Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using Insertion-Deletion (InDel) and Simple Sequence Repeat (SSR) markers

BMC Genetics

Yingzhong Zhao¹  Ju Mei¹  Ye Tao²  Hongyan Liu¹  Minmin Yang¹  Kun Wu¹ 

[1] Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Sesame Genetic Improvement Laboratory, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, Hubei 430062, China;Shanghai Major Biological Medicine Technology Co., Ltd, Shanghai 201203, China

关键词: Allele distribution;    Population structure;    Genetic diversity;    Microsatellites;    InDel;    Sesame;   

Others  :  866598
DOI  :  10.1186/1471-2156-15-35

 received in 2013-11-18, accepted in 2014-03-10,  发布年份 2014

【 摘 要 】

Background

Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design.

Results

Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines.

Conclusions

This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic drift or selection during breeding processes. Comparative analysis of allele distribution revealed genetic divergence between improved cultivars and landraces, as well as between cultivars released in different years. These results will be useful for assessing cultivars and for marker-assisted breeding in sesame.

【 授权许可】

   
2014 Wu et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 2.

【 参考文献 】

• [1]Bedigian D: Evolution of sesame revisited: domestication, diversity and prospects. Genet Resour Crop Ev 2003, 50(7):779-787.
• [2]Zhang H, Miao H, Wang L, Qu L, Liu H, Wang Q, Yue M: Genome sequencing of the important oilseed crop Sesamum indicum L. Genome Biol 2013, 14(1):401.
• [3]Anilakumar KR, Pal A, Khanum F, Bawa AS: Nutritional, medicinal and industrial uses of sesame (Sesamum indicum L.) seeds-an overview. Agric conspec sci 2010, 75(4):159-168.
• [4]Namiki M: The Chemistry and Physiological Functions of Sesame. Food Rev Int 1995, 11(2):281-329.
• [5]Moazzami AA, Kamal-Eldin A: Sesame seed is a rich source of dietary lignans. J Am Oil Chem Soc 2006, 83(8):719-723.
• [6]Zhang YX, Sun JA, Zhang XR, Wang LH, Che Z: Analysis on Genetic Diversity and Genetic Basis of the Main Sesame Cultivars Released in China. Agr Sci China 2011, 10(4):509-518.
• [7]Zhang YX, Zhang XR, Che Z, Wang LH, Wei WL, Li DH: Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection. BMC Genet 2012, 13:102.
• [8]Reif JC, Zhang P, Dreisigacker S, Warburton ML, Van Ginkel M, Hoisington D, Bohn M, Melchinger AE: Wheat genetic diversity trends during domestication and breeding. Theor Appl Genet 2005, 110(5):859-864.
• [9]Lu YL, Yan JB, Guimaraes CT, Taba S, Hao ZF, Gao SB, Chen SJ, Li JS, Zhang SH, Vivek BS, Magorokosho C, Mugo S, Makumbi D, Parentoni SN, Shah T, Rong TZ, Crouch JH, Xu YB: Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet 2009, 120(1):93-115.
• [10]Qian W, Ge S, Hong DY: Assessment of genetic variation of Oryza granulata detected by RAPDs and ISSRs. Acta Bot Sin 2000, 42(7):741-750.
• [11]Plaschke J, Ganal MW, Roder MS: Detection of Genetic Diversity in Closely-Related Bread Wheat Using Microsatellite Markers. Theor Appl Genet 1995, 91(6–7):1001-1007.
• [12]Manifesto MM, Schlatter AR, Hopp HE, Suarez EY, Dubcovsky J: Quantitative evaluation of genetic diversity in wheat germplasm using molecular markers. Crop Sci 2001, 41(3):682-690.
• [13]Xu P, Wu XH, Wang BG, Liu YH, Qin DH, Ehlers JD, Close TJ, Hu TT, Lu ZF, Li GJ: Development and polymorphism of Vigna unguiculata ssp. unguiculata microsatellite markers used for phylogenetic analysis in asparagus bean (Vigna unguiculata ssp. sesquipedialis (L.) Verdc.). Mol Breeding 2010, 25(4):675-684.
