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"Mapping"

Research Articles

Genomic and Evolutionary Insights on Two Coix lacryma-jobi L. Varieties (kiboa and tapol) Using PLOP-FISH and Molecular Phylogenetics Based on ITS 1 and 4 Loci
Walter Clint E. Bayani, Reggie Y. Dela Cruz, Eliazar Alumbro Peniton, Joliesa Mae S. Toledo, Glenda Z. Doblas
Plant Breed. Biotech. 2026;14:76-87.
Published online April 13, 2026
DOI: https://doi.org/10.9787/PBB.2026.14.76

Coix lacryma-jobi L. is a cereal crop belonging to the Poaceae family, valued for its nutritional, medicinal, and ornamental uses. Among its varieties, two prominent landraces, C. lacryma-jobi var. kiboa and var. tapol, are cultivated for their distinct grain morphologies and favorable agronomic traits. However, despite its economic importance, detailed cytogenetic and molecular phylogenetic studies remain limited. This study presents a cytogenetic and molecular phylogenetic analysis of C. lacryma-jobi L. var. kiboa and tapol. Partial cytogenomic characterization on the 45S and 5S rDNA loci as well as Arabidopsis- type telomeric repeats using pre-labeled oligomer probes for fluorescence in situ hybridization (PLOP-FISH) technique confirmed a diploid chromosome number of 2n = 20 in both varieties. The 45S and 5S rDNA loci were localized on the nucleolar organizer region (NOR) of the short arm of chromosome 1 and the long arm of chromosome 4, respectively, indicating conserved chromosomal arrangements. Additionally, Arabidopsis-type telomeric repeats were detected at the terminal regions of all chromosomes. Chromosome sizes ranged from 2.98 ± 0.07 to 3.74 ± 0.11 μm in var. kiboa and from 3.42 ± 0.08 to 4.12 ± 0.05 μm in var. tapol. Phylogenetic analyses based on the internal transcribed spacer (ITS1 and ITS4) genes revealed a close genetic relationship between the two varieties, supporting their shared evolutionary lineage. These findings enhanced our understanding of adlay genetic diversity and provide foundational insights for plant breeding improvement, conservation strategies, and future genomic research.

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QTL Mapping for Heading Date and Yield-Related Traits in a Doubled Haploid Population Derived from Two Korean Wheat Cultivars
Sumin Hong, Kyeong-Min Kim, Changhyun Choi, Seong-Woo Cho, Chul Soo Park, Youngjun Mo
Plant Breed. Biotech. 2023;11(3):197-207.   Published online September 1, 2023
DOI: https://doi.org/10.9787/PBB.2023.11.3.197

Understanding the genetics underlying heading date and yield-related traits is essential in wheat breeding for maximizing productivity under different environments. Using doubled haploid lines derived from two Korean wheat cultivars, we identified seven stable quantitative trait loci (QTLs) for yield-related traits, i.e., days to heading date (QDhd.jbnu-3B, QDhd.jbnu-6B, and QDhd.jbnu-7D), culm length (QCl.jbnu-6A), thousand kernel weight (QTkw.jbnu-6A), kernels per spike (QKps.jbnu-3B) and test weight (QTw.jbnu-1A). Compared to the lines carrying the allele for late heading, those carrying the allele for early heading at QDhd.jbnu-3B, QDhd.jbnu-6B, and QDhd.jbnu-7D headed 3.1, 2.0, and 1.7 days earlier, respectively. Interestingly, when the alleles for early heading at the three QTLs were accumulated, heading date was accelerated by approximately one week, indicating that these QTLs provide useful genetic resources to fine-tune heading date. However, as the alleles for early heading at all three QTLs were associated with decreased kernels per spike, caution is required when deploying them to minimize the negative impacts on yield. Our study provides useful information for developing wheat cultivars with optimal heading date and enhanced productivity.

