The Promise of Agriculture Genomics
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International Journal of Genomics The Promise of Agriculture Genomics Guest Editors: Wenqin Wang, Xuan H. Cao, Mihai Miclăuş, Jianhong Xu, and Wenwei Xiong The Promise of Agriculture Genomics International Journal of Genomics The Promise of Agriculture Genomics Guest Editors: Wenqin Wang, Xuan H. Cao, Mihai Miclaus, Jianhong Xu, and Wenwei Xiong Copyright © 2017 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “International Journal of Genomics.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Jacques Camonis, France Sylvia Hagemann, Austria Graziano Pesole, Italy Prabhakara V. Choudary, USA Henry Heng, USA Giulia Piaggio, Italy Martine A. Collart, Switzerland Eivind Hovig, Norway Mohamed Salem, USA Marco Gerdol, Italy Giuliana Napolitano, Italy Brian Wigdahl, USA Soraya E. Gutierrez, Chile Ferenc Olasz, Hungary Jinfa Zhang, USA M. Hadzopoulou-Cladaras, Greece Elena Pasyukova, Russia Contents The Promise of Agriculture Genomics Wenqin Wang, Xuan H. Cao, Mihai Miclăus,, Jianhong Xu, and Wenwei Xiong Volume 2017, Article ID 9743749, 3 pages Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection Hien Trinh, Khoa Truong Nguyen, Lam Van Nguyen, Huy Quang Pham, Can Thu Huong, Tran Dang Xuan, LaHoangAnh,MarioCaccamo,SarahAyling,NguyenThuyDiep,CuongNguyen,KhuatHuuTrung,and Tran Dang Khanh Volume 2017, Article ID 9272363, 11 pages Genetic Diversity and Association Analysis for Solvent Retention Capacity in the Accessions Derived from Soft Wheat Ningmai 9 Peng Jiang, Ping-Ping Zhang, Xu Zhang, and Hong-Xiang Ma Volume 2017, Article ID 2413150, 8 pages Development of a New Marker System for Identification of Spirodela polyrhiza and Landoltia punctata Bo Feng, Yang Fang, Zhibin Xu, Chao Xiang, Chunhong Zhou, Fei Jiang, Tao Wang, and Hai Zhao Volume 2017, Article ID 5196763, 8 pages The Power of CRISPR-Cas9-Induced Genome Editing to Speed Up Plant Breeding HieuX.Cao,WenqinWang,HienT.T.Le,andGiangT.H.Vu Volume2016,ArticleID5078796,10pages Gene Expression Analysis of Alfalfa Seedlings Response to Acid-Aluminum Peng Zhou, Liantai Su, Aimin Lv, Shengyin Wang, Bingru Huang, and Yuan An Volume 2016, Article ID 2095195, 13 pages Role of Recombinant DNA Technology to Improve Life Suliman Khan, Muhammad Wajid Ullah, Rabeea Siddique, Ghulam Nabi, Sehrish Manan, Muhammad Yousaf, and Hong wei Hou Volume 2016, Article ID 2405954, 14 pages Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species Suliman Khan, Ghulam Nabi, Muhammad Wajid Ullah, Muhammad Yousaf, Sehrish Manan, Rabeea Siddique, and Hongwei Hou Volume 2016, Article ID 3460416, 8 pages Genetic Diversity of Cowpea (Vigna unguiculata (L.) Walp.) Accession in Kenya Gene Bank Based on Simple Sequence Repeat Markers EmilyN.Wamalwa,JohnMuoma,andClabeWekesa Volume 2016, Article ID 8956412, 5 pages Effect on Soil Properties of BcWRKY1 Transgenic Maize with Enhanced Salinity Tolerance Xing Zeng, Yu Zhou, Zhongjia Zhu, Hongyue Zu, Shumin Wang, Hong Di, and Zhenhua Wang Volume 2016, Article ID 6019046, 13 pages Molecular Cloning, Characterization, and mRNA Expression of Hemocyanin Subunit in Oriental River Prawn Macrobrachium nipponense Youqin Kong, Liqiao Chen, Zhili Ding, Jianguang Qin, Shengming Sun, Ligai Wang, and Jinyun Ye Volume 2016, Article ID 6404817, 9 pages Transcriptome Analyses Reveal Lipid Metabolic Process in Liver Related to the Difference of Carcass Fat Content in Rainbow Trout (Oncorhynchus mykiss) Guo Hu, Wei Gu, Peng Sun, Qingli Bai, and Bingqian Wang Volume 2016, Article ID 7281585, 10 pages Genome-Wide Analysis of Genes Encoding Methionine-Rich Proteins in Arabidopsis and Soybean Suggesting Their Roles in the Adaptation of Plants to Abiotic Stress Ha Duc Chu, Quynh Ngoc Le, Huy Quang Nguyen, and Dung Tien Le Volume 2016, Article ID 5427062, 8 pages SSR Mapping of QTLs Conferring Cold Tolerance in an Interspecific Cross of Tomato Yang Liu, Tengxia Zhou, Haiyan Ge, Wen Pang, Lijie Gao, Li Ren, and Huoying Chen Volume 2016, Article ID 3219276, 6 pages Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress in Brassica rapa L. (Inbred Line “Chiifu”) Soon-Wook Kwon, Mijeong Kim, Hijin Kim, and Joohyun Lee Volume 2016, Article ID 4235808, 9 pages Hindawi International Journal of Genomics Volume 2017, Article ID 9743749, 3 pages http://dx.doi.org/10.1155/2017/9743749 Editorial The Promise of Agriculture Genomics 1 2 3 4 5 Wenqin Wang, Xuan H. Cao, Mihai Miclsus,, Jianhong Xu, and Wenwei Xiong 1 Shanghai Jiaotong