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Volume 4(2); May 2016

Review Articles

Repeat Evolution in Brassica rapa (AA), B. oleracea (CC), and B. napus (AACC) Genomes
Nomar Espinosa Waminal, Sampath Perumal, Jonghoon Lee, Hyun Hee Kim, Tae-Jin Yang
Plant Breed. Biotech. 2016;4(2):107-122.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.107

The genus Brassica is an important resource for major agricultural products such as oils, vegetable and fodder. The Brassiceae tribe-specific whole-genome triplication that occurred ~15.9 million years ago influenced the speciation and morphological diversification that has been exploited in agriculture, making Brassica an excellent model system for studying polyploidization-mediated evolution. Genome sequencing and comparative genome analysis have revealed conserved structures and uncovered the genome evolution of Brassica species. While chromosome shuffling and asymmetric subgenome gene retention are widely reported in Brassica species, limited information is available about the dynamics of repetitive elements (REs), which are central to epigenetic mechanisms and thus play a pivotal role in plant genome adaptation and evolution. The assembled reference genome sequences of B. rapa (AA) and B. oleracea (CC), and their derived allotetraploid, B. napus (AACC), cover 58%, 86%, and 75% of their respective estimated genome sizes. The remaining non-assembled genome portions vary between these three genome sequences, and the major components remain hidden in each genome. Here, we review the dynamics of the major Brassica repeats that have played roles in speciation of the AA, CC, and AACC genomes. We show that 10 major Brassica repeats appear to occupy more than 50% of each respective unassembled genome sequence, yet represent less than 1% of assembled reference genome sequences. We have estimated their genome proportions using whole-genome Illumina reads and cytogenetic analyses in an attempt to understand the role of these repeats in genome evolution.