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  • Variations in Major Agronomic Traits of Durum Wheat Germplasm Under Different Nitrogen Fertilization Levels
    Hosun Cheon, Sun-Hwa Kwak, Sieun Choi, Sukyeung Lee, Jinhee Park, Kyung-Min Kim, Chul Soo Park, Youngjun Mo
    Korean Journal of Breeding Science.2024; 56(3): 281.     CrossRef
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Fine-Mapping of a Major Quantitative Trait Locus q2ID1 for Rice Stem Diameter
Ye-Ji Lee, Yeisoo Yu, Hyeonso Ji, Gang-Sub Lee, Nam-In Hyung, Keunpyo Lee, Tae-Ho Kim
Plant Breed. Biotech. 2021;9(4):298-309.   Published online December 1, 2021
DOI: https://doi.org/10.9787/PBB.2021.9.4.298

Rice culm is an important trait for determining rice lodging yield, and stem diameter has been suggested as a yield-related trait; however, studies for the genetic basis of its phenotypic variation are still required. In this study, we used 160 recombination inbred lines derived from a cross of two different rice varieties [‘Milyang23’ (Tongil rice) and ‘Giho’ (japonica)] for quantitative trait locus (QTL) mapping with nine stem traits. The analysis showed that QTLs for the diameters of the first, second, third and fourth internode traits were independently separated in the top of chromosome 1, whereas four lengths of internodes were estimated as being related to the semidwarf1 (sd1) gene. A major-effect QTL (q2ID1) was identified that the overlapped region of our previous mapping with a large genomic region. Therefore, we performed high-resolution genetic mapping for fine-mapping of q2ID1 to a ~140 kb region between Ind1_1 and Ind1_2 of genetic markers, with candidate genes predicted using a reference genome. We ultimately identified nine of the 15 candidate genes with specific gene functions and analyzed the sequence variations between two parents. These results offer valuable gene and/or genetic information on stem diameter to improve lodging resistance and yield.

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  • Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice (Oryza sativa L.)
    Ognigamal Sowadan, Shanbin Xu, Yulong Li, Everlyne Mmbone Muleke, Hélder Manuel Sitoe, Xiaojing Dang, Jianhua Jiang, Hui Dong, Delin Hong
    Genes.2024; 15(1): 105.     CrossRef
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Review

The production of chili pepper (Capsicum annuum L.) is hindered by several biotic factors even though striding progresses were made in genetic improvement in the last two decades. Among the advancements were the fast-track genetic improvement of disease-resistant varieties by the use of marker-assisted selection (MAS) and the conventional breeding-based introgression of major resistance genes. Marker development, marker-based identification and fine mapping have revealed a large number of resistance genes, from which cloning of some candidate genes demonstrated the applicability and versatility of map-based cloning for disease resistance. In some of the recent fine mapping of disease resistance QTLs, closely linked DNA markers were identified, which in turn resulted in the rapid introgression of target gene(s) into breeding lines. Also, progresses were made on the characterization and map-based cloning of resistance genes conferring broad-spectrum resistance. As the number of identified and characterized resistance genes and the DNA markers linked to resistance genes are steadily generated, the development of multiple/durable resistance to major chili pepper diseases is accelerated by MAS. In the present review, the development of molecular markers, marker-based mapping of genes conferring resistance to ten major chili pepper diseases were discussed, focusing on the recent advancements in major and QTL-spanning resistance gene mapping. The review provides up-to-date insights into the development of DNA markers linked to disease resistance genes and the cloning of resistance genes, which are all so crucial in pepper breeding for disease resistance.

