@article{lee_siddique_jang_kim_choi_kwon_kang_2024, title={Identification of QTLs associated with resistance to bacterial wilt in pepper (Capsicum annuum L.) through bi-parental QTL mapping and genome-wide association analysis}, volume={329}, ISSN={0304-4238}, url={http://dx.doi.org/10.1016/j.scienta.2024.112987}, DOI={10.1016/j.scienta.2024.112987}, abstractNote={Ralstonia solanacearum is responsible for causing bacterial wilt (BW) disease in solanaceous crops, leading to significant crop losses. The challenge in controlling this disease lies in its soil-borne nature and the complex genetic architecture of R. solanacearum. Moreover, the complex oligogenic nature of resistance genes makes breeding resistant cultivars in peppers difficult. In this study, we combined bi-parental quantitative trait loci (QTL) mapping and a genome-wide association study (GWAS) to map loci associated with BW resistance. An F5:7 recombinant inbred lines were subjected to genotyping by sequencing (GBS) and the GWAS panel was genotyped using an Illumina PepperSNP 16 K array genotyping platform. A significant QTL (QTL.Bw5) was identified on the telomeric region of chromosome 5. GWAS analysis also identified four loci associated with BW resistance (GWAS.Bw.4, GWAS.Bw.5, GWAS.Bw.8.1, and GWAS.Bw.8.2) on chromosomes 4, 5, and 8. Our study revealed 13 candidate genes within QTL regions and in the vicinity of GWAS single-nucleotide polymorphisms (SNPs) based on their biological gene functions. A majority of these candidate genes were associated with plant stress, defense, or hormone signaling pathways. The QTLs and GWAS-SNPs related to BW resistance will provide valuable information for further characterizing resistance genes and developing markers to facilitate the breeding of resistant pepper cultivars.}, journal={Scientia Horticulturae}, publisher={Elsevier BV}, author={Lee, Joung-Ho and Siddique, Muhammad Irfan and Jang, Siyoung and Kim, Geon-Woo and Choi, Gyung Ja and Kwon, Jin-Kyung and Kang, Byoung-Cheorl}, year={2024}, month={Apr}, pages={112987} }
 @article{siddique_silverman_louws_panthee_2024, title={Quantitative Trait Loci Mapping for Bacterial Wilt Resistance and Plant Height in Tomatoes}, volume={13}, ISSN={["2223-7747"]}, url={https://doi.org/10.3390/plants13060876}, DOI={10.3390/plants13060876}, abstractNote={Bacterial wilt (BW) of tomatoes, caused by Ralstonia solanacearum, is a devastating disease that results in large annual yield losses worldwide. Management of BW of tomatoes is difficult due to the soil-borne nature of the pathogen. One of the best ways to mitigate the losses is through breeding for disease resistance. Moreover, plant height (PH) is a crucial element related to plant architecture, which determines nutrient management and mechanical harvesting in tomatoes. An intraspecific F2 segregating population (NC 11212) of tomatoes was developed by crossing NC 84173 (tall, BW susceptible) × CLN1466EA (short, BW resistant). We performed quantitative trait loci (QTL) mapping using single nucleotide polymorphic (SNP) markers and the NC 11212 F2 segregating population. The QTL analysis for BW resistance revealed a total of three QTLs on chromosomes 1, 2, and 3, explaining phenotypic variation (R2) ranging from 3.6% to 14.9%, whereas the QTL analysis for PH also detected three QTLs on chromosomes 1, 8, and 11, explaining R2 ranging from 7.1% to 11%. This work thus provides information to improve BW resistance and plant architecture-related traits in tomatoes.}, number={6}, journal={PLANTS-BASEL}, author={Siddique, Muhammad Irfan and Silverman, Emily and Louws, Frank and Panthee, Dilip R.}, year={2024}, month={Mar} }
 @misc{siddique_younis_gururani_venkatesh_2023, title={Application of TILLING as a Reverse Genetics Tool to Discover Mutation in Plants Genomes for Crop Improvement}, ISBN={9789811697197 9789811697203}, url={http://dx.doi.org/10.1007/978-981-16-9720-3_9}, DOI={10.1007/978-981-16-9720-3_9}, abstractNote={The deployment of mutant resources for plant functional genomics is ever increasing with the availability of genome information of economically important crops. Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach for high-throughput discovery of induced mutations in the desired gene(s) from a mutant population developed through mutagenesis. TILLING accelerates trait discovery and crop genetic improvement. TILLING strategies for several crops have been developed for the identification of the desired mutants. The combined use of TILLING and the high-throughput sequencing technologies can overcome the bottlenecks of traditional TILLING approaches and facilitates the rapid discovery of useful mutations. Several important mutants related to economically important traits have been identified in agronomic and horticultural crops by employing TILLING by sequencing (TbyS) and, thus, have sizeable potential in crop improvement. In this chapter, we highlight significant developments in the use of TILLING strategies along with the application of high-throughput techniques, such as high-resolution melting (HRM) and next-generation sequencing (NGS) in the discovery of mutations and further discuss the challenges and prospects of TILLING in modern crop breeding.}, journal={Mutation Breeding for Sustainable Food Production and Climate Resilience}, publisher={Springer Nature Singapore}, author={Siddique, M. I. and Younis, A. and Gururani, M. A. and Venkatesh, J.}, year={2023}, pages={233–268} }
 @article{lee_siddique_kim_lee_han_kim_lee_2023, title={CRISPR/Cas9-mediated gene editing to confer turnip mosaic virus (TuMV) resistance in Chinese cabbage (<i>Brassica rapa</i>)}, volume={10}, ISSN={2052-7276}, url={http://dx.doi.org/10.1093/hr/uhad078}, DOI={10.1093/hr/uhad078}, abstractNote={Abstract}, number={6}, journal={Horticulture Research}, publisher={Oxford University Press (OUP)}, author={Lee, Ye-Rin and Siddique, Muhammad Irfan and Kim, Do-Sun and Lee, Eun Su and Han, Koeun and Kim, Sang-Gyu and Lee, Hye-Eun}, year={2023}, month={Apr} }
 @article{venkatesh_kim_siddique_kim_lee_kang_2023, title={CopE and TLR6 RNAi-mediated tomato resistance to western flower thrips}, volume={22}, ISSN={2095-3119}, url={http://dx.doi.org/10.1016/j.jia.2022.12.009}, DOI={10.1016/j.jia.2022.12.009}, abstractNote={The western flower thrips (WFT; Frankliniella occidentalis) is a mesophyll cell feeder that damages many crops. Management of WFT is complex due to factors such as high fecundity, short reproduction time, ability to feed on a broad range of host plants, and broad pesticide resistance. These challenges have driven research into developing alternative pest control approaches for WFT. This study analyzed the feasibility of a biological control-based strategy to manage WFT using RNA interference (RNAi)-mediated silencing of WTF endogenous genes. For the delivery of RNAi, we developed transgenic tomato lines expressing double-stranded RNA (dsRNA) of coatomer protein subunit epsilon (CopE) and Toll-like receptor 6 (TLR6) from WFT. These genes are involved in critical biological processes of WFT, and their dsRNA can be lethal to these insects when ingested orally. Adult WFT that fed on the transgenic dsRNA-expressing tomato flower stalk showed increased mortality compared with insects that fed on wild-type samples. In addition, WFT that fed on TLR6 and CopE transgenic tomato RNAi lines showed reduced levels of endogenous CopE and TLR6 transcripts, suggesting that their mortality was likely due to RNAi-mediated silencing of these genes. Thus, our findings demonstrate that transgenic tomato plants expressing dsRNA of TLR6 and CopE can be lethal to F. occidentalis, suggesting that these genes may be deployed to control insecticide-resistant WFT.}, number={2}, journal={Journal of Integrative Agriculture}, publisher={Elsevier BV}, author={Venkatesh, Jelli and Kim, Sung Jin and Siddique, Muhammad Irfan and Kim, Ju Hyeon and Lee, Si Hyeock and Kang, Byoung Cheorl}, year={2023}, month={Feb}, pages={471–480} }
 @article{patil_kim_kang_lee_mekonnen_siddique_han_2023, title={Genetic Analyses of Bolting Time in Radish (Raphanus sativus L.)}, volume={41}, number={1}, journal={Journal of Horitucultural Science and Technology}, author={Patil, A.S. and Kim, G.W. and Kang, M.Y. and Lee, H.Y. and Mekonnen, S.A. and Siddique, M.I. and Han, K.}, year={2023}, pages={215} }
