticum aestivum L.) genotypes with simple sequence repeat markers linked to drought tolerance
  Ruhangiz Mammadova, Zeynal Akparov, Ahmad Amri, Allah Bakhsh, Fida Alo, Shader Alizade, Nurlan Amrahov, Firuza Yunisova
  Genetic Resources and Crop Evolution.2025; 72(1): 315.     CrossRef
• Association mapping for Striga resistance and agronomic‐related traits in sorghum
  Wilbert T. Mutezo, Moosa M. Sedibe, Justice Norvienyeku, Bingting Lai
  The Plant Genome.2025;[Epub]     CrossRef
• Biochemical characteristics of bread wheat genotypes related to SSR markers in moisture stress conditions
  Fatemeh Bavandpouri, Ezatollah Farshadfar, Kianoosh Cheghamirza, Mohsen Farshadfar
  Genetic Resources.2025; 6(12): 171.     CrossRef
• Agronomic and Molecular Identification of Drought-Tolerant Bread Wheat Varieties in Iran
  Arezoo Karkhaneh, Hooman Salari, Kianoosh Cheghamirza, Leila Zarei
  Journal of Plant Growth Regulation.2025; 44(6): 3039.     CrossRef
• Multivariate Analysis Techniques and Tolerance Indices for Detecting Bread Wheat Genotypes of Drought Tolerance
  Ibrahim Al-Ashkar
  Diversity.2024; 16(8): 489.     CrossRef
• Combining Genetic and Phenotypic Analyses for Detecting Bread Wheat Genotypes of Drought Tolerance through Multivariate Analysis Techniques
  Mohammed Sallam, Abdelhalim Ghazy, Abdullah Al-Doss, Ibrahim Al-Ashkar
  Life.2024; 14(2): 183.     CrossRef
• Assessing Heat Stress Tolerance of Wheat Genotypes through Integrated Molecular and Physio-Biochemical Analyses
  Mohammed Sallam, Ibrahim Al-Ashkar, Abdullah Al-Doss, Khalid A. Al-Gaadi, Ahmed M. Zeyada, Abdelhalim Ghazy
  Agronomy.2024; 14(9): 1999.     CrossRef
• Assessment of genetic variation among wheat genotypes for drought tolerance utilizing microsatellite markers and morpho-physiological characteristics
  Sheikh Faruk Ahmed, Jalal Uddin Ahmed, Mehfuz Hasan, Mohammed Mohi-Ud-Din
  Heliyon.2023; 9(11): e21629.     CrossRef
• Molecular cytological analysis of alien introgressions in common wheat lines created by crossing of Triticum aestivum with T. dicoccoides and T. dicoccum
  О. A. Orlovskaya, I. N. Leonova, L. A. Solovey, N. I. Dubovets
  Vavilov Journal of Genetics and Breeding.2023; 27(6): 553.     CrossRef
• Research Advances in Diversity of Wheat Genetic Resources
  Do Yoon Hyun, Jae Yoon Kim
  Korean Journal of Breeding Science.2023; 55(4): 350.     CrossRef
• Assessment of Genetic Diversity of Bread Wheat Genotypes for Drought Tolerance Using Canopy Reflectance-Based Phenotyping and SSR Marker-Based Genotyping
  Mohammed Mohi-Ud-Din, Md. Alamgir Hossain, Md. Motiar Rohman, Md. Nesar Uddin, Md. Sabibul Haque, Eldessoky S. Dessoky, Mohammed Alqurashi, Salman Aloufi
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• Enzyme activity and population genetic structure analysis in wheat associated with resistance to Bipolaris sorokiniana-common root rot diseases
  Fatemeh Qalavand, Mehdi Nasr Esfahani, Jafar Vatandoost, Davood Amin Azarm
  Phytochemistry.2022; 200: 113208.     CrossRef

