Cytoplasmic diversity of the cotton genus as revealed by chloroplast microsatellite markers

Genetic Resources and Crop Evolution

Volumn 61, Issue 1, 2014, Pages 107-119

  Li, Pengbo ^a,b   Li, Zhaohu ^a   Liu, Huimin ^b   Hua, Jinping ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b Shanxi Academy of Agricultural Sciences   (China)

Author keywords

Chloroplast; cpSSR; Genetic differentiation; Gossypium

Indexed keywords

GOSSYPIUM; GOSSYPIUM ARBOREUM; GOSSYPIUM BARBADENSE; GOSSYPIUM HERBACEUM; GOSSYPIUM HIRSUTUM;

EID: 84892900843     PISSN: 09259864     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10722-013-0018-9     Document Type: Article

References (61)

1. Álvarez I, Cronn R, Wendel JF (2005) Phylogeny of the new world diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes. Plant Syst Evol 252: 199-214.
2. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36: 181-186.
3. Armbruster U, Pesaresi P, Pribil M, Hertle A, Leister D (2011) Update on chloroplast research: new tools, new topics, and new trends. Mol Plant 4: 1-16.
4. Clegg MT, Gaut BS, Learn GH Jr, Morton BR (1994) Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci USA 91: 6795-6801.
5. Cronn RC, Zhao X, Paterson AH, Wendel JF (1996) Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J Mol Evol 42: 685-705.
6. Cronn RC, Small RL, Haselkorn T, Wendel JF (2002) Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Am J Bot 89: 707-725.
7. Cronn R, Small RL, Haselkorn T, Wendel JF (2003) Cryptic repeated genomic recombination during speciation in Gossypium gossypioides. Evolution 57: 2475-2489.
8. Doyle JJ, Morgante M, Tingey SV, Powell W (1998) Size homoplasy in chloroplast microsatellites of wild perennial relatives of soybean (Glycine subgenus Glycine). Mol Biol Evol 15: 215-218.
9. Endrizzi JE, Turcotte EL, Kohel RJ (1985) Genetics, cytogenetics, and evolution of Gossypium. Adv Genet 23: 271-375.
10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
11. Frankham R, Ballou JD, Briscoe DA (2004) A primer of conservation genetics. Cambridge University Press, Cambridge.
12. Fryxell PA (1979) The natural history of the cotton tribe. Texas A & M University Press, College station, TX.
13. Fryxell PA (1992) A revised taxonomic interpretation of Gossypium L. (Malvaceae). Rheedea 2: 108-165.
14. Goremykin VV, Hirsch-Ernst KI, Wölfl S, Hellwig FH (2003) Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol Biol Evol 20: 1499-1505.
15. Harris SA, Robinson JP, Juniper BE (2002) Genetic clues to the origin of the apple. Trends Genet 18: 426-430.
16. Ibrahim RIH, Azuma JI, Sakamoto M (2006) Complete nucleotide sequence of cotton (Gossypium barbadense L.) chloroplast genome with a comparative analysis of sequence among 9 dicot plants. Genes Genet Syst 81: 311-321.
17. Ibrahim RIH, Azuma JI, Sakamoto M (2007) PCR-RFLP analysis of the whole chloroplast DNA from three cultivated species of cotton (Gossypium L.). Euphytica 156: 47-56.
18. Ishii T, Mori N, Ogihara Y (2001) Evaluation of allelic diversity at chloroplast microsatellite loci among common wheat and its ancestral species. Theor Appl Genet 103: 896-904.
19. Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann Mo Bot Gard 87: 482-498.
20. Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H (2006) The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics 7: 61.
21. Leister D (2003) Chloroplast research in the genomic age. Trends Genet 19: 47-56.
22. Li W-T, Peng Y-Y, Wei Y-M, Baum BR, Zheng Y-L (2009) Relationships among Avena species as revealed by consensus chloroplast simple sequence repeat (ccSSR) markers. Genet Resour Crop Evol 56: 465-480.
23. Li R, Zhang H, Zhou X, Guan Y, Yao F, Song G, Wang J, Zhang C (2010) Genetic diversity in Chinese sorghum landraces revealed by chloroplast simple sequence repeats. Genet Resour Crop Evol 57: 1-15.
24. Liu Q, Brubaker CL, Green AG, Marshall DR, Sharp PJ, Singh SP (2001) Evolution of the FAD2-1 fatty acid desaturase 5' UTR intron and the molecular systematics of Gossypium (Malvaceae). Am J Bot 88: 92-102.
25. Maqbool A, Zahur M, Irfan M, Younas M, Barozai K, Rashid B, Husnain T, Riazuddin S (2008) Identification and expression of six drought-responsive transcripts through differential display in desi cotton (Gossypium arboreum). Mol Biol 42: 492-498.
26. Martin W, Deusch O, Stawski N, Grünheit N, Goremykin V (2005) Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends Plant Sci 10: 204-209.
27. Meyer VG (1975) Male sterility from Gossypium harknessii. J Hered 66: 23-27.
28. Nei M, Li W (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76: 5269-5273.
29. Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski JA (1995) Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci USA 92: 7759-7763.
30. Powell WM, Morgante JJ, Doyle JW, McNicol SV (1996) Gene pool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics 144: 793-803.
31. Provan J, Corbett G, McNicol JW, Powell W (1997) Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats. Genome 40: 104-110.
32. Provan J, Lawrence P, Young G, Wright F, Bird R, Paglia G, Cattonaro F, Morgante M, Powell W (1999a) Analysis of the genus Zea (Poaceae) using polymorphic chloroplast simple sequence repeats. Plant Syst Evol 218: 245-256.
33. Provan J, Russell JR, Booth A, Power W (1999b) Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum. Mol Ecol 8: 505-511.
34. Provan J, Soranzo N, Wilson NJ, McNicol JW, Morgante M, Powell W (1999c) The use of uniparentally inherited simple sequence repeat markers in plant population studies and systematics. In: Hollingsworth PM, Bateman RM, Gornall RJ (eds) Molecular systematics and plant evolution. Taylor and Francis, London, pp 35-50.
35. Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16: 142-147.
36. Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, Jansen RK (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8: 174.
37. Rose O, Falush D (1998) A threshold size for microsatellite expansion. Mol Biol Evol 15: 613-615.
38. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
39. Salmaso M, Vannozzi A, Lucchin M (2010) Chloroplast microsatellite markers to assess genetic diversity and origin of an endangered Italian grapevine collection. Am J Enol Vitic 61: 551-556.
40. Seelanan T, Schnabel A, Wendel JF (1997) Congruence and consensus in the cotton tribe. Syst Bot 22: 259-290.
41. Seelanan T, Brubaker CL, Stewart JM, Craven LA, Wendel JF (1999) Molecular systematics of Australian Gossypium section Grandicalyx (Malvaceae). Syst Bot 24: 183-208.
42. Shaw J, Lickey EB, Beck JT, Farmer SB, Liu WS, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (2005) The tortoise and the hareII: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92: 142-166.
43. Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in Angiosperms: the tortoise and the hare III. Am J Bot 94: 275-288.
44. Small RL, Wendel JF (2000) Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium L. Malvaceae). Mol Phylogenet Evol 16: 73-84.
45. Song GL, Cui RX, Wang KB, Guo LP, Li SH, Wang CY, Zhang XD (1998) A rapid improved CTAB method for extraction of cotton genomic DNA. Acta Gossypii Sin 10: 273-275.
46. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105-1109.
47. Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5: 123-135.
48. Ulloa M, Saha S, Jenkins JN, Meredith WR Jr, McCarty JC Jr, Stelly DM (2005) Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotton (Gossypium hirsutum L.) Joinmap. J Hered 96: 132-144.
49. van de Peer Y, De Wachter Y (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10: 569-570.
50. Wendel JF (1989) New World tetraploid cottons contain Old World cytoplasm. Proc Nat Acad Sci USA 86: 4132-4136.
51. Wendel JF, Albert VA (1992) Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Syst Bot 17: 115-143.
52. Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. Adv Agron 78: 139-186.
53. Wendel JF, McD SJ, Rettig JH (1991) Molecular evidence for homoploid reticulate evolution in Australian species of Gossypium. Evolution 45: 694-711.
54. Wills DM, Hester ML, Liu A, Burke JM (2005) Chloroplast SSR polymorphisms in the compositae and the mode of organellar inheritance in Helianthus annuus. Theor Appl Genet 110: 941-947.
55. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84: 9054-9058.
56. Won H, Renner SS (2005) The chloroplast trnT-trnF region in the seed plant lineage Gnetales. J Mol Evol 61: 425-436.
57. Wu GY, Pan HZ, Wu H (1999) Experiments in biochemistry and molecular biology data handbook. Science Press, Beijing.
58. Wu YX, Daud MK, Chen L, Zhu SJ (2007) Phylogenetic diversity and relationship among Gossypium germplasm using SSRs markers. Plant Syst Evol 268: 199-208.
59. Xu Q, Xiong GJ, Li PB, He F, Huang Y, Wang KB, Li ZH, Hua JP (2012) Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids. PLoS ONE 7: e37128.
60. Yang AH, Zhang JJ, Yao XH, Huang HW (2011) Chloroplast microsatellite markers in Liriodendron tulipifera (Magnoliaceae) and cross-species amplification in L. chinense. Am J Bot 98: e123-e126.
61. Zamani-Nour S, Clemens R, Möllers C (2013) Cytoplasmic diversity of Brassica napus L., Brassica oleracea L. and Brassica rapa L. as determined by chloroplast microsatellite markers. Genet Resour Crop Evol 60: 953-965.