 @article{adhikari_siddique_louws_panthee_2023, title={Identification of quantitative trait loci associated with bacterial spot race T4 resistance in intra-specific populations of tomato (Solanum lycopersicum L.)}, volume={18}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0295551}, DOI={10.1371/journal.pone.0295551}, abstractNote={Bacterial spot of tomato is a serious disease caused by at least four species and four races of Xanthomonas- X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (race T3 and T4), and X. gardneri, with X. perforans race T4 being predominant in the southeast USA. Practical management of this disease is challenging because of the need for more effective chemicals and commercially resistant cultivars. Identification of genetic resistance is the first step to developing a disease-resistant variety. The objective of this study was to identify quantitative trait loci (QTL) conferring resistance to race T4 in two independent recombinant inbred lines (RILs) populations NC 10204 (intra-specific) and NC 13666 (interspecific) developed by crossing NC 30P x NC22L-1(2008) and NC 1CELBR x PI 270443, respectively. Seven QTLs on chromosomes 2, 6, 7, 11, and 12 were identified in NC 10204. The QTL on chromosome 6 explained the highest percentage of phenotypic variance (up to 21.3%), followed by the QTL on chromosome 12 (up to 8.2%). On the other hand, the QTLs on chromosomes 1, 3, 4, 6, 7, 8, 9, and 11 were detected in NC 13666. The QTLs on chromosomes 6, 7, and 11 were co-located in NC 10204 and NC 13666 populations. The donor of the resistance associated with these QTL in NC 10204 is a released breeding line with superior horticultural traits. Therefore, both the donor parent and the QTL information will be useful in tomato breeding programs as there will be minimal linkage drag associated with the bacterial spot resistance.}, number={12}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Adhikari, Pragya and Siddique, Muhammad Irfan and Louws, Frank J. and Panthee, Dilip R.}, editor={Pandey, Abhay K.Editor}, year={2023}, month={Dec}, pages={e0295551} }
 @inproceedings{siddique_blume_zhang_panthee_2023, title={Mapping QTL for Septoria Leaf Spot Resistance in Tomato}, booktitle={Annual conference of American Society of Horticultural Science}, author={Siddique, M.I. and Blume, Jackie and Zhang, Jianbo and Panthee, Dilip}, year={2023}, month={Aug} }
 @article{adhikari_siddique_louws_sim_panthee_2023, title={Molecular mapping of quantitative trait loci for resistance to early blight in tomatoes}, volume={14}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2023.1135884}, DOI={10.3389/fpls.2023.1135884}, abstractNote={Early blight (EB), caused by Alternaria linariae (Neerg.) (syn. A. tomatophila) Simmons, is a disease that affects tomatoes (Solanum lycopersicum L.) throughout the world, with tremendous economic implications. The objective of the present study was to map the quantitative trait loci (QTL) associated with EB resistance in tomatoes. The F2 and F2:3 mapping populations consisting of 174 lines derived from NC 1CELBR (resistant) × Fla. 7775 (susceptible) were evaluated under natural conditions in the field in 2011 and in the greenhouse in 2015 by artificial inoculation. In all, 375 Kompetitive Allele Specific PCR (KASP) assays were used for genotyping parents and the F2 population. The broad-sense heritability estimate for phenotypic data was 28.3%, and 25.3% for 2011, and 2015 disease evaluations, respectively. QTL analysis revealed six QTLs associated with EB resistance on chromosomes 2, 8, and 11 (LOD 4.0 to 9.1), explaining phenotypic variation ranging from 3.8 to 21.0%. These results demonstrate that genetic control of EB resistance in NC 1CELBR is polygenic. This study may facilitate further fine mapping of the EB-resistant QTL and marker-assisted selection (MAS) to transfer EB resistance genes into elite tomato varieties, including broadening the genetic diversity of EB resistance in tomatoes.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Adhikari, Tika B. and Siddique, Muhammad Irfan and Louws, Frank J. and Sim, Sung-Chur and Panthee, Dilip R.}, year={2023}, month={May} }
 @misc{siddique_younis_naing_kim_2022, title={Cisgenic Crops and Disease Resistance}, ISBN={9783031066276 9783031066283}, ISSN={2662-3188 2662-3196}, url={http://dx.doi.org/10.1007/978-3-031-06628-3_8}, DOI={10.1007/978-3-031-06628-3_8}, abstractNote={Plant breeding is a continuous process in which genetic variation and heritability of a trait are essential. Cisgenesis and intragenesis are biotechnology techniques employed to generate additional genetic diversity in the current germplasm to improve their productivity. The development in sequencing approaches and the genome information accessibility simplifies isolation of integral Cis-genes, in conjunction with related promoter/terminator from the same species, and are introduced into the identical or a closely related genome, sexually compatible species, whereas in intragenesis, diverse coding and controlling sequences are accumulated either in a sense or in antisense alignment. This chapter illustrates the present status, applications, constraints, and prospects of cisgenesis and intragenesis to improve crop disease resistance. Further comparisons of cisgenesis, intragenesis, and transgenesis in an era of genome editing to develop cisgenic crops were described. This technique has been utilized to develop disease-resistant cultivars, such as the late blight-resistant potato, by transferring gene Rpi-sto1, Rpi-vnt1.1; similarly, scab resistance gene HcrVF2 for the development of apple cultivars and Vvtl-1, NtpII genes for grapes resistant to fungal diseases. Therefore, we can infer cisgenesis as an influential substitute to transfer the desired gene without linkage drag. Hence, it can be concluded that both cisgenic and intragenic derived genetically modified plants (GMP) are as sustainable and eco-friendly as traditionally bred plants and, therefore, excused from GMP regulation.}, journal={Concepts and Strategies in Plant Sciences}, publisher={Springer International Publishing}, author={Siddique, Muhammad Irfan and Younis, Adnan and Naing, Aung Htay and Kim, Chang Kil}, year={2022}, pages={145–167} }
 @article{ilyas_jin_siddique_lee_kim_chua_2022, title={DIANA: A deep learning-based paprika plant disease and pest phenotyping system with disease severity analysis}, volume={13}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2022.983625}, DOI={10.3389/fpls.2022.983625}, abstractNote={The emergence of deep neural networks has allowed the development of fully automated and efficient diagnostic systems for plant disease and pest phenotyping. Although previous approaches have proven to be promising, they are limited, especially in real-life scenarios, to properly diagnose and characterize the problem. In this work, we propose a framework which besides recognizing and localizing various plant abnormalities also informs the user about the severity of the diseases infecting the plant. By taking a single image as input, our algorithm is able to generate detailed descriptive phrases (user-defined) that display the location, severity stage, and visual attributes of all the abnormalities that are present in the image. Our framework is composed of three main components. One of them is a detector that accurately and efficiently recognizes and localizes the abnormalities in plants by extracting region-based anomaly features using a deep neural network-based feature extractor. The second one is an encoder–decoder network that performs pixel-level analysis to generate abnormality-specific severity levels. Lastly is an integration unit which aggregates the information of these units and assigns unique IDs to all the detected anomaly instances, thus generating descriptive sentences describing the location, severity, and class of anomalies infecting plants. We discuss two possible ways of utilizing the abovementioned units in a single framework. We evaluate and analyze the efficacy of both approaches on newly constructed diverse paprika disease and pest recognition datasets, comprising six anomaly categories along with 11 different severity levels. Our algorithm achieves mean average precision of 91.7% for the abnormality detection task and a mean panoptic quality score of 70.78% for severity level prediction. Our algorithm provides a practical and cost-efficient solution to farmers that facilitates proper handling of crops.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Ilyas, Talha and Jin, Hyungjun and Siddique, Muhammad Irfan and Lee, Sang Jun and Kim, Hyongsuk and Chua, Leon}, year={2022}, month={Oct} }
