Development of a core set of SSR markers for the characterization of Gossypium germplasm

Euphytica

Volumn 187, Issue 2, 2012, Pages 203-213

  Yu, John Z ^a,h   Fang, David D ^b   Kohel, Russell J ^a   Ulloa, Mauricio ^c   Hinze, Lori L ^a   Percy, Richard G ^a   Zhang, Jinfa ^d   Chee, Peng ^e   Scheffler, Brian E ^f   Jones, Don C ^g  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b SOUTHERN REGIONAL RESEARCH CENTER   (United States)

^c U S DEPARTMENT OF AGRICULTURE   (United States)

^d NEW MEXICO STATE UNIVERSITY   (United States)

^e UNIVERSITY OF GEORGIA   (United States)

^f AGRICULTURAL RESEARCH SERVICE   (United States)

^g Agricultural and Environmental Research Division   (United States)

^h SOUTHERN PLAINS AGRICULTURAL RESEARCH CENTER   (United States)

Author keywords

Chromosome location; Cotton (Gossypium spp.); Genetic diversity; Polymorphism information content (PIC); Simple sequence repeats (SSR) markers

Indexed keywords

GOSSYPIUM; GOSSYPIUM HIRSUTUM;

EID: 84865744232     PISSN: 00142336     EISSN: 15735060     Source Type: Journal    
DOI: 10.1007/s10681-012-0643-y     Document Type: Article

References (32)