Citations

Citations to this article as recorded by  
  • Effects of a Coal-derived Soil Amendment on Plant Growth of Sweet Pepper (Capsicum annuum) and Rhizosphere Microbial Communities
    Xing-Feng Huang, Paul H. Fallgren, Kenneth F. Reardon, Song Jin
    Journal of Soil Science and Plant Nutrition.2026; 26(1): 2799.     CrossRef
  • Integrating Hybrid and Molecular Breeding as Approaches in Vegetable Breeding Strategies
    Janko Červenski, Srđan Zec, Gordana Tamindžić, Dragana Miljaković, Jelena Marinković, Boris Adamović, Đorđe Vojnović, Aleksandra Ilić
    Horticulturae.2026; 12(6): 666.     CrossRef
  • Molecular and genomic insights into viral resistance in Capsicum spp.: pathogenesis, defense mechanisms, and breeding innovations
    Jayabalan Shilpha, Won-Hee Kang
    Frontiers in Plant Science.2025;[Epub]     CrossRef
  • Fine mapping of the Chilli veinal mottle virus resistance 4 (cvr4) gene in pepper (Capsicum annuum L.)
    Joung-Ho Lee, Jung-Min Kim, Jin-Kyung Kwon, Byoung-Cheorl Kang
    Theoretical and Applied Genetics.2025;[Epub]     CrossRef
  • Wild-type and resistance-breaking strains of tomato spotted wilt virus differentially upregulate the immunosuppressive epoxyoctadecamonoenoic acid biosynthesis of its insect vector, Frankliniella occidentalis
    Niayesh Shahmohammadi, Falguni Khan, Donghee Lee, Daehong Lee, Yonggyun Kim
    Journal of General Virology .2025;[Epub]     CrossRef
  • Development of SNP Markers for ms3 Gene of Genetic Male Sterility in Pepper (Capsicum annuum L.)
    Soeun Lee, Bora Geum, Jundae Lee
    Korean Journal of Breeding Science.2025; 57(4): 391.     CrossRef
  • Cleaved Amplified Polymorphic Sequence Markers in Horticultural Crops: Current Status and Future Perspectives
    Krishnanand P. Kulkarni, Richmond K. Appiah, Umesh K. Reddy, Kalpalatha Melmaiee
    Agronomy.2024; 14(11): 2598.     CrossRef
  • The landscape of sequence variations between resistant and susceptible hot peppers to predict functional candidate genes against bacterial wilt disease
    Ji-Su Kwon, Junesung Lee, Jayabalan Shilpha, Hakgi Jang, Won-Hee Kang
    BMC Plant Biology.2024;[Epub]     CrossRef
  • Phenotypical and molecular characterization of new pepper genotypes resistant to Chili pepper mild mottle virus firstly detected in Europe and other tobamoviruses
    Mikel Ojinaga, Ana Aragones, Mónica Hernández, Santiago Larregla
    Scientia Horticulturae.2024; 330: 113074.     CrossRef
  • Assessment of elite pepper breeding lines using molecular markers
    Ercan Ekbiç, Ceylan Özlem Okay
    Plant Biotechnology Reports.2024; 18(4): 515.     CrossRef
  • Current knowledge and breeding strategies for management of aphid-transmitted viruses of pepper (Capsicum spp.) in Africa
    Herbaud P. F. Zohoungbogbo, Fabrice Vihou, Enoch G. Achigan-Dako, Derek W. Barchenger
    Frontiers in Plant Science.2024;[Epub]     CrossRef
  • Comparison of effectiveness of molecular markers linked to Me1 and N genes in pepper (Capsicum annuum L.) (Solanales: Solanaceae)
    Gülsüm Uysal, Zübeyir Devran
    Turkish Journal of Entomology.2024; 48(2): 239.     CrossRef
  • Pepper mild mottle virus: a formidable foe of capsicum production—a review
    Nidhi Kumari, Vivek Sharma, Priyankaben Patel, P. N. Sharma
    Frontiers in Virology.2023;[Epub]     CrossRef
  • Development and Application of a Cleaved Amplified Polymorphic Sequence Marker (Phyto) Linked to the Pc5.1 Locus Conferring Resistance to Phytophthora capsici in Pepper (Capsicum annuum L.)
    Giacomo Bongiorno, Annamaria Di Noia, Simona Ciancaleoni, Gianpiero Marconi, Vincenzo Cassibba, Emidio Albertini
    Plants.2023; 12(15): 2757.     CrossRef
  • QTL Mapping for Resistance to Bacterial Wilt Caused by Two Isolates of Ralstonia solanacearum in Chili Pepper (Capsicum annuum L.)
    Saeyoung Lee, Nidhi Chakma, Sunjeong Joung, Je Min Lee, Jundae Lee
    Plants.2022; 11(12): 1551.     CrossRef
  • A multiplex RT-PCR assay for detection of emergent pepper Tsw resistance-breaking variants of tomato spotted wilt virus in South Korea
    Sun-Jung Kwon, Young-Eun Cho, Hee-Seong Byun, Hae-Ryun Kwak, Jang-Kyun Seo
    Molecular and Cellular Probes.2022; 61: 101792.     CrossRef
  • Advances in S gene targeted genome-editing and its applicability to disease resistance breeding in selected Solanaceae crop plants
    Geleta Dugassa Barka, Jundae Lee
    Bioengineered.2022; 13(6): 14646.     CrossRef
  • Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)
    Dennis N. Lozada, Guillermo Nunez, Phillip Lujan, Srijana Dura, Danise Coon, Derek W. Barchenger, Soumaila Sanogo, Paul W. Bosland
    BMC Plant Biology.2021;[Epub]     CrossRef
  • Resistance-Breaking Tomato Spotted Wilt Virus Variant that Recently Occurred in Pepper in South Korea is a Genetic Reassortant
    Sun-Jung Kwon, Young-Eun Cho, Oh-Hun Kwon, Hyung-Gon Kang, Jang-Kyun Seo
    Plant Disease.2021; 105(10): 2771.     CrossRef
  • Identification of QTLs Controlling α-Glucosidase Inhibitory Activity in Pepper (Capsicum annuum L.) Leaf and Fruit Using Genotyping-by-Sequencing Analysis
    Doie Park, Geleta Dugassa Barka, Eun-Young Yang, Myeong-Cheoul Cho, Jae Bok Yoon, Jundae Lee
    Genes.2020; 11(10): 1116.     CrossRef
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Research Articles
Characterization and Genetic Mapping of White-Spotted Leaf (wspl) Mutant in Rice
Backki Kim, Hyerim Lee, Zhuo Jin, Dongryung Lee, Hee-Jong Koh
Plant Breed. Biotech. 2019;7(4):340-349.   Published online December 1, 2019
DOI: https://doi.org/10.9787/PBB.2019.7.4.340