 @article{siddique_lee_ahn_kusumawardhani_safitri_harpenas_kwon_kang_2022, title={Genotyping-by-sequencing-based QTL mapping reveals novel loci for Pepper yellow leaf curl virus (PepYLCV) resistance in Capsicum annuum}, volume={17}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0264026}, DOI={10.1371/journal.pone.0264026}, abstractNote={Disease caused by Pepper yellow leaf curl virus (PepYLCV) is one of the greatest threats to pepper (Capsicum spp.) cultivation in the tropics and subtropics. Resistance to PepYLCV was previously identified in a few Capsicum accessions, but no resistance QTLs have been mapped. This study aimed to elucidate the genetics of PepYLCV resistance in C. annuum L. Augmented inoculation by the viruliferous whitefly Bemisia tabaci was used to evaluate parental lines and an F2 segregating population derived from a cross between resistant C. annuum line LP97 and susceptible C. annuum line ECW30R. Final evaluation was performed six weeks after inoculation using a standardized 5-point scale (0 = no symptoms to 4 = very severe symptoms). A high-density linkage map was constructed using genotyping-by-sequencing (GBS) to identify single-nucleotide polymorphism (SNP) markers associated with PepYLCV resistance in the F2 population. QTL analysis revealed three QTLs, peplcv-1, peplcv-7, and peplcv-12, on chromosomes P1, P7, and P12, respectively. Candidate genes associated with PepYLCV resistance in the QTL regions were inferred. In addition, single markers Chr7-LCV-7 and Chr12-LCV-12 derived from the QTLs were developed and validated in another F2 population and in commercial varieties. This work thus provides not only information for mapping PepYLCV resistance loci in pepper but also forms the basis for future molecular analysis of genes involved in PepYLCV resistance.}, number={2}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Siddique, Muhammad Irfan and Lee, Joung-Ho and Ahn, Jung-Hwan and Kusumawardhani, Meirina Kartika and Safitri, Ramadhani and Harpenas, Asep and Kwon, Jin-Kyung and Kang, Byoung-Cheorl}, editor={Rahimi, MehdiEditor}, year={2022}, month={Feb}, pages={e0264026} }
 @article{hanif_khan_kiran_ul haq_ali_niaz_ali_arshad_ansari_alharbi_et al._2022, title={Interactive effect of organic and mineral phosphorus on volatile compounds, morphology, and physiology of garlic (Allium sativum L.)}, volume={34}, ISSN={["2213-686X"]}, DOI={10.1016/j.jksus.2022.102351}, abstractNote={Phosphorus (P) is a macronutrient required by the plants for their normal growth and development. However, the impacts of different forms of P have been rarely tested on the morphology, physiology, and biochemical attributes of garlic (Allium sativum L.) This study examined interactive effect of mineral-P (mP) as single super phosphate (SSP), and organic-P (oP) as farmyard manure (FYM) on morphological, physiological traits and volatile sulfur containing compounds of garlic. The treatments included T0 = control, T1 = 50 kg ha−1 mP, T2 = 70 kg ha−1 mP, T3 = 90 kg ha−1 mP, T4 = 50 kg ha−1 mP + oP ≈ 50 kg ha−1, T5 = 70 kg ha−1 mP + oP ≈ 60 kg ha−1, T6 = 90 kg ha−1 mP + oP ≈ 30 kg ha−1, and T7 = 50 kg ha−1 mP + oP ≈ 90 kg ha−1. The plant morphological and physiological traits as well as contents of the volatile sulfur containing compounds were significantly altered by the interactive effect of mP and oP. The garlic plants that were treated with T7 generated the maximum bulb output (4382.96 kg ha−1), followed by those fertilized with T5, T6, T2, and T4 which produced 4205.43, 4164.10, 3992.73, and 3916.30 kg ha−1, respectively. The harvest was brought down to 3722.80 kg ha−1 in T3, and it was just 3509.95 kg ha−1 in T1. The response of volatile sulfur containing compounds in garlic leaves (detected by GC–MS and HPLC analysis) indicated that in T7 enormously higher count of constituents in garlic leaves were determined which include aldehydes (3.254 µg/g), hydrocarbons(1.245 µg/g), esters (0.547 µg/g), acids (1.658 µg/g), sulfides (4.985 µg/g), ketones (1.254 µg/g), ethers (8.888 µg/g), alkaloids (0.357 µg/g), heterocyclic polymers (2.684 µg/g), cyclomethycaines (1.854 µg/g), polyolefins (0.214 µg/g), furfuryl and furan derivatives (0.987 µg/g), phenols (0.666 µg/g) and diterpenes(1.256 µg/g). It is noticeable that in absence of oP, the highest level of mP could not improve the volatile compounds, but higher rate of oP even under lower portion of mP recorded higher concentration of the volatile compounds in garlic leaves. Therefore, combined application of organic and mineral P is recommended for better yield and quality of garlic.}, number={8}, journal={JOURNAL OF KING SAUD UNIVERSITY SCIENCE}, author={Hanif, Medhia and Khan, Rabia and Kiran, Javeria and Ul Haq, Inzamam and Ali, Shahbaz and Niaz, Yasir and Ali, Azad and Arshad, Muhammad and Ansari, Mohammad Javed and Alharbi, Sulaiman Ali and et al.}, year={2022}, month={Nov} }
 @article{asekova_oh_kulkarni_siddique_lee_kim_lee_kim_oh_ha_et al._2021, title={An Integrated Approach of QTL Mapping and Genome-Wide Association Analysis Identifies Candidate Genes for Phytophthora Blight Resistance in Sesame (Sesamum indicum L.)}, volume={12}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85101963790&partnerID=MN8TOARS}, DOI={10.3389/fpls.2021.604709}, abstractNote={Phytophthora blight (PB) caused byPhytophthora nicotianaeis a highly destructive disease in sesame (Sesamum indicumL.). In this study, we used linkage mapping and genome-wide association study (GWAS) to identify quantitative trait loci (QTL) and candidate genes associated with PB resistance. The QTL mapping in 90 RILs of the Goenbaek × Osan cross using genotyping-by-sequencing detected significant QTLs for PB resistance on chromosome 10, explaining 12.79%–13.34% of phenotypic variation. Association of this locus to PB resistance was also revealed through bulked segregant analysis in second RIL population (Goenbaek × Milsung cross) comprising 188 RILs. The GWAS of 87 sesame accessions evaluated against threeP. nicotianaeisolates identified 29 SNPs on chromosome 10 significantly associated with PB resistance. These SNPs were located within a 0.79 Mb region, which co-located with the QTL intervals identified in RIL populations, and hence scanned for identifying candidate genes. This region contained several defense-related candidateRgenes, five of which were selected for quantitative expression analysis. One of these genes,SIN_1019016was found to show significantly higher expression in the resistant parent compared to that in the susceptible parents and selected RILs. Paired-end sequencing of the geneSIN_1019016in parental cultivars revealed two synonymous SNPs between Goenbaek and Osan in exon 2 of coding DNA sequence. These results suggestedSIN_1019016as one of the candidate gene conferring PB resistance in sesame. The findings from this study will be useful in the marker-assisted selection as well as the functional analysis of PB resistance candidate gene(s) in sesame.}, journal={Frontiers in Plant Science}, author={Asekova, S. and Oh, E. and Kulkarni, K.P. and Siddique, M.I. and Lee, M.H. and Kim, J.I. and Lee, J.-D. and Kim, M. and Oh, K.-W. and Ha, T.-J. and et al.}, year={2021} }
 @article{lee_siddique_kwon_kang_2021, title={Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici}, volume={12}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2021.694136}, DOI={10.3389/fmicb.2021.694136}, abstractNote={Phytophthora capsici is an oomycete pathogen responsible for damping off, root rot, fruit rot, and foliar blight in popular vegetable and legume crops. The existence of distinct aggressiveness levels and physiological races among the P. capsici population is a major constraint to developing resistant varieties of host crops. In the present study, we compared the genomes of three P. capsici isolates with different aggressiveness levels to reveal their genomic differences. We obtained genome sequences using short-read and long-read technologies, which yielded an average genome size of 76 Mbp comprising 514 contigs and 15,076 predicted genes. A comparative genomic analysis uncovered the signatures of accelerated evolution, gene family expansions in the pathogenicity-related genes among the three isolates. Resequencing two additional P. capsici isolates enabled the identification of average 1,023,437 SNPs, revealing the frequent accumulation of non-synonymous substitutions in pathogenicity-related gene families. Furthermore, pathogenicity-related gene families, cytoplasmic effectors and ATP binding cassette (ABC) transporters, showed expansion signals in the more aggressive isolates, with a greater number of non-synonymous SNPs. This genomic information explains the plasticity, difference in aggressiveness levels, and genome structural variation among the P. capsici isolates, providing insight into the genomic features related to the evolution and pathogenicity of this oomycete pathogen.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Lee, Joung-Ho and Siddique, Muhammad Irfan and Kwon, Jin-Kyung and Kang, Byoung-Cheorl}, year={2021}, month={Aug} }
 @article{lee_kim_lee_han_siddique_back_kim_lee_2021, title={Evaluation of Gummy Stem Blight Resistance and Selection for Development of Inbred Line in Wild Watermelon (Citrullus spp}, volume={39}, number={2}, journal={Journal of Horticultural Science and Technology}, author={Lee, E.S. and Kim, D.S. and Lee, H.E. and Han, K. and Siddique, M.I. and Back, C.G. and Kim, S.G. and Lee, O.}, year={2021}, pages={211–212} }
 @inproceedings{kim_solomon_han_lee_patil_siddique_ahn_2021, title={Fine Mapping and Candidate Capup Gene Identification Controlling Fruit Orientation in Pepper (Capsicum spp.)}, booktitle={Korean Society of Breeding Studies}, author={Kim, T.G. and Solomon, A.M. and Han, K. and Lee, H.Y. and Patil, A. and Siddique, M.I. and Ahn, J.}, year={2021}, pages={289} }
