New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum？？EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. 1. Introduction Molecular markers provide valuable information in assessing the genetic variability, generating linkage maps, enabling better understanding of the genome organization, and deciphering quantitative trait loci (QTLs). Initial effort to map the cotton genome using an F2 population utilized 705 restriction fragment length polymorphism (RFLP) probes that were polymorphic between G. hirsutum and G. barbadense and generated 41 linkage groups spanning 4675？cM [1]. Genetic variation at molecular level in cotton has been characterized using isozyme/allozyme markers [2], RFLPs [1, 3, 4], AFLPs [5, 6], and microsatellites [7, 8] in G. hirsutum and its related species. A comprehensive comparative genetic map with 2584？loci at ~1.72？cM intervals for tetraploid (AtDt) cotton and with 662 loci at ~1.96？cM intervals for diploid (D) genome was constructed using RFLPs, genomic SSRs, and sequence tagged sites (STS) as probes [9]. Advances in technology have facilitated sequencing of complete transcriptomes and genomes that are accessible through public domain databases. Increasing number of expressed sequence tags (ESTs) for cotton facilitated the identification of simple sequence repeat (SSR) regions from the ESTs through data mining
References
[1]
A. J. Reinisch, J. M. Dong, C. L. Brubaker, D. M. Stelly, J. F. Wendel, and A. H. Paterson, “A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome,” Genetics, vol. 138, no. 3, pp. 829–847, 1994.
[2]
J. F. Wendel, C. L. Brubaker, and A. E. Percival, “Genetic diversity in Gossypium hirsutum and the origin of upland cotton,” American Journal of Botany, vol. 79, no. 11, pp. 1291–1310, 1992.
[3]
Z. W. Shappley, J. N. Jenkins, C. E. Watson, A. L. Kahler, and W. R. Meredith, “Establishment of molecular markers and linkage groups in two F2 populations of upland cotton,” Theoretical and Applied Genetics, vol. 92, no. 8, pp. 915–919, 1996.
[4]
Z. W. Shappley, J. N. Jenkins, W. R. Meredith, and J. C. McCarty Jr., “An RFLP linkage map of Upland cotton, Gossypium hirsutum L,” Theoretical and Applied Genetics, vol. 97, no. 5-6, pp. 756–761, 1998.
[5]
M. K. Rana, V. P. Singh, and K. V. Bhat, “Assessment of genetic diversity in upland cotton (Gossypium hirsutum L.) breeding lines by using amplified fragment length polymorphism (AFLP) markers and morphological characteristics,” Genetic Resources and Crop Evolution, vol. 52, no. 8, pp. 989–997, 2005.
[6]
A. M. Abdalla, O. U. K. Reddy, K. M. El-Zik, and A. E. Pepper, “Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP,” Theoretical and Applied Genetics, vol. 102, no. 2-3, pp. 222–229, 2001.
[7]
J. M. Lacape, D. Dessauw, M. Rajab, J. L. Noyer, and B. Hau, “Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs,” Molecular Breeding, vol. 19, no. 1, pp. 45–58, 2007.
[8]
S. Liu, R. G. Cantrell, J. C. McCarty, and J. M. Stewart, “Simple sequence repeat-based assessment of genetic diversity in cotton race stock accessions,” Crop Science, vol. 40, no. 5, pp. 1459–1469, 2000.
[9]
J. Rong, C. Abbey, J. E. Bowers et al., “A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium),” Genetics, vol. 166, no. 1, pp. 389–417, 2004.
[10]
S. N. Qureshi, S. Saha, R. V. Kantety, and J. N. Jenkins, “Molecular biology and physiology: EST-SSR: a new class of genetic markers in cotton,” Journal of Cotton Science, vol. 8, no. 2, pp. 112–123, 2004.
[11]
S. Samuel Yang, F. Cheung, J. J. Lee et al., “Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton,” Plant Journal, vol. 47, no. 5, pp. 761–775, 2006.
[12]
J. A. Udall, J. M. Swanson, K. Haller et al., “A global assembly of cotton ESTs,” Genome Research, vol. 16, no. 3, pp. 441–450, 2006.
[13]
P. W. Chee, J. Rong, D. Williams-Coplin, S. R. Schulze, and A. H. Paterson, “EST derived PCR-based markers for functional gene homologues in cotton,” Genome, vol. 47, no. 3, pp. 449–462, 2004.
[14]
Z. Han, C. Wang, X. Song et al., “Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton,” Theoretical and Applied Genetics, vol. 112, no. 3, pp. 430–439, 2006.
[15]
Z. G. Han, W. Z. Guo, X. L. Song, and T. Z. Zhang, “Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton,” Molecular Genetics and Genomics, vol. 272, no. 3, pp. 308–327, 2004.
[16]
Y. H. Park, M. S. Alabady, M. Ulloa et al., “Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population,” Molecular Genetics and Genomics, vol. 274, no. 4, pp. 428–441, 2005.
[17]
W. Gao, Z. J. Chen, J. Z. Yu, R. J. Kohel, J. E. Womack, and D. M. Stelly, “Wide-cross whole-genome radiation hybrid mapping of the cotton (Gossypium barbadense L.) genome,” Molecular Genetics and Genomics, vol. 275, no. 2, pp. 105–113, 2006.
[18]
S. Saha, D. A. Raska, and D. M. Stelly, “Upland cotton (Gossypium hirsutum L.) x Hawaiian cotton (G. tomentosum Nutt. ex Seem.) F1 hybrid hypoaneuploid chromosome substitution series,” Journal of Cotton Science, vol. 10, no. 4, pp. 263–272, 2006.