• [14]Laurentin HE, Karlovsky P: Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasm collection using amplified fragment length polymorphism (AFLP). BMC Genet 2006, 7:10.
• [15]Laurentin H, Karlovsky P: AFLP fingerprinting of sesame (Sesamum indicum L.) cultivars: identification, genetic relationship and comparison of AFLP informativeness parameters. Genet Resour Crop Ev 2007, 54(7):1437-1446.
• [16]Zhang YX, Zhang XR, Hua W, Wang LH, Che Z: Analysis of genetic diversity among indigenous landraces from sesame (Sesamum indicum L.) core collection in China as revealed by SRAP and SSR markers. Genes Genom 2010, 32(3):207-215.
• [17]Bhat KV, Babrekar PP, Lakhanpaul S: Study of genetic diversity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers. Euphytica 1999, 110(1):21-33.
• [18]Ercan AG, Taskin M, Turgut K: Analysis of genetic diversity in Turkish sesame (Sesamum indicum L.) populations using RAPD markers. Genet Resour Crop Ev 2004, 51(6):599-607.
• [19]Salazar B, Laurentin H, Davila M, Castillo MA: Reliability of the RAPD technique for germplasm analysis of sesame (Sesamum indicum L.) from Venezuela. Interciencia 2006, 31(6):456-460.
• [20]Kim DH, Zur G, Danin-Poleg Y, Lee SW, Shim KB, Kang CW, Kashi Y: Genetic relationships of sesame germplasm collection as revealed by inter-simple sequence repeats. Plant Breed 2002, 121(3):259-262.
• [21]Kumar H, Kaur G, Banga S: Molecular Characterization and Assessment of Genetic Diversity in Sesame (Sesamum indicum L.) Germplasm Collection Using ISSR Markers. J Crop Improv 2012, 26(4):540-557.
• [22]Dixit A, Jin MH, Chung JW, Yu JW, Chung HK, Ma KH, Park YJ, Cho EG: Development of polymorphic microsatellite markers in sesame (Sesamum indicum L.). Mol Ecol Notes 2005, 5(4):736-738.
• [23]Hongyan L, Kun W, Minmin Y, Yang Z, Yingzhong Z: DNA Fingerprinting of Sesame (Sesamum indicum L.) Varieties (Lines) from Recent National Regional Trials in China. Acta Agron Sin 2012, 38(04):596-605.
• [24]Cho YI, Park JH, Lee CW, Ra WH, Chung JW, Lee JR, Ma KH, Lee SY, Lee KS, Lee MC, Park YJ: Evaluation of the genetic diversity and population structure of sesame (Sesamum indicum L.) using microsatellite markers. Genes Genom 2011, 33(2):187-195.
• [25]Zhang HY, Wei LB, Miao HM, Zhang TD, Wang CY: Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genomics 2012, 13:316. BioMed Central Full Text
• [26]Wang L, Zhang Y, Qi X, Gao Y, Zhang X: Development and characterization of 59 polymorphic cDNA-SSR markers for the edible oil crop Sesamum indicum (Pedaliaceae). Am J Bot 2012, 99(10):e394-398.
• [27]Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A: The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breeding 1996, 2(3):225-238.
• [28]Zhang P, Li J, Li X, Liu X, Zhao X, Lu Y: Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS One 2011, 6(12):e27565.
• [29]Patzak J, Paprstein F, Henychova A, Sedlak J: Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus x domestica) genetic resources. Genome 2012, 55(9):647-665.
• [30]Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater JM, Zyprian E, Moreira FM, Grando MS: Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biol 2013, 13:39. BioMed Central Full Text
• [31]Frascaroli E, Schrag TA, Melchinger AE: Genetic diversity analysis of elite European maize (Zea mays L.) inbred lines using AFLP, SSR, and SNP markers reveals ascertainment bias for a subset of SNPs. Theor Appl Genet 2013, 126(1):133-141.