The anaerobic germination 1 (AG1) locus, which confers tolerance to the anaerobic germination of rice seed, has been previously identified and a gel-based InDel DNA marker developed for marker-assisted selection (MAS). However, there is a need for marker development for high-throughput genotyping in order to increase the breeding efficiency. Single nucleotide polymorphisms (SNPs)-based Kompetitive Allele Specific PCR (KASP) markers enable high-accuracy and high-throughput analyses for the genotyping of AG1 locus. In the present study, we developed one AG1 InDel-specific and four flanking KASP markers, which can be used as the foreground and recombination markers, respectively, for the AG1 locus. Of those, three KASP markers developed were validated with Dasan-AG1 (BC₃F₂) segregating lines; the AG1 InDel-specific KASP marker was 100% consistent with the existing AG1 gel-based marker, while the two flanking markers showed 70.3 and 66.7 percent consistency to the AG1 gel-based marker, respectively. In addition, the five KASP markers developed were further used to genotype 78 Korean and 95 foreign rice varieties. The genotyping results with 172 varieties revealed that most of the Korean varieties possessed the AG1 locus; however, a wide variation was observed in the foreign varieties for AG1 locus. Hence, the KASP markers developed for AG1 locus show promise as useful tools for expediting the breeding of varieties tolerant to anaerobic germination stress via high-throughput genotyping.

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• KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance
  Bhawna Dipta, Salej Sood, Vikas Mangal, Vinay Bhardwaj, Ajay Kumar Thakur, Vinod Kumar, Brajesh Singh
  Molecular Biology Reports.2024;[Epub]     CrossRef
• Development and Validation of Kompetitive Allele-Specific Polymerase Chain Reaction Markers for Seed Protein Content in Soybean
  Shuangzhe Li, Chenyijun Guo, Xuezhen Feng, Jing Wang, Wenjing Pan, Chang Xu, Siming Wei, Xue Han, Mingliang Yang, Qingshan Chen, Jinxing Wang, Limin Hu, Zhaoming Qi
  Plants.2024; 13(24): 3485.     CrossRef
• KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)
  Hamza Ashfaq, Reena Rani, Naila Perveen, Allah Ditta Babar, Umer Maqsood, Muhammad Asif, Katherine A. Steele, Muhammad Arif
  Euphytica.2023;[Epub]     CrossRef
• Development of SNP Marker Set to Select Varieties Tolerant to Multiple Abiotic Stresses in Rice
  Jung-Woo Lee, Jung-Seok Oh, Soo-Cheul Yoo
  Plant Breeding and Biotechnology.2023; 11(3): 208.     CrossRef
• Gene-Based Allele Specific Marker for Resistance to Phytophthora sojae in Soybean (Glycine max L.)
  Young Eun Jang, Sungwoo Lee
  Plant Breeding and Biotechnology.2021; 9(2): 164.     CrossRef

Salinity stress is one of the important abiotic stresses in crops. In this study, ten different concentrations of NaCl solutions were tested to determine the optimal level of NaCl concentration for salinity tolerance test at the germination stage in peanut, and 0.6% NaC1 was suitable for the test. A total of 249 peanut accessions were tested with 0.6% NaC1 and radical root lengths of the accessions were measured. The results showed that there were significant genetic variations on the tolerance to salinity stress among the tested accessions. Through a Genome-Wide Association Study (GWAS) using the Axiom_Arachis array with 58K SNPs, three putative SNPs with significant relation to radicle root length were identified on chromosomes Aradu.A03, Araip.B01, and Araip.B05.

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• Physiological and biochemical mechanisms underlying the role of anthocyanin in acquired tolerance to salt stress in peanut (Arachis hypogaea L.)
  Guanghui Li, Xin Guo, Yanbin Sun, Sunil S. Gangurde, Kun Zhang, Fubin Weng, Guanghao Wang, Huan Zhang, Aiqin Li, Xingjun Wang, Chuanzhi Zhao
  Frontiers in Plant Science.2024;[Epub]     CrossRef
• Designing future peanut: the power of genomics-assisted breeding
  Ali Raza, Hua Chen, Chong Zhang, Yuhui Zhuang, Yasir Sharif, Tiecheng Cai, Qiang Yang, Pooja Soni, Manish K. Pandey, Rajeev K. Varshney, Weijian Zhuang
  Theoretical and Applied Genetics.2024;[Epub]     CrossRef
• Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut
  Sunil S. Gangurde, Janila Pasupuleti, Sejal Parmar, Murali T. Variath, Deekshitha Bomireddy, Surendra S. Manohar, Rajeev K. Varshney, Prashant Singam, Baozhu Guo, Manish K. Pandey
  Frontiers in Genetics.2023;[Epub]     CrossRef
• Genome-wide association study as a powerful tool for dissecting competitive traits in legumes
  Pusarla Susmitha, Pawan Kumar, Pankaj Yadav, Smrutishree Sahoo, Gurleen Kaur, Manish K. Pandey, Varsha Singh, Te Ming Tseng, Sunil S. Gangurde
  Frontiers in Plant Science.2023;[Epub]     CrossRef

