Scientia Agricultura Sinica ›› 2015, Vol. 48 ›› Issue (17): 3316-3332.doi: 10.3864/j.issn.0578-1752.2015.17.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Crop Genomics and Crop Science Revolutions

JIA Ji-zeng, GAO Li-feng, ZHAO Guang-yao, ZHOU Wen-bin, ZHANG Wei-jian   

  1. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081
  • Received:2015-03-06 Online:2015-09-01 Published:2015-09-01

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Abstract: Development in the field of crop sciences is playing an important role in increasing yield throughout the world. The history of the first Green Revolution was overviewed in this paper. According to the initiation time, gene donors and increased yield caused by dwarfing breeding over the same period, China should be one of the origins and initiators of the first Green Revolution. The achievements in crop scientific researches including Chinese Green Revolution and hybrid rice have made great contributions to crop production all over the world. However, China is facing serious challenges in crop production. Over the decades after the first Green Revolution, the increasing percentage of production per year attributed to genetic breeding for major crops accounts for only 0.7%-0.9%, far from the required 1.7% in China. The efficiency of fertilization and watering is only one third of that in developed countries. Although agricultural mechanization improved a lot in China, big gaps still existed in comparison with developed countries. The quality of agricultural products can’t meet requirements, and food safety is still a big problem. In view of the above, a new Green Revolution, aimed at higher yielding, higher efficiency, better quality, and friendly environment, is imperative. Although traditional crop sciences have made great contributions to crop yield, they are not competent enough to complete the new Green Revolution. Crop genomics is booming as a new subject in the biological sciences. The finished genome sequencing for many crops has advanced crop sciences to genomic era, which highlights the genomics-based crop research. Genomics has promoted five distinct improvements in crop sciences: (1) Great progresses in germplasm-based researches have been achieved, such as the construction of core collection of crop germplasms, cloning of agricultural important genes, development and application of germplasm resources, and introduction of new subject of germplasm variome. (2) Breakthroughs in theory and methology for crop breeding resulted in a new subject of breeding genomics. (3) The effect of environment and cultivation management on gene expression and regulation will be clarified. A lot of genes regulated by environmental factors will be discovered. These will direct cultivation research to cultivation genomics. (4) The breeding level for minor crops will be improved rapidly. Therefore, the research gaps between major and minor crops are narrowing. Nowadays, crop sciences are developing at an unprecedented high speed. The development of germplasm variome, breeding genomics and culture genomics will lead to revolutions in crop sciences and hence result in a new green revolution. Some problems in scientific research of crop sciences in China were listed, including organizations, topics, materials used, and achievements transformation. How to deal with them and which are the directions are also discussed in this review.

Key words: crop science, genomics, crop germplasm, crop breeding, crop cultivation

