The Reduced-representation Genome Sequencing Technology: Application in Plant Genetic Analysis

doi:10.11924/j.issn.1000-6850.casb2021-0380

Abstract

Abstract:

Reduced-representation Genome Sequencing (RRGS) is a technology developed on the basis of next-generation sequencing to sequence specific regions based on enzyme digestion to reduce the complexity of the genome. This methodological step is simple, low cost, independent of the reference genome, and enables molecular markers at the genome-wide level. This paper summarizes the development process and main technical types of RRGS, and sums up the application of RRGS in plant genetic map construction, quantitative trait locus mapping, and population genetic analysis. At the same time, the defects and deficiencies in the analysis of population genetics by RRGS are put forward, in order to provide reference for the research methods of plant genetic evolution, trait mapping, and etc.

Key words: reduced-representation genome sequencing, molecular marker, genetic map, quantitative trait locus, population genetics

CLC Number:

S184

DONG Yuqing, WEI Xueping, QIANG Tingyan, ZHANG Bengang, QI Yaodong, LIU Haitao. The Reduced-representation Genome Sequencing Technology: Application in Plant Genetic Analysis[J]. Chinese Agricultural Science Bulletin, 2022, 38(8): 25-32.

Figures/Tables 2

References 72

[1]	SANGER F, NICKLEN S, COULSON A R. DNA sequencing with chain-terminating inhibitors[J]. Proceedings of the national academy of sciences, 1977, 74(12):5463-5467. doi: 10.1073/pnas.74.12.5463 URL
[2]	MARGULIES M, EGHOLM M, ALTMAN W E, et al. Genome sequencing in microfabricated high-density picolitre reactors[J]. Nature, 2005, 437(7057):376-380. doi: 10.1038/nature03959 URL
[3]	FULLER C W, MIDDENDORF L R, BENNER S A, et al. The challenges of sequencing by synjournal[J]. Nature Biotechnology, 2009, 27(11):1013-23. doi: 10.1038/nbt.1585 URL
[4]	SHENDURE J, JI H. Next-generation DNA sequencing[J]. Nature biotechnology, 2008, 26(10):1135-45. doi: 10.1038/nbt1486 URL
[5]	BOTSTEIN D, WHITE R L, SKOLNICK M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. Am J hum genet, 1980, 32(3):314-31.
[6]	CHEE M, YANG R, HUBBELL E, et al. Accessing genetic information with high-density DNA arrays[J]. Science (New York, NY), 1996, 274(5287):610-4. doi: 10.1126/science.274.5287.610 URL
[7]	JARNE P, LAGODA P J. Microsatellites, from molecules to populations and back[J]. Trends in ecology & evolution, 1996, 11(10):424-9. doi: 10.1016/0169-5347(96)10049-5 URL
[8]	WANG D G, FAN J B, SIAO C J, et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome[J]. Science (New York, NY), 1998, 280(5366):1077-82. doi: 10.1126/science.280.5366.1077 URL
[9]	LEY T J, MARDIS E R, DING L, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome[J]. Nature, 2008, 456(7218):66-72. doi: 10.1038/nature07485 URL
[10]	Miller M R, Dunham J P, Amores A, et al. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers[J]. Genome res, 2007, 17(2):240-8. doi: 10.1101/gr.5681207 URL
[11]	HOHENLOHE P A, AMISH S J, CATCHEN J M, et al. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout[J]. Molecular ecology resources, 2011, 11 Suppl 1:117-122. doi: 10.1111/j.1755-0998.2010.02967.x URL
[12]	VAN TASSELL C P, SMITH T P, MATUKUMALLI L K, et al. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries[J]. Nat methods, 2008, 5(3):247-52. doi: 10.1038/nmeth.1185 URL
[13]	LI X, WANG S, XUN X, et al. A carotenoid oxygenase is responsible for muscle coloration in scallop[J]. Biochimica et biophysica acta Molecular and cell biology of lipids, 2019, 1864(7):966-975.
[14]	BAIRD N A, ETTER P D, ATWOOD T S, et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers[J]. PLoS One, 2008, 3(10):e3376. doi: 10.1371/journal.pone.0003376 URL
[15]	王洋坤, 胡艳, 张天真. RAD-seq技术在基因组研究中的现状及展望[J]. 遗传, 2014, 36(1):41-9.
[16]	MU X Y, TONG L, SUN M, et al. Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data[J]. Mol Phylogenet Evol, 2020, 147:106802. doi: 10.1016/j.ympev.2020.106802 URL
[17]	KAJIYA-KANEGAE H, TAKANASHI H, FUJIMOTO M, et al. RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG[J]. Plant & cell physiology, 2020, 61(7):1262-72.
[18]	NATARAJAN S, HOSSAIN M R, KIM H T, et al. ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry (Fragaria x ananassa)[J]. 3 Biotech, 2020, 10(8):353. doi: 10.1007/s13205-020-02291-5 URL
[19]	ESPOSITO S, CARDI T, CAMPANELLI G, et al. ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean 'da serbo' type long shelf-life germplasm[J]. Horticulture research, 2020, 7:134. doi: 10.1038/s41438-020-00353-6 URL