Citations

Citations to this article as recorded by  
  • Construction and evaluation of Brassica rapa orphan genes overexpression library
    Mingliang Jiang, Zongxiang Zhan, Xiaonan Li, Zhongyun Piao
    Frontiers in Plant Science.2025;[Epub]     CrossRef
  • Fluorescence in situ Hybridization Analysis of Oligonucleotide 5S Ribosomal DNA, 45S Ribosomal DNA, and (TTTAGGG)3 Locations in Gloriosa superba L.
    Hongyou Zhao, Duo Wang, Haitao Li, Shuang Li, Yanfang Wang, Anshun Xu, Chunyong Yang, Ge Li, Yanqian Wang, Lixia Zhang
    Cytogenetic and Genome Research.2024; : 1.     CrossRef
  • Exploring the mechanism of blindness physiopathy in Brassica oleracea var italica L. by comprehensive transcriptomics and metabolomics analysis
    Alvaro Lopez-Zaplana, Juan Nicolas-Espinosa, Lorena Albaladejo-Marico, Micaela Carvajal
    Plant Physiology and Biochemistry.2024; 206: 108304.     CrossRef
  • Chromosome-scale reference genome of broccoli (Brassica oleracea var. italica Plenck) provides insights into glucosinolate biosynthesis
    Qiuyun Wu, Shuxiang Mao, Huiping Huang, Juan Liu, Xuan Chen, Linghui Hou, Yuxiao Tian, Jiahui Zhang, Junwei Wang, Yunsheng Wang, Ke Huang
    Horticulture Research.2024;[Epub]     CrossRef
  • Physical mapping of ribosomal DNA sites and genome size in polyploid series of Urochloa humidicola (Rendle) Morrone & Zuloaga (Poaceae)
    Ana Gabriela Damasceno, Marco Túlio Mendes Ferreira, Isadora Cardoso Soares, Sanzio Carvalho Lima Barrios, Cacilda Borges Do Valle, Vânia Helena Techio
    Botany Letters.2023; 170(4): 634.     CrossRef
  • Evolutionary expansion and expression dynamics of cytokinin-catabolizing CKX gene family in the modern amphidiploid mustard (Brassica sp.)
    Aniruddhabhai Khuman, Vijay Kumar, Bhupendra Chaudhary
    3 Biotech.2022;[Epub]     CrossRef
  • Evolutionary divergence in embryo and seed coat development of U’s Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas
    Peng Gao, Teagen D. Quilichini, Hui Yang, Qiang Li, Kirby T. Nilsen, Li Qin, Vivijan Babic, Li Liu, Dustin Cram, Asher Pasha, Eddi Esteban, Janet Condie, Christine Sidebottom, Yan Zhang, Yi Huang, Wentao Zhang, Pankaj Bhowmik, Leon V. Kochian, David Konki
    New Phytologist.2022; 233(1): 30.     CrossRef
  • Comparative triple-color FISH mapping in eleven Senna species using rDNA and telomeric repeat probes
    Thi Hong Nguyen, Nomar Espinosa Waminal, Do Sin Lee, Remnyl Joyce Pellerin, Thanh Dat Ta, Nicole Bon Campomayor, Byung Yong Kang, Hyun Hee Kim
    Horticulture, Environment, and Biotechnology.2021; 62(6): 927.     CrossRef
  • Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy
    Nomar Espinosa Waminal, Remnyl Joyce Pellerin, Sang-Ho Kang, Hyun Hee Kim
    Frontiers in Plant Science.2021;[Epub]     CrossRef
  • Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines
    Sampath Perumal, Nomar Espinosa Waminal, Jonghoon Lee, Hyun-Jin Koo, Boem-soon Choi, Jee Young Park, Kyounggu Ahn, Tae-Jin Yang
    Horticultural Plant Journal.2021; 7(6): 539.     CrossRef
  • Comparative Molecular Cytogenetic Analysis of Ribosomal DNAs Distribution inBrassicaSpecies
    Franklin H. Mancia, Jung Sun Kim, Yoon-Jung Hwang
    Korean Journal of Breeding Science.2021; 53(3): 206.     CrossRef
  • Omics: The way forward to enhance abiotic stress tolerance inBrassica napusL
    Ali Raza, Ali Razzaq, Sundas Saher Mehmood, Muhammad Azhar Hussain, Su Wei, Huang He, Qamar U Zaman, Zhang Xuekun, Cheng Yong, Mirza Hasanuzzaman
    GM Crops & Food.2021; 12(1): 251.     CrossRef
  • Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites
    Nicole Bon Campomayor, Nomar Espinosa Waminal, Byung Yong Kang, Thi Hong Nguyen, Soo-Seong Lee, Jin Hoe Huh, Hyun Hee Kim
    Cells.2021; 10(9): 2358.     CrossRef
  • Gene duplication and stress genomics in Brassicas: Current understanding and future prospects
    Shayani Das Laha, Smritikana Dutta, Anton R. Schäffner, Malay Das
    Journal of Plant Physiology.2020; 255: 153293.     CrossRef
  • BrmiR828 Targets BrPAP1, BrMYB82, and BrTAS4 Involved in the Light Induced Anthocyanin Biosynthetic Pathway in Brassica rapa
    Bo Zhou, Jingtong Leng, Yanyun Ma, Pengzhen Fan, Yuhua Li, Haifang Yan, Qijiang Xu
    International Journal of Molecular Sciences.2020; 21(12): 4326.     CrossRef
  • Comparative Cyto-molecular Analysis of Repetitive DNA Provides Insights into the Differential Genome Structure and Evolution of Five Cucumis Species
    Shuqiong Yang, Chunyan Cheng, Xiaodong Qin, Xiaqing Yu, Qunfeng Lou, Ji Li, Chuntao Qian, Jinfeng Chen
    Horticultural Plant Journal.2019; 5(5): 192.     CrossRef
  • FISH mapping of rDNA and telomeric repeats in 10 Senna species
    Remnyl Joyce Pellerin, Nomar Espinosa Waminal, Hyun Hee Kim
    Horticulture, Environment, and Biotechnology.2019; 60(2): 253.     CrossRef
  • Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa
    Mingliang Jiang, Xiangshu Dong, Hong Lang, Wenxing Pang, Zongxiang Zhan, Xiaonan Li, Zhongyun Piao
    International Journal of Molecular Sciences.2018; 19(7): 2064.     CrossRef
  • Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax
    Junki Lee, Nomar Espinosa Waminal, Hong-Il Choi, Sampath Perumal, Sang-Choon Lee, Van Binh Nguyen, Woojong Jang, Nam-Hoon Kim, Li-zhi Gao, Tae-Jin Yang
    Scientific Reports.2017;[Epub]     CrossRef
  • Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution
    Sampath Perumal, Nomar Espinosa Waminal, Jonghoon Lee, Junki Lee, Beom-Soon Choi, Hyun Hee Kim, Marie-Angèle Grandbastien, Tae-Jin Yang
    Scientific Reports.2017;[Epub]     CrossRef
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Modification of Fatty Acid Profiles of Rapeseed (Brassica napus L.) Oil for Using as Food, Industrial Feed-Stock and Biodiesel
Ujjal Kumar Nath, Hoy-Taek Kim, Khadiza Khatun, Jong-In Park, Kwon-Kyoo Kang, Ill-Sup Nou
Plant Breed. Biotech. 2016;4(2):123-134.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.123

Rapeseed is a member of family Brassicaceae, cultivated as oil crop. Rapeseed oil is being utilized from early civilization, but its popularity being declined from the mid-nineteenth century due to presence of erucic acid (C22:1) and glucosinolates. Thereby, several attempts have been made to develop cultivars free from those toxins. In the past 20 years, breeders got success in developing ‘00’-quality rapeseed, known as ‘Canola’. The target mutagenesis of fae-1 and fae-2 of Brassica napus ensured such success. Thereafter, ‘canola’ regains its market as a healthy vegetable oil. Moreover, high oleic acid rapeseed lines, with 86% oleic acid, have been developed by using chemical mutagenesis of FAD2 alleles responsible for desaturation of oleic acid (C18:1) to linoleic acid (C18:2). Recently, high erucic acid rapeseed oil regained interest for biodegradable plastic, cosmetic, emollient industries and for biodiesel. Therefore, breeding approaches have been pursued; unfortunately, that were failed to reach erucic acid level beyond 50% in seed-oil. Rapeseed genotypes over-expressed with Ld-LPAAT separately and Ld-LPAAT-FAE chimaric construct together were tried but failed to reach the erucic acid content more than 60%. Thereof, combined effort of conventional breeding and transgenic approaches are brought together to overcome three hypothesized bottlenecks; reviewed in this article, which restricted erucic acid level near to 60%. Finally, rapeseed genotypes with 78% erucic acid were developed successfully. This material is now available in Germany for using in emollient industries and for biodiesel. Therefore, this article is reviewed on the current status and future outlook for modification of fatty acid profiles of rapeseed oil for its end-use as food, industrial feed-stock and biodiesel.

