Biotechnology Bulletin ›› 2021, Vol. 37 ›› Issue (1): 246-254.doi: 10.13560/j.cnki.biotech.bull.1985.2020-1008
Previous Articles Next Articles
GUO Li-li(), LI Yu-ying, GUO Da-long, HOU Xiao-gai()
Received:
2020-08-10
Online:
2021-01-26
Published:
2021-01-15
Contact:
HOU Xiao-gai
E-mail:guolili@haust.edu.cn;hkdhxg@haust.edu.cn
GUO Li-li, LI Yu-ying, GUO Da-long, HOU Xiao-gai. Research Progress on High-density Genetic Linkage Map Construction of Important Ornamental Plants:a Review[J]. Biotechnology Bulletin, 2021, 37(1): 246-254.
[1] | 阮成江, 何祯祥, 钦佩. 中国植物遗传连锁图谱构建研究进展[J]. 西北植物学报, 2002(6):246-256. |
Ruan CJ, He ZX, Qin P. Research progress of plant genetic linkage map in China[J]. Journal of Northwest Botany, 2002(6):246-256. | |
[2] | Zhang L, Guo DL, Guo LL, et al. Construction of a high-density genetic map and QTLs mapping with GBS from the interspecific F1 population of P. ostii ‘Fengdan Bai’ and P. suffruticosa ‘Xin Riyuejin’[J]. Scientia Horticulturae, 2019,246:190-200. |
[3] | Zhang QX, Chen WB, Sun LD, et al. The genome of Prunus mume[J]. Nature Communications, 2012,3(1):1318. |
[4] |
Wei FS, Zhang JW, Zhou SG, et al. The physical and genetic framework of the maize B73 genome[J]. PLoS Genetics, 2009,5(11):e1000715.
URL pmid: 19936061 |
[5] | Bradbury P, Parker T, Hamblin MT, et al. Assessment of power and false discovery rate in genome-wide association studies using the barley cap germplasm[J]. Crop Science, 2011,51(1):52-59. |
[6] |
Xie SQ, Feng JY, Zhang YM. Linkage group correction using epistatic distorted markers in F2 and backcross populations[J]. Heredity, 2014,112(5):479-488.
URL pmid: 24595363 |
[7] |
Botstein D, White RL, Skolnick M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. American Journal of Human Genetics, 1980,32(3):314-331.
URL pmid: 6247908 |
[8] |
Ganal MW, Altmann T, Roeder MS. SNP identification in crop plants[J]. Current Opinion in Plant Biology, 2009,12(2):211-217.
doi: 10.1016/j.pbi.2008.12.009 URL pmid: 19186095 |
[9] |
Jiang Z, Wang H, Michal JJ, et al. Genome wide sampling sequencing for SNP genotyping:methods, challenges and future development[J]. International Journal of Biological Sciences, 2016,12(1):100-108.
URL pmid: 26722221 |
[10] | 巴桑玉珍. 基于SLAF-seq技术构建青稞遗传图谱及抗倒伏相关性状的QTL分析[D]. 成都:四川农业大学, 2018. |
Basang YZ. Construction of high-density genetic map and QTL analysis of lodging resistance based on SLAF-seq technique in hulless barley[D]. Chengdu:Sichuan Agricultural University, 2018. | |
[11] | 杜庆章. 利用连锁与连锁不平衡联合作图解析毛白杨重要性状的等位遗传变异[D]. 北京:北京林业大学, 2014. |
Du QZ. Dissection of allelic variation underlying important traits in Populus tomentosa Carr. by using joint linkage and linkage disequilibrium mapping[D]. Beijing:Beijing Forestry University, 2014. | |
[12] | 李博. 毛白杨与毛新杨转录组图谱构建及若干性状的遗传学联合分析[D]. 北京:北京林业大学, 2009. |
Li B. Construction of transcriptome maps and QTL analyses of some complex traits by integrating genomics and transcriptomics for Populus tomentosa Carr. and P. tomentosa × P. bolleana[D]. Beijing:Beijing Forestry University, 2009. | |
[13] | 李旭冉. 美洲黑杨×小叶杨遗传连锁图谱构建[D]. 南京:南京林业大学, 2012. |
Li XR. A molecular genetic linkage map for hybrid population of Populus deltoids × Populus simonii[D]. Nanjing:Nanjing Forestry University, 2012. | |
[14] | 尹佟明, 沈永宝, 郑阿宝. 林木遗传图谱构建研究概述[J]. 江苏林业科技, 2000(6):38-43. |
Yin TM, Shen YB, Zheng AB. Introduction to genetic map construction in forest trees[J]. Journal of Jiangsu Forestry Science & Technology, 2000(6):38-43. | |
[15] |
Harushima Y, Yano M, Shomura A, et al. A high-density rice genetic linkage map with 2275 markers using a single F2 population[J]. Genetics, 1998,148(1):479-494.