University, Shanghai, China 2Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany 3National R&D Institute for Biological Sciences, Cluj-Napoca, Romania 4Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Zhejiang 310058, China 5Montclair State University, Montclair, NJ, USA Correspondence should be addressed to Wenqin Wang; [email protected] Received 31 January 2017; Accepted 1 February 2017; Published 5 March 2017 Copyright © 2017 Wenqin Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. With the fact of growing global population, changing climate, genomic sequences of model plants. Almost every species- and environmental pressure, there is an urgent need to specific genome can be sequenced with affordable price and accelerate breeding novel crops with higher production, thus offer great opportunities for targeted crop breeding. droughtorheattolerance,andlesspesticideusage.Advances Furthermore, genomics is playing a very crucial role in biodi- in genomics offer the potential to speed up the process of versity conservation. Advanced genomics helps in identifying developing crops with promising agronomic traits. Agricul- the segments of the genome responsible for adaptation. It can ture genomics is the application of genomics in agriculture also improve our understanding of microevolution through to improve the productivity and sustainability in crop and a better understanding of natural selection, mutation, and livestock production. With the combination of traditional recombination, as summarized in S. Khan et al.’s article. and high-throughput sequencing platforms, there has been a Understanding the structure, organization, and dynamics tremendous increase in genomic resources available, includ- of genomes in plant species can provide insights into how ing expressed sequence tags (ESTs), BAC end sequence, genes have been adapted by natural and artificial selection genetic sequence polymorphisms, gene expression profiling, to respond to environmental constraints and the potential of whole-genome (re)sequencing, and genome-wide associa- their manipulation for crop improvement. tion studies. Given the emergence of genomic sequencing Conventional breeding in agriculture is based exclu- and expansion of bioinformatic tools, we are shifting from sively on phenotypic selection. Until the availability of ge- single gene study to whole-genome analysis, which offers nomic sequence for model plants, comparative genomics a broader view of how all genes work together. Therefore, approaches were successful for identifying homologues/ this special issue was organized, comprising eleven original orthologues or cloning species-specific genes by using se- research papers and three reviews aimed to highlight recent quence conservation or synteny from model plant systems. advances in (1) comparative genomics for plant breeding, The group of D. T. Le surveyed the genomes of Arabidopsis (2) transcriptome analysis for plant breeding, (3) genotyping and soybean for genes encoding Met-rich proteins (MRPs) and marker-assisted breeding, and (4) recombinant DNA basedonsequencesimilarity.GenesencodingMRPswere technology (Figure 1). classified into functional categories including RNA transcrip- tion, protein modification, and calcium signaling. It was Comparative Genomics for Plant Breeding.Todate,the found that MRPs were mainly responsible for drought and genome sequences for more than 55 plant species (mainly salinity stress in Arabidopsis and soybean. model plants, such as Arabidopsis, rice, and maize) have Predicting gene function solely based on homology to been produced. The 1000-plant (one KP or 1 KP) initiative is others can sometimes be difficult. Thus, proteomics (the underway. As a result, scientists are not totally dependent on large-scale analysis of proteins) will greatly contribute to our 2 International Journal of Genomics Comparative genomics for breeding Genomics Breeding 4 5 3 6 Genotyping and marker-assisted 2 7 breeding 8 1 9 32 31 30 10 29 28 11 27 Transcriptome analysis for breeding 26 12 25 24 13 23 14 22 21 15 20 16 19 18 17 Recombinant DNA technology Figure 1: Advances in this special issue. understanding of gene function in the postgenomic era. The but also in other crops under aluminum-acid stress. The tran- group of J. Lee used shotgun proteomic analysis to quantify script levels of MRP-coding genes under normal and stress the protein in Brassica rapa under drought treatment. Their conditions in Arabidopsis and soybean were also studied by results showed