Synteny of Cotton SSR Markers Genomes Paves the Way for Resistance Against Black Root Rot Disease in Cotton

Trinh Ngoc Ai, Anh Phu Nam Bui

Abstract


Background: Black root rot disease is documented for substantial reducing cotton yield and fiber quality. The isolation of candidate resistant genes in tetraploid genome AADD cotton species (2n=4x=52) remains challenging in the absence of research of black root rot resistance on progenitor DD genome diploid cotton. In this study, by exploiting Phytozome database, a comparative map of the black root rot-resistance quantitative trait loci in DD genome was constructed.

Methods: Simple sequence repeats markers associated with these three quantitative trait loci in the AA genome were used as “anchored-probes” frameworks for establishing relationships between the two cotton genomes AA and DD.

Results: Our findings showed that there