[20]	LIU J X, ZHOU M Y, YANG G Q, et al. ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa-Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae)[J]. Mol phylogenet evol, 2020, 146:106758. doi: 10.1016/j.ympev.2020.106758 URL
[21]	BARBANTI A, Torrado H, Macpherson E, et al. Helping decision making for reliable and cost-effective 2b-RAD sequencing and genotyping analyses in non-model species[J]. Molecular ecology resources, 2020, 20(3).
[22]	SUI J, LUAN S, DAI P, et al. High accuracy of pooled DNA genotyping by 2b-RAD sequencing in the Pacific white shrimp, Litopenaeus vannamei[J]. PLoS One, 2020, 15(7):e0236343. doi: 10.1371/journal.pone.0236343 URL
[23]	HUANG X, JIANG Y, ZHANG W, et al. Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)[J]. BMC genomics, 2020, 21(1):313. doi: 10.1186/s12864-020-6730-x URL
[24]	PETERSON B K, WEBER J N, KAY E H, 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
[25]	WANG S, MEYER E, MCKAY J K, et al. 2b-RAD: a simple and flexible method for genome-wide genotyping[J]. Nat methods, 2012, 9(8):808-810.
[26]	ELSHIRE R J, GLAUBITZ J C, SUN Q, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species[J]. PLoS one, 2011, 6(5):e19379. doi: 10.1371/journal.pone.0019379 URL
[27]	张羽, 周婉莹, 孙旺. 基于限制性内切酶简化基因组测序的两种主要技术[J]. 分子植物育种, 2020, 18(11):3562-3570.
[28]	POLAND J A, BROWN P J, SORRELLS M E, et al. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach[J]. plos one, 2012, 7(2):e32253. doi: 10.1371/journal.pone.0032253 URL
[29]	WANG Y, CAO X, ZHAO Y, et al. Optimized double-digest genotyping by sequencing (ddGBS) method with high-density SNP markers and high genotyping accuracy for chickens[J]. plos one, 2017, 12(6):e0179073. doi: 10.1371/journal.pone.0179073 URL
[30]	ENCISO-RODRíguez F E, OSORIO-GUARín J A, GARZóN-MARTínez G A, et al. Optimization of the genotyping-by-sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa[J]. PLoS one, 2020, 15(8):e0238383. doi: 10.1371/journal.pone.0238383 URL
[31]	SUN X, LIU D, ZHANG X, 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
[32]	代慧英, 张玉琮, 单文娟. 基于SLAF-seq技术的动物基因组应用及进展[J]. 生物技术, 2020, 30(3):290-294.
[33]	熊燕, 张金柱, 董婕, 等. 简化基因组测序技术在观赏植物中的应用研究进展[J]. 园艺学报, 2020, 47(6):1194-1202.
[34]	WEI Q, WANG W, HU T, et al. Construction of a SNP-Based Genetic Map Using SLAF-Seq and QTL Analysis of Morphological Traits in Eggplant[J]. Front genet, 2020, 11:178. doi: 10.3389/fgene.2020.00178 URL
[35]	FANG H, LIU H, MA R, et al. Genome-wide assessment of population structure and genetic diversity of Chinese Lou onion using specific length amplified fragment (SLAF) sequencing[J]. PLoS one, 2020, 15(5):e0231753. doi: 10.1371/journal.pone.0231753 URL
[36]	YANG B, ZHANG G, GUO F, et al. A Genomewide Scan for Genetic Structure and Demographic History of Two Closely Related Species, Rhododendron dauricum and R. mucronulatum (Rhododendron, Ericaceae)[J]. Front Plant Sci, 2020, 11:1093. doi: 10.3389/fpls.2020.01093 URL
[37]	DAVEY J W, HOHENLOHE P A, ETTER P D, et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J]. Nature reviews genetics, 2011, 12(7):499-510. doi: 10.1038/nrg3012 URL
[38]	ALTSHULER D, POLLARA V J, COWLES C R, et al. An SNP map of the human genome generated by reduced representation shotgun sequencing[J]. Nature, 2000, 407(6803):513-516. doi: 10.1038/35035083 URL
[39]	KERSTENS H H, CROOIJMANS R P, VEENENDAAL A, et al. Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey[J]. BMC genomics, 2009, 10:479. doi: 10.1186/1471-2164-10-479 URL
[40]	SUN Z, BAHETI S, MIDDHA S, et al. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing[J]. Bioinformatics, 2012, 28(16):2180-2181. doi: 10.1093/bioinformatics/bts337 URL
[41]	VAN ORSOUW N J, HOGERS R C, 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. doi: 10.1371/journal.pone.0001172 URL
[42]	边力, 王军. 简化基因组测序技术及其在海洋生物研究中的应用[J]. 厦门大学学报:自然科学版, 2017, 56(1):3-12.
[43]	GOMPERT Z, Forister M L, Fordyce J A, et al. Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies[J]. Mol Ecol, 2010, 19(12):2455-2473.
[44]	MAMMADOV J A, CHEN W, REN R, et al. Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.]genome for use in marker-assisted breeding[J]. TAG Theoretical and applied genetics theoretische und angewandte genetik, 2010, 121(3):577-588. doi: 10.1007/s00122-010-1331-8 URL
[45]	GROVER A, SHARMA P C. Development and use of molecular markers: past and present[J]. Critical reviews in biotechnology, 2016, 36(2):290-302. doi: 10.3109/07388551.2014.959891 URL
[46]	MARRANO A, BIROLO G, PRAZZOLI M L, et al. SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)[J]. PLoS one, 2017, 12(1):e0170655. doi: 10.1371/journal.pone.0170655 URL
[47]	薛晓杰, 杜晓云, 盖艺, 等. 基于GBS测序开发SNP在植物上的应用进展[J]. 江苏农业科学, 2020, 36(2):290-302.
