Progress on genomics and locus of important agronomic traits in Chenopodium quinoa
Received date: 2022-09-02
Revised date: 2022-10-10
Online published: 2022-10-27
Supported by
the Fundamental Research Program of Shanxi Province(202103021223158);the Scientific Research Project of Shanxi Province Outstanding Doctoral Work Award Fund(SXBYKY2022022);the Doctoral research Project of Shanxi Agricultural University(2021BQ82)
Quinoa (Chenopodium quinoa, Willd.) as a new health food in the 20th century, its comprehensive nutritional composition, stress resistance and other characteristics have been paid much of attention, and enjoys the reputation of “nutritional gold”, “vegetarian king” and “food in the future” in the world. In recent years, with the rapid development of genomics and high-throughput sequencing technology, the high-quality whole genome sequence of quinoa has been completed, and the omics analysis and functional research of a series of key genes have been gradually carried out. In this review, we summarize the research progress in quinoa genomics, gene family analysis of important transcription factors, genetic map construction, QTL mapping of important traits, and genes for important agronomic and yield traits. Moreover, according to the current status of quinoa breeding, this paper also put forward five key problems in quinoa breeding, and pointed out four important directions of genetic improvement and breeding of quinoa in the future, so as to provide reference for the realization of directional genetic improvement of quinoa in the future.
Key words： quinoa; genomics; genetic breeding; traits; genes
Linghong Li, Tong Gou, Aixia Ren, Pengcheng Ding, Wen Lin, Xiangyun Wu, Min Sun, Zhiqiang Gao . Progress on genomics and locus of important agronomic traits in Chenopodium quinoa[J]. Hereditas(Beijing), 2022 , 44(11) : 1009 -1027 . DOI: 10.16288/j.yczz.22-289
| [1] | Organization FA. Genebank standards for plant genetic resources for food and agriculture. Genebank Stand Plant Genet Resour Food Agric, 2013, 11(1): 1-16. |
| [2] | Yan F, Li QQ, Dong Y, Ji SD. Industry status and development countermeasures of Chenopodium quinoa. Heilongjiang Agric Sci, 2021, (9): 98-100. |
| [2] | 闫锋, 李清泉, 董扬, 季生栋. 藜麦产业现状及发展对策. 黑龙江农业科学, 2021, (9): 98-100. |
| [3] | Ren GX, Yang XS, Me Y. Current situation of Chinese quinoa industry. Crop Sci, 2015, (5): 1-5. |
| [3] | 任贵兴, 杨修仕, 么杨. 中国藜麦产业现状. 作物杂志, 2015, (5): 1-5. |
| [4] | Kolano B, McCann J, Orzechowska M, Siwinska D, Temsch E, Weiss-Schneeweiss H. Molecular and cytogenetic evidence for an allotetraploid origin of Chenopodium quinoa and C. berlandieri (Amaranthaceae). Mol Phylogenet Evol, 2016, 100: 109-123. |
| [5] | Yasui Y, Hirakawa H, Oikawa T, Toyoshima M, Matsuzaki C, Ueno M, Mizuno N, Nagatoshi Y, Imamura T, Miyago M, Tanaka K, Mise K, Tanaka T, Mizukoshi H, Mori M, Fujita Y. Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties. DNA Res, 2016, 23(6): 535-546. |