URL pmid: 9475757 |
[16] |
Causse MA, Fulton TM, Cho YG, et al. Saturated molecular map of the rice genome based on an interspecific backcross population[J]. Genetics, 1994,138(4):1251-1274.
URL pmid: 7896104 |
[17] |
Lu CF, Shen LS, He P, et al. Comparative mapping of QTLs for agronomic traits of rice across environments by using a doubled-haploid population[J]. Theoretical and Applied Genetics, 1997,94(1):145-150.
URL pmid: 19352757 |
[18] | Muehlbauer GJ, Specht JE, Thomas-Compton MA, et al. Near-isogenic lines-a potential resource in the integration of conventional and molecular marker linkage maps[J]. Crop Science, 1988,28(5):729-735. |
[19] |
Watanabe S, Xia ZJ, Hideshima R, et al. A map-based cloning strategy employing a residual heterozygous line reveals that the gigantea gene is involved in soybean maturity and flowering[J]. Genetics, 2011,188(2):395-407.
URL pmid: 21406680 |
[20] |
Mei HW, Xu JL, Li ZK, et al. QTLs influencing panicle size detected in two reciprocal introgressive line(IL)populations in rice(Oryza sativa L.)[J]. Theoretical and Applied Genetics, 2006,112(4):648-656.
doi: 10.1007/s00122-005-0167-0 URL |
[21] | 徐礼羿. 茶树SNP高密度遗传连锁图谱构建与数量性状候选基因挖掘[D]. 武汉:华中农业大学, 2019. |
Xu LY. Construction of high-density SNP genetic map and identification of candidate genes for quantitative traits in Camellia sinensis[D]. Wuhan:Huazhong Agricultural University, 2019. | |
[22] | Devi AM, Goel S, Misra AK. Generation of silver stained TE-AFLP markers in tea(Camellia sinensis)and their assessment in filling gaps with construction of a genetic linkage map[J]. Scientia Horticulturae, 2015,192:293-301. |
[23] |
Grattapaglia D, Bertolucci FLG, Penchel R, et al. Genetic mapping of quantitative trait loci controlling growth and wood quality traits in Eucalyptus grandis using a maternal half-sib family and RAPD markers[J]. Genetics, 1996,144(3):1205-1214.
URL pmid: 8913761 |
[24] | 王莹. 利用RAD-seq测序构建美洲黑杨×小叶杨高密度遗传连锁图谱[D]. 南京:南京林业大学, 2014. |
Wang Y. Construction of a high-density linkage map of P. deltoids×P. Simonii using restriction-site associated DNA sequencing[D]. Nanjing:Nanjing Forestry University, 2014. | |
[25] | 周文才, 左继林, 赵松子, 等. 林木遗传图谱的构建策略及存在的问题[J]. 南方林业科学, 2016,44(2):62-66. |
Zhou WC, Zuo JL, Zhao SZ, et al. Construction strategies of genetic linkage map of forest trees and existing problems[J]. South China Forestry Science, 2016,44(2):62-66. | |
[26] | 刘更森. 苹果SSR和SNP标记开发及在遗传图谱构建和品种鉴定中的应用[D]. 长沙:湖南农业大学, 2018. |
Liu GS. Development of apple SSR and SNP markers and application in genetic map construction and cultivar identification[D]. Changsha:Hunan Agricultural University, 2018. | |
[27] | 胡建林. 油菜巢式关联作图群体的遗传特性及开花期QTL解析[D]. 武汉:华中农业大学, 2019. |
Hu JL. Genetic properties and flowering time QTL analysis of a nested association mapping population in rapeseed[D]. Wuhan:Huazhong Agricultural University, 2019. | |
[28] |
Davey JW, Hohenlohe PA, Etter PD, et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J]. Nature Reviews Genetics, 2011,12(7):499-510.
URL pmid: 21681211 |
[29] |
Van Tassell CP, Smith TPL, Matukumalli LK, et al. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries[J]. Nature Methods, 2008,5(3):247-252.