[48]	XIAO B, TAN Y, LONG N, et al. SNP-based genetic linkage map of tobacco (Nicotiana tabacum L.) using next-generation RAD sequencing[J]. Journal of Biological Research (Thessalonike, Greece), 2015, 22:11.
[49]	WANG J, WANG Z, DU X, et al. A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq[J]. PLoS One, 2017, 12(6):e0179717. doi: 10.1371/journal.pone.0179717 URL
[50]	PALUMBO F, QI P, PINTO V B, et al. Construction of the First SNP-Based Linkage Map Using Genotyping-by-Sequencing and Mapping of the Male-Sterility Gene in Leaf Chicory[J]. Front plant Sci, 2019, 10:276. doi: 10.3389/fpls.2019.00276 URL
[51]	VERMA S, GUPTA S, BANDHIWAL N, et al. High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS)[J]. Sci Rep, 2015, 5:17512. doi: 10.1038/srep17512 URL
[52]	HUANG L, YANG Y, ZHANG F, et al. A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage[J]. Sci Rep, 2017, 7:46305. doi: 10.1038/srep46305 URL
[53]	LI X, XU J, DUAN S, et al. Mapping and QTL Analysis of Early-Maturity Traits in Tetraploid Potato (Solanum tuberosum L.)[J]. Int J Mol Sci, 2018, 19(10):3065. doi: 10.3390/ijms19103065 URL
[54]	XU P, XU S, WU X, et al. Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd[J]. The Plant journal : for cell and molecular biology, 2014, 77(3):430-442. doi: 10.1111/tpj.2014.77.issue-3 URL
[55]	GRAMLICH S, WAGNER N D, HÖRANDL E. RAD-seq reveals genetic structure of the F(2)-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression[J]. BMC plant Biol, 2018, 18(1):317. doi: 10.1186/s12870-018-1552-6 URL
[56]	Zhou M, Yang G, Sun G, et al. Resolving complicated relationships of the Panax bipinnatifidus complex in southwestern China by RAD-seq data[J]. Mol Phylogenet Evol, 2020, 149:106851. doi: 10.1016/j.ympev.2020.106851 URL
[57]	BAI B, WANG L, ZHANG Y J, et al. Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm[J]. Scientific reports, 2018, 8(1):691. doi: 10.1038/s41598-017-18613-2 URL
[58]	MAYES S, JACK P L, CORLEY R H, et al. Construction of a RFLP genetic linkage map for oil palm (Elaeis guineensis Jacq.)[J]. Genome, 1997, 40(1):116-22. doi: 10.1139/g97-016 URL
[59]	KUMAR A, ZHAO Y, ZHAO Y, et al. High-density genetic linkage-map construction of hawthorn and QTL mapping for important fruit traits[J]. Plos One, 2020, 15(2):e0229020. doi: 10.1371/journal.pone.0229020 URL
[60]	ZHANG F, KANG J, LONG R, et al. High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq[J]. BMC plant biology, 2019, 19(1):165. doi: 10.1186/s12870-019-1770-6 URL
[61]	CARRASCO B, GONZález M, GEBAUER M, et al. Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling[J]. PLoS one, 2018, 13(12):e0208032. doi: 10.1371/journal.pone.0208032 URL
[62]	LIU T, GUO L, PAN Y, et al. Construction of the first high-density genetic linkage map of Salvia miltiorrhiza using specific length amplified fragment (SLAF) sequencing[J]. Scientific reports, 2016, 6(1):24070. doi: 10.1038/srep24070 URL
[63]	JAMANN T M, BALINT-KURTI P J, HOLLAND J B. QTL mapping using high-throughput sequencing[J]. Methods in molecular biology (Clifton, NJ), 2015, 1284:257-85.
[64]	DU H, ZHANG H, WEI L, et al. A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.)[J]. BMC Plant Biol, 2019, 19(1):588. doi: 10.1186/s12870-019-2172-5 URL
[65]	LI B, TIAN L, ZHANG J, et al. Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max[J]. BMC genomics, 2014, 15(1):1086. doi: 10.1186/1471-2164-15-1086 URL
[66]	XU L Y, WANG L Y, WEI K, et al. High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing[J]. BMC genomics, 2018, 19(1):955. doi: 10.1186/s12864-018-5291-8 URL
[67]	GANGADHARA Rao P, BEHERA TK, GAIKWAD A B, et al. Mapping and QTL Analysis of Gynoecy and Earliness in Bitter Gourd (Momordica charantia L.) Using Genotyping-by-Sequencing (GBS) Technology[J]. Front Plant Sci, 2018, 9:1555. doi: 10.3389/fpls.2018.01555 URL
[68]	LU J, LIU Y, XU J, et al. High-Density Genetic Map Construction and Stem Total Polysaccharide Content-Related QTL Exploration for Chinese Endemic Dendrobium (Orchidaceae)[J]. Front plant Sci, 2018, 9:398. doi: 10.3389/fpls.2018.00398 URL
[69]	KANG Y J, LEE B M, NAM M, et al. Identification of quantitative trait loci associated with flowering time in perilla using genotyping-by-sequencing[J]. Molecular biology reports, 2019, 46(4):4397-4407. doi: 10.1007/s11033-019-04894-5 URL
[70]	REN G, MATEO R G, LIU J, et al. Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing[J]. New phytol, 2017, 213(3):1500-1512. doi: 10.1111/nph.2017.213.issue-3 URL
[71]	FENG J, ZHAO S, LI M, et al. Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq[J]. Genomics, 2020, 112(2):197819-87.
[72]	FENG L, RUHSAM M, WANG Y H, et al. Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region[J]. Mol Ecol, 2020, 29(10):1791-1805. doi: 10.1111/mec.v29.10 URL