| [6] | Jarvis DE, Ho YS, Lightfoot DJ, Schm?ckel SM, Li B, Borm TJA, Ohyanagi H, Mineta K, Michell CT, Saber N, Kharbatia NM, Rupper RR, Sharp AR, Dally N, Boughton BA, Woo YH, Gao G, Schijlen EGWM, Guo XJ, Momin AA, Negr?o S, Al-Babili S, Gehring C, Roessner U, Jung C, Murphy K, Arold ST, Gojobori T, van der Linden CG, van Loo EN, Jellen EN, Maughan PJ, Tester M. The genome of Chenopodium quinoa. Nature, 2017, 542(7641): 307-312. |
| [7] | Wang KY, Li L, Li SK, Sun HH, Zhao MZ, Zhang MP, Wang Y. Characterization of the complete chloroplast genome of Chenopodium quinoa Willd. Mitochondrial DNA B Resour, 2017, 2(2): 812-813. |
| [8] | Stevens MR, Coleman CE, Parkinson SE, Maughan PJ, Zhang HB, Balzotti MR, Kooyman DL, Arumuganathan K, Bonifacio A, Fairbanks DJ, Jellen EN, Stevens JJ. Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins. Theor Appl Genet, 2006, 112(8): 1593-1600. |
| [9] | Morales A, Zurita-Silva A, Maldonado J, Silva H. Transcriptional responses of Chilean quinoa (Chenopodium quinoa Willd.) under water deficit conditions uncovers ABA-independent expression patterns. Front Plant Sci, 2017, 8: 216. |
| [10] | Liu Q, Zhang GY, Chen SY. Structure and regulatory function of plant transcription factors. Chin Sci Bull, 2001, 46: 271-278. |
| [11] | Alshareef NO, Rey E, Khoury H, Tester M, Schm?ckel SM. Genome wide identification of NAC transcription factors and their role in abiotic stress tolerance in Chenopodium quinoa. bioRxiv, 2019, Doi: 10.1101/693093. |
| [12] | Zhang DL.Identification and analysis of quinoa MADS-box gene family and study on agrobacterium- mediated root transformation[Dissertation]. Yantai University, 2021. |
| [12] | 张东亮.藜麦MADS-box基因家族的鉴定与分析及发根农杆菌介导的根转化研究[学位论文]. 烟台大学, 2021. |
| [13] | Yue H, Chang X, Zhi YQ, Wang L, Xing GW, Song WN, Nie XJ. Evolution and identification of the WRKY gene family in quinoa (Chenopodium quinoa). Genes (Basel), 2019, 10(2): 131. |
| [14] | Li KY, Fan Y, Zhou GY, Liu XJ, Chen SS, Chang XC, Wu WQ, Duan LL, Yao MX, Wang R, Wang ZL, Yang MF, Ding YQ, Ren MJ, Fan Y, Zhang LY. Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions. BMC Genomics, 2022, 23(1): 499. |
| [15] | Zhang YM, Zhu LL, Chen ZG. Identification and expression analysis of NHX gene family in quinoa under salt stress. Biotechnology Bulletin, 2022, 1-10. |
| [15] | 张业猛, 朱丽丽, 陈志国. 藜麦NHX基因家族鉴定及盐胁迫下表达分析. 生物技术通报, 2022, 1-10. |
| [16] | Xiao YL.Identification analysis and functional vertification of TCP gene family in Chenopodium quinoa[Dissertation]. Shandong Normal University, 2021. |
| [16] | 肖玉林.藜麦TCP基因家族鉴定分析与功能验证[学位论文]. 山东师范大学, 2021. |
| [17] | Cao HQ.Isolation and molecular characterization of quinoa SPL family genes[Dissertation]. Shanxi University, 2021. |
| [17] | 曹华麒.藜麦SPL家族基因的分离和分子特性分析[学位论文]. 山西大学, 2021. |
| [18] | Tashi G, Zhan HS, Xing GW, Chang X, Zhang H, Nie XJ, Ji WQ. Genome-wide identification and expression analysis of heat shock transcription factor family in Chenopodium quinoa Willd. Agron, 2018, 8(7): 103. |