URL pmid: 18297082 |
[30] | Van Orsouw N, Hogers RCJ, Janssen A, et al. Complexity reduction of polymorphic sequences(CRoPS):a novel approach for large-scale polymorphism discovery in complex genomes[J]. PLoS One, 2007,2(11):e1172. |
[31] |
Miller MR, Dunham JP, Amores A, et al. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA(RAD)markers[J]. Genome Research, 2007,17(2):240-248.
doi: 10.1101/gr.5681207 URL pmid: 17189378 |
[32] |
Peterson BK, Weber JN, Kay EH, et al. Double digest RADseq:an inexpensive method for de novo SNP discovery and genotyping in model and non-model species[J]. PLoS One, 2012,7(5):e37135.
doi: 10.1371/journal.pone.0037135 URL pmid: 22675423 |
[33] |
Wang S, Meyer E, McKay JK, et al. 2b-RAD:a simple and flexible method for genome-wide genotyping[J]. Nature Methods, 2012,9(8):808-810.
doi: 10.1038/nmeth.2023 URL pmid: 22609625 |
[34] |
Sun XW, Liu DY, Zhang XF, et al. SLAF-seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing[J]. PLoS One, 2013,8(3):e58700.
doi: 10.1371/journal.pone.0058700 URL pmid: 23527008 |
[35] |
Andolfatto P, Davison D, Erezyilmaz D, et al. Multiplexed shotgun genotyping for rapid and efficient genetic mapping[J]. Genome Research, 2011,21(4):610-617.
doi: 10.1101/gr.115402.110 URL |
[36] |
Elshire RJ, Glaubitz JC, Sun Q, et al. A robust, simple genotyping-by-sequencing(GBS)approach for high diversity species[J]. PLoS One, 2011,6(5):e19379.
URL pmid: 21573248 |
[37] | Singh BD, Singh AK. Marker-assisted plant breeding:principles and practices[M]. New Delhi:Springer, 2015. |
[38] | 谢尚潜. 偏分离群体遗传图谱矫正QTL定位及其软件研制[D]. 南京:南京农业大学, 2013. |
Xie SQ. Genetic map correction, quantitative trait locus mapping and software development in segregation distortion population[D]. Nanjing:Nanjing Agricultural University, 2013. | |
[39] |
Lander ES, Green P, Abrahamson J, et al. Mapmaker:an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations[J]. Genomics, 1987,1(2):174-181.
URL pmid: 3692487 |
[40] | Van Ooijen J, JoinMap® 4, software for the calculation of genetic linkage maps in experimental populations[J]. Kyazma BV Wageningen, 2006,33(10):1371. |
[41] | 童春发. 林木遗传图谱构建和QTL定位的统计方法[J]. 南京林业大学学报:自然科学版, 2004(1):109. |
Tong CF. Statistical methods for constructing genetic linkage maps and mapping QTLs in forest trees[J]. Journal of Nanjing Forestry University:Natural Sciences Edition, 2004(1):109. | |
[42] |
Cai CF, Cheng FY, Wu J, et al. The first high-density genetic map construction in tree peony(Paeonia Sect. Moutan)using genotyping by specific-locus amplified fragment sequencing[J]. PLoS One, 2015,10(5):e0128584.
URL pmid: 26010095 |
[43] | Li S, Lv SZ, Yu K, et al. Construction of a high-density genetic map of tree peony(Paeonia suffruticosa Andr. Moutan)using restriction site associated DNA sequencing(RADseq)approach[J]. Tree Genetics & Genomes, 2019,15(4):63. |
[44] | Vukosavljev M, Arens P, Voorrips R, et al. High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array[J]. Horticulture Research, 2016,3:16052. |
[45] |
Yan M, Byrne DH, Klein PE, et al. Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map[J]. Horticulture Research, 2018,5:17.
doi: 10.1038/s41438-018-0021-6 URL pmid: 29619228 |
[46] |
Li SB, Yang GQ, Yang SH, et al. The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose[J]. Scientific Reports, 2019,9:5985.
doi: 10.1038/s41598-019-42428-y URL pmid: 30979937 |
[47] | Sun LD, Wang YQ, Yan XL, et al. Genetic control of juvenile growth and botanical architecture in an ornamental woody plant, Prunus mume Sieb. et Zucc. as revealed by a high-density linkage map[J]. BMC Genetics, 2014,15:S1. |
[48] |
Zhang J, Zhang QX, Cheng TR, et al. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant(Prunus mume Sieb. et Zucc)[J]. DNA Research, 2015,22(3):183-191.