[19]
D. Stelly, S. Saha, D. Raska, J. Jenkins, J. McCarty, and O. Gutierrez, “Registration of 17 upland (Gossypium hirsutum) cotton germplasm lines disomic for different G. barbadense chromosome or arm substitutions,” Crop Science, vol. 45, no. 6, pp. 2663–2665, 2005.
[20]
S. Saha, J. N. Jenkins, J. Wu et al., “Effects of chromosome-specific introgression in upland cotton on fiber and agronomic traits,” Genetics, vol. 172, no. 3, pp. 1927–1938, 2006.
[21]
N. Gutierrez, C. M. Avila, G. Duc et al., “CAPs markers to assist selection for low vicine and convicine contents in faba bean (Vicia faba L.),” Theoretical and Applied Genetics, vol. 114, no. 1, pp. 59–66, 2006.
[22]
A. Blenda, J. Scheffler, B. Scheffler et al., “CMD: a Cotton Microsatellite Database resource for Gossypium genomics,” BMC Genomics, vol. 7, no. 1, article 132, 2006.
[23]
R. J. Kohel, J. Yu, Y. H. Park, and G. R. Lazo, “Molecular mapping and characterization of traits controlling fiber quality in cotton,” Euphytica, vol. 121, no. 2, pp. 163–172, 2001.
[24]
G. Figliuolo and P. Perrino, “Genetic diversity and intra-specific phylogeny of Triticum turgidum L. subsp. dicoccon (Schrank) Thell. revealed by RFLPs and SSRs,” Genetic Resources and Crop Evolution, vol. 51, no. 5, pp. 519–527, 2004.
[25]
R. V. Kantety, M. La Rota, D. E. Matthews, and M. E. Sorrells, “Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat,” Plant Molecular Biology, vol. 48, no. 5-6, pp. 501–510, 2002.
[26]
S. Rozen and H. Skaletsky, “Primer3 on the WWW for general users and for biologist programmers,” Methods in Molecular Biology, vol. 132, no. 3, pp. 365–386, 2000.
[27]
S. Shete, H. Tiwari, and R. C. Elston, “On estimating the heterozygosity and polymorphism information content value,” Theoretical Population Biology, vol. 57, no. 3, pp. 265–271, 2000.
[28]
K. F. Manly, R. H. Cudmore, and J. M. Meer, “Map Manager QTX, cross-platform software for genetic mapping,” Mammalian Genome, vol. 12, no. 12, pp. 930–932, 2001.
[29]
I. Eujayl, M. Baum, W. Powell, W. Erskine, and E. Pehu, “A genetic linkage map of lentil (Lens sp.) based on RAPD and AFLP markers using recombinant inbred lines,” Theoretical and Applied Genetics, vol. 97, no. 1-2, pp. 83–89, 1998.
[30]
C. M. Ronning, S. S. Stegalkina, R. A. Ascenzi et al., “Comparative analyses of potato expressed sequence tag libraries,” Plant Physiology, vol. 131, no. 2, pp. 419–429, 2003.
[31]
S. Doganlar, J. Dodson, B. Gabor, T. Beck-Bunn, C. Crossman, and S. D. Tanksley, “Molecular mapping of the py-1 gene for resistance to corky root rot (Pyrenochaeta lycopersici) in tomato,” Theoretical and Applied Genetics, vol. 97, no. 5-6, pp. 784–788, 1998.
[32]
D. M. Stelly, S. Saha, D. A. Raska, J. N. Jenkins, J. C. McCarty, and O. A. Gutierrez, “Registration of 17 upland (Gossypium hirsutum) cotton germplasm lines disomic for different G. barbadense chromosome or arm substitutions,” Crop Science, vol. 45, pp. 2663–2665, 2003.
[33]
J. F. Wendel and R. C. Cronn, “Polyploidy and the evolutionary history of cotton,” Advances in Agronomy, vol. 78, pp. 139–186, 2003.
[34]
J. F. Wendel and V. A. Albert, “Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications,” Systematic Botany, vol. 17, pp. 115–143, 1992.
[35]
T. Seelanan, A. Schnabel, and J. F. Wendel, “Congruence and consensus in the cotton tribe (Malvaceae),” Systematic Botany, vol. 22, no. 2, pp. 259–290, 1997.
[36]
R. L. Small and J. F. Wendel, “Phylogeny, duplication, and intraspecific variation of Adh sequences in new world diploid cottons (Gossypium L., Malvaceae),” Molecular Phylogenetics and Evolution, vol. 16, no. 1, pp. 73–84, 2000.
[37]
R. C. Cronn, R. L. Small, T. Haselkorn, and J. F. Wendel, “Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes,” American Journal of Botany, vol. 89, no. 4, pp. 707–725, 2002.
[38]
J. F. Wendel, “New world tetraploid cottons contain old world cytoplasm,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, pp. 4132–4136, 1989.
[39]
J. F. Wendel, R. Rowley, and J. M. Stewart, “Genetic diversity in and phylogenetic relationships of the Brazilian endemic cotton, Gossypium mustelinum (Malvaceae),” Plant Systematics and Evolution, vol. 192, no. 1-2, pp. 49–59, 1994.
[40]
O. T. Westengen, Z. Huamán, and M. Heun, “Genetic diversity and geographic pattern in early South American cotton domestication,” Theoretical and Applied Genetics, vol. 110, no. 2, pp. 392–402, 2005.
[41]
Y. H. Park, M. S. Alabady, M. Ulloa et al., “Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population,” Molecular Genetics and Genomics, vol. 274, no. 4, pp. 428–441, 2005.
[42]
W. Guo, W. Wang, B. Zhou, and T. Zhang, “Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium,” Theoretical and Applied Genetics, vol. 112, no. 8, pp. 1573–1581, 2006.