• [32]Wurschum T, Langer SM, Longin CF, Korzun V, Akhunov E, Ebmeyer E, Schachschneider R, Schacht J, Kazman E, Reif JC: Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theor Appl Genet 2013, 126(6):1477-1486.
• [33]Wei LB, Zhang HY, Zheng YZ, Miao HM, Zhang TZ, Guo WZ: A Genetic Linkage Map Construction for Sesame (Sesamum indicum L.). Genes Genom 2009, 31(2):199-208.
• [34]Britten RJ, Rowen L, Williams J, Cameron RA: Majority of divergence between closely related DNA samples is due to indels. Proc Natl Acad Sci USA 2003, 100(8):4661-4665.
• [35]Liu B, Wang Y, Zhai W, Deng J, Wang H, Cui Y, Cheng F, Wang XW, Wu J: Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theor Appl Genet 2013, 126(1):231-239.
• [36]Pacurar DI, Pacurar ML, Street N, Bussell JD, Pop TI, Gutierrez L, Bellini C: A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions. J Exp Bot 2012, 63(7):2491-2501.
• [37]Ollitrault F, Terol J, Martin AA, Pina JA, Navarro L, Talon M, Ollitrault P: Development of Indel Markers from Citrus Clementina (Rutaceae) Bac-End Sequences and Interspecific Transferability in Citrus. Am J Bot 2012, 99(7):E268-E273.
• [38]Hou XH, Li LC, Peng ZY, Wei BY, Tang SJ, Ding MY, Liu JJ, Zhang FX, Zhao YD, Gu HY, Qu LJ: A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis. Plant J 2010, 63(5):880-888.
• [39]Heesacker A, Kishore VK, Gao WX, Tang SX, Kolkman JM, Gingle A, Matvienko M, Kozik A, Michelmore RM, Lai Z, Rieseberg LH, Knapp SJ: SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility. Theor Appl Genet 2008, 117(7):1021-1029.
• [40]Hayashi K, Yoshida H, Ashikawa I: Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes. Theor Appl Genet 2006, 113(2):251-260.
• [41]Garcia-Lor A, Luro F, Navarro L, Ollitrault P: Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies. Mol Genet Genomics 2012, 287(1):77-94.
• [42]Raman H, Raman R, Wood R, Martin P: Repetitive indel markers within the ALMT1 gene conditioning aluminium tolerance in wheat (Triticum aestivum L.). Mol Breeding 2006, 18(2):171-183.
• [43]Vasemagi A, Gross R, Palm D, Paaver T, Primmer CR: Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon. BMC Genomics 2010, 11:156. BioMed Central Full Text
• [44]Ke T, Dong CH, Mao H, Zhao YZ, Chen H, Liu HY, Dong XY, Tong CB, Liu SY: Analysis of expression sequence tags from a full-length-enriched cDNA library of developing sesame seeds (Sesamum indicum). BMC Plant Biol 2011, 11:180. BioMed Central Full Text
• [45]Spandana B, Reddy VP, Prasanna GJ, Anuradha G, Sivaramakrishnan S: Development and characterization of microsatellite markers (SSR) in Sesamum (Sesamum indicum L.) species. Appl Biochem Biotechnol 2012, 168(6):1594-1607.
• [46]Yue WD, Wei LB, Zhang TD, Li C, Miao HM, Zhang HY: Analysis of genetic diversity and population structure of germplasm resources in sesame (Sesamum indicum L.) by SSR markers. Acta Agronomica Sinica (Chinese) 2012, 38(12):2286-2296.
• [47]Wei W, Zhang Y, Lu H, Li D, Wang L, Zhang X: Association Analysis for Quality Traits in a Diverse Panel of Chinese Sesame (Sesamum indicum L.) Germplasm. J Integr Plant Biol 2013, 55(8):745-758.
• [48]Yang X, Yan J, Shah T, Warburton ML, Li Q, Li L, Gao Y, Chai Y, Fu Z, Zhou Y, Xu S, Bai G, Meng Y, Zheng Y, Li J: Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection. Theor Appl Genet 2010, 121(3):417-431.
• [49]Wei W, Zhang Y, Lu H, Wang L, Li D, Zhang X: Population Structure and Association Analysis of Oil Content in a Diverse Set of Chinese Sesame (Sesamum indicum L.) Germplasm. Agr Sci China 2012, 45(10):1895-1903.
• [50]Nyongesa B, Were B, Gudu S, Dangasuk O, Onkware A: Genetic diversity in cultivated sesame (Sesamum indicum L.) and related wild species in East Africa. J Crop Sci Biot 2013, 16(1):9-15.