| [19] | Shi PB, He B, Fei YY, Wang J, Wang WY, Wei FY, Lv YD, Gu MF. Identification and expression analysis of GRF transcription factor family of Chenopodium quinoa. Acta Agron Sin, 2019, 45(12): 1841-1850. |
| [19] | 时丕彪, 何冰, 费月跃, 王军, 王伟义, 魏福友, 吕远大, 顾闽峰. 藜麦GRF转录因子家族的鉴定及表达分析. 作物学报, 2019, 45(12): 1841-1850. |
| [20] | Zhu MX, Yang YS, Yang XL, Zhang F, Yang LY, Wang CY. Identification and expression analysis of WOX transcription factor family of Chenopodium quinoa. J Nat Sci Hunan Norm Univ, 2020, 43(4): 43-49. |
| [20] | 朱满喜, 杨雅舒, 杨小兰, 张芳, 杨利艳, 王创云. 藜麦WOX转录因子家族的鉴定及表达分析. 湖南师范大学自然科学学报, 2020, 43(4): 43-49. |
| [21] | Zhang DL, Wu XL, Tian XQ, Chu J, Guo SL, Chen SH. Identification and expression of CqKEA gene family in Chenopodium quinoa. Journal of Yantai University Natural Science and Engineering Edition, 2021, 34(4): 400-405. |
| [21] | 张东亮, 吴筱林, 田晓芹, 褚晶, 郭善利, 陈世华. 藜麦CqKEA基因家族的鉴定及表达. 烟台大学学报(自然科学与工程版), 2021, 34(4): 400-405. |
| [22] | Shi XD, Sun MH, Wu Q, Tian YS, Xu Y. Identification and expression analysis of fatty acid export gene family in Chenopodium quinoa. Genomics Appl Biol, 2020, 39(12): 5652-5659. |
| [22] | 时小东, 孙梦涵, 吴琪, 田银帅, 徐莺. 藜麦脂肪酸转运基因家族FAX的鉴定与表达分析. 基因组学与应用生物学, 2020, 39(12): 5652-5659. |
| [23] | Zhu MX, Zhang YR, Yang YS, Yang XL, Wang CY, Deng Y, Zhao L, Zhang LG, Qin LX, Yang LY. Identification and expression analysis of NLP transcription factor family of Chenopodium quinoa Willd. Acta Agric Boreali-Sin, 2021, 36(4): 37-46. |
| [23] | 朱满喜, 张玉荣, 杨雅舒, 杨小兰, 王创云, 邓妍, 赵丽, 张丽光, 秦丽霞, 杨利艳. 藜麦NLP转录因子家族的鉴定及表达分析. 华北农学报, 2021, 36(4): 37-46. |
| [24] | Maughan PJ, Smith SM, Rojas-Beltrán JA, Elzinga D, Raney JA, Jellen EN, Bonifacio A, Udall JA, Fairbanks DJ. Single nucleotide polymorphism identification, characterization, and linkage mapping in quinoa. Plant Genome, 2012, 5(3): 114-125. |
| [25] | Fairbanks DJ, Waldrigues A, Ruas CF, Maughan PJ, Robinson LR, Andersen WR, Riede CR, Pauley CS, Caetano LG, Arantes OMN, Fungaro MHP, Vidotto MC, Jankevicius SE. Efficient characterization of biological diversity using field DNA extraction and random amplified polymorphic DNA markers. Braz J Genet, 1993, 16(1): 11-22. |
| [26] | Maughan PJ, Bonifacio A, Jellen EN, Stevens MR, Coleman CE, Ricks M, Mason SL, Jarvis DE, Gardunia BW, Fairbanks DJ. A genetic linkage map of quinoa (Chenopodium quinoa) based on AFLP, RAPD, and SSR markers. Theor Appl Genet, 2004, 109(6): 1188-1195. |
| [27] | Mason SL, Stevens MR, Jellen EN, Bonifacio A, Fairbanks DJ, Coleman CE, Mccarty RR, Rasmussen AG, Maughan PJ. Development and use of microsatellite markers for germplasm characterization in quinoa (Chenopodium quinoa Willd.). Crop Sci, 2005, 45(4): 1618-1630. |
| [28] | Zhang TF, Gu MF, Liu YH, Lv YD, Zhou L, Lu HY, Liang SQ, Bao HB, Zhao H. Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing. BMC Genomics, 2017, 18(1): 685. |
| [29] | Jarvis DE, Kopp OR, Jellen EN, Mallory MA, Pattee J, Bonifacio A, Coleman CE, Stevens MR, Fairbanks DJ, Maughan PJ. Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.). J Genet, 2008, 87(1): 39-51. |