Salinity is a common and increasing problem in many coastal rice producing areas around the world. Salinity tolerance at the reproductive stage in rice is crucial as it determines grain yield. An F₂ mapping population was developed from two modern rice cultivars contrasting in tolerance: NSIC Rc222 (a high-yielding salt-sensitive variety released in the Philippines) and BRRI dhan 47 (a salt-tolerant variety released in Bangaldesh). The performance of the F₂ population showed transgressive segregation in the yield components under salinity stress of EC 10 dS/m under salinized field conditions. Ninety-six single nucleotide polymorphism (SNP) markers using 96-plex Fluidigm^TM genotyping were used to construct a linkage map of 1306.2 cM (Kosambi), with an average interval size of 13.6 cM. Seven putative quantitative trait loci (QTLs) for reproductive stage salinity tolerance traits having LOD values ranging from 2.9 to 4.1 were identified on chromosomes 1, 2, 5 and 11, explaining 13.4 to 18.4% of the phenotypic variation. Results of this mapping study identified a genomic region on chromosome 2 that confers salinity tolerance at the reproductive stage as measured by the number of filled spikelets, percent filled spikelets and yield. This study reports the molecular mapping of QTLs controlling reproductive-stage salinity tolerance-related traits, which will be useful in marker-assisted selection and breeding population development in rice.

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• Identification of QTLs for reproductive stage salinity tolerance in rice using a cross between CSR28 and BRRI dhan28
  Sejuti Mondal, Robert Vaughn, Endang M. Septiningsih, Rakesh K. Singh, Michael J. Thomson
  Crop Science.2025;[Epub]     CrossRef
• Meta-analysis of identified genomic regions and candidate genes underlying salinity tolerance in rice (Oryza sativa L.)
  Pratik Satasiya, Sanyam Patel, Ritesh Patel, Om Prakash Raigar, Kaushal Modha, Vipul Parekh, Haimil Joshi, Vipul Patel, Ankit Chaudhary, Deepak Sharma, Maulik Prajapati
  Scientific Reports.2024;[Epub]     CrossRef
• Evaluation of salinity tolerance of lowland rice genotypes (Oryza sativa L.) at the reproductive stage
  Rafaliarivony Safidimanjato, Lisy Tiana Ranarijaona Hery, Rasoafalimanana Mbolarinosy, Radanielina Tendro, Wissuwa Matthias
  African Journal of Agricultural Research.2023; 19(10): 945.     CrossRef
• Mapping and Identification a Salt-Tolerant QTL in a Salt-Resistant Rice Landrace, Haidao86
  Lixia Xie, Chongke Zheng, Wen Li, Menglin Pu, Guanhua Zhou, Wei Sun, Xiu Wu, Xiangyu Zhao, Xianzhi Xie
  Journal of Plant Growth Regulation.2022; 41(6): 2347.     CrossRef
• Mapping QTLs for Reproductive Stage Salinity Tolerance in Rice Using a Cross between Hasawi and BRRI dhan28
  Sejuti Mondal, Endang M. Septiningsih, Rakesh K. Singh, Michael J. Thomson
  International Journal of Molecular Sciences.2022; 23(19): 11376.     CrossRef
• Identification of Quantitative Trait Loci Related to Salt Tolerance of Indica Rice RIL Population in Different Growth Stages
  S. M. M. Razi, R. Shirzadian-Khorramabad, H. Sabouri, B. Rabiei, H. H. Moghadam
  Russian Journal of Genetics.2022; 58(9): 1091.     CrossRef
• Genetic Mapping to Detect Stringent QTLs Using 1k-RiCA SNP Genotyping Platform from the New Landrace Associated with Salt Tolerance at the Seedling Stage in Rice
  Sheikh Maniruzzaman, Mohammad Akhlasur Rahman, Mehfuz Hasan, Mohammad Golam Rasul, Abul Hossain Molla, Hasina Khatun, Salma Akter
  Plants.2022; 11(11): 1409.     CrossRef
• QTL MAPPING FOR SALT TOLERANCE AT REPRODUCTIVE STAGE IN RICE: A MINIREVIEW
  Nguyen Sao MAI, Yoshihiko HIRAI
  Journal of Environmental Science for Sustainable Society.2021; 10(Supplement): MR08_p31.     CrossRef
• Identification and Validation of QTLs for Yield and Yield Components under Long-Term Salt Stress Using IR64 CSSLs in the Genetic Background of Koshihikari and Their Backcross Progenies
  Nguyen Sao Mai, Dao Duy Hanh, Mai Nakashima, Kotaro Kumamoto, Nguyen Thi Thu Thuy, Tohru Kobata, Kuniyuki Saitoh, Yoshihiko Hirai
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• Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel
  Caijin Chen, Gareth J. Norton, Adam H. Price
  Frontiers in Plant Science.2020;[Epub]     CrossRef