• [51]Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao J: Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor Appl Genet 2010, 121(3):475-487.
• [52]Das B, Sengupta S, Parida SK, Roy B, Ghosh M, Prasad M, Ghose TK: Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India. BMC Genet 2013, 14:71.
• [53]Chen X, Min D, Yasir TA, Hu YG: Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLoS One 2012, 7(9):e44510.
• [54]Zhang L, Liu D, Guo X, Yang W, Sun J, Wang D, Sourdille P, Zhang A: Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers. BMC Genet 2011, 12:42.
• [55]Yang X, Gao S, Xu S, Zhang Z, Prasanna BM, Li L, Li J, Yan J: Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Mol Breeding 2011, 28(4):511-526.
• [56]Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith JS, Jaqueth J, Smith OS, Doebley J: An analysis of genetic diversity across the maize genome using microsatellites. Genetics 2005, 169(3):1617-1630.
• [57]Roy A, Bandyopadhyay A, Mahapatra AK, Ghosh SK, Singh NK, Bansal KC, Koundal KR, Mohapatra T: Evaluation of genetic diversity in jute (Corchorus species) using STMS, ISSR and RAPD markers. Plant Breed 2006, 125(3):292-297.
• [58]Zhao WG, Mia XX, Jia SH, Pan YL, Huang Y: Isolation and characterization of microsatellite loci from the mulberry, Morus L. Plant Sci 2005, 168(2):519-525.
• [59]Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X: Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 2011, 12:451. BioMed Central Full Text
• [60]Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA: Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 2008, 3(10):e3376.
• [61]Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH: Stacks: building and genotyping loci de novo from short-read sequences. G3 (Bethesda) 2011, 1(3):171-182.
• [62]Lee WH, Vega VB: Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies. Bioinformatics 2004, 20(16):2863-2864.
• [63]Liang HW, Wang CZ, Li Z, Luo XZ, Zou GW: Improvement of the silver-stained technique of polyacrylamide gel electrophoresis. Yi Chuan 2008, 30(10):1379-1382.
• [64]Nei M: Genetic distance between populations. Am Nat 1972, 283:292.
• [65]Liu K, Muse SV: PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 2005, 21(9):2128-2129.
• [66]Laurentin H: Data analysis for molecular characterization of plant genetic resources. Genet Resour Crop Ev 2009, 56(2):277-292.
• [67]Fisher RA: On the interpretation of χ 2 from contingency tables, and the calculation of P. J Roy Stat Soc 1922, 85(1):87-94.
• [68]Rousset F: genepop’007: a complete re‐implementation of the genepop software for Windows and Linux. Mol Ecol Resour 2008, 8(1):103-106.
• [69]Pritchard JK, Stephens M, Donnelly P: Inference of Population Structure Using Multilocus Genotype Data. Genetics 2000, 155(2):945-959.
• [70]Falush D, Stephens M, Pritchard JK: Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003, 164(4):1567-1587.
• [71]Evanno G, Regnaut S, Goudet J: Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 2005, 14(8):2611-2620.
• [72]Jakobsson M, Rosenberg NA: CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 2007, 23(14):1801-1806.
• [73]Xu P, Wu X, Wang B, Luo J, Liu Y, Ehlers J, Close T, Roberts P, Lu Z, Wang S: Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies. Heredity 2012, 109(1):34-40.
• [74]Rohlf FJ: NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.1. 2000.
• [75]Excoffier L, Laval G, Schneider S: Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol Bioinform 2005, 1:47-50.