| [30] | Cervantes DP, Van Loo E. QTL Mapping for agromorphological traits in quinoa (Chenopodium quinoa Willd.). Wageningen University, 2017. |
| [31] | Patiranage DSR, Rey E, Emrani N, Wellman G, Schmid K, Schm?ckel SM, Tester M, Jung C. Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history. eLife, 2020, 11: e66873. |
| [32] | Maldonado-Taipe N, Barbier F, Schmid K, Jung C, Emrani N. High-density mapping of quantitative trait loci controlling agronomically important traits in quinoa (Chenopodium quinoa Willd.). Front Plant Sci, 2022, 13: 916067. |
| [33] | Pin PA, Nilsson O. The multifaceted roles of FLOWERING LOCUS T in plant development. Plant Cell Environ, 2012, 35(10): 1742-1755. |
| [34] | Golicz AA, Steinfort U, Arya H, Singh MB, Bhalla PL. Analysis of the quinoa genome reveals conservation and divergence of the flowering pathways. Funct Integr Genomics, 2020, 20(2): 245-258. |
| [35] | Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP. 'Green revolution' genes encode mutant gibberellin response modulators. Nature, 1999, 400(6741): 256-261. |
| [36] | Winkler RG, Freeling M. Physiological genetics of the dominant gibberellin-nonresponsive maize dwarfs, Dwarf8 and Dwarf9. Planta, 1994, 193: 341-348. |
| [37] | Maliro MFA, Guwela VF, Nyaika J, Murphy KM. Preliminary studies of the performance of quinoa (Chenopodium quinoa Willd.) genotypes under irrigated and rainfed conditions of central Malawi. Front Plant Sci, 2017, 8: 227. |
| [38] | Silverstone AL, Ciampaglio CN, Sun T. The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. Plant Cell, 1998, 10(2): 155-169. |
| [39] | Song XJ, Huang W, Shi M, Zhu MZ, Lin HX. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet, 2007, 39(5): 623-630. |
| [40] | Wang SG, Ma BT, Gao Q, Jiang GJ, Zhou L, Tu B, Qin P, Tan XQ, Liu PX, Kang YH, Wang YP, Chen WL, Liang CZ, Li SG. Dissecting the genetic basis of heavy panicle hybrid rice uncovered Gn1a and GS3 as key genes. Theor Appl Genet, 2018, 131(6): 1391-1403. |
| [41] | Bartrina I, Otto E, Strnad M, Werner T, Schmülling T. Cytokinin regulates the activity of reproductive meristems, flower organ size, ovule formation, and thus seed yield in Arabidopsis thaliana. Plant Cell, 2011, 23(1): 69-80. |
| [42] | Ballester P, Ferrándiz C. Shattering fruits: variations on a dehiscent theme. Curr Opin Plant Biol, 2017, 35: 68-75. |
| [43] | Hofmann NR. SHAT1, a new player in seed shattering of rice. Plant Cell, 2012, 24(3): 839. |
| [44] | Liljegren SJ, Ditta GS, Eshed Y, Savidge B, Bowman JL, Yanofsky MF. Shatterproof MADS-box genes control seed dispersal in Arabidopsis. Nature, 2000, 404(6779): 766-770. |
| [45] | Fiallos-Jurado J, Pollier J, Moses T, Arendt P, Barriga- Medina N, Morillo E, Arahana V, de Lourdes Torres M, Goossens A, Leon-Reyes A. Saponin determination, expression analysis and functional characterization of saponin biosynthetic genes in Chenopodium quinoa leaves. Plant Sci, 2016, 250: 188-197. |