Spotted leaf mutants which produce necrotic lesions spontaneously are important sources to study programmed cell death in plant defense responses. A novel white-spotted leaf (wspl) mutant was induced from Ilpum, Korean japonica rice cultivar by the treatment of ethyl methane sulfonate (EMS). The phenotype of wspl mutant differed from that of other spotted leaf mutants in that not only brown spots but also white lesion mimic spots were observed on the tip of the leaves from the vegetative stage. Strong nitro blue tetrazolium (NBT) and 3, 3ʹ-diaminobenzidine (DAB) staining were observed on the older leaf of wspl mutant in microscopic reactive oxygen species (ROS) assay, and the chlorophyll content of wspl mutant maintained longer than wild-type in the old leaves. Genetic analysis revealed that the wspl mutant trait was controlled by a single recessive gene and the locus of wspl gene was mapped on the long arm of chromosome 5 between the flanking markers S05100 and S05112 (4.1 Mb). Through the combination of the genetic mapping and SNP analysis, two candidate genes for white-spotted leaf were identified in the genic region. A novel phenotype of white-spotted leaf mutant has not yet been reported, thus further study of the wspl mutant will contribute to understanding of the molecular mechanisms involved in lesion mimic phenotype in rice.

Citations

Citations to this article as recorded by  
  • Next generation sequencing-based MutMap identifies genomic regions associated with strong culm in rice
    Pritam Kanti Guha, Anil A. Hake, Kalyani M. Barbadikar, Potupureddi Gopi, Nakul D. Magar, Vishalakshi Balija, C. G. Gokulan, Madhavilatha Kommana, Md Jamaloddin, Anjana Sharma, Raju Madanala, A. Chandra Sekhar, D. Vijaya Raghava Prasad, D. Vijaya Lakshmi,
    Journal of Crop Science and Biotechnology.2026;[Epub]     CrossRef
  • Rice Lesion Mimic Mutants (LMM): The Current Understanding of Genetic Mutations in the Failure of ROS Scavenging during Lesion Formation
    Sang Gu Kang, Kyung Eun Lee, Mahendra Singh, Pradeep Kumar, Mohammad Nurul Matin
    Plants.2021; 10(8): 1598.     CrossRef
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Mapping QTLs for Leafspot Resistance in Peanut Using SNP-Based Next-Generation Sequencing Markers
Yuya Liang, Michael Baring, Shichen Wang, Endang M. Septiningsih
Plant Breed. Biotech. 2017;5(2):115-122.   Published online June 1, 2017
DOI: https://doi.org/10.9787/PBB.2017.5.2.115

Leafspot is one of the major diseases of peanut (Arachis hypogaea L.) that can cause more than 50% yield loss. The
objective
of this study was to identify and map quantitative trait loci (QTLs) for resistance to leafspot disease. An F2:6 recombinant inbred line (RIL) population, derived from a released cultivar Tamrun OL07 and a highly tolerant breeding line Tx964117, were used as a mapping population. A total of 90 RILs were planted for disease phenotyping in Yoakum, Texas in 2010 and 2012. A genetic map spanning the 20 linkage groups was developed using 1,211 SNP markers based on double digest restriction-site associated DNA sequencing (ddRAD-seq). A total of six quantitative trait loci (QTLs) were identified, with LOD score values of 3.2–5.0 and phenotypic variance explained ranging from 11%–24%. Major QTLs identified in this study may be used as potential targets for peanut improvement to leafspot disease through molecular breeding.