 @article{solomon_kim_han_lee_patil_siddique_ahn_kang_2021, title={Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)}, volume={12}, url={http://dx.doi.org/10.3389/fpls.2021.675474}, DOI={10.3389/fpls.2021.675474}, abstractNote={The orientation of fruits is a distinguishing morphological feature of pepper (Capsicum spp.) varieties. The pendent (downward curved) growth of the fruit stalks, known as pedicels, is highly correlated with fruit weight and pedicel length. A previous genetic analysis revealed that the pendent fruit orientation is governed by a dominant gene, and incomplete inheritance is also observed in some Capsicum accessions. To identify and localize this gene, a single quantitative trait locus (QTL) analysis was performed on one F2 and two recombinant inbred line (RIL) populations, and a genome-wide association study (GWAS) was performed using a core collection. Common QTL regions associated with fruit orientation were detected on chromosome 12. A total of 187,966 SNPs were identified in a genotyping-by-sequencing (GBS) for GWAS analysis of 196 Capsicum annuum, 25 Capsicum baccatum, 21 Capsicum chinense, and 14 Capsicum frutescens accessions, representing the germplasm collection of South Korea. The results of these analyses enabled us to narrow down the CapUp region of interest to 200–250 Mbp on chromosome 12. Seven candidate genes were found to be located between two markers that were completely cosegregated with the fruit orientation phenotype. The findings and markers developed in this study will be helpful for additional understanding of pepper fruit development and breeding for fruit orientation.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Solomon, Abate Mekonnen and Kim, Tae-Gun and Han, Koeun and Lee, Hea-Young and Patil, Abhinandan and Siddique, Muhammad Irfan and Ahn, Jeonghwan and Kang, Byoung-Cheorl}, year={2021}, month={Jun} }
 @inproceedings{han_lee_lee_siddique_lee_park_kim_2021, title={Genetic mapping of a locus for restorer gene of Ogura cytoplasmic male sterility in radish (Raphanus sativus L.)}, booktitle={Annual Conference of the Korean Society for Breeding Science}, author={Han, Koeun and Lee, Jieun and Lee, Eun-Su and Siddique, M.I. and Lee, Hye-Eun and Park, Han Yong and Kim, Do-Sun}, year={2021}, month={Jul} }
 @inproceedings{siddique_lee_lee_lee_han_kim_2021, title={Genome editing of eIF4E1 in Chinese cabbage confers resistance to turnip mosaic virus}, booktitle={Annual Fall Conference of the Korean Society of the Horticultural Science}, author={Siddique, M.I. and Lee, Ye-Rin and Lee, Hye-Eun and Lee, Eun Su and Han, Koeun and Kim, Do-Sun}, year={2021}, month={Oct} }
 @article{lee_siddique_lee_lee_han_kim_2021, title={Genome editing of eIF4E1 in Chinese cabbage confers resistance to turnip mosaic virus}, volume={39}, number={2}, journal={Journal of Horticultural Science and Technology}, author={Lee, H.E. and Siddique, M.I. and Lee, Y.R. and Lee, E.S. and Han, K. and Kim, D.S.}, year={2021}, pages={210} }
 @article{lee_kim_han_choi_han_lee_kim_lee_siddique_lee_2021, title={Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (Allium cepa L.)}, volume={10}, ISSN={2223-7747}, url={http://dx.doi.org/10.3390/plants10112267}, DOI={10.3390/plants10112267}, abstractNote={Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F2 segregating population derived from a cross between the doubled haploid line ‘16P118’ and inbred line ‘Sweet Green’ through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (qSC4.1), glucose (qGC5.1), fructose (qFC5.1), and total sugar content (qTSC5.1) explaining the phenotypic variation (R2%) ranging from 6.07–11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.}, number={11}, journal={Plants}, publisher={MDPI AG}, author={Lee, Ye-Rin and Kim, Cheol Woo and Han, JiWon and Choi, Hyun Jin and Han, Koeun and Lee, Eun Su and Kim, Do-Sun and Lee, Jundae and Siddique, Muhammad Irfan and Lee, Hye-Eun}, year={2021}, month={Oct}, pages={2267} }
 @inproceedings{han_jo_yeum_manivannan_siddique_2021, title={Identification of QTLs controlling fruit firmness of octoploid strawberry (Fragaria× ananassa) by integrating GWAS and QTL analysis}, volume={2021}, number={1}, booktitle={Korean Society of Breeding Studies}, author={Han, K. and Jo, J. and Yeum, J.G. and Manivannan, A. and Siddique, M.I.}, year={2021}, pages={100–100} }
 @article{siddique_han_lee_lee_lee_lee_lee_kim_2021, title={QTL Analysis for Chlorophyll Content in Strawberry (Fragaria × ananassa Duch.) Leaves}, volume={11}, ISSN={2077-0472}, url={http://dx.doi.org/10.3390/agriculture11111163}, DOI={10.3390/agriculture11111163}, abstractNote={Chlorophyll is an important factor facilitating plants to capture, allocate and transforms light energy and plays a major role in yield formation. Strawberry is one of the most important fruit crops worldwide. Breeding strawberry for better light utilization by improving photosynthetic efficiency can improve the yield potential. In strawberry, genetic studies have been done for several traits, but no reports on the genetic mapping of chlorophyll content in leaves. In the present study, we used two independent F2 mapping populations (BS-F2 and BC-F2) and, Axiom 35 K strawberry chip and genotyping-by-sequencing derived single nucleotide polymorphisms based linkage maps to identify the quantitative trait loci (QTLs) controlling leaf chlorophyll content. SPAD values were used to estimate the leaf chlorophyll content of parental lines and F2 populations. A total of seven QTLs, including major and minor effects, common and specific to populations, were identified across the strawberry genome explaining phenotypic variation (R2) ranging from 1.4 to 26.4%. Candidate genes associated with the photosynthesis and chlorophyll content were inferred in commonly detected QTLs. This work thus provides not only information for novel loci controlling chlorophyll content in strawberry leaves but also forms the basis for future marker assisted breeding in strawberry to select the plants for required chlorophyll content.}, number={11}, journal={Agriculture}, publisher={MDPI AG}, author={Siddique, Muhammad Irfan and Han, Koeun and Lee, Jieun and Lee, Eun Su and Lee, Ye-Rin and Lee, Hye-Eun and Lee, Sun Yi and Kim, Do-Sun}, year={2021}, month={Nov}, pages={1163} }
 @article{lee_kim_kim_huh_back_lee_siddique_han_lee_lee_2021, title={QTL Mapping for Gummy Stem Blight Resistance in Watermelon (Citrullus spp.)}, volume={10}, ISSN={2223-7747}, url={http://dx.doi.org/10.3390/plants10030500}, DOI={10.3390/plants10030500}, abstractNote={Watermelon (Citrulluslanatus) is an economically important fruit crop worldwide. Gummy stem blight (GSB) is one of the most damaging diseases encountered during watermelon cultivation. In the present study, we identified quantitative trait loci (QTLs) associated with GSB resistance in an F2 population derived from a cross between maternal-susceptible line ‘920533’ (C. lanatus) and the paternal-resistant line ‘PI 189225’ (C. amarus). The resistance of 178 F2 plants was assessed by two different evaluation methods, including leaf lesion (LL) and stem blight (SB). To analyze the QTLs associated with GSB resistance, a linkage map was constructed covering a total genetic distance of 1070.2 cM. QTL analysis detected three QTLs associated with GSB resistance on chromosome 8 and 6. Among them, two QTLs, qLL8.1 and qSB8.1 on chromosome 8 identified as major QTLs, explaining 10.5 and 10.0% of the phenotypic variations localizing at same area and sharing the same top markers for both LL and SB traits, respectively. A minor QTL, qSB6.1, explains 9.7% of phenotypic variations detected on chromosome 6 only for the SB trait. High-throughput markers were developed and validated for the selection of resistant QTLs using watermelon accessions, and commercial cultivars. Four potential candidate genes were predicted associated with GSB resistance based on the physical location of flanking markers on chromosome 8. These findings will be helpful for the development of watermelon cultivars resistant to GSB.}, number={3}, journal={Plants}, publisher={MDPI AG}, author={Lee, Eun Su and Kim, Do-Sun and Kim, Sang Gyu and Huh, Yun-Chan and Back, Chang-Gi and Lee, Ye-Rin and Siddique, Muhammad Irfan and Han, Koeun and Lee, Hye-Eun and Lee, Jundae}, year={2021}, month={Mar}, pages={500} }
 @inproceedings{siddique_han_lee_lee_lee_lee_lee_kim_2021, title={QTL mapping for the leaf chlorophyll content in octoploid strawberry (Fragaria x ananassa}, booktitle={Annual Conference of the Korean Society for Breeding Science}, author={Siddique, M.I. and Han, Koeun and Lee, Jieun and Lee, Hye-Eun and Lee, Ye-Rin and Lee, Sun Yi and Lee, Eun Su and Kim, Do-Sun}, year={2021}, month={Jul} }
 @inproceedings{siddique_han_lee_lee_lee_lee_lee_kim_2021, title={QTL mapping for the leaf chlorophyll content in strawberry (Fragaria x ananassa)}, volume={2021}, number={1}, booktitle={Korean Society of Breeding Studies}, author={Siddique, M.I. and Han, K. and Lee, J. and Lee, H.E. and Lee, Y.R. and Lee, S.Y. and Lee, E.S. and Kim, D.S.}, year={2021}, pages={295} }