Citations

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    Sk Mosaraf Ahammed, Amit Kumar Roy, Xue-Zhi Li, Fahad Al Basir, Priti Kumar Roy
    Frontiers in Applied Mathematics and Statistics.2026;[Epub]     CrossRef
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    Discover Agriculture.2026;[Epub]     CrossRef
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    Khalid Mahmood, Abdul Majid Khan, Wajiha Anum, Abid Ali, Rana Tauqeer Ahmad, Rana Imtiaz Ahmed, Imran Akhtar, Nadia Manzoor, Asad- ur- Rehman Ch., Naeem Arshad Maan, Noorah AlKubaisi, Mohamed S. Elshikh, Rashid Iqbal, Umair Riaz, Gang Deng, Saltanat Aghay
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    Jaehee Jeong, Da-Hee An, Hyun-Min Cho, Young-Lok Cha, Ji-Bong Choi, Dong-Sung Kim, Soo-Yeon Kim
    Korean Journal of Breeding Science.2025; 57(2): 55.     CrossRef
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    Proceedings on applied botany, genetics and breeding.2025; 186(2): 121.     CrossRef
  • Genotyping-by-Sequencing Analysis Reveals Associations between Agronomic and Oil Traits in Gamma Ray-Derived Mutant Rapeseed (Brassica napus L.)
    Woon Ji Kim, Baul Yang, Dong-Gun Kim, Sang Hoon Kim, Ye-Jin Lee, Juyoung Kim, So Hyeon Baek, Si-Yong Kang, Joon-Woo Ahn, Yu-Jin Choi, Chang-Hyu Bae, Kanivalan Iwar, Seong-Hoon Kim, Jaihyunk Ryu
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    Journal of Crop Breeding.2024; 16(49): 74.     CrossRef
  • HO-CR and HOLL-CR: new forms of winter oilseed rape (Brassica napus L.) with altered fatty acid composition and resistance to selected pathotypes of Plasmodiophora brassicae (clubroot)
    Stanisław Spasibionek, Katarzyna Mikołajczyk, Marcin Matuszczak, Joanna Kaczmarek, Noor Ramzi, Małgorzata Jędryczka
    Journal of Applied Genetics.2024; 65(3): 439.     CrossRef
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    Yunliang Li, Sally L. Vail, Melissa M. Arcand, Bobbi L. Helgason
    Phytobiomes Journal.2023; 7(1): 125.     CrossRef
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    S Virgian, A Aunillah, D Listyati, M Herman, D Pranowo, E Wardiana
    IOP Conference Series: Earth and Environmental Science.2022; 974(1): 012124.     CrossRef
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    Nisha Kumari, Ram Avtar, Vivek K. Singh, Neeraj Kumar, Mahavir Bishnoi, Manjeet Singh, Rajeev Varshney
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    Biomass and Bioenergy.2022; 163: 106521.     CrossRef
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    Biological Communications.2020;[Epub]     CrossRef
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    Vaccines.2020; 8(3): 468.     CrossRef
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    Ahmed A. AbdulJabbar, Bahar J. Mahmood, Sirwan T. Salih
    Al-Mustansiriyah Journal of Science.2020; 31(3): 65.     CrossRef
  • Marker assisted selection of new high oleic and low linolenic winter oilseed rape (Brassica napus L.) inbred lines revealing good agricultural value
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  • 26 Crossref
Research on Biotic and Abiotic Stress Related Genes Exploration and Prediction in Brassica rapa and B. oleracea: A Review
Md. Abdul Kayum, Hoy-Taek Kim, Ujjal Kumar Nath, Jong-In Park, Kang Hee Kho, Yong-Gu Cho, Ill-Sup Nou
Plant Breed. Biotech. 2016;4(2):135-144.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.135

Global population is increasing day-by-day, simultaneously, crop production need to increase proportionately. Whereas, increase crop production being restricted due to abiotic and biotic stresses. Abiotic stresses are adversely affected crop growth and development, leading to crop loss globally and thereby causing huge amount of economic loss as well. Contrary, pathogens are attacked the plants imposing biotic stress and severely hampers the yield. Therefore, it is prime need to understand the molecular mechanism and genes involved to minimize the biotic and abiotic stresses for mitigating the Brassica vegetable crop losses. The stress responsive, pathogens related genes are involved in tolerance or resistance to stress in plants that are cross-talk with different types of stress components in signal transduction pathways. The plants have their own mechanism to overcome biotic and abiotic stresses to follow the abscisic acid (ABA)-dependent and ABA-independent pathways. Several transcription factors such as WRKY, Alfin-like, MYB, NAC, DREB, CBF are integrating to various stress signals and controlling the gene expression through networking with their related cis-elements. To develop stress tolerance and/or resistant crops plants, there is need to realize both of the plant and pathogenic disease development mechanisms. Therefore, this article is focused on (i) major and devastating stresses on vegetable crops, (ii) role of genes to overcome the stresses, and (iii) differential genes expressed under biotic and abiotic stresses in Brassica oleracea and B. rapa for getting insight of the mechanisms of development of resistance lines.