[1]    http://www.fao.org/home/en/.
[2]    Zhang C, Gao L, Sun J, Jia J, Ren Z. Haplotype variation of     Green Revolution gene Rht-D1 during wheat domestication and improvement. Journal of Integrative Plant Biology, 2014, 56(8): 774-780.
[3]    Paterson A H, Bowers J E, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti A K, Chapman J, Feltus F A, Gowik U, Grigoriev I V, Lyons E, Maher C A, Martis M, Narechania A, Otillar R P, Penning B W, Salamov A A, Wang Y, Zhang L, Carpita N C, Freeling M, Gingle A R, Hash C T, Keller B, Klein P, Kresovich S, McCann M C, Ming R, Peterson D G, Mehboob ur R, Ware D, Westhoff P, Mayer K F, Messing J, Rokhsar D S. The Sorghum bicolor genome and the diversification of grasses. Nature, 2009, 457(7229): 551-556.
[4]    Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X, Jing R, Zhang C, Ma Y, Gao L, Gao C, Spannagl M, Mayer K F, Li D, Pan S, Zheng F, Hu Q, Xia X, Li J, Liang Q, Chen J, Wicker T, Gou C, Kuang H, He G, Luo Y, Keller B, Xia Q, Lu P, Wang J, Zou H, Zhang R, Xu J, Gao J, Middleton C, Quan Z, Liu G, Wang J, Yang H, Liu X, He Z, Mao L, Wang J. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature, 2013, 496(7443): 91-95.
[5]    Li Y H, Zhou G, Ma J, Jiang W, Jin L G, Zhang Z, Guo Y, Zhang J, Sui Y, Zheng L, Zhang S S, Zuo Q, Shi X H, Li Y F, Zhang W K, Hu Y, Kong G, Hong H L, Tan B, Song J, Liu Z X, Wang Y, Ruan H, Yeung C K, Liu J, Wang H, Zhang L J, Guan R X, Wang K J, Li W B, Chen S Y, Chang R Z, Jiang Z, Jackson S A, Li R, Qiu L J. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nature Biotechnology, 2014, 32(10): 1045-1052.
[6]    Mikkelsen T S, Hiller L W, Eichler E, Zody M C, Jaffe D B, Yang S P, Enard W, Hellmann I, Lindblad-toh K, Altheide T K, Archidiacono N, Bork P, Butler J, Chang J I, Cheng Z, Chinwalla A T, de Jong P, Delehaunty K D, Fronick C, et al.Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 2005, 437(7055): 69-87.
[7]    王述民, 张宗文. 世界粮食和农业植物遗传资源保护与利用现状. 植物遗传资源学报, 2011, 12(3): 325-338.
Wang S M, Zhang Z W. The state of the world’s plant genetic resources for food and agriculture. Journal of Plant Genetic Resources, 2011, 12(3): 325-338. (in Chinese)
[8]    Ring H, Kwok P, Cotton R. Human Variome Project: An international collaboration to catalogue human genetic variation. Pharmacogenomics, 2006, 7(7): 969-972.
[9]    Gore M A, Chia J M, Elshire R J, Sun Q, Ersoz E S, Hurwitz B L, Peiffer J A, McMullen M D, Grills G S, Ross-Ibarra J, Ware D H, Buckler E S. A first-generation haplotype map of maize. Science, 2009, 326(5956): 1115-1117.
[10]   Chia J, Song C, Bradbury P, Costich D, de Leon N, Doebley J, Elshire R, Gaut B, Geller L, Glaubitz J, Gore M, Guill K, Holland J, Hufford M, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna B, Pyhajarvi T, Rong T, Sekhon R, Sun Q, Tenaillon M, Tian F, Wang J, Xu X, Zhang Z, Kaeppler S, Ross-Ibarra J, McMullen M, Buckler E, Zhang G, Xu Y, Ware D. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics, 2012, 44(7): 803-807.
[11]   Hufford M, Xu X, van Heerwaarden J, Pyhajarvi T, Chia J, Cartwright R, Elshire R, Glaubitz J, Guill K, Kaeppler S, Lai J, Morrell P, Shannon L, Song C, Springer N, Swanson-Wagner R, Tiffin P, Wang J, Zhang G, Doebley J, McMullen M, Ware D, Buckler E, Yang S, Ross-Ibarra J. Comparative population genomics of maize domestication and improvement. Nature Genetics, 2012, 44(7): 808-811.
[12]   Huang X, Kurata N, Wei X, Wang Z, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B. A map of rice genome variation reveals the origin of cultivated rice. Nature, 2012, 490(7421): 497-501.
[13]   Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, Li W, Guo Y, Deng L, Zhu C, Fan D, Lu Y, Weng Q, Liu K, Zhou T, Jing Y, Si L, Dong G, Huang T, Lu T, Feng Q, Qian Q, Li J, Han B. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nature Genetics, 2012, 44(1): 32-39.
[14]   Xu X, Liu X, Ge S, Jensen J, Hu F, Li X, Dong Y, Gutenkunst R, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology, 2012, 30(1): 105-111.
[15]   Morris G P, Ramu P, Deshpande S P, Hash C T, Shah T, Upadhyaya H D, Riera-Lizarazu O, Brown P J, Acharya C B, Mitchell S E, Harriman J, Glaubitz J C, Buckler E S, Kresovich S. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(2): 453-458.
[16]   Jia G, Huang X, Zhi H, Zhao Y, Zhao Q, Li W, Chai Y, Yang L, Liu K, Lu H, Zhu C, Lu Y, Zhou C, Fan D, Weng Q, Guo Y, Huang T, Zhang L, Lu T, Feng Q, Hao H, Liu H, Lu P, Zhang N, Li Y, Guo E, Wang S, Wang S, Liu J, Zhang W, Chen G, Zhang B, Li W, Wang Y, Li H, Zhao B, Li J, Diao X, Han B. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nature Genetics, 2013, 45(8): 957-961.
[17]   Lam H, Xu X, Liu X, Chen W, Yang G, Wong F, Li M, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun S, Zhang G. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics, 2010, 42(12): 1053-1059.