Two consecutive cycles of selection were imposed on five F₂ populations of bread wheat. The first cycle was a divergent selection for spike length conducted in favorable environment (optimal sowing date) and the response was measured under favorable and heat stress conditions of a late sowing date. Positive responses to selection for longer spikes were obtained under favorable (13.43%) heat stress (8.66%) conditions, whereas the responses for shorter spikes were 2.24 and 5.02% in the two environments, respectively. The realized heritability of spike length was greater under favorable conditions (0.25–0.56) than under heat stress (0.18–0.41). Concurrent positive responses to selection for longer spikes were obtained in grain yield per spike under favorable (25.35%) and heat stress (13.65%) environments. Selection for greater number of grains per spike imposed on F₃ plants selected for spike length under heat stress resulted in significant responses (14.65%). Selection for greater number of grains per spike resulted in correlated responses in grain yield per spike (17.64%). The concurrent positive responses produced in spike length in F₄ with selection for number of grains per spike (averaged 9.20%) was almost equal to that produced by the direct selection in F₃ (8.66%), indicating that selection advance effected in F₃ has been maintained in F₄. High F₄/F₃ regression was obtained for spike length under heat stress (b = 0.85 ± 0.07), indicating high heritability. In conclusion, phenotypic selection for longer spikes under heat stress followed by a cycle of selection for number of grains per spike was capable of improving heat tolerance in wheat.

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• Analysis of Wheat Spike Morphological Traits by 2D Imaging
  Fujun Sun, Shusong Zheng, Zongyang Li, Qi Gao, Ni Jiang
  Plant Phenomics.2025; 7(3): 100096.     CrossRef
• Morpho-Colorimetric Diversity and Genome-Wide Association Study of Wheat Spike Architecture Based on Image Processing Under Well-Watered and Rain-Fed Conditions
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  Journal of Plant Growth Regulation.2025; 44(2): 850.     CrossRef
• Direct and Indirect Selection for Grain Yield and Grain Weight in Late Generations of Bread Wheat under Drought Stress and Normal Irrigation Environments
  Rasha E. Mahdy, Dikhnah Ashehri, Hanan Ali Alatawi, Hadba Al-Amrah, Ezzat E. Mahdy
  Plants.2022; 11(12): 1604.     CrossRef
• Effect of long-term heat stress on grain yield, pollen grain viability and germinability in bread wheat (Triticum aestivum L.) under field conditions
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• Evaluation of Triticum durum–Aegilops tauschii derived primary synthetics as potential sources of heat stress tolerance for wheat improvement
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  Plant Genetic Resources: Characterization and Utilization.2021; 19(1): 74.     CrossRef

The SUBMERGENCE 1 (SUB1) locus, conferring tolerance to complete inundation, was identified, and gel-based DNA markers, AEX1 and GnS2, were previously developed for marker-assisted breeding (MAB). However, a high throughput and high specific method, at low cost, is still required to detect Sub1 alleles. Kompetitive Allele Specific PCR (KASP) markers enable high throughput analysis for a large number of seeds, as well as detection of both alleles, in a single reaction. In this study, we developed KASP markers that can distinguish specific alleles at Sub1A loci based on single nucleotide polymorphisms (SNPs). Marker validations were carried out by genotyping of a segregating population with the developed KASP markers. The results from KASP assay and gel-based marker analysis were consistent for Sub1A alleles. KASP markers developed for Sub1A would be helpful due to high accuracy, low cost, and a high throughput genotyping feature in MAB.