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    3 Biotech.2018;[Epub]     CrossRef
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Research Articles
Differential Expression of Flowering Genes between Rapid- and Slow-Cycling Brassica rapa
Hayong Song, Xiangshu Dong, Hankuil Yi, Ill-Sup Nou, Yoonkang Hur
Plant Breed. Biotech. 2016;4(2):145-157.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.145

Flowering time is a very important agronomic trait in Brassica crops and regulation of the time is one of major factor in the breeding program. To understand the control of flowering time in Brassica rapa, we have carried out Br300K microarray with two contrasting Brassica inbred lines, Rapid Cycling B. rapa (RCBr) as rapid cycling type and B. rapa ssp. pekinensis inbred line Chiifu as slow flowering phenotype. Reproductive process-related genes were specifically expressed in RCBr, whereas environmental stimuli-responsive genes in Chiifu. Flowering stimulating genes, such as BrFT and BrSOC1, were preferentially expressed in RCBr, while flowering repressing genes, such as BrFLC and BrMAF4, expressed in Chiifu. Several paralogues present in B. rapa, BrFLCs and BrCOLs, were expressed with paralog-specific pattern depending on flowering phenotypes: i.e., BrFLC1 and BrFLC2, major floral repressors, were expressed in Chiifu, BrFLCL/BrFLC5 in RCBr and BrFLC3 in both plants. The expression of several flowering repressing genes was gradually decreased in RCBr growth, but increased in Chiifu growth. However, the expression of genes involved in photoperiodic flowering was no difference between these two plants under LD and SD conditions, indicating photoperiodic pathway is not major factor to distinguish fast vs. slow flowering in B. rapa. The mechanism underlined in the rapid or fast flowering of RCBr would be further elucidated in association with the controlling mechanism of its short life span.

Citations

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Assessment of the Response of Beta Carotene Enhanced Transgenic Soybeans to Soybean Mosaic Virus (SMV)
Yang Qin, Kong-Sik Shin, Jang-Kyun Seo, Myung-Ho Lim, Young-Soo Chung, Hyun-Suk Cho, Seong-Kon Lee, Hee-Jong Woo
Plant Breed. Biotech. 2016;4(2):158-169.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.158

Beta-carotene, a defense chemical, is synthesized by the carotenoid biosynthesis pathway. In the present study, a transgenic soybean line, with a single copy insertion of phytoene synthase and carotene desaturase genes, having high beta-carotene content was studied for its response to systemically inoculated Soybean mosaic virus (SMV). Beta-carotene-enhanced transgenic soybean showed similar leaf and seed symptoms, viral RNA, and protein expression compared to the non-genetically modified (GM) ‘Kwangan’ control. Total antioxidant contents in the non-GM ‘Kwangan’ line were increased after SMV attack in both leaves and seeds; however, the antioxidant contents in the beta-carotene-enhanced soybean line have no significant changes. In addition, both GM and non-GM soybean were detected increased lipid hydroperoxide concentrations in leaves and seeds after SMV infection, even though they did not reach a statistical significant level. Abscisic acid (ABA) levels in beta-carotene-enhanced transgenic soybean seeds was determined 35-fold increase after SMV infections caused a lower seed germination rate and a higher SMV transmission rate to subsequent generations, compared to those of non-GM ‘Kwangan’. Thus, we concluded that the additional production of beta-carotene did not confer resistance of beta-carotene-enhanced transgenic soybean to SMV infections, but caused mass accumulations of ABA in seeds.

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    Yang Qin, Hee-Jong Woo, Kong-Sik Shin, Myung-Ho Lim, Seong-Kon Lee
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  • Nutritional composition analysis for beta-carotene-enhanced transgenic soybeans (Glycine max L.)
    Yang Qin, Soo-Yun Park, Seon-Woo Oh, Myung-Ho Lim, Kong-Sik Shin, Hyun-Suk Cho, Seong-Kon Lee, Hee-Jong Woo
    Applied Biological Chemistry.2017; 60(3): 299.     CrossRef
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Breeding of Black Soybean Line with ti and le Allele
Sangwoo Choi, Sungjin Han, Mikyung Sung, Jong Il Chung
Plant Breed. Biotech. 2016;4(2):170-175.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.170

Soybean is an economically important leguminous seed crop for feed and food products that are rich in seed protein, oil and saccharides. Also, black soybean has been known as medicinal food. However, Kunitz trypsin inhibitor (KTI) and lectin proteins are a main antinutritional factor in mature black soybean seed. The genetic removal of the KTI and lectin proteins will improve the nutritional value of black soybean seed. The
objective
of this research was to develop a new black soybean lines with double recessive allele for both KTI and lectin protein. A total of 179 F2 seeds were obtained from the cross of ‘Gaechuck#1’ (Le/Le, ti/ti genotype) and ‘LE-16’ (le/le, Ti/Ti genotype) parents. The segregation ratios for the presence or absence of KTI and lectin proteins in the F2 seed generation were well fitted to an expected 3:1 ratio. The segregation ratios of 9:3:3:1 (113 Ti_Le_:28 Ti_lele:30 titiLe_:8 titilele) between Ti gene and Le gene in F2 seed generation were observed (χ2=3.71, P=0.5–0.1). From eight F2 seeds with double recessive allele (ti/ti, le/le genotype), one new strain (titilele, both KTI, and lectin protein free) was developed. New strain has black seed coat, black hilum and green cotyledon in mature seed and 100-seed weight was 19.5 g. This strain will be helpful in breeding program for selecting black soybean line with lacking both KTI and lectin protein.