 @article{siddique_din_ahmad_ali_naz_alam_ullah_2020, title={Bioefficacy of Some Aqueous Phytoextracts Against Clavibacter Michiganensis Subsp. Michiganensis (Smith), the Cause of Bacterial Canker of Tomato}, volume={72}, ISSN={0367-4223 1439-0345}, url={http://dx.doi.org/10.1007/s10343-020-00503-9}, DOI={10.1007/s10343-020-00503-9}, abstractNote={Abstract}, number={3}, journal={Gesunde Pflanzen}, publisher={Springer Science and Business Media LLC}, author={Siddique, Muhammad and Din, Naseerud and Ahmad, Musharaf and Ali, Asad and Naz, Ishrat and Alam, Syed Sartaj and Ullah, Najeeb}, year={2020}, month={May}, pages={207–217} }
 @article{siddique_back_lee_jo_jang_han_venkatesh_kwon_jo_kang_2020, title={Development and Characterization of an Ethyl Methane Sulfonate (EMS) Induced Mutant Population in <i>Capsicum annuum</i> L.}, volume={9}, url={https://www.mdpi.com/2223-7747/9/3/396}, DOI={10.3390/plants9030396}, abstractNote={Plant breeding explores genetic diversity in useful traits to develop new, high-yielding, and improved cultivars. Ethyl methane sulfonate (EMS) is a chemical widely used to induce mutations at loci that regulate economically essential traits. Additionally, it can knock out genes, facilitating efforts to elucidate gene functions through the analysis of mutant phenotypes. Here, we developed a mutant population using the small and pungent ornamental Capsicum annuum pepper “Micro-Pep”. This accession is particularly suitable for mutation studies and molecular research due to its compact growth habit and small size. We treated 9500 seeds with 1.3% EMS and harvested 3996 M2 lines. We then selected 1300 (32.5%) independent M2 families and evaluated their phenotypes over four years. The mutants displayed phenotypic variations in plant growth, habit, leaf color and shape, and flower and fruit morphology. An experiment to optimize Targeting Induced Local Lesions IN Genomes (TILLING) in pepper detected nine EMS-induced mutations in the eIF4E gene. The M2 families developed here exhibited broad phenotypic variation and should be valuable genetic resources for functional gene analysis in pepper molecular breeding programs using reverse genetics tools, including TILLING.}, number={3}, journal={Plants}, publisher={MDPI AG}, author={Siddique, Muhammad Irfan and Back, Seungki and Lee, Joung-Ho and Jo, Jinkwan and Jang, Siyoung and Han, Koeun and Venkatesh, Jelli and Kwon, Jin-Kyung and Jo, Yeong Deuk and Kang, Byoung-Cheorl}, year={2020}, month={Mar}, pages={396} }
 @article{kim_pa wai_siddique_mo_yoo_kim_hong_2020, title={First report of phytophthora leaf blight and vine rot of kudzu (Pueraria lobata) in Korea}, volume={26}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85091878925&partnerID=MN8TOARS}, DOI={10.5423/RPD.2020.26.2.103}, abstractNote={Evaluations were made for the effects of cheese whey treatment on infection of pepper plants by cucumber mosaic virus-Vch (CMV-Vch) and pepper mottle virus-Kr (PepMoV-Kr). In a greenhouse, pepper plants sprayed with whey, prior to inoculation by CMV-Vch using aphids, showed a viral infection rate significantly lower (6.6%) than for the control (23.3%). In an open field experiment, in which CMV infection relied on natural transmission by aphids, pepper plants were sprayed with undiluted whey once a week, starting on the transplanting date (May 2) to the end of June. On June 5, these whey-sprayed plants showed a CMV infection rate reduced by 18.9% and 16.7%, compared to untreated and pesticide-treated plants, respectively. In the greenhouse, pepper plants inoculated with PepMoV-Kr mixed with whey showed a viral infection rate decreased by 60% compared to the control. The accumulated amount of PepMoV-Kr coat protein was less than that for the virusonly control at 6 days post inoculation (dpi), but increased up to a similar level as the control at 9 dpi. This study showed that cheese whey is effective in reducing infection of both CMV and PepMoV in pepper plants.}, number={2}, journal={Research in Plant Disease}, author={Kim, B.-S. and Pa Wai, K.P. and Siddique, M.I. and Mo, H.-S. and Yoo, H.J. and Kim, H.S. and Hong, S.-B.}, year={2020}, pages={109–115} }
 @inproceedings{siddique_2019, title={Combined Linkage and Association Mapping Reveals Novel QTLs and Candidate Genes for Phytophthora capsici Root Rot in Capsicum annuum}, booktitle={International Horticulture Conference}, author={Siddique, M.I.}, year={2019}, month={Feb} }
 @inproceedings{siddique_lee_kang_2019, title={Comparative genomic analysis of three isolates of Phytophthora capsici}, booktitle={Kim Dae-jung Convention Center}, author={Siddique, M.I. and Lee, Joung-Ho and Kang, Byoung-Cheorl}, year={2019} }
 @article{siddique_lee_ro_han_venkatesh_solomon_patil_changkwian_kwon_kang_2019, title={Identifying candidate genes for Phytophthora capsici resistance in pepper (Capsicum annuum) via genotyping-by-sequencing-based QTL mapping and genome-wide association study}, volume={9}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-019-46342-1}, DOI={10.1038/s41598-019-46342-1}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Siddique, Muhammad Irfan and Lee, Hea-Young and Ro, Na-Young and Han, Koeun and Venkatesh, Jelli and Solomon, Abate Mekonnen and Patil, Abhinandan Surgonda and Changkwian, Amornrat and Kwon, Jin-Kyung and Kang, Byoung-Cheorl}, year={2019}, month={Jul} }
 @inproceedings{patil_kang_lee_mekonnen_siddique_han_2019, place={MY Kang, HY Lee, SA Mekonnen, MI}, title={Integrated bi-parental quantitative trait loci mapping and genome-wide association provides novel candidate genes for plant height and habits in pepper (Capsicum annuum) using a superior Dempsey reference genome}, volume={2019}, number={1}, booktitle={Korean Society of Breeding Studies}, publisher={Siddique, K Han. Korean Society of Breeding Studies}, author={Patil, A.S. and Kang, M.Y. and Lee, H.Y. and Mekonnen, S.A. and Siddique, M.I. and Han, K.}, year={2019}, pages={230–230} }
 @article{changkwian_venkatesh_lee_han_kwon_siddique_solomon_choi_kim_seo_et al._2019, title={Physical localization of the root-knot nematode (Meloidogyne incognita) resistance locus Me7 in pepper (Capsicum annuum)}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85069497776&partnerID=MN8TOARS}, DOI={10.3389/fpls.2019.00886}, abstractNote={The root-knot nematode (RKN) Meloidogyne incognita severely reduces yields of pepper (Capsicum annuum) worldwide. A single dominant locus, Me7, conferring RKN resistance was previously mapped on the long arm of pepper chromosome P9. In the present study, the Me7 locus was fine mapped using an F2 population of 714 plants derived from a cross between the RKN-susceptible parent C. annuum ECW30R and the RKN-resistant parent C. annuum CM334. CM334 exhibits suppressed RKN juvenile movement, suppressed feeding site enlargement and significant reduction in gall formation compared with ECW30R. RKN resistance screening in the F2 population identified 558 resistant and 156 susceptible plants, which fit a 3:1 ratio confirming that this RKN resistance was controlled by a single dominant gene. Using the C. annuum CM334 reference genome and BAC library sequencing, fine mapping of Me7 markers was performed. The Me7 locus was delimited between two markers G21U3 and G43U3 covering a physical interval of approximately 394.7 kb on the CM334 chromosome P9. Nine markers co-segregated with the Me7 gene. A cluster of 25 putative nucleotide-binding site and leucine-rich repeat (NBS-LRR)-type disease resistance genes were predicted in the delimited Me7 region. We propose that RKN resistance in CM334 is mediated by one or more of these NBS-LRR class R genes. The Me7-linked markers identified here will facilitate marker-assisted selection (MAS) for RKN resistance in pepper breeding programs, as well as functional analysis of Me7 candidate genes in C. annuum.}, journal={Frontiers in Plant Science}, author={Changkwian, A. and Venkatesh, J. and Lee, J.-H. and Han, J.-W. and Kwon, J.-K. and Siddique, M.I. and Solomon, A.M. and Choi, G.-J. and Kim, E. and Seo, Y. and et al.}, year={2019} }
 @inproceedings{siddique_2019, title={QTL Mapping and Genome-Wide Association Study for Phytophthora capsici Resistance in Pepper (Capsicum annuum) and Comparative Genomic Analysisof P. capsici Isolates}, booktitle={11th Plant Genomics and Breeding Workshop}, author={Siddique, M.I.}, year={2019}, month={Jun} }
 @inproceedings{back_jo_siddique_kang_2018, title={Identification of eIF4E Mutants in EMS-induced Pepper (Capsicum annuum) Populations by TILLING (Targeting Induced Local Lesions IN Genomes)}, booktitle={Annual Spring Conference of the Korean Society of the Horticultural Science}, author={Back, Seungki and Jo, Jinkwan and Siddique, M.I. and Kang, Byoung-cheorl}, year={2018} }
 @inproceedings{siddique_lee_lee_han_venkatesh_kwon_kang_2018, title={QTL and GWAS Analysis of Phytophthora Resistance in Capsicum}, volume={2018}, number={1}, booktitle={Korean Society of Breeding Studies}, author={Siddique, M.I. and Lee, H.Y. and Lee, H.Y. and Han, K. and Venkatesh, J. and Kwon, J.K. and Kang, B.C.}, year={2018}, pages={13} }