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• Identification of KASP-SNP markers correlated with both growth and hypoxia tolerance traits in blunt snout bream (Megalobrama amblycephala)
  Yanluo Zhuo, Han Wang, Guanghai Dong, Huihu Wang, Guodong Zheng, Shuming Zou
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• Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1
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• Development of Kompetitive Allele Specific PCR Markers for Anaerobic Germination 1 Locus in Rice
  Jung-Woo Lee, Joong Hyoun Chin, Soo-Cheul Yoo
  Plant Breeding and Biotechnology.2021; 9(1): 20.     CrossRef

Temperatures that extend beyond normal levels of tolerance cause severe stress to plants, especially during the reproductive and grain filling/ripening stages. Heat stress leads to serious yield losses in many crop plants, including rice (Oryza sativa). In view of the current scenario of global climate change, frequent fluctuations and a significant increase in average temperatures will pose challenges to protecting those yields. Therefore, elucidating the molecular mechanisms that make crop plants more tolerant of heat, particularly in organs at the reproductive stage, is of utmost importance. Precise molecular information will be helpful for the manipulation and exploration of relevant genes for use in crop improvement programs. In this review, we highlight recent progress in research on the molecular responses to high temperatures in pollen and seed and provide a perspective on the development of heat tolerance in rice cultivars. The responsible mechanism is a very complex phenomenon that involves several biochemical and physiological changes, molecular responses, and a series of signal transductions. Improving our understanding requires detailed knowledge at various omics levels. Recent technological advancements have accelerated genomics, transcriptomics, and proteomics studies in rice, a model crop plant. Here, we discuss those technological and omics approaches being taken to investigate the heat tolerance mechanism, particularly in rice. In addition, we address the tools being used to identify key genes and QTLs that can then be utilized for molecular breeding and biotechnology.

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Pyropia tenera is an intertidal red alga of commercial significance owing to its popularity as a health-promoting seafood product. This alga grows in marine environments and is frequently exposed to high salinity and osmotic stress, which impact its growth. Therefore, the enhancement of stress tolerance in P. tenera is critical. In the present work, we aimed to elucidate the mechanisms underlying abiotic stress tolerance in this species; specifically, we identified the P. tenera S-adenosylmethionine synthetase-encoding gene (PtSAMS) and characterized its biological function. This gene, which is known to play a role in stress tolerance in other plants, was cloned and overexpressed in Escherichia coli under high-salinity conditions. The PtSAMS gene was found to encode a 385-amino-acid protein with a molecular weight of 41.8 kDa. In silico sequence alignment and phylogenetic analysis of the PtSAMS amino acid sequence showed that the encoded protein comprises three conserved domains and two motifs that are highly conserved in other plants. Growth assay results indicated that PtSAMS-overexpressing E. coli cells exhibit enhanced tolerance to salt stress. The results suggest that PtSAMS expression is induced by a combination of ion toxicity and osmotic stress resulting from exposure to high salinity in marine environments, and that this gene is expressed at housekeeping levels owing to growth in such conditions. The findings suggest that PtSAMS could be used as a potentially valuable bioresource with utility in the genetic engineering of salt stress-tolerant crop plants.

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• Gibberellin mediates spermidine-induced salt tolerance and the expression of GT-3b in cucumber
  Yu Wang, Xiaowen Gong, Weikang Liu, Lei Kong, Xinyu Si, Shirong Guo, Jin Sun
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Maize (Zea mays L.) is a crop in a tropical region which resists growing under sensitive temperature. This study was conducted to evaluate the performance of Canadian maize inbred lines under controlled cold stress conditions (5°C, 10°C, and 23°C). Data were recorded by measuring germination rate, index, root length, and seed vigour index values. Five higher and three lower tolerant inbred lines were shortlisted. The data were analyzed using analysis of variance, while mean values were compared using Tukey’s Honest Significant Difference Test at α=0.05 and at α=0.01. Using Genstat software, correlation was done. A strong correlation (P<0.05) was found between germination rate and germination index under all stress conditions. Root length and vigour index were also strongly correlated with germination rate under 5°C stress condition and compared to 10°C and 23°C stress conditions. Our results suggested that five (CO439, CO438, CO450, CO435, and CO445) among 22 maize inbred lines performed better under 5°C cold stress condition and thus had the potential to develop maize hybrids to increase grain yield under environmentally stressful conditions in South Korea.