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    Gyung Young Kang, Sang Woo Choi, Won Gi Chae, Jong Il Chung
    Journal of Plant Biotechnology.2020; 47(2): 118.     CrossRef
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Optimization of Temperature Regime to Screen Cold Tolerant Rice Seedlings
Ung-Jo Hyun, Sang-Min Yeo, Sang-Bok Lee, Jeong-Heui Lee, Jong-Min Jeong, Yeaul-Kyu Seong, Dae-Ha Seo, Yong-Jae Won, Eok-Keun Ahn, Jeom Ho Lee, Jun-Cheol Mun, Cheol-Seong Jang
Plant Breed. Biotech. 2016;4(2):176-187.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.176

Low temperature stress at the seedling stage of rice is an important factor causing the leaf discoloration, wilting and consequently leads to non-uniform crop maturation. In order to screen the cold tolerance elite lines efficiently, the five cold treatment conditions with different water and air temperature were designed and treated at seedling stage. For the evaluation of seedling tolerance, the injury was scored by visual rate and measured by Soil and Plant Analyzer Development (SPAD) meter. In the reactions of varieties for each treatment, the treatment ‘B’ condition, 12ºC mean water with 24ºC mean air, shows clear discoloration, so it’s correlation coefficient was highest (r=−0.9, P<0.0001) among the treatments. In the treatment condition for screening the cold-tolerance elite line, the cultivar, treatment and their interaction significantly affect the SPAD value. The ‘A’ treatment, 12ºC mean water with 34ºC mean air, was the best way to observe the variation between the elite lines. On the basis of the Duncan’s test for SPAD value of cultivars, Keumo (moderate tolerant), Saetbyeol (sensitive) and Seolak (tolerant) were selected as check varieties. To study its impacts at the paddy field, the changes of crop characteristics such as height, panicle length, number of tiller and heading were investigated. In later growth period, the seedling treatment impact at the paddy field leads to heading delay. Due to the low temperature stress at the seedling stage induced by 12ºC mean cold water, Japonica and Tongil group shows the heading delay 4 to 7 and 8 to 11 days respectively.

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    Sa-Eun Park, Ngoc Ha Luong, Sang-Nag Ahn, Kyu-Chan Shim
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  • 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
  • Haplotype analysis of Tongil-type rice varieties through sequence polymorphism analysis of cold tolerance-enhancing genes
    Youngeun Lee, Sais-Beul Lee, Ju-Won Kang, Jun-Hyeon Cho, Dong-Soo Park, Jong-Hee Lee, Dongjin Shin, Byung Jun Jin
    Journal of Plant Biotechnology.2024;[Epub]     CrossRef
  • Temporal Changes of Leaf Spectral Properties and Rapid Chlorophyll—A Fluorescence under Natural Cold Stress in Rice Seedlings
    Árpád Székely, Tímea Szalóki, Mihály Jancsó, János Pauk, Csaba Lantos
    Plants.2023; 12(13): 2415.     CrossRef
  • Efficient Cold Tolerance Evaluation of Four Species of Liliaceae Plants through Cell Death Measurement and Lethal Temperature Prediction
    Woo-Hyeong Yang, Seong-Hyeon Yong, Dong-Jin Park, Sung-Jin Ahn, Do-Hyun Kim, Kwan-Been Park, Eon-Ju Jin, Myung-Suk Choi
    Horticulturae.2023; 9(7): 751.     CrossRef
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Identification of Quantitative Trait Loci Associated with Grain Shape Using Cheongchenong/Nagdong Double Haploid Lines in Rice
Home Regina Wacera, Hyun-Suk Lee, Kyung-Min Kim
Plant Breed. Biotech. 2016;4(2):188-197.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.188

We performed a molecular marker-based analysis of quantitative trait loci (QTLs) for the traits that determine appearance quality of the grains using 120 double haploid (DH) lines developed by anther culture from F1 hybrid of a cross between Cheongcheong (Oryza sativa L. ssp. Indica) and Nagdong (Oryza sativa L. ssp. Japonica). The traits studied included grain length, grain width, grain thickness, length to width ration and thousand grain weight. This experiment was conducted with two replications of 2013 and 2014. A linkage map with 217 DNA markers was constructed spanning across 2,067.1 centiMorgans (cM) at an average interval of 9.5 cM between markers and covering 12 rice chromosomes. Interval mapping procedure was used to identify the QTLs controlling five grain traits and QTLs detected were further confirmed using composite interval mapping. A total of 24 QTLs affecting grain appearances were identified and mapped on all the twelve chromosomes for 2 years at grain quality. Nine of the 24 QTLs were reproducibly detected in two year trials. Major QTL for grain length was detected on chromosome 5 in 2013 with a phenotypic variation of 64% and chromosome 7 in 2014 that explained 55% of the phenotypic variation. The QTL findings in this study will in future faciltate the gene isolation and breeding application for improvement of rice grain shape and yield.