URL pmid: 25776277 |
[49] |
He YX, Yuan WJ, Dong MF, et al. The first genetic map in sweet Osmanthus(Osmanthus fragrans lour. )using specific locus amplified fragment sequencing[J]. Frontiers in Plant Science, 2017,8:1621.
doi: 10.3389/fpls.2017.01621 URL pmid: 29018460 |
[50] | Yang M, Han YN, VanBuren R, et al. Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar[J]. BMC Genomics, 2012,13(1):653. |
[51] | Zhang Q, Li LT, VanBuren R, et al. Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map[J]. BMC Genomics, 2014,15(1):372. |
[52] | 刘艳玲. 莲野生居群遗传多样性评价及高密度遗传连锁图谱的构建[D]. 武汉:华中农业大学, 2013. |
Liu YL. Assessment of genetic diversity among lotus populations and construction of a high-density genetic linkage map of lotus[D]. Wuhan:Huazhong Agricultural University, 2013. | |
[53] |
Ming R, VanBuren R, Liu YL, et al. Genome of the long-living sacred lotus(Nelumbo nucifera Gaertn. )[J]. Genome Biology, 2013,14(5):R41
doi: 10.1186/gb-2013-14-5-r41 URL pmid: 23663246 |
[54] |
Liu ZW, Zhu HL, Liu YP, et al. Construction of a high-density, high-quality genetic map of cultivated lotus(Nelumbo nucifera)using next-generation sequencing[J]. BMC Genomics, 2016,17(1):466.
doi: 10.1186/s12864-016-2781-4 URL |
[55] | Gui ST, Peng J, Wang XL, et al. Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements[J]. Plant Journal, 2018,94(4):721-734. |
[56] | 严寒松. 中国莲高密度遗传图谱的构建及花瓣数控制基因的定位[D]. 福州:福建农林大学, 2019. |
Yan HS. High-density genetic Map and QTL mapping of genes controlling petal number in lotus[D]. Fuzhou:Fujian Agriculture and Forestry University, 2019. | |
[57] | Van Geest G, Bourke PM, Voorrips RE, et al. An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis[J]. Theoretical and Applied Genetics, 2017,130(12):2527-2541. |
[58] | Song XB, Xu YH, Gao K, et al. High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum(Chrysanthemum × morifolium Ramat. )[J]. Horticulture Research, 2020,7(1):108. |
[59] | Li J, Xu YC, Wang ZH. Construction of a high-density genetic map by RNA sequencing and eQTL analysis for stem length and diameter in Dendrobium(Dendrobium nobile × Dendrobium wardianum)[J]. Industrial Crops and Products, 2019,128:48-54. |
[60] | Lu JJ, Zhao HY, Suo NN, et al. Genetic linkage maps of Dendrobium moniliforme and D. officinale based on EST-SSR, SRAP, ISSR and RAPD markers[J]. Scientia Horticulturae, 2012,137:1-10. |
[61] | Lu JJ, Liu YY, Xu J, et al. High-density genetic map construction and stem total polysaccharide content-related qtl exploration for Chinese Endemic Dendrobium(Orchidaceae)[J]. Frontiers in Plant Science, 2018,9:398. |
[62] | 阮莹. 矮牵牛遗传图谱构建及重瓣分子标记筛选[D]. 武汉:华中农业大学, 2019. |
Ruan Y. Construction of genetic linkage map and screening of molecular markers associated with double flower trait in Petunia[D]. Wuhan:Huazhong Agricultural University, 2019. | |
[63] | Yagi M, Shirasawa K, Waki T, et al. Construction of an SSR and RAD marker-based genetic linkage map for Carnation(Dianthus caryophyllus L.)[J]. Plant Molecular Biology Reporter, 2017,35(1):110-117. |
[64] | Hirakawa H, Sumitomo K, Hisamatsu T, et al. De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis[J]. DNA Research, 2019,26(3):195-203. |
[65] | Zhang LS, Chen F, Zhang XT, et al. The water lily genome and the early evolution of flowering plants[J]. Nature, 2020,577:79-84. |
[66] | Povilus RA, DaCosta JM, Grassa C, et al. Water lily(Nymphaea thermarum)genome reveals variable genomic signatures of ancient vascular cambium losses[J]. Proceedings of the National Academy of Sciences of the United States of America, 2020,117(15):8649-8656. |
[67] | Wang Y, Fan GY, Liu YM, et al. The sacred lotus genome provides insights into the evolution of flowering plants[J]. Plant Journal, 2013,76(4):557-567. |