物种	酶切技术	标记位点数目	遗传图谱			QTL 定位	群体遗传		参考文献
物种	酶切技术	标记位点数目	连锁群数量	图谱总长	平均遗传距离	QTL 定位	居群/个体/亚群数目	研究地区	参考文献
油棕	RAD	10023	16	2938.2	0.29				[57]
山楂	RAD	6384	17	2470.02	0.41	果实农艺性状			[59]
紫苜蓿	RAD	4346	32	父本3455 母本 4381	父本3.00 母本1.32	产量相关性状			[60]
李	GBS	1441	8	617	0.96				[61]
丹参	SLAF	5164	8	1516.43	0.29				[62]
芝麻	SLAF	2159	13	2128.51	0.99	种子相关性状			[64]
大豆	SLAF	5785	20	2255.18	0.43	异黄酮含量			[65]
茶树	2b-RAD	4217	15	1678.52	0.40	类黄酮及咖啡因含量			[66]
苦瓜	GBS	2013	20	2329.2	1.16	雌蕊数、性别比、节数和初花日			[67]
铁皮石斛	SLAF	8573	19	2737.49	0.32	茎总多糖含量			[68]
紫苏	GBS	2518	10	1309.39	0.56	花期相关性状			[69]
西藏报春	RAD	8930					16/293/4	青藏高原地区	[70]
甘薯	RAD	97010					/81/5	中国、美国、日本、澳大利亚、坦桑尼亚	[71]
大黄	SLAF	5256					46/218/5	横断山区及毗邻地区	[72]