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  • Combined Linkage Mapping and Genome-Wide Association Study Identified QTLs Associated with Grain Shape and Weight in Rice (Oryza sativa L.)
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Parentage Confirmation of Korean Bred Pear Cultivars by Simple Sequence Repeat SSR Genotyping and S-Genotypes Analysis
Hoy-Taek Kim, Arif Hasan Khan Robin, Ill-Sup Nou
Plant Breed. Biotech. 2016;4(2):198-211.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.198

Identification and authentication of parentage are important for effective pear breeding. Within Korean pear cultivars discrepancies are often reported between parents and offspring in skin color of fruits and also in S-genotypes suggesting that reported parentage was often inappropriate. In Korea, the parentage of the most of pear cultivars was never confirmed at the molecular level. Simple sequence repeat (SSR) genotyping and S-genotype analysis are considered effective in identifying parents. In this study, parentage of nine Korean bred cultivars was confirmed using SSR genotyping and S-genotype analysis. A total of 53 SSR markers were used. Six different haplotype-specific endonucleases were used for restriction cleavage of S-genotypes. Most of the Korean bred cultivars had six comparatively shorter S-RNase, S1, S3, S4, S5, S6, or S7 of 450 bp in length whereas the Japanese control cultivars had four other comparatively longer S-RNase. Out of nine pear cultivars only ‘Chuwhangbae’ and ‘Whangkeumbae’ had identical SSR genotypes and S-genotype with previously reported parents. For another cultivar, ‘Sujeonbae’, the parents were the mutants of reported parent, ‘Niitaka’. For four other cultivars, SSR and S-genotypes of offspring matched with only one reported parent ‘Niitaka’ but those of another parent did not match. For the two other pear cultivars ‘Soowhangbae’ and ‘Sooyoung’ none of reported parents were confirmed by SSR genotyping and S-genotype analysis. Historically, the parent ‘Niitaka’ was predominant in the Korean pear breeding programs because of its high yield potential and quality. The methods have been used in this study could be used to identify pear cultivars with diverse S-genotypes to eliminate any existing obscure parent-offspring relations.

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  • Genetic Differentiation of Ornamental and Fruit-Bearing Prunus laurocerasus Revealed by SSR and S-Locus Markers
    Attila Hegedűs, Péter Honfi, Sezai Ercisli, Gulce Ilhan, Endre György Tóth, Júlia Halász
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  • Quantitative Trait Loci Analysis Related to Fruit Quality Traits in Interspecific Hybrid Derived from the Cross Between ‘Manpungbae’ and ‘Oharabeni’ Pear (Pyrus spp.)
    Keumsun Kim, Haewon Jung, Kyungho Won, Seok Kyu Yun, Young Sik Cho, Eu Ddeum Choi, Ung Yang
    Korean Journal of Breeding Science.2025; 57(4): 455.     CrossRef
  • Construction of a Bin Genetic Map and QTL Mapping of Red Skin in Interspecific Pear Population
    Xiaojie Zhang, Mengyue Tang, Jianying Peng, Hui Ma, Yuxing Zhang
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  • Phenotypic assessment of pear varieties in mutual pollination
    Nina Mozhar, E. Egorov, I. Ilina, N. Zaporozhets, E. Yakimenko
    BIO Web of Conferences.2021; 34: 01012.     CrossRef
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Characterization and Expression Analysis of Peroxidases and Glucan Synthase Like Genes in Cucumis melo L
Jewel Howlader, Kanij Rukshana Sumi, Hoy-Taek Kim, Arif Hasan Khan Robin, Jong-In Park, Mi-Young Chung, Ill-Sup Nou
Plant Breed. Biotech. 2016;4(2):212-224.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.212

Powdery mildew (PM) is a severe fungal disease for melon cultivation worldwide. Stress resistance related genes could be important tools to address this problem. In this study, we retrieved defense related peroxidase and glucan synthase genes from Melon Genome Database ‘Melonomics’. Thereafter, we analyzed the genes in silico. We conducted protein blast in the NCBI database and found a high degree of homology among them. Based on the highest protein homology we named two isoforms of Cucumis melo peroxidase 2-like genes (CmPrx2-1 and CmPrx2-2) and one glucan synthase1-like gene (CmGLS1). In reverse transcription- polymerase chain reaction (PCR), all 3 genes showed organ specific expression in a C. melo line, SCNU1154. Real-time quantitative PCR expression of these 3 genes was conducted in the infected leaf samples by PM fungus Podosphaera xanthii and also treated leaf samples by exogenous phytohormones (salicylic acid and methyl jasmonate). The CmPrx2-2 gene was up-regulated in response to all seven races of PM fungus whereas up-regulation or down-regulation of CmPrx2-1 gene was race-specific. The CmGLS1 gene was down-regulated in response to all races except one race. The CmPrx2-1, CmPrx2-2, and CmGLS1 genes were up-regulated under both salicylic acid and methyl jasmonate treatments but their level of expression was higher in salicylic acid treated plants compared to methyl jasmonate. Therefore, we speculate that defense response of the three tested genes is largely mediated by the salicylic acid signaling pathway under PM infection. Taken together, the data presented herein may be useful resources in the development of PM stress resistant in C. melo L.

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    Chahak Jain, Shilpa Gupta, Sat Pal Sharma, Manjeet Kaur Sangha, Navraj Kaur Sarao, Anu Kalia, Shabda Verma
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    Jinu Jacob, Madhu Pusuluri, Balakrishna Domathoti, Indra Kanta Das
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Identification of a New Race and Development of DNA Markers Associated with Powdery Mildew in Melon
Hoy-Taek Kim, Jong-In Park, Arif Hasan Khan Robin, Tomoko Ishikawa, Maki Kuzuya, Manabu Horii, Katsutoshi Yashiro, Ill-Sup Nou
Plant Breed. Biotech. 2016;4(2):225-233.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.225