[68] | Lv SZ, Cheng S, Wang ZY, et al. Draft genome of the famous ornamental plant Paeonia suffruticosa[J]. Ecology and Evolution, 2020,10(11):4518-4530. |
[69] | Yang XL, Yue YZ, Li HY, et al. The chromosome-level quality genome provides insights into the evolution of the biosynjournal genes for aroma compounds of Osmanthus fragrans[J]. Horticulture Research, 2018,5:72. |
[70] | Yagi M, Kosugi S, Hirakawa H, et al. Sequence analysis of the genome of Carnation(Dianthus caryophyllus L.)[J]. DNA Research, 2014,21(3):231-241. |
[71] | Zhang GQ, Xu Q, Bian C, et al. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution[J]. Scientific Reports, 2016,6:19029 |
[72] | Huang JZ, Lin CP, Cheng T, et al. The genome and transcriptome of Phalaenopsis yield insights into floral organ development and flowering regulation[J]. Peerj, 2016,4:e2017. |
[73] | Cai J, Liu X, Vanneste K, et al. The genome sequence of the orchid Phalaenopsis equestris[J]. Nature Genetics, 2015,47(1):65-72. |
[74] | Bombarely A, Moser M, Amrad A, et al. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida[J]. Nature Plants, 2016,2:16074. |
[1] | YU Shi-zhou, CAO Ling-gai, WANG Shi-ze, LIU Yong, BIAN Wen-jie, REN Xue-liang. Development Core SNP Markers for Tobacco Germplasm Genotyping [J]. Biotechnology Bulletin, 2023, 39(3): 89-100. |
[2] | CHEN Yi-dan, ZHANG Yu, YANG Jie, ZHANG Qin, JIANG Li. Exploration of Key Functional Genes Affecting Milk Production Traits in Dairy Cattle Based on RNA-seq [J]. Biotechnology Bulletin, 2020, 36(9): 244-252. |
[3] | YU Jun-jian, CHI Mei-li, JIA Yong-yi, LIU Shi-li, ZHU Jun-quan, GU Zhi-min. Tetra-primer Amplification Refractory Mutation System PCR and Its Application in Fauna and Flora Genetics and Breeding Research [J]. Biotechnology Bulletin, 2020, 36(5): 32-38. |
[4] | LI Xiao-kai, FAN Yi-xing, QIAO Xian, ZHANG Lei, WANG Feng-hong, WANG Zhi-ying, WANG Rui-jun, ZHANG Yan-jun, LIU Zhi-hong, WANG Zhi-xin, HE Li-bing, LI Jin-quan, SU Rui, ZHANG Jia-xin. Research Progress of Goat Genome and Genetic Variation Map [J]. Biotechnology Bulletin, 2020, 36(4): 175-184. |
[5] | HUANG Long, WU Ben-li, HE Ji-xiang, CHEN Jing, SONG Guang-tong, WANG Xiang, ZHANG Ye, WU Song. SNP Identification of MyoD1 Gene and Its Correlation with Growth Traits in Pelodiscus sinensis [J]. Biotechnology Bulletin, 2019, 35(4): 76-81. |
[6] | GUO Meng-meng, ZHOU Yan-qing, DUAN Hong-ying, YANG Ke, SHAO Lu-ying. Development of SNP Marker Based on the Rehmannia glutinosa Transcriptome Database and Construction of DNA Fingerprint in Rehmannia [J]. Biotechnology Bulletin, 2019, 35(11): 224-230. |
[7] | Gong Jing, Liu Chunjie, Miao Xiaoping, Guo Anyuan. Research Progress of the Human Long Non-coding RNA Related SNP Identification and Function Prediction [J]. Biotechnology Bulletin, 2015, 31(11): 27-34. |
[8] | Wang Chunxia, Lin Jiajuan, Liu Xuanxuan, Li Yuan, Fang Xingtang. Single Nucleotide Polymorphism of MDFI Gene and Association with Body Size Traits in Haimen Goats [J]. Biotechnology Bulletin, 2013, 0(9): 99-104. |
[9] | Zhang Xiaomeng, Ma Pu, Wang Hongdi, Wang Xiuli. Progresses of SNPs Studies in Aquaculture Animals [J]. Biotechnology Bulletin, 2013, 0(8): 7-11. |
[10] | Zhang Yinhong, Li Huifang, Zhu Wenqi. Single Nucleotide Polymorphism Analysis of Duck Adiponectin Gene [J]. Biotechnology Bulletin, 2013, 0(5): 126-129. |
[11] | Wang Qingyao, Rao Huachun, Diao Yong, Yang Huiyong. Recent Development of Allele-specific Amplification in SNP Genotyping [J]. Biotechnology Bulletin, 2013, 0(12): 62-67. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||