 @inproceedings{siddique_han_kang_2017, title={Evaluation of phenotypic variants and identification of non-pungent mutants among EMS-treated M2 populations}, volume={2017}, number={1}, booktitle={Korean Society of Breeding Studies}, publisher={Korean Society of Breeding Studies}, author={Siddique, M.I. and Han, K. and Kang, B.C.}, year={2017}, pages={72} }
 @article{lee_an_siddique_han_choi_kwon_kang_2017, title={Identification and molecular genetic mapping of Chili veinal mottle virus (ChiVMV) resistance genes in pepper (Capsicum annuum)}, volume={37}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85029234622&partnerID=MN8TOARS}, DOI={10.1007/s11032-017-0717-6}, number={10}, journal={Molecular Breeding}, author={Lee, J.-H. and An, J.-T. and Siddique, M.I. and Han, K. and Choi, S. and Kwon, J.-K. and Kang, B.-C.}, year={2017} }
 @article{siddique_wai_mo_yoo_jang_jeon_hwang_kim_2017, title={Resistance to Phytophthora capsici, Restorer-offertility
Genotype for Cytoplasmic Male Sterility
and Chemical Quality Components of Breeding
Lines Developed for Improvement of Subicho, a
Land Race of Pepper in Yeongyang}, volume={35}, ISSN={1226-8763 2465-8588}, url={http://dx.doi.org/10.12972/kjhst.20170080}, DOI={10.12972/kjhst.20170080}, abstractNote={Over the last 25 years, a breeding line of pepper (Capsicum spp.) PVR Subi has been bred by the introduction of the Phytophthora capsici resistance found in pepper line PI201234 and the field resistance to viruses found in pepper accession KC00406 into a small-fruited, earlymaturing, and good-tasting land race, Subicho, in Yeongyang. In 2009, PVR Subi was crossed with a new version of Subi (New Subi) and an accession, KC01522, with mild and good dry fruit quality. This was done to meet growers’ demands for larger-fruited, open-pollinated local cultivars adapted to conditions in the Subi area of Yeongyang. Twenty-nine F5 and 37 F6 lines that developed from the two crosses were evaluated for resistance to P. capsici by pathogen inoculation at the seedling stage. Selected lines were grown to record horticultural characters in F5 and to analyze chemical quality components such as capsaicinoids, sugar and color in F6. Most of the breeding lines carried pathogen resistance comparable with the commercial resistant hybrid control cultivar, ‘Baerota’, and many lines were found to contain higher capsaicinoid and sugar levels, as well as ASTA color value, than the commercial control. All the breeding lines were identified as restorer-of-fertility lines with N(S)RfRf genotype, producing stable male fertile F1 plants in crosses with a cytoplasmic male sterile line (CMS). These breeding lines are promising as basic materials for selection of open-pollinated cultivars adapted to grow in Yeongyang, and as pollen parents for a hybrid seed production system using cytoplasmic male sterility.}, number={6}, journal={Horticultural Science and Technology}, publisher={Korean Society of Horticultural Science}, author={Siddique, Muhammad Irfan and Wai, Khin Pa Pa and Mo, Hwang-Sung and Yoo, Hee-Ju and Jang, Kil-Su and Jeon, Su-Gyeong and Hwang, Ji-Eun and Kim, Byung-Soo}, year={2017}, month={Dec}, pages={758–768} }
 @article{kim_siddique_mo_yoo_wai_jang_hwang_jeon_2016, title={Breeding a landrace of capsicum pepper in Yeongyang, ‘Subicho’, for resistance to <i>Phytophthora capsici}, volume={1127}, ISSN={0567-7572 2406-6168}, url={http://dx.doi.org/10.17660/ActaHortic.2016.1127.17}, DOI={10.17660/ActaHortic.2016.1127.17}, number={1127}, journal={Acta Horticulturae}, publisher={International Society for Horticultural Science (ISHS)}, author={Kim, B.S. and Siddique, M.I. and Mo, H. and Yoo, H. and Wai, K.P.P. and Jang, K.S. and Hwang, J. and Jeon, S.}, year={2016}, month={Nov}, pages={97–102} }
 @article{byeon_abebe_jegal_wai_siddique_mo_yoo_jang_hwang_jeon_et al._2016, title={Characterization of Sources of Resistance to Bacterial Spot in Capsicum Peppers}, volume={34}, url={https://publons.com/wos-op/publon/27107934/}, DOI={10.12972/KJHST.20160082}, abstractNote={A total of 33 accessions of pepper (Capsicum spp.), including previously reported and newly discovered sources of resistance to bacterial spot caused by Xanthomonas euvesicatoria , were evaluated for their resistance to bacterial spot. The selected accessions were then grown and their horticultural characteristics were recorded. In a test for hypersensitive resistance (HR) to four races (P1, P3, P7, P8) of the pathogen found in Korea, KC00939 and Chilbok No.2, which carry the Bs2 gene, exhibited a hypersensitive response to all four races, as expected. Chilbok No.3, which carries the Bs3 gene, showed a hypersensitive reaction to race 1 and 7, as expected. KC00939 exhibited a high ASTA color value and tolerance to multiple infections from a viral complex of Cucumber mosaic virus (CMV) and Broad bean wilt virus (BBWV). Thus, this accession represents a promising genetic resource for breeding cultivars with multiple disease resistance and strong red coloration. KC01327, KC01617, KC01015, KC01760, KC01779, KC01137, KC01328, KC01006, KC00127, KC01704, and KC00995 did not exhibit hypersensitivity but showed a high level of general resistance when evaluated by spray inoculation. KC01617, KC01760, KC01779, KC01137, KC01704, and KC01777 are newly identified sources of resistance to bacterial spot. The previously and newly identified sources of resistance to bacterial spot evaluated in this study, including information about their resistance to CMV and BBWV complex in the field, the contents of pungent and sweet taste components, and the color values of dry fruits, will be useful for breeding pepper cultivars with resistance to bacterial spot. Additional key words: Capsicum spp., general resistance, hypersensitive resistance, race, Xanthomonas euvesicatoria Received: January 14, 2016 Revised: May 9, 2016 Accepted: August 25, 2016 Copyrightc2016 Korean Society for Horticultural Science. This is an Open-Access article distributed under the terms of the Creative Commons Attribution NonCommercial License which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 이 논문은 2013년도 정부(교육부)의 재원으로 한국연 구재단의 지원을 받아 수행된 기초연구사업(No. 2013R1A1A2008630), 농림축산식품부 농림축산식품 연구센터지원사업 (과제번호 710001-07)과 농촌진 흥청 농업생명자원관리기관사업의 지원에 의해 이루어 진 것임. Korean J. Hortic. Sci. Technol. 34(5):779-789, 2016 http://dx.doi.org/10.12972/kjhst.20160082 pISSN : 1226-8763 eISSN : 2465-8588 OPEN ACCESS 고추 세균성점무늬병 저항성 유전자원과 그 주요 특성 Korean Journal of Horticultural Science & Technology 780 서 언 한국에서 고추는 독특한 매운맛으로 인해 채소작물 중에서 가장 많이 재배되고 있으며 전체 채소류 재배면적 246,725ha 중 에서 약 17%를 차지하는(MAFRA, 2015) 경제적으로 매우 중요한 작물 중 하나이다. 고추에는 비타민이 풍부하며 특히 비타 민 C가 다량 함유되어 있고, 특유의 매운맛을 내는 성분인 capsaicinoids가 들어있어서 조미료로서 가치가 높다. Capsaicinoids 는 또한 항균, 항암, 항산화 등 다양한 생리활성 효과가 밝혀지면서 고추의 수요는 꾸준히 증가하고 있다(Yang et al., 2012). 그러나 고추 재배농가에서는 재배 기간 중 여러가지 병해충의 발생으로 수량 감소와 품질 저하의 어려움을 겪고있다. 발생 하는 병해충 중 고추 세균성점무늬병은 세계의 고추 재배지역에 걸쳐 특히, 열대 및 아열대 지역에서 고추에 심각한 병으로서, 25-30°C의 온난 다습한 환경에서 크게 증가하며 고추의 잎, 줄기 및 과실에 점무늬를 형성하여 조기 낙엽을 초래하고 과실의 품질을 떨어뜨려 농가에 경제적으로 큰 피해를 준다(Jones et al., 1998; Stall et al., 2009). 과거 국내에서 세균성점무늬병은 탄 저병이나 역병처럼 농가의 관심을 끌지 못하였으나, 태풍이 지나가는 해에 비바람에 의해 동시다발적으로 광범위하게 확산되 고 한 번 발병한 후에는 방제가 어려워 큰 피해를 줄 수 있는 주요 병의 하나가 되었다. 최근 지구 온난화로 기후 변화가 잦은 상 태에서 국내에서도 고추 과실의 성숙과 수확에 중요한 시기인 7–8월에 집중되는 호우로 인해 기온이 상승하고 높은 습도가 지속되어 지역에 따라 세균성점무늬병의 발생이 증가하고 있다. 세균성점무늬병을 방제하기 위하여 종자 소독, 윤작, 살균제 살포, 길항 미생물의 이용 등 다양한 방법이 제시되고 있지만 살균제에 대한 내성균의 출현에 따른 방제효과 감소 등의 문제가 드러남에 따라 고추 세균성점무늬병에 대한 저항성 유전자원의 수집과 이의 활용으로 저항성 품종을 육성하여 재배하는 것이 가장 친환경적이고, 경제적이며 효율적인 방제 방법으로 기대된다(Lee and Cho, 1996). 고추와 토마토에 발생하는 세균성점무늬병 병원균은 종래 Xanthomonas campestris pv. vesicatoria로 표기되었으나 최근의 분자유전학적 분류 체계의 발전으로 Xanthomonas euvesicacoria, X. vesicatoria, X. perforans 및 X. gardneri의 4종으로 세분 되고 있다. 이 중에서 X. euvesicatoria, X. vesicatoria 및 X. gardneri가 고추를 침해하며 X. perforans는 토마토만 침입하는 것 으로 알려져 있다(Jones et al., 1998). 고추의 세균성점무늬병에는 X. euvesicatoria가 주요 원인 균종인 것으로 보인다(Jones et al., 1998, 2004; EPPO, 2013). X. euvesicatoria의 병원성 변이형(race)은 기주 식물의 과민반응형 저항성(hypersensitive resistance) 유전자와의 특이적 반응에 따라 현재까지 race 0부터 race 10까지 분류하고 있으나(Sahin and Miller, 1998; Kousik and Ritchie, 1999; Stall et al., 2009) 국내에서는 오랜 기간 race 1과 race 3만 알려졌으며(Kim et al., 1990; Pae et al., 1994; Lee and Cho, 1996), 최근 Bs4 유전자를 보유한 PI235047을 이용하여 race 7과 race 8까지 분류되었다(Wai et al., 2015). 세균성점무늬병에 대한 저항성은 미국식물도입국(PI) 계통들에서 고도의 저항성이 보고되었는데(Sowell, 1960), 이들 계통 중 PI163192, PI260435, PI271322, PI235047에서 발견된 과민반응형 저항성 유전자는 각각 Bs1, Bs2, Bs3, Bs4로 명명되었 다. 이들의 과민반응형(hypersensitive reaction, HR) 저항성은 병원균이 침입하면 즉각적으로 침입부위를 중심으로 조직이 괴 사하면서 방어조직을 형성하여 병의 진행을 막는 현상으로서 각 계통의 유전양식은 서로 독립적으로 단일 우성유전자에 지배 되며(Cook and Stall, 1963, 1969; Cook and Guevara, 1984; Kim and Hartmanm, 1985; Hibberd et al., 1987; Sahin and Miller, 1998), 유전자–유전자 양식(gene–for–gene model)에 따라 병원세균에 들어있는 비병원성 유전자(avirulence gene) 와의 상호작용에 따라 과민형 반응을 나타낸다(Minsavage et al., 1990; Stall et al., 2009; Wai et al., 2015). 이러한 주동 유전자 는 여교잡법으로 실용품종에 도입하기 쉬우나 새로운 race에 쉽게 무력화되는 문제가 있다. 한편 저항성 계통 중에는 race에 비 특이적으로 반응하는 일반 저항성(non–hypersensitive resistance, NHR)이 있으며 일반 저항성 유전성분은 고추의 양적 저항 성(quantitative resistance)을 형성한다(Sowell, 1960; Cook and Stall, 1963). 이는 과민반응형 저항성이 병원균 변이에 취약한 문제점을 보완할 수 있기 때문에 매우 중요하다고 생각된다. 따라서 보다 지속적이고 안정한 저항성 품종을 육성하기 위해서 는 과민반응형 저항성 뿐만 아니라 일반 저항성을 품종 육성에 활용하는 것이 필요하다. 이를 위해 다양한 저항성 유전자원의 확보는 다양한 육종 수요와 병원균의 변이에 대처하기 위해서 매우 중요한 일이 될 것이다. 과민반응형 저항성 유전자가 발견 고추 세균성점무늬병 저항성 유전자원과 그 주요 특성 Korean Journal of Horticultural Science & Technology 781 된 PI163192, PI260435, PI271322에도 일반 저항성 유전성분이 함께 들어있는 것으로 관찰되었으며(Kim and Hartmanm, 1985; Kim et al., 1991; Jones et al., 2002), 본 실험실에서 지난 수년간 수집해온 PI계통과 베트남, 라오스 수집종에서도 다수 검색되었다(Tran and Kim, 2007; Kim et al., 2009). 본 연구에서는 그간에 수집해온 저항성 유전자원의 세균성점무늬병 저항성 정도와 육종 소재로서의 원예적 가치를 검토하 기 위해 X. euvesicatoria균에 대한 저항성을 검정하고, 오이모자이크바이러스(CMV)와 잠두시들음바이러스(BBWV)가 복합 적으로 발생하는 포장에서의 바이러스병 발병도와 과실의 함유성분 등의 주요 원예적 특성을 조사 분석하였다.}, number={5}, journal={Horticultural Science and Technology}, author={Byeon, S. and Abebe, A.M. and Jegal, Y. and Wai, K.P.P. and Siddique, M.I. and Mo, H.-S. and Yoo, H.J. and Jang, K. and Hwang, J. and Jeon, S. and et al.}, year={2016}, pages={779–789} }