[18]   Qi J, Liu X, Shen D, Miao H, Xie B, Li X, Zeng P, Wang S, Shang Y, Gu X, Du Y, Li Y, Lin T, Yuan J, Yang X, Chen J, Chen H, Xiong X, Huang K, Fei Z, Mao L, Tian L, Stadler T, Renner S S, Kamoun S, Lucas W J, Zhang Z, Huang S. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nature Genetics, 2013, 45(12): 1510-1515.
[19]   Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X, Huang Z, Li J, Zhang C, Wang T, Zhang Y, Wang A, Zhang Y, Lin K, Li C, Xiong G, Xue Y, Mazzucato A, Causse M, Fei Z, Giovannoni J J, Chetelat R T, Zamir D, Stadler T, Li J, Ye Z, Du Y, Huang S. Genomic analyses provide insights into the history of tomato breeding. Nature Genetics, 2014, 46(11): 1220-1226.
[20]   Palmgren M, Edenbrandt A, Vedel S, Andersen M, Landes X, Østerberg J, Falhof J, Olsen L, Christensen S, Sandøe P, Gamborg C, Kappel K, Thorsen B, Pagh P. Are we ready for back-to-nature crop breeding? Trends in Plant Science, 2015, 20(3): 155-164.
[21]   李俊, 魏会廷, 胡晓蓉, 李朝苏, 汤永禄, 刘登才, 杨武云. 川麦42中源于人工合成小麦的一个高产位点鉴定. 作物学报, 2011, 37(2): 255-262.
Li J, Wei H T, Hu X R, Li C S, Tang Y L, Liu D C, Yang W Y. Identification of a high-yield introgression locus from synthetic hexaploid wheat in Chuanmai 42. Acta Agronomica Sinica, 2011, 37(2): 255-262. (in Chinese)
[22]   Yoon D B, Kang K H, Kim H J, Ju H G, Kwon S J, Suh J P, Jeong O Y, Ahn S N. Mapping quantitative trait loci for yield components  and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theoretical and Applied Genetics, 2006, 112(6): 1052-1062.
[23]   Liu S, Zhou R, Dong Y, Li P, Jia J. Development, utilization of introgression lines using a synthetic wheat as donor. Theoretical and Applied Genetics, 2006, 112(7): 1360-1373.
[24]   Eshed Y, Zamir D. An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics, 1995, 141(3): 1147-1162.
[25]   Xing Y, Zhang Q. Genetic and molecular bases of rice yield. Annual Review of Plant Biology, 2010, 61(1): 421-442.
[26]   Shang Y, Ma Y, Zhou Y, Zhang H, Duan L, Chen H, Zeng J, Zhou Q, Wang S, Gu W, Liu M, Ren J, Gu X, Zhang S, Wang Y, Yasukawa K, Bouwmeester H J, Qi X, Zhang Z, Lucas W J, Huang S. Biosynthesis, regulation, and domestication of bitterness in cucumber. Science, 2014, 346(6213): 1084-1088.
[27]   Chen H, Xie W, He H, Yu H, Chen W, Li J, Yu R, Yao Y, Zhang W, He Y, Tang X, Zhou F, Deng X W, Zhang Q. A high-density SNP genotyping aArray for rice biology and molecular breeding. Molecular Plant, 2014, 7(3): 541-553.
[28]   Unterseer S, Bauer E, Haberer G, Seidel M, Knaak C, Ouzunova M, Meitinger T, Strom T M, Fries R, Pausch H, Bertani C, Davassi A, Mayer K F, Schon C C. A powerful tool for genome analysis in maize: Development and evaluation of the high density 600K SNP genotyping array. BMC Genomics, 2014, 15: 823.
[29]   Yu H, Xie W, Li J, Zhou F, Zhang Q. A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnology Journal, 2014, 12(1): 28-37.
[30]   Kumar K, Kumar M, Kim S R, Ryu H, Cho Y G. Insights into genomics of salt stress response in rice. Rice, 2013, 6(1): 1-15.
[31]   Kawaura K, Mochida K, Yamazaki Y, Ogihara Y. Transcriptome analysis of salinity stress responses in common wheat using a 22K oligo-DNA microarray. Functional & Integrative Genomics, 2006, 6(2): 132-142.
[32]   Tuberosa R, Salvi S. Genomics-based approaches to improve drought tolerance of crops. Trends in Plant Science, 2006, 11(8): 405-412.
[33]   Wang D, Pan Y, Zhao X, Zhu L, Fu B, Li Z. Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice. BMC Genomics, 2011, 12(1): 149.
[34]   Degenkolbe T, Do P T, Kopka J, Zuther E, Hincha D K, Köhl K I. Identification of drought tolerance Mmarkers in a diverse population of rice cultivars by expression and metabolite profiling. PLoS ONE, 2013, 8(5): e63637.
[35]   Qin D, Wu H, Peng H, Yao Y, Ni Z, Li Z, Zhou C, Sun Q. Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using wheat genome array. BMC Genomics, 2008, 9(1): 432.
[36]   Lian X, Wang S, Zhang J, Feng Q, Zhang L, Fan D, Li X, Yuan D, Han B, Zhang Q. Expression Profiles of 10,422 Genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray. Plant Molecular Biology, 2006, 60(5): 617-631.
[37]   Gelli M, Duo Y, Konda A, Zhang C, Holding D, Dweikat I. Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling. BMC Genomics, 2014, 15(1): 179.
[38]   Li L, Liu C, Lian X. Gene expression profiles in rice roots under low phosphorus stress. Plant Molecular Biology, 2010, 72(4/5): 423-432.
[39]   Zheng L, Huang F, Narsai R, Wu J, Giraud E, He F, Cheng L, Wang F, Wu P, Whelan J, Shou H. Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings. Plant Physiology, 2009, 151(1): 262-274.
[40]   Ma T L, Wu W H, Wang Y. Transcriptome analysis of rice root responses to potassium deficiency. BMC Plant Biology, 2012, 12(1): 161.
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