Citations

Citations to this article as recorded by  
  • Discovery of the genomic region and candidate gene for qELSB02.1, a novel and stable major QTL associated with peanut early leaf spot resistance
    Zhijun Xu, Sheng Zhao, Xuejiao Zhang, Qibiao Li, Lei Xu, Qian Yang, Li Huang, Huifang Jiang
    Journal of Integrative Agriculture.2026;[Epub]     CrossRef
  • Genome-Wide Dissection of Early and Late Leaf Spot Resistance in Advanced Peanut Backcross Lines Carrying Introgressions from Arachis stenosperma and Arachis batizocoi
    Namrata Maharjan, Mounirou H. Alyr, David J. Bertioli, Soraya C. M. Leal-Bertioli
    Agronomy.2026; 16(12): 1129.     CrossRef
  • Next-Generation Sequencing in the Development of Climate-Resilient and Stress-Responsive Crops – A Review
    Amitava Roy, Suman Dutta, Sumanta Das, Malini Roy Choudhury
    The Open Biotechnology Journal.2024;[Epub]     CrossRef
  • High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing
    Ping Lin, Jingyu Chai, Anni Wang, Huiqi Zhong, Kailiang Wang
    International Journal of Molecular Sciences.2024; 25(16): 8840.     CrossRef
  • High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance
    Jiaowen Pan, Xiaojie Li, Chun Fu, Jianxin Bian, Zhenyu Wang, Conghui Yu, Xiaoqin Liu, Guanghao Wang, Ruizheng Tian, Xiaofeng Song, Changsheng Li, Han Xia, Shuzhen Zhao, Lei Hou, Meng Gao, Hailing Zi, David Bertioli, Soraya Leal-Bertioli, Manish K. Pandey,
    Theoretical and Applied Genetics.2024;[Epub]     CrossRef
  • Validation of SNP markers associated with late leaf spot resistance in groundnut
    Benjamin Aboagye Danso, Daniel Kwadjo Dzidzienyo, John Saviour Yaw Eleblu, Sylvester Addy, William Manilal, Kwadwo Ofori, James Yaw Asibuo
    Cogent Food & Agriculture.2024;[Epub]     CrossRef
  • Advances in omics research on peanut response to biotic stresses
    Ruihua Huang, Hongqing Li, Caiji Gao, Weichang Yu, Shengchun Zhang
    Frontiers in Plant Science.2023;[Epub]     CrossRef
  • An Overview of Mapping Quantitative Trait Loci in Peanut (Arachis hypogaea L.)
    Fentanesh C. Kassie, Joël R. Nguepjop, Hermine B. Ngalle, Dekoum V. M. Assaha, Mesfin K. Gessese, Wosene G. Abtew, Hodo-Abalo Tossim, Aissatou Sambou, Maguette Seye, Jean-François Rami, Daniel Fonceka, Joseph M. Bell
    Genes.2023; 14(6): 1176.     CrossRef
  • Quantitative Trait Analysis Shows the Potential for Alleles from the Wild Species Arachis batizocoi and A. duranensis to Improve Groundnut Disease Resistance and Yield in East Africa
    Danielle A. Essandoh, Thomas Odong, David K. Okello, Daniel Fonceka, Joël Nguepjop, Aissatou Sambou, Carolina Ballén-Taborda, Carolina Chavarro, David J. Bertioli, Soraya C. M. Leal-Bertioli
    Agronomy.2022; 12(9): 2202.     CrossRef
  • Optimization of Protoplast Isolation and Transformation for a Pilot Study of Genome Editing in Peanut by Targeting the Allergen Gene Ara h 2
    Sudip Biswas, Nancy J. Wahl, Michael J. Thomson, John M. Cason, Bill F. McCutchen, Endang M. Septiningsih
    International Journal of Molecular Sciences.2022; 23(2): 837.     CrossRef
  • Genetic diversity analysis among late leaf spot and rust resistant and susceptible germplasm in groundnut (Arachis hypogea L.)
    Sushmita Mandloi, M.K. Tripathi, Sushma Tiwari, Niraj Tripathi
    Israel Journal of Plant Sciences.2022; 69(3-4): 163.     CrossRef