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• The Effect of Plasma-Activated Water on Zea mays L. Landraces Under Abiotic Stress
  Paula-Maria Galan, Silvia Strajeru, Danela Murariu, Catalin-Ioan Enea, Denisa-Elena Petrescu, Alina-Carmen Tanasa, Dumitru-Dorel Blaga, Livia-Ioana Leti
  Agriculture.2025; 15(19): 2037.     CrossRef
• Low temperature elicits differential biochemical and antioxidant responses in maize (Zea mays) genotypes with different susceptibility to low temperature stress
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• Genome-wide association mapping in maize: status and prospects
  Kumari Shikha, J. P. Shahi, M. T. Vinayan, P. H. Zaidi, A. K. Singh, B. Sinha
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A total of six markers RM3586 and RM160 on chromosome 3 and RM3735, RM3471, RM3687 and RM3536 on chromosome 4 were used to select promising lines in backcrossing populations for heat tolerance at flowering stage in rice. Fifty lines selected in BC₃F₂, BC₄F₁, and BC₄F₂ and parents were planted in 2013, and 2014 dry seasons at the CLRRI field under natural heat stress and greenhouse to evaluate heat tolerance at the reproductive period. Heat tolerance scoring under field condition was based on percentage of unfilled grains. All selected lines exhibited their homozygous alleles with two heat tolerance germplasm N22 or Dular in QTL loci. Twelve lines harboring homozygous alleles to QTL loci RM3586 on chromosome 3 and RM3735 on chromosome 4, respectively were selected and evaluated to agronomic traits and yield potential. Four lines BC4-1-10-1 from OM5930/N22//4 *OM5930, BC4-5-8 from OM5930/Dular//4*OM5930, BC4-5-9-4 from AS996/N22//4*AS996, and BC4-6-3 from AS996/Dular//4 *AS996, respectively were finally selected to would be for regional adaptable test in Central Coast of Vietnam under heat stress condition to release to rice farmers.

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• Decrypting molecular mechanism of heat stress tolerance in rice to tackle climate change challenges through recent approaches
  Neeraj Kumar, Seyed Mahdi Hosseiniyan Khatibi, Deepak Sharma, Faraz Azeem, Ganesh Kumar Koutu, Jauhar Ali
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• Rice Heat Tolerance Breeding: A Comprehensive Review and Forward Gaze
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The increased severity and frequency of flooding is causing greater yield reductions in most rice-growing areas. To address this, popular cultivars were improved through introgression of SUB1, an FR13A-derived QTL conferring submergence tolerance at the vegetative stage, using marker-assisted backcrossing (MABC). Ciherang-Sub1, one of these improved near isogenic lines (NILs), showed significantly higher tolerance compared to the original cultivar while retaining its desirable agronomic qualities. However, due to the current shift to direct seeding, seed germination may also be adversely affected by flooding; thus the addition of major QTLs which can confer anaerobic germination (AG) tolerance will be highly beneficial. The AG tolerance QTL, qAG-9-2, also referred to as AG1, derived from Khao Hlan On, a Myanmar landrace, has been introgressed into the elite cultivar IR64 to produce IR64-AG1. This research focused on the transfer of AG1 to Ciherang-Sub1 via MABC, using IR64-AG1, a closely-related donor. Introgression of AG1 and recovery of the Ciherang genome was done in two backcross generations followed by one generation of selfing. The use of a closely-related donor shortened the development period to two years which could have been further reduced if a larger BC₁F₁ population had been used. Phenotypic evaluation showed that introgression of AG1 significantly increased AG tolerance compared to Ciherang-Sub1, and that the newly developed Ciherang-Sub1+AG1 retained the submergence tolerance from SUB1. The approach is very promising for faster development of improved lines using closely-related cultivars or improved lines as donors for introducing key traits.

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Most eukaryotic organisms display specialized cellular and behavioral oscillations with a period of approximately 24 hours, which are called circadian rhythms. The biological clock generates a rhythm that conveys temporal information over a day. Through this system, most eukaryotic organisms appropriately respond to daily or seasonal environmental changes by regulating their physiology and development in a time-dependent manner, conferring the organism with an adaptive advantage. In plants, the endogenous timing system also controls many important physiological processes including flower opening, hormone synthesis, metabolic pathways and gene expression so that these sessile species may survive efficiently in changing environments. Temperature compensation (TC) is one of the defining features of the clock mechanism. Under this mechanism, the pace of the clock, or period, remains stable over a broad range of physiologically relevant temperatures, which is unlikely to happen in other biochemical reactions. Thus, this mechanism allows organisms to sustain their ordinary life in various thermal environments by providing an accurate measure of the passage of time, regardless of the ambient temperature. Considering the current global climate changes our planet is undergoing, understanding the fundamental mechanism underlying TC cannot be overemphasized. In this review, we discuss the molecular organization of the plant circadian clock and the concept of TC, as well as the significance of plant TC in conferring fitness under the current increasing thermal environments.