1. Abdurakhmonov IY, Kohel RJ, Yu JZ, Pepper AE, Abdullaev AA, Kushanov FN, Salakhutdinov IB, Buriev ZT, Saha S, Scheffler BE, Jenkins JN, Abdukarimov A (2008) Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics 92(6): 478-487. doi: 10. 1016/j. ygeno. 2008. 07. 013.
2. Abdurakhmonov IY, Saha S, Jenkins J, Buriev Z, Shermatov S, Scheffler B, Pepper A, Yu J, Kohel R, Abdukarimov A (2009) Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica 136(3): 401-417. doi: 10. 1007/s10709-008-9337-8.
3. Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape JM, Yu JZ, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu SL, Zhang TZ, Fang DQ, Pepper A, Kumpatla S, Jacobs J, Tomkins J, Cantrell R, Main D (2006) CMD: a cotton microsatellite database resource for Gossypium genomics. BMC Genomics 7: 132-141. doi: 13210. 1186/1471-2164-7-132.
4. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3): 314-331.
5. Campbell BT, Saha S, Percy R, Frelichowski J, Jenkins JN, Park W, Mayee CD, Gotmare V, Dessauw D, Giband M, Du X, Jia Y, Constable G, Dillon S, Abdurakhmonov IY, Abdukarimov A, Rizaeva SM, Abdullaev A, Barroso PAV, Pádua JG, Hoffmann LV, Podolnaya L (2010) Status of the global cotton germplasm resources. Crop Sci 50(4): 1161-1179. doi: 10. 2135/cropsci2009. 09. 0551.
6. Endrizzi JE, Turcotte EL, Kohel RJ (1985) Genetics, cytology, and evolution of Gossypium. In: Caspari EW, John GS (eds) Advances in genetics, vol 23. Academic Press, New York, pp 271-375.
7. Esbroeck G, Bowman DT (1998) Cotton germplasm diversity and its importance to cultivar development. J Cotton Sci 2(3): 121-129.
8. Fang D, Xiao J, Canci P, Cantrell R (2010) A new SNP haplotype associated with blue disease resistance gene in cotton (Gossypium hirsutum L.). Theor Appl Genet 120(5): 943-953. doi: 10. 1007/s00122-009-1223-y.
9. Garcia-Vallvé S, Palau J, Romeu A (1999) Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Mol Biol Evol 16(9): 1125-1134.
10. Gill KS, Gill BS, Endo TR (1993) A chromosome region-specific mapping strategy reveals gene-rich telomeric ends in wheat. Chromosoma 102(6): 374-381. doi: 10. 1007/bf00360401.
11. Guo WZ, Cai CP, Wang CB, Han ZG, Song XL, Wang K, Niu XW, Wang C, Lu KY, Shi B, Zhang TZ (2007) A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics 176(1): 527-541. doi: 10. 1534/genetics. 107. 070375.
12. Jordan GE, Piel WH (2008) PhyloWidget: web-based visualizations for the tree of life. Bioinformatics 24(14): 1641-1642. doi: 10. 1093/bioinformatics/btn235.
13. Kohel RJ, Richmond TR, Lewis CF (1970) Texas marker-1. Description of a genetic standard for Gossypium hirsutum. Crop Sci 10: 670-671.
14. Kohel RJ, Yu JZ (2002) Molecular characterization of Gossypium germplasm for cotton improvement. In: Engels JMM, Rao VR, Brown AHD, Jackson MT (eds) Managing plant genetic resources. CAB International Publishing, Wallingford, pp 67-75.
15. Kohel RJ, Yu JZ, Park Y-H, Lazo G (2001) Molecular mapping and characterization of traits controlling fiber quality in cotton. Euphytica 121(2): 163-172. doi: 10. 1023/a: 1012263413418.
16. Lacape JM, Dessauw D, Rajab M, Noyer JL, Hau B (2007) Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs. Mol Breed 19(1): 45-58. doi: 10. 1007/s11032-006-9042-1.
17. Lacape JM, Jacobs J, Arioli T, Derijcker R, Forestier-Chiron N, Llewellyn D, Jean J, Thomas E, Viot C (2009) A new interspecific, Gossypium hirsutum × G. barbadense, RIL population: towards a unified consensus linkage map of tetraploid cotton. Theor Appl Genet 119(2): 281-292. doi: 10. 1007/s00122-009-1037-y.
18. Lee JA (1984) Cotton as a world crop. In: Kohel RJ, Lewis CF (eds) Cotton, agronomy monograph 24. American Society of Agronomy, Madison, pp 1-25.
19. Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21(9): 2128-2129.
20. Liu D, Guo X, Lin Z, Nie Y, Zhang X (2006) Genetic diversity of Asian cotton (Gossypium arboreum L.) in China evaluated by microsatellite analysis. Genet Res Crop Evol 53(6): 1145-1152. doi: 10. 1007/s10722-005-1304-y.
21. Percival AE, Wendel JF, Stewart JM (1999) Taxonomy and germplasm resources. In: Smith CW, Cothren JT (eds) Cotton: origin, history, technology, and production. Wiley, New York, pp 33-63.
22. Stelly DM, Saha S, Raska DA, Jenkins JN, McCarty JC, Gutierrez OA (2005) Registration of 17 upland (Gossypium hirsutum) cotton germplasm lines disomic for different G. barbadense chromosome or arm substitutions. Crop Sci 45(6): 2663-2665.
23. Stewart JM (1994) Potential for crop improvement with exotic germplasm and genetic engineering. Paper presented at the Challenging the Future: Proceedings of the World Cotton Research Conference-1. Brisbane, Australia, 14-17 February.
24. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277(5329): 1063-1066.
25. van Deynze A, Stoffel K, Lee M, Wilkins TA, Kozik A, Cantrell RG, Yu JZ, Kohel RJ, Stelly DM (2009) Sampling nucleotide diversity in cotton. BMC Plant Biol 9: 125. doi: 12510. 1186/1471-2229-9-125.
26. Wallace T, Bowman D, Campbell B, Chee P, Gutierrez O, Kohel R, McCarty J, Myers G, Percy R, Robinson F, Smith W, Stelly D, Stewart J, Thaxton P, Ulloa M, Weaver D (2009) Status of the USA cotton germplasm collection and crop vulnerability. Genet Res Crop Evol 56(4): 507-532. doi: 10. 1007/s10722-008-9382-2.
27. Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. In: Advances in agronomy, vol 78. Academic Press, San Diego, pp 139-186.
28. Xu ZY, Kohel RJ, Song GL, Cho JM, Alabady M, Yu J, Koo P, Chu J, Yu SX, Wilkins TA, Zhu YX, Yu JZ (2008) Gene-rich islands for fiber development in the cotton genome. Genomics 92(3): 173-183. doi: 10. 1016/j. ygeno. 2008. 05. 010.
29. Yu JZ (2004) A standard panel of Gossypium genotypes established for systematic characterization of cotton microsatellite markers. An electronic newsletter of applied plant breeding sponsored Food and Agriculture Organization of the United Nations. Plant Breed News Ed 148(107): 148.
30. Yu JZ, Kohel RJ (2001) Cotton genome research in the United States. In: Jenkins JN, Saha S (eds) Genetic improvement of cotton: emerging technologies. The Science Publishers Inc., Polymouth, pp 103-121.
31. Yu JZ, Kohel RJ, Fang DD, Cho J, van Deynze A, Ulloa M, Hoffman SM, Pepper AE, Stelly DM, Jenkins JN, Saha S, Kumpatla SP, Shah MR, Hugie WV, Percy RG (2012) A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. Genes Genomes Genet 2: 43-58.
32. Yu Y, Yuan DJ, Liang SG, Li XM, Wang XQ, Lin ZX, Zhang XL (2011) Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. BMC Genomics 12: 15. doi: 1510. 1186/1471-2164-12-15.