  • Functional Allele Validation by Gene Editing to Leverage the Wealth of Genetic Resources for Crop Improvement
    Michael J. Thomson, Sudip Biswas, Nikolaos Tsakirpaloglou, Endang M. Septiningsih
    International Journal of Molecular Sciences.2022; 23(12): 6565.     CrossRef
  • Peanut leaf spot caused by Nothopassalora personata
    D. F. Giordano, N. Pastor, S. Palacios, C. M. Oddino, A. M. Torres
    Tropical Plant Pathology.2021; 46(2): 139.     CrossRef
  • Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice
    John Carlos I. Ignacio, Maricris Zaidem, Carlos Casal, Shalabh Dixit, Tobias Kretzschmar, Jaime M. Samaniego, Merlyn S. Mendioro, Detlef Weigel, Endang M. Septiningsih
    Plants.2021; 10(4): 705.     CrossRef
  • Identification of QTLs associated with Sclerotinia blight resistance in peanut (Arachis hypogaea L.)
    Yuya Liang, John M. Cason, Michael R. Baring, Endang M. Septiningsih
    Genetic Resources and Crop Evolution.2021; 68(2): 629.     CrossRef
  • Improved Transformation and Regeneration of Indica Rice: Disruption of SUB1A as a Test Case via CRISPR-Cas9
    Yuya Liang, Sudip Biswas, Backki Kim, Julia Bailey-Serres, Endang M. Septiningsih
    International Journal of Molecular Sciences.2021; 22(13): 6989.     CrossRef
  • Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value
    Tinashe Zenda, Songtao Liu, Anyi Dong, Jiao Li, Yafei Wang, Xinyue Liu, Nan Wang, Huijun Duan
    Frontiers in Plant Science.2021;[Epub]     CrossRef
  • Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences
    Carolina Chavarro, Ye Chu, Corley Holbrook, Thomas Isleib, David Bertioli, Ran Hovav, Christopher Butts, Marshall Lamb, Ronald Sorensen, Scott A. Jackson, Peggy Ozias-Akins
    G3 Genes|Genomes|Genetics.2020; 10(7): 2297.     CrossRef
  • Major QTLs for Resistance to Early and Late Leaf Spot Diseases Are Identified on Chromosomes 3 and 5 in Peanut (Arachis hypogaea)
    Ye Chu, Peng Chee, Albert Culbreath, Thomas G. Isleib, C. Corley Holbrook, Peggy Ozias-Akins
    Frontiers in Plant Science.2019;[Epub]     CrossRef
  • Groundnut (Arachis hypogaeaL.) improvement in sub-Saharan Africa: a review
    Seltene Abady, Hussein Shimelis, Pasupuleti Janila, Jacob Mashilo
    Acta Agriculturae Scandinavica, Section B — Soil & Plant Science.2019; 69(6): 528.     CrossRef
  • Mapping of Quantitative Trait Loci for Yield and Grade Related Traits in Peanut (Arachis hypogaeaL.) Using High-Resolution SNP Markers
    Yuya Liang, Michael R. Baring, Endang M. Septiningsih
    Plant Breeding and Biotechnology.2018; 6(4): 454.     CrossRef
  • A SNP-Based Linkage Map Revealed QTLs for Resistance to Early and Late Leaf Spot Diseases in Peanut (Arachis hypogaea L.)
    Suoyi Han, Mei Yuan, Josh P. Clevenger, Chun Li, Austin Hagan, Xinyou Zhang, Charles Chen, Guohao He
    Frontiers in Plant Science.2018;[Epub]     CrossRef
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Quantitative Trait Loci Associated with Heat Tolerance in Rice (Oryza sativa L.)
Bui Chi Buu, Pham Thi Thu Ha, Bui Phuoc Tam, Tran Thi Nhien, Nguyen Van Hieu, Nguyen Trong Phuoc, Luong the Minh, Ly Hau Giang, Nguyen Thi Lang
Plant Breed. Biotech. 2014;2(1):14-24.   Published online March 31, 2014
DOI: https://doi.org/10.9787/PBB.2014.2.1.014

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.