Powdery mildew disease caused by an obligatory parasitic fungus Podosphaera xanthii is a serious problem of melon (Cucumis melo L.) production worldwide. Severity of problem is further associated with emergence of new races over the years. In this study a new race of powdery mildew fungus was discovered from Ibaraki, Japan. The race was different from all other existing races of P. xanthii occurring in Japan. Phenotypic and genetic analysis established the new fungus type as a new race, N5. Ten melon lines were infected with a total of eight fungal races including the new N5 race and it was found that all melon lines had different disease reactions against the new race compared to other seven races. Only four melon genotypes were found resistant out of 42 commercial cultivars and lines were tested. Disease reactions of two sets of F2 populations and one set of backcross population revealed that two separate epistatic gene loci located in two different linkage groups (LG), LG II and LG XII, interact together for the resistant or susceptible reaction of melon lines. A total of six simple sequence repeat (SSR) markers were found polymorphic in melon lines out of 16 tested in response to N5 race. Two different sets of F2 populations between resistant and susceptible melon lines were assessed with two polymorphic SSR markers located in two different groups, LG II and LG XII. SSR genotyping yielded 78% and 94% expected polymerase chain reaction fragments in favor of resistance or susceptibility of F2 populations of CM17187×PMR5 and PMR45×PMR5 of melon lines, respectively.

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    Journal of Plant Pathology.2025; 108(1): 777.     CrossRef
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    Aleš Lebeda, Eva Křístková, Barbora Mieslerová, Narinder P. S. Dhillon, James D. McCreight
    Critical Reviews in Plant Sciences.2024; 43(4): 211.     CrossRef
  • Identification of powdery mildew resistance quantitative trait loci in melon and development of resistant near-isogenic lines through marker-assisted backcrossing
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  • Identification of Gene Responsible for Conferring Resistance against Race KN2 of Podosphaera xanthii in Melon
    Sopheak Kheng, San-Ha Choe, Nihar Sahu, Jong-In Park, Hoy-Taek Kim
    International Journal of Molecular Sciences.2024; 25(2): 1134.     CrossRef
  • Fine mapping and identification of candidate genes associated with powdery mildew resistance in melon (Cucumis melo L.)
    Xiaoyu Duan, Yue Yuan, Núria Real, Mi Tang, Jian Ren, Jiaqi Wei, Bin Liu, Xuejun Zhang
    Horticulture Research.2024;[Epub]     CrossRef
  • Inheritance of Resistance to Race 5 of Powdery Mildew Fungus Podosphaera xanthii in Melon and Development of Race 5-Specific High Resolution Melting Markers
    Jeong-Eui Hong, Mohammad Rashed Hossain, Hee-Jeong Jung, Ill-Sup Nou
    Plant Breeding and Biotechnology.2022; 10(4): 272.     CrossRef
  • Development of powdery mildew race 5-specific SNP markers in Cucumis melo L. using whole-genome resequencing
    Jewel Howlader, Yeji Hong, Sathishkumar Natarajan, Kanij Rukshana Sumi, Hoy-Taek Kim, Jong-In Park, Ill-Sup Nou
    Horticulture, Environment, and Biotechnology.2020; 61(2): 347.     CrossRef
  • Genetic Mapping and Nucleotide Diversity of Two Powdery Mildew Resistance Loci in Melon (Cucumis melo)
    Cui Haonan, Ding Zhuo, Fan Chao, Zhu Zicheng, Zhang Hao, Gao Peng, Luan Feishi
    Phytopathology®.2020; 110(12): 1970.     CrossRef
  • PCR-Based InDel Marker Associated with Powdery Mildew-Resistant MR-1
    Yu-Ri Choi, Jae Yong Lee, Seongbin Hwang, Hyun Uk Kim
    Agronomy.2020; 10(9): 1274.     CrossRef
  • Identification of Two New Races of Podosphaera xanthii Causing Powdery Mildew in Melon in South Korea
    Ye-Ji Hong, Mohammad Rashed Hossain, Hoy-Taek Kim, Jong-In Park, Ill-Sup Nou
    The Plant Pathology Journal.2018; 34(3): 182.     CrossRef
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Genotypic Variation among Okra (Abelmoschus esculentus (L.) Moench) Germplasms in South India
Kishor Doddanakatte Shivaramegowda, Arya Krishnan, Yogeesh Kebbahalli Jayaramu, Vinod Kumar, Yashoda, Hee-Jong Koh
Plant Breed. Biotech. 2016;4(2):234-241.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.234

Thirty-six okra germplasms were grown and evaluated for yield and yield related traits at the Department of Plant Breeding and Genetics, Vellayani, Trivandrum, Kerala. The germplasms studied possessed sufficient variability for all the traits. High genotypic coefficient of variation (GCV) and phenotypic coefficient of variation (PCV) were noticed for almost all characters and narrow difference between GCV and PCV suggest that environmental influence is minimal for the traits studied. High estimates of heritability coupled with high to moderate genetic advance as percent over mean was recorded for all the characters considered. Yield had positive and significant association with number of fruits per plant, fruit weight, fruit girth and number of primary branches indicating that selection based on these characters may improve yield. Principal component analysis indicated that first three principal components contributed for sixty percent total variation among ten characters describing accessions. The cluster analysis revealed that hybridization of cluster I with cluster IV would be beneficial to develop promising varieties under diverse climatic conditions in India.