Drought is one of the most important abiotic factors affecting wheat production and development of tolerant genotypes is limited by the lack of effective selection criteria. A genetic analysis of drought tolerance indices at seedling stage (i.e. root length, shoot length, root/shoot ratio and seedling dry weight) was performed for a seven-parent half diallel cross of bread wheat (Triticum aestivum L.) in Egypt. The parents and their F₂ progenies were evaluated in the laboratory under osmotic stress induced by polyethylene glycol (PEG) with five treatments (i.e. 0, 5, 10, 15 and 20% PEG-6000). Grain yield per spike was also evaluated under drought stressed field conditions. The parent P₇ had maximum root and shoot lengths under stress conditions, highest root/shoot ratio under 20% PEG and higher grain yield per spike than the other parents suggesting that P₇ possessed stress tolerance genes. Grain yield/spike was significantly correlated with root length (r= 0.41, P<0.05) and seedling dry weight (r= 0.46, P<0.05) at 15% PEG. Both additive and non-additive gene effects were involved in the genetic control of all traits. Rather low to moderately narrow-sense heritability was obtained for root length (0.18 and 0.12) and shoot length (0.19 and 0.12) at 15 and 20% PEG, respectively; root/shoot ratio (0.15) and seedling dry weight (0.16) at 15% PEG. Moderate genetic advance was observed for root length (41.24%) and shoot length (29.96%) under stress conditions suggesting that selection could be practiced on both traits for improving drought tolerance in wheat breeding programs.

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A set of five Korean rice cultivars and seven drought-tolerant indica lines were screened under irrigated non-stress and drought-stressed conditions in the 2011 and 2012 dry seasons at IRRI, Philippines. The drought-stressed experiment received mild to moderate stress. Under drought stress, ‘IR86918-B-439-B’ had the highest grain yield among all tested lines and ‘Hanarembyeo’ had the highest grain yield among the five Korean rice cultivars. ‘IR86918-B-439-B’ also had the highest yield under irrigated non-stress conditions. The grain yield of ‘Hanareumbyeo’ was similar to ‘IR86918-B-439-B’ under non-stress conditions. SSR marker analysis was performed using 125 SSR markers for detection of polymorphic markers between the Korean rice cultivars and the drought-tolerant indica lines, and for genetic diversity analysis. Twelve polymorphic markers were identified in the region of three major drought QTLs (DTY1.1, DTY2.2, DTY3.1) in two of the Korean rice cultivars and three of the drought-tolerant lines. These polymorphic markers will be useful as foreground genotyping markers for drought-QTL introgression in Korean rice genetic backgrounds.

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Common wheat (Triticum aestivum L.) and durum wheat (T. turgidum L. subsp. Durum) are major staple food crops in the world. However, their production are limited by environmental stress such as drought. In order to evaluate wheat’s response to drought, a total of 77 common wheat and durum wheat consisted of 19 Korean common wheat, 30 Tunisian common wheat and 28 Tunisian durum wheat were used in this study. Drought stress was applied for 21 days by suspending water application starting at the third leaf-expansion stage, followed by watering for the recovery of wheat until harvesting. Phenotypic parameters such as plant height, leaf length, tiller number, chlorophyll content, days to flowering and dry weight were scored during and after the treatment. Drought tolerance trait index (DTTI) and drought tolerance index (DTI) were calculated and used as criteria for selection of drought tolerance. At the end of treatment, most of the parameters except tiller numbers significantly decreased. Even after re-watering, plant height, leaf length, and dry weight continuously decreased. However, leaf chlorophyll content, and days to flowering of both stressed and non-stressed plants showed no significant differences. A total of 17 drought tolerance related simple sequence repeats (SSR) markers were used to identify genetic distance between Korean and Tunisian cultivars and elucidate possible use of marker systems for drought resistance. The common wheat and durum wheat cultivars formed different clusters for drought tolerance (resistance, moderate resistance, susceptible) using the SSR data. The results obtained in this study could help to increase genetic resources and breeding program for drought tolerance.