Citations

Citations to this article as recorded by  
  • Morphological and Physiological Responses of Two Tropical Rice (Oryza sativa) Varieties to High-Temperature Stress
    V. S. Anup, Pallot Sindhumole, Jiji Joseph, Deepu Mathew, M. S. Parvathi, B. R. Vishnu
    Agricultural Research.2026; 15(1): 44.     CrossRef
  • Unlocking the potential of rice for thermotolerance using simple sequence repeat (SSR) marker-based assessment of genetic variability and population structure
    Ravi Teja Seelam, Venkata Ramana Rao Puram, Veronica Nallamothu, Sudhir Kumar Injeti, Vani Praveena Madhunapantula
    Genetic Resources and Crop Evolution.2025; 72(1): 947.     CrossRef
  • Dissecting genetic variation for agro-morphological traits of elevated temperature under CO2-temperature gradient chamber and validation of markers linked to heat tolerance of rice (Oryza sativa L.)‏ cultivars of north-eastern Himalayan Region
    Amit Kumar, Letngam Touthang, Shankar. P. Das, R. Krishnappa, Avinash Pandey, Arvind Prasad, Shiv Poojan Singh, Simardeep Kaur, C. Aochen, Veerendra Kumar Verma, N. Umakanta, A. Gangarani Devi, Harendra Verma, E. Lamalakshmi Devi, Samarendra Hazarika, Vin
    Euphytica.2024;[Epub]     CrossRef
  • Comparative Genetic Diversity Assessment and Marker–Trait Association Using Two DNA Marker Systems in Rice (Oryza sativa L.)
    Mohammed I. Al-daej, Adel A. Rezk, Mohamed M. El-Malky, Tarek A. Shalaby, Mohamed Ismail
    Agronomy.2023; 13(2): 329.     CrossRef
  • Physiological and molecular implications of multiple abiotic stresses on yield and quality of rice
    Beena Radha, Nagenahalli Chandrappa Sunitha, Rameswar P. Sah, Md Azharudheen T. P., G. K. Krishna, Deepika Kumar Umesh, Sini Thomas, Chandrappa Anilkumar, Sameer Upadhyay, Awadhesh Kumar, Manikanta Ch L. N., Behera S., Bishnu Charan Marndi, Kadambot H. M.
    Frontiers in Plant Science.2023;[Epub]     CrossRef
  • Identification of simple sequence repeat markers linked to heat tolerance in rice using bulked segregant analysis in F2 population of NERICA-L 44 × Uma
    K. Stephen, K. Aparna, R. Beena, R. P. Sah, Uday Chand Jha, Sasmita Behera
    Frontiers in Plant Science.2023;[Epub]     CrossRef
  • Molecular characterization and varietal identification for multiple abiotic stress tolerance in rice (Oryza sativa L.)
    Alif Ali, Beena R, Chennamsetti Lakshmi Naga Manikanta, Swapna Alex, Soni KB, Viji MM
    Oryza-An International Journal on Rice.2022; 59(1): 59.     CrossRef
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    V. Vishnu Prasanth, Kumari Ramana Basava, M. Suchandranath Babu, Venkata Tripura V.G.N., S. J. S. Rama Devi, S. K. Mangrauthia, S. R. Voleti, N. Sarla
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Mapping a New Source of Self-fertility in Perennial Ryegrass (Lolium perenne L.)
Andrea Arias Aguirre, Bruno Studer, Javier Do Canto, Ursula Frei, Thomas Lübberstedt
Plant Breed. Biotech. 2013;1(4):385-395.   Published online December 31, 2013
DOI: https://doi.org/10.9787/PBB.2013.1.4.385

There is a rising interest of moving towards hybrid breeding in outcrossing species. Self-compatibility (SC), which occurs at low rates in self-incompatible species, could be used to develop inbred lines, a key requirement for hybrid breeding programs. In perennial ryegrass, the existence of SC independent from the self-incompatibility (SI) loci S and Z has been reported.

In this study, we used 98 F2 individuals from a cross between a self-compatible ecotype and an individual of the VrnA mapping population that were tested with markers for two candidate linkage groups 3 and 5 as well as markers for candidate regions at the S and Z locus. We were able to determine a tentative location of a SC locus and tested the possible interaction to other loci involved in SI and SC. This information will help to fine map the SC locus, and for marker-assisted selection.