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    Andrews Appiah, Richard Akromah, Alexander Wireko Kena, Benjamin Annor, Stephen Amoah, Emmanuel Yaw Owusu, Benjamin Karikari
    Ecological Genetics and Genomics.2025; 35: 100347.     CrossRef
  • Genotypic Variation in Root System Architecture in Okra (Abelmoschus esculentus (L.) Moench) for Adaptive Breeding in Soil Resource‐Limited Environments
    Godswill Hygienus, Vincent Agyemang Opoku, Mathias Neumann Andersen, Paul Agu Asare, Michael Osei Adu
    Journal of Agronomy and Crop Science.2025;[Epub]     CrossRef
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  • Isolation of yellow vein mosaic virus (YVMV)‐resistant mutants of okra (Abelmoschus esculentus L.) through applied mutagenesis
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Plant Breed. Biotech. 2016;4(2):242-251.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.242

Blackberries (Rubus fruticosus L.) are a good source of antioxidants and contain appreciable levels of functional compounds. This study was carried out to evaluate fruit qualities (pH, soluble solids content, titratable acidity, and minerals), functional compounds (total phenolic content, total flavonoid content, anthocyanins, and ellagic acid), and antioxidant activity among five mutated blackberry lines over three ripening stages to examine the effect of fruit maturation on functional compounds and antioxidant activity. The content of sugars, total phenolic content, total flavonoid content, and anthocyanins (cyanidin-3-O-glucoside, cyanidin-3-O-xyloside, cyanidin-3-O-malonylglucoside, and cyanidin-3-O-dioxalylglucoside) increased as fruit development advanced, whereas the ellagic acid content decreased as the fruit became more mature. Among the minerals tested, potassium showed the highest concentrations at all stages of development. The antioxidant activity was correlated with total phenolic content (P≤0.01), total flavonoid content (P≤0.01), and total anthocyanins (P≤0.05). The results indicate that Maple and B201 lines contained the highest anthocyanin content and exhibited greater antioxidant activity.

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Phenotypic Analysis of Seed Yield and Yield Components in Cowpea (Vigna unguiculata L., Walp)
Olawale Mashood Aliyu, Bukola Oluwaseun Makinde
Plant Breed. Biotech. 2016;4(2):252-261.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.252

Poor seed yield remains a great challenge for cowpea production in sub-Sahara Africa and continuous evaluation of available genetic resource to develop high and stable yielding varieties is the panacea to this regional food security conundrum. In this study, 21 cowpea breeding lines were evaluated for phenotypic analysis of seed yield components for two years in a randomized complete block design of 3 replications. All the yield components exhibited significant genotypic variation, while flowering, pod maturity and seed yield traits recorded significant variation for years and its interactions. These cowpeas, which are predominantly early-medium maturing biotypes, exhibited relative phenotypic stability for the yield components across years (seasons) except seed yield, being a final product of complex physiological process. Relationships between flowering/pod maturity and seed size were positive and significant. By contrast, pods/plant, seeds/plant and total seed yield recorded negative correlations with pod maturity. However, seeds/plant and pods/plant are the most contributory components to seed-yield with correlation coefficients of r=0.95, 0.89, respectively. Although seed size had negative correlation with seeds/pod, but strong linkage between seed number (seeds/pod, seeds/plant) and seed yield; and additive gene nature of seed size, suggest a weak size-number trade-off in cowpea. Genetic variance components indicates high genetic contributions over non-genetic to plant phenotypic variability with high heritability values (0.75–0.91). Six cowpea lines (IT10K-837-1, IT07K-299-6, IT10K-815-5, IT10K-817-7, IT08K-150-24, and IT11K-61-82) with multiple quality yield traits could be selected for immediate farmers use and future genetic improvement.

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Estimates of Genetic Variability for Seedling Traits in Fluted Pumpkin (Telfairia occidentalis Hook. F)
Lawrence Stephen Fayeun, Lateef Akinkunle Hammed, Olusegun Adebayo Oduwaye, Jide Umar Madike, Edith Uqueen Ushie
Plant Breed. Biotech. 2016;4(2):262-270.   Published online May 31, 2016
DOI: https://doi.org/10.9787/PBB.2016.4.2.262

An experiment was conducted to evaluate genetic variation among twenty-one fluted pumpkin genotypes for seedling traits. The seeds of the fluted pumpkin were germinated in nursery bags filled with saw dust at the Federal University of Agriculture, Abeokuta and the Federal University of Technology, Akure, Nigeria between July and August, 2013. The experiment was laid out in completely randomized design with three replications. Characters evaluated were emergence percentage (E%), emergence index, emergence index rate, vine length (cm), leaf area (cm2), number of leaves, shoot dry weight (g), and seedling vigour index (SVI). Significant (P≤0.05) differences were observed among the fluted pumpkin genotypes for the evaluated characters. High E% was observed for genotypes Ftn45 (94.80%), Ftn43 (93.30%), Ftn57 (93.30%), Fte41 (90.0%), Ftn61 (86.70%), and Ftm11 (83.30%). Also, these genotypes had above average values for SVI. High phenotypic coefficients of variation and genotypic coefficients of variation were observed for leaf area (75.44%) and dry shoot weight (55.85%), respectively while heritability estimates above 50% was observed for leaf area (82.0%), dry weight (77.78%), E% (70.84%), and SVI (51.98%). The genetic advance was high for E% (38.37), SVI (38.09), and leaf area. SVI, E%, vine length, and leaf area had significant positive correlation with most of the traits therefore, they can be used as selection criteria in fluted pumpkin. Therefore, genetic improvement of early seedling can be used for selection programme in fluted pumpkin.

Citations

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