 @article{abebe_wai_siddique_mo_yoo_jegal_byeon_jang_jeon_hwang_et al._2016, title={Evaluation of Phytophthora root rot- and bacterial wilt-resistant inbred lines and their crosses for use as rootstocks in pepper (Capsicum annuum L.)}, volume={57}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85007448343&partnerID=MN8TOARS}, DOI={10.1007/s13580-016-0050-8}, number={6}, journal={Horticulture Environment and Biotechnology}, author={Abebe, A.M. and Wai, K.P.P. and Siddique, M.I. and Mo, H.-S. and Yoo, H.J. and Jegal, Y. and Byeon, S.-E. and Jang, K.-S. and Jeon, S.-G. and Hwang, J.-E. and et al.}, year={2016}, pages={598–605} }
 @inproceedings{siddique_han_kang_2016, title={Exploring Resistance against Phytophthora capsici in Pepper}, booktitle={Ramda Plaza Hotel}, author={Siddique, M.I. and Han, Koeun and Kang, Byoung-Cheorl}, year={2016} }
 @article{dong_han_siddique_kwon_zhao_wang_kang_2016, title={Gene-Based Markers for the <i>Tomato Yellow Leaf Curl Virus}, volume={4}, ISSN={2287-9366}, url={http://dx.doi.org/10.9787/pbb.2016.4.1.79}, DOI={10.9787/pbb.2016.4.1.79}, abstractNote={The viral disease induced by Tomato yellow leaf curl virus (TYLCV) reduces tomato (Solanum lycopersicum) yield significantly in tropical and subtropical regions. A number of loci, including Ty-1 to Ty-5, conferring resistance to TYLCV have been described and introgressed into modern tomato cultivars. The availability of molecular markers linked to these genes would expedite the introgression of TYLCV resistance into commercial cultivars. In the present study, we developed gene-based markers linked to the Ty-3 gene using a segregating population derived from a cross between the TYLCV-resistant line S. lycopersicum ‘A45’ and the susceptible line S. lycopersicum ‘A39’. Agrobacterium-mediated screening was used to test TYLCV resistance of plants in the segregating population, and the resistance was evaluated by a visual scoring method and polymerase chain reaction analysis. By comparing sequences of the Ty-3 genes of the resistant and susceptible lines, two high-resolution melting (HRM) markers (Ty3-HRM1 and Ty3-HRM2) and one sequence characterized amplified region (SCAR) marker (Ty3-SCAR1) were developed. The HRM markers were based on single nucleotide polymorphisms at the 13th exon and the 15th intron, whereas the SCAR marker was based on a 246-bp deletion in the 16th intron. These gene-based markers will be useful tools for marker-assisted selection in breeding programs to improve TYLCV resistance of tomato.}, number={1}, journal={Plant Breeding and Biotechnology}, publisher={Korean Society of Breeding Science}, author={Dong, Panpan and Han, Koeun and Siddique, Muhammad Irfan and Kwon, Jin-Kyung and Zhao, Meiai and Wang, Fu and Kang, Byoung-Cheorl}, year={2016}, month={Feb}, pages={79–86} }
 @inproceedings{lee_an_han_choi_siddique_kang_2016, title={Genetic mapping of resistance sources against ChiVMV (Chili veinal mottle virus) in hot pepper}, booktitle={Ramda Plaza Hotel}, author={Lee, Joung-Ho and An, Jeong-Tak and Han, Koeun and Choi, Seula and Siddique, M.I. and Kang, Byoung-Cheorl}, year={2016} }
 @inproceedings{siddique_han_hwang_jeong_kang_2015, series={Annual Spring Conference of the Korean Society for Horticultural Science}, title={Assessment of EMS mutagenic effects in Capsicum annuum population for the identification of non-pungent mutants}, booktitle={Annual Spring Conference of the Korean Society for Horticultural Science}, author={Siddique, M.I. and Han, Koeun and Hwang, Doyeon and Jeong, Hee-Jin and Kang, Byoung-Cheorl}, year={2015}, collection={Annual Spring Conference of the Korean Society for Horticultural Science} }
 @inproceedings{jeong_siddique_an_kim_choi_struss_kang_2015, title={Characterization and interaction analysis of two QTLs, QTL5-1 and QTL5-2, controlling Phytophthora capsici resistance in Capsicum annuum using near-isogenic lines}, booktitle={Korea Breeding Society Next Generation BG21 Project Group GSP Project Group Joint Symposium}, author={Jeong, H.S. and Siddique, M.I. and An, J.T. and Kim, K.T. and Choi, G.J. and Struss, D. and Kang, B.C.}, year={2015}, pages={130–130} }
 @inproceedings{siddique_han_hwang_jeong_rai_kang_2015, title={Development of EMS mutant populations in Capsicum annuum and identification of non-pungent mutants}, booktitle={Annual Conference of the Korean Society for Breeding Science}, author={Siddique, M.I. and Han, Koeun and Hwang, Doyeon and Jeong, Hee-Jeonn and Rai, Arti and Kang, Byoung- Cheorl}, year={2015} }
 @article{younis_riaz_mushtaq_tahir_siddique_2015, title={Evaluation of the Suitability of Sewage and Recycled Water for Irrigation of Ornamental Plants}, volume={46}, url={https://publons.com/wos-op/publon/13339175/}, DOI={10.1080/00103624.2014.956886}, abstractNote={The present study was conducted to evaluate the potential benefits and risks of the sewage water and recycled treated water on three ornamental plant species, including Umbrella plant (Cyperus alternifolius), Euonymus (Euonymus japonicas), and Dracaena (Cordyline terminalis). Plants in the pots were irrigated with equal volumes of water in 2-day intervals. Treatment plants were analyzed for sodium (Na), potassium (K), copper (Cu), iron (Fe), and lead (Pb) concentrations, in roots and shoots. The experiment was conducted by using a completely randomized design (CRD) with five replications. Data were analyzed using analysis of variance technique and least significance difference (LSD) test was applied at 5% probability level. Plants species performed better in sewage water after recycled water, in terms of growth, number of leaves, chlorophyll content, and leaf thickness, which proved sewage water accelerates the growth and development of ornamental foliage plants, but plants irrigated with this water exhibited greater concentration of Pb than other treatments.}, number={1}, journal={Communications in Soil Science and Plant Analysis}, author={Younis, A. and Riaz, A. and Mushtaq, N. and Tahir, Z. and Siddique, M.I.}, year={2015}, pages={62–79} }
 @article{wai_siddique_mo_yoo_byeon_jegal_mekuriaw_kim_2015, title={Pathotypes of Bacterial Spot Pathogen Infecting Capsicum Peppers in Korea}, volume={31}, url={https://publons.com/wos-op/publon/27107937/}, DOI={10.5423/PPJ.NT.05.2015.0074}, abstractNote={Sixty-seven isolates of bacterial spot pathogen (Xanthomonas spp.) collected from six provinces of Korea were tested for the identification of their pathotypes and determination of their distribution throughout Korea in an effort to genetically manage the disease. Near isogenic lines of Early Calwonder (Capsicum annuum) pepper plants carrying Bs1, Bs2 and Bs3, and PI235047 (C. pubescens) were used as differential hosts. Race P1 was found to be predominant, followed by race P7, and races P3 and P8 were also observed. This is the first report of races P7 and P8 in Korea. The races P7 and P8 were differentiated from the former races P1 and P3, respectively, on the basis of their ability to elicit hypersensitive reactions to PI235047.}, number={4}, journal={Plant Pathology Journal}, author={Wai, K.P.P. and Siddique, M.I. and Mo, H.-S. and Yoo, H.J. and Byeon, S.-E. and Jegal, Y. and Mekuriaw, A.A. and Kim, B.-S.}, year={2015}, pages={428–432} }