| [46] | Balzotti MRB, Thornton JN, Maughan PJ, Mcclellan DA, Stevens MR, Jellen EN, Fairbanks DJ, Coleman CE. Expression and evolutionary relationships of the Chenopodium quinoa 11S seed storage protein gene. Int J Plant Sci, 2008, 169(2): 281-291. |
| [47] | Nakamura S, Ikegami A, Mizuno M, Yagi F, Nomura K. The expression profile of lectin differs from that of seed storage proteins in Castanea crenata trees. Biosci Biotechnol Biochem, 2004, 68(8): 1698-1705. |
| [48] | Ruiz KB, Biondi S, Martínez EA, Orsini F, Antognoni F, Jacobsen SE. Quinoa - a model crop for understanding salt-tolerance mechanisms in halophytes. Plant Biosyst, 2016, 150(2): 357-371. |
| [49] | Maughan PJ, Turner TB, Coleman CE, Elzinga DB, Jellen EN, Morales JA, Udall JA, Fairbanks DJ, Bonifacio A. Characterization of salt overly sensitive 1 (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd.). Genome, 2009, 52(7): 647-657. |
| [50] | Schm?ckel SM, Lightfoot DJ, Razali R, Tester M, Jarvis DE. Identification of putative transmembrane proteins involved in salinity tolerance in Chenopodium quinoa by integrating physiological data, RNAseq, and SNP analyses. Front Plant Sci, 2017, 8: 1023. |
| [51] | B?hm J, Messerer M, Müller HM, Scholz-Starke J, Gradogna A, Scherzer S, Maierhofer T, Bazihizina N, Zhang H, Stigloher C, Ache P, Al-Rasheid KAS, Mayer KFX, Shabala S, Carpaneto A, Haberer G, Zhu JK, Hedrich R. Understanding the molecular basis of salt sequestration in epidermal bladder cells of Chenopodium quinoa. Curr Biol, 2018, 28(19): 3075-3085.e7. |
| [52] | Imamura T, Yasui Y, Koga H, Takagi H, Abe A, Nishizawa K, Mizuno N, Ohki S, Mizukoshi H, Mori M. A novel WD40-repeat protein involved in formation of epidermal bladder cells in the halophyte quinoa. Commun Biol, 2020, 3(1): 513. |
| [53] | Liu JX, Wang RM, Liu WY, Zhang HL, Guo YD, Wen RY. Genome-wide characterization of heat-shock protein 70s from Chenopodium quinoa and expression analyses of Cqhsp70s in response to drought stress. Genes (Basel), 2018, 9(2): 35. |
| [54] | Golldack D, Li C, Mohan H, Probst N. Tolerance to drought and salt stress in plants: unraveling the signaling networks. Front Plant Sci, 2014, 5: 151. |
| [55] | Liu HC, Liao HT, Charng YY.The role of class A1 heat shock factors (HSFA1s) in response to heat and other stresses in Arabidopsis. Plant Cell Environ, 2011, 34(5): 738-751. |
| [56] | Hinojosa L, Sanad MNME, Jarvis DE, Steel P, Murphy K, Smertenko A. Impact of heat and drought stress on peroxisome proliferation in quinoa. Plant J, 2019, 99(6): 1144-1158. |
| [57] | Jacobsen SE, Christiansen JL, Rasmussen J. Weed harrowing and inter-row hoeing in organic grown quinoa (Chenopodium quinoa Willd.). Outlook Agric, 2010, 39(3): 223-227. |
| [58] | Mestanza U, Riegel R, Silva H, Vásquez SC. Characterization of the acetohydroxyacid synthase multigene family in the tetraploide plant Chenopodium quinoa. Electron J Biotechnol, 2015, 18(6): 393-398. |
| [59] | Ceccato DV, Bertero HD, Batlla D. Environmental control of dormancy in quinoa (Chenopodium quinoa) seeds: two potential genetic resources for pre-harvest sprouting tolerance. Seed Sci Res, 2011, 21(2): 133-141. |