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A total of 310 BC₂F₂ lines derived from the cross of OM5930/N22 were evaluated for heat stress at flowering. Genetic map was set up with 264 polymorphic SSRs to detect linkage to the target traits. The map covers 2,741.63 cM with an average interval of 10.55 cM between two marker loci. Markers associated with heat tolerance were located mostly on chromosomes 3, 4, 6, 8, 10 and 11. The proportion of phenotypic variation explained by each QTL ranged from 17.1% for RM160 to 36.2% for RM3586. Four QTLs were detected for filled grains per panicle on chromosome 4 at the interval of RM468 - RM7076 and RM241 - RM26212, explaining 13.1 and 31.0% of the total phenotypic variation, respectively. Two QTLs controling unfilled grain percentage was also detected at loci RM554 and RM3686 on chromosome 3 explaining 25.0 and 11.2% of the total phenotypic variance. One QTL was detected for 1,000-grain weight located at the locus RM103 on chromosome 6, explaining 30.6% of the total phenotypic variance. Also, a QTL at the locus RM5749 on chromosome 4 was identified which explained 10.8% of the total phenotypic variance of grain yield. A single QTL at the interval of RM3586- RM160 on chromosome 3 was detected in conformity with the QTL findings for heat tolerance in previous studies.

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A total of 23 elite rice cultivars from eight countries were evaluated for cold tolerance using two screening methods at Chuncheon Substation, National Institute of Crop Science (NICS), Republic of Korea. The rice cultivars Jinbu, Mustaqillik, and Avangard showed cold tolerance and high spikelet fertility (63–79%) in cold-water irrigation screening. Under greenhouse screening, five cultivars (Giza 177, Avangard, Mustaqillik, Jinbu, and Jungan) showed high cold tolerance and high spikelet fertility (71–81%). Simple sequence repeat (SSR) marker analysis of 21 genotypes revealed two major clusters, the japonica and indica groups, with a genetic similarity of 0.69. Out of 21 rice cultivars, only four (Giza 178 from Egypt, Attey and Zakha from Bhutan, and Millin from Australia) fell under the indica cluster. The cold-tolerant varieties Jinbu, Mustaqillik, and Avangard were clustered with the japonica group, which had genetic similarity of 0.83. These varieties are considered as potential germplasm that will help diversify the japonica gene pool for cold-tolerant rice breeding. A one-way linear analysis of variance identified a significant relationship between individual alleles and traits. Three SSR markers were significantly associated with spikelet fertility under cold-water irrigation on chromosomes 1, 2, and 7. Five SSR markers were associated with spikelet fertility under a cool-environment greenhouse on chromosomes 8, 9, 10, and 12. The SSR markers associated with cold tolerance may also be useful as selection markers in indica/japonica cross combinations to improve cold tolerance.

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Grape (Vitis spp.), which is an important economic fruit crop worldwide, is the fourth most common fruit produced in Korea. Low temperature is one of the most important environmental factors that affect the successful cultivation of grapes. To screen for specific expression of abiotic stress-related genes against cold treatment in ‘Campbell Early’ and ‘Muscat Bailey A’ grapevines, the expression of various defense-related genes was investigated by real-time PCR and semi-quantitative RT-PCR. Among 67 genes analyzed by real-time PCR and RT-PCR, 43 and 10 were found to be up-regulated, while 4 and 37 were down-regulated in low temperature treated ‘Campbell Early’ and ‘Muscat Baily A’ grapevines, respectively. Genes encoding cold induced protein (CIP), lipoxygenase (LOX), glutathione S-transferase (GST), polygalacturonase-inhibiting protein (PGIP), and cold acclimation specific protein (CAS15A) were up-regulated, while those encoding cinnamyl alcohol dehydrogenase 2 (CAD2) and cold acclimation protein (WCS120) were down-regulated by low temperature treatment in both ‘Campbell Early’ and ‘Muscat Bailey A’. These changes in gene expression showed that defense response-related genes for cold acclimation were induced and wheat cold-specific gene decreased in grapevines. Among tested genes, the transcript levels of CLP, cell wall protein (CW), TIP, TLP, and WRKY transcription factor 10 (WRKY10) increased considerably in response to low temperature in ‘Campbell Early’ grapevine. These findings suggest that differentially expressed genes could be utilized as candidates for useful genetic resources and molecular markers after additional confirmation in various grapevine cultivars treated with low temperature in breeding programs for grapes with cold-tolerance.

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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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