 @article{jang_han_jo_jeong_siddique_kang_2015, title={Substitution of a Dysfunctional pAMT Allele Results in Low-Pungency but High Levels of Capsinoid in <i>Capsicum chinense</i> ‘Habanero’}, volume={3}, ISSN={2287-9366}, url={http://dx.doi.org/10.9787/pbb.2015.3.2.119}, DOI={10.9787/pbb.2015.3.2.119}, abstractNote={Capsinoids are the class of secondary metabolites identified in non-pungent peppers exhibiting the same bioactive properties as capsaicinoid. Previously, it has been demonstrated that capsinoid production is controlled by the capsaicin synthase ( CS ) gene and the putative-aminotransferase ( pAMT ) gene. In this study, we report that C. chinense ‘SNU11-001’ containing high levels of capsinoid has an early stop codon in pAMT resulted from 403 bp and 8 bp insertions deletion in the third and sixth exons. In order to know whether CS expression is correlated with the level of capsinoid, CS and pAMT expressions were determined using SNU11-001 and four Capsicum accessions with different pungency level. RT-PCR analysis showed higher transcription levels of CS in pungent accessions but no clear differences in pAMT expression. To investigate the effect of the substitution of the pAMT allele of C. chinense ‘Habanero’ with the dysfunctional pAMT allele of SNU11-001, an F 2 population was constructed by a cross between aforementioned parental lines. Molecular markers were developed to distinguish CS and pAMT genotypes of SNU11-001 and Habanero and F 2 plants were genotyped. All F 2 plants having the pAMT genotype of SNU11-001 contained high levels of capsinoid while very low levels of capsaicinoid. There was no significant difference in levels of capsinoid among the F 2 plants regardless of CS genotypes. This may be due to strong CS expression of both parental lines. In conclusion, our results show that it is possible to develop a new Habanero cultivar with high capsinoid content by introducing a dysfunctional pAMT allele.}, number={2}, journal={Plant Breeding and Biotechnology}, publisher={Korean Society of Breeding Science}, author={Jang, Siyoung and Han, Koeun and Jo, Yeoung Deuk and Jeong, Hee-Jin and Siddique, Muhammad Irfan and Kang, Byoung-Cheorl}, year={2015}, month={Jun}, pages={119–128} }
 @article{younis_riaz_ahmed_siddique_tariq_hameed_nadeem_2014, title={Anatomical changes induced by NaCl stress in root and stem of Gazania harlequin L}, volume={2}, journal={Agricultural Communications}, author={Younis, A. and Riaz, A. and Ahmed, I. and Siddique, M.I. and Tariq, U. and Hameed, M. and Nadeem, M.}, year={2014}, pages={8–14} }
 @inproceedings{siddique_2014, title={Breeding Local Cultivars of Capsicum Pepper Resistant to Phytophthora capsici and their Restorer of Fertility Genotype interacting with Cytoplasmic Male Sterility Adapted to Yeongyang}, booktitle={Plant Factory conference}, author={Siddique, M.I.}, year={2014}, month={Nov} }
 @inproceedings{kim_siddique_mo_yoo_wai_jang_hwang_jeon_2014, title={Breeding a landrace of capsicum pepper in Yeongyang, 'Subicho', for resistance to Phytophthora capsici}, booktitle={XXIX International Horticultural Congress on Horticulture: Sustaining Lives, Livelihoods and Landscapes (IHC2014): International Symposium on Plant Breeding in Horticulture}, author={Kim, B.S. and Siddique, M.I. and Mo, H. and Yoo, H. and Wai, K.P.P. and Jang, K.S. and Hwang, J. and Jeon, S.}, year={2014} }
 @phdthesis{siddique_2014, title={Evaluation and Characterization of Phytophthora Resistant Breeds of Yeongyang Local Cultivars of Pepper (Capsicum annuum L.) MI Siddique}, school={Kyungpook National University}, author={Siddique, M.I.}, year={2014} }
 @article{siddique_mo_wai_kim_2014, title={Fertility-restoring Genotype Interacting with Male Sterile Cytoplasm of Youngyang Local Breeds of Pepper Resistant to Phytophthora capsici}, volume={32}, number={1}, journal={Journal of Horticultural Science and Technology}, author={Siddique, M.I. and Mo, H. and Wai, K.P.P. and Kim, B.S.}, year={2014}, pages={109–109} }
 @inproceedings{siddique_wai_yoo_mo_kim_2014, title={Fertility–Restoring Genotype interacting with Male Sterile Cytoplasm of Yeongyang Local Breeds of Pepper, Resistant to Phytophthora Capsici}, booktitle={Annual Spring Conference of the Korean Society for Horticultural Science}, author={Siddique, M.I. and Wai, Khin Pa Pa and Yoo, Hee Ju and Mo, Hwang Sung and Kim, Byung-Soo}, year={2014} }
 @article{mo_kim_wai_siddique_yoo_kim_2014, title={New sources of resistance to Phytophthora capsici in Capsicum spp.}, volume={55}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84897777217&partnerID=MN8TOARS}, DOI={10.1007/s13580-014-0016-7}, number={1}, journal={Horticulture Environment and Biotechnology}, author={Mo, H. and Kim, S. and Wai, K.P.P. and Siddique, M.I. and Yoo, H. and Kim, B.-S.}, year={2014}, pages={50–55} }
 @inproceedings{kim_wai_siddique_mo_2014, title={Phytophthora Leaf Blight and Vine Rot of Kudzu (Pueraria thunbergiana)}, booktitle={2014 Conference of The Korean Society of Plant Pathology}, author={Kim, Byung-Soo and Wai, Khin Pa Pa and Siddique, M.I. and Mo, Hwang Sung}, year={2014} }
 @article{ramzan_younis_riaz_ali_siddique_lim_2014, title={Pre-planting Exogenous Application of Gibberellic Acid Influences Sprouting, Vegetative Growth, Flowering, and Subsequent Bulb Characteristics of 'Ad-Rem' Tulip}, volume={55}, url={https://publons.com/wos-op/publon/13339187/}, DOI={10.1007/S13580-014-0113-7}, number={6}, journal={Horticulture, Environment, and Biotechnology}, author={Ramzan, F. and Younis, A. and Riaz, A. and Ali, S. and Siddique, M.I. and Lim, K.-B.}, year={2014}, pages={479–488} }
 @article{younis_siddique_kim_lim_2014, title={RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding}, volume={10}, url={https://publons.com/wos-op/publon/13339184/}, DOI={10.7150/IJBS.10452}, abstractNote={RNA interference (RNAi) is a promising gene regulatory approach in functional genomics that has significant impact on crop improvement which permits down-regulation in gene expression with greater precise manner without affecting the expression of other genes. RNAi mechanism is expedited by small molecules of interfering RNA to suppress a gene of interest effectively. RNAi has also been exploited in plants for resistance against pathogens, insect/pest, nematodes, and virus that cause significant economic losses. Keeping beside the significance in the genome integrity maintenance as well as growth and development, RNAi induced gene syntheses are vital in plant stress management. Modifying the genes by the interference of small RNAs is one of the ways through which plants react to the environmental stresses. Hence, investigating the role of small RNAs in regulating gene expression assists the researchers to explore the potentiality of small RNAs in abiotic and biotic stress management. This novel approach opens new avenues for crop improvement by developing disease resistant, abiotic or biotic stress tolerant, and high yielding elite varieties.}, number={10}, journal={International Journal of Biological Sciences}, author={Younis, A. and Siddique, M.I. and Kim, C.-K. and Lim, K.-B.}, year={2014}, pages={1150–1158} }
 @article{younis_riaz_siddique_lim_hwang_khan_2013, title={Anatomical and Morphological Variation in Dracaena reflexa ‘Variegata’ Grown in Different Organic Potting Substrates}, volume={21}, ISSN={1225-5009 2287-772X}, url={http://dx.doi.org/10.11623/frj.2013.21.4.32}, DOI={10.11623/frj.2013.21.4.32}, abstractNote={Potting media are an integral part of potted plants production system, formulated by a mixture of various raw materials to act as a substrate for plant support and source of nutrition. There is a wide range of potting media available, which are used for quality production of high-value plants worldwide. In this study, quality assessment of Dracaena plants grown in different potting media like: mushroom compost, peat, sand, farmyard manure, coconut coir, and leaf compost in different combinations were carried out. A mixture of sand, mushroom compost, coconut coir, and peat proved to be the best, by promoting root and shoot growth, leaf area, fresh and dry weights of root and shoot, and also improved overall quality of the plant. Media containing garden soil alone or a mixture of sand and leaf compost produced the lowest quality of plants with considerable reduction in most of the growth parameters. Anatomical parameters showed weak relation to media composition as compared to other morphological features. The best medium was made with sand, mushroom compost, coconut coir, peat, that produced plants with thick epidermis and larger pith cells, but thin endodermis and smaller metaxylem vessels in their roots. As moisture availability was sufficient enough in this medium combination, the development of water storing tissue may not contribute significantly. However, epidermis can play a decisive role in protecting roots from external environmental hazards.}, number={4}, journal={Korean Society for Floricultural Science}, publisher={Korean Society for Floricultural Science}, author={Younis, Adnan and Riaz, Atif and Siddique, Muhammad Irfan and Lim, Ki-Byung and Hwang, Yoon-Jung and Khan, Muhammad Asif}, year={2013}, month={Dec}, pages={162–171} }
 @inproceedings{siddique_mo_kim_2012, title={Testing Resistance in Selected Breeds of Yeongyang Pepper (Capsicum annuum) against Phytophthora capsici}, booktitle={Research day at Kyungpook National University}, author={Siddique, M.I. and Mo, Hwangsung and Kim, Byung-Soo}, year={2012} }