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  • Mapping quantitative trait loci associated with self-(in)compatibility in goji berries (Lycium barbarum)
    Cuiping Wang, Ken Qin, Xiaohui Shang, Yan Gao, Jiali Wu, Haijun Ma, Zhaojun Wei, Guoli Dai
    BMC Plant Biology.2024;[Epub]     CrossRef
  • Assessing inbreeding in perennial ryegrass (Lolium perenne) as a step towards F1 hybrid breeding
    Caitlin Harris, Madison Hall, Ruby Arrowfield, Rowan Herridge, Colin Eady, Richard Macknight, Lynette Brownfield
    Plant Breeding.2023; 142(4): 518.     CrossRef
  • Characterization and practical use of self-compatibility in outcrossing grass species
    Claudio Cropano, Iain Place, Chloé Manzanares, Javier Do Canto, Thomas Lübberstedt, Bruno Studer, Daniel Thorogood
    Annals of Botany.2021; 127(7): 841.     CrossRef
  • Identification of Candidate Genes for Self-Compatibility in Perennial Ryegrass (Lolium perenne L.)
    Claudio Cropano, Chloé Manzanares, Steven Yates, Dario Copetti, Javier Do Canto, Thomas Lübberstedt, Michael Koch, Bruno Studer
    Frontiers in Plant Science.2021;[Epub]     CrossRef
  • Genetic Variability in Winter Rye (Secale cereale L.) Accessions at Early Stage of Self-Pollination Manifested through Fertility, Plant Height and Secalins
    N. Daskalova, S. Doneva, P. Spetsov
    Cytology and Genetics.2021; 55(1): 96.     CrossRef
  • A new genetic locus for self-compatibility in the outcrossing grass species perennial ryegrass (Lolium perenne)
    Lucy M Slatter, Susanne Barth, Chloe Manzanares, Janaki Velmurugan, Iain Place, Daniel Thorogood
    Annals of Botany.2021; 127(6): 715.     CrossRef
  • Pattern of inheritance of a self‐fertility gene in an autotetraploid perennial ryegrass (Lolium perenne) population
    Javier Do Canto, Bruno Studer, Ursula Frei, Thomas Lübberstedt, Odd Arne Rognli
    Plant Breeding.2020; 139(1): 207.     CrossRef
  • Fine mapping a self-fertility locus in perennial ryegrass
    Javier Do Canto, Bruno Studer, Ursula Frei, Thomas Lübberstedt
    Theoretical and Applied Genetics.2018; 131(4): 817.     CrossRef
  • A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae) Population
    Daniel Thorogood, Steven Yates, Chloé Manzanares, Leif Skot, Matthew Hegarty, Tina Blackmore, Susanne Barth, Bruno Studer
    Frontiers in Plant Science.2017;[Epub]     CrossRef
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Phenotypic Characterization and Genetic Mapping of An Open-hull Sterile Mutant in Rice
Yoye Yu, Rihua Piao, Wenzhu Jiang, Sunghan Kim, Hee-Jong Koh
Plant Breed. Biotech. 2013;1(1):24-32.   Published online March 31, 2013
DOI: https://doi.org/10.9787/PBB.2013.1.1.024

Rice hulls remain closed throughout the ripening period to maintain internal humidity of the grains. An Open-hull sterile mutant was induced by N-methyl-N-nitrosourea (MNU) treatment on Sinsunchalbyeo rice, a japonica type. This mutant showed open hulls even in the ripening stages and fully mature grains. In addition, several altered characteristics were observed, including of narrowed palea, decreased grain size, partial pollen sterility and erect panicle. Microscopic analysis showed that the palea was positioned slightly inside the lemma, and the size of palea decreased in the mutant. Genetic analysis of F2 and F3 segregation populations derived from the cross between the Open-hull sterile mutant (Oryza sativa ssp. japonica) and Milyang23 (O. sativa ssp. indica) indicated that the Open-hull trait was controlled by a single recessive allele. The fine-mapping with STS (sequence tagged site) markers revealed that the mutant gene was located on the short arm of chromosome 3. We were able to narrow it down until 30.6Kb where three candidate genes were found.

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  • Fine Mapping and Candidate-Gene Analysis of an open glume multi-pistil 3 (mp3) in Rice (Oryza sativa L.)
    Yongshu Liang, Junyi Gong, Yuxin Yan, Tingshen Peng, Jinyu Xiao, Shuang Wang, Wenbin Nan, Xiaojian Qin, Hanma Zhang
    Agriculture.2022; 12(10): 1731.     CrossRef
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