| [60] | Xi WY, Liu C, Hou XL, Yu H.Mother of FT and TFL1 regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis. Plant Cell, 2010, 22(6): 1733-1748. |
| [61] | López-Marqués RL, N?rrevang AF, Ache P, Moog M, Visintainer D, Wendt T, ?sterberg JT, Dockter C, J?rgensen ME, Salvador AT, Hedrich R, Gao CX, Jacobsen SE, Shabala S, Palmgren M. Prospects for the accelerated improvement of the resilient crop quinoa. J Exp Bot, 2020, 71(18): 5333-5347. |
| [62] | Nakamura S, Pourkheirandish M, Morishige H, Kubo Y, Nakamura M, Ichimura K, Seo S, Kanamori H, Wu JZ, Ando T, Hensel G, Sameri M, Stein N, Sato K, Matsumoto T, Yano M, Komatsuda T. Mitogen-activated protein kinase kinase 3 regulates seed dormancy in barley. Curr Biol, 2016, 26(6): 775-781. |
| [63] | Danielsen S, Bonifacio A, Ames T. Diseases of quinoa (Chenopodium quinoa). Food Rev Int, 2006, 19(1-2): 43-59. |
| [64] | Khalifa W, Thabet M. Variation in downy mildew (Peronospora variabilis G?um) resistance of some quinoa (Chenopodium quinoa Willd.) cultivars under Egyptian conditions. Middle East J Agric, 2018, 7(2): 671-682. |
| [65] | Mhada M, Ezzahiri B, Benlhabib O. Assessment of downy mildew resistance (Peronospora farinosa) in a quinoa (Chenopodium quinoa Willd.) germplasm. Int J Agric Biol Eng, 2014, 8(3): 277-280. |
| [66] | Ochoa J, Frinking HD, Jacobs T. Postulation of virulence groups and resistance factors in the quinoa/downy mildew pathosystem using material from Ecuador. Plant Pathol, 1999, 48(3): 425-430. |
| [67] | Rasmussen C, Lagnaoui A, Esbjerg P. Advances in the knowledge of quinoa pests. Food Rev Int, 2003, 19(1-2): 61-75. |
| [68] | Pereira E, Encina-Zelada C, Barros L, Gonzales-Barron U, Cadavez V, Ferreira ICFR. Chemical and nutritional characterization of quinoa (Chenopodium quinoa Willd.) grains: A good alternative to nutritious food. Food Chem, 2019, 280: 110-114. |
| [69] | Ruiz KB, Biondi S, Oses R, Acu?a-Rodríguez IS, Antognoni F, Martinez-Mosqueira EA, Coulibaly A, Canahua-Murillo A, Pinto M, Zurita-Silva A, Bazile D, Jacobsen SE, Molina-Montenegro MA. Quinoa biodiversity and sustainability for food security under climate change. A review. Agron Sustainable Dev, 2014, 34(2): 349-359. |
| [70] | Zurita-Silva A, Fuentes F, Zamora P, Jacobsen SE, Schwember AR. Breeding quinoa (Chenopodium quinoa Willd.): potential and perspectives. Mol Breed, 2014, 34(1): 13-30. |
| [71] | Lin C, Liu ZJ, Dong YM, Michel V, Mao ZC. Domesticated cultivation and genetic breeding of Chenopodium quinoa. Hereditas(Beijing), 2019, 41(11): 1009-1022. |
| [71] | 林春, 刘正杰, 董玉梅, Michel Vales, 毛自朝. 藜麦的驯化栽培与遗传育种. 遗传, 2019, 41(11): 1009-1022. |
| [72] | Ma XL, Zhang QY, Zhu QL, Liu W, Chen Y, Qiu R, Wang B, Yang ZF, Li HY, Lin YR, Xie YY, Shen RX, Chen SF, Wang Z, Chen YL, Guo JX, Chen LT, Zhao XC, Dong ZC, Liu YG. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in Monocot and Dicot plants. Mol Plant, 2015, 8(8): 1274-1284. |
/
| 〈 |
|
〉 |
www.chinagene.cn
备案号：京ICP备09063187号