物种	酶切技术	标记位点数目	遗传图谱			QTL 定位	群体遗传		参考文献
物种	酶切技术	标记位点数目	连锁群数量	图谱总长	平均遗传距离	QTL 定位	居群/个体/亚群数目	研究地区	参考文献
油棕	RAD	10023	16	2938.2	0.29				[57]
山楂	RAD	6384	17	2470.02	0.41	果实农艺性状			[59]
紫苜蓿	RAD	4346	32	父本3455 母本 4381	父本3.00 母本1.32	产量相关性状			[60]
李	GBS	1441	8	617	0.96				[61]
丹参	SLAF	5164	8	1516.43	0.29				[62]
芝麻	SLAF	2159	13	2128.51	0.99	种子相关性状			[64]
大豆	SLAF	5785	20	2255.18	0.43	异黄酮含量			[65]
茶树	2b-RAD	4217	15	1678.52	0.40	类黄酮及咖啡因含量			[66]
苦瓜	GBS	2013	20	2329.2	1.16	雌蕊数、性别比、节数和初花日			[67]
铁皮石斛	SLAF	8573	19	2737.49	0.32	茎总多糖含量			[68]
紫苏	GBS	2518	10	1309.39	0.56	花期相关性状			[69]
西藏报春	RAD	8930					16/293/4	青藏高原地区	[70]
甘薯	RAD	97010					/81/5	中国、美国、日本、澳大利亚、坦桑尼亚	[71]
大黄	SLAF	5256					46/218/5	横断山区及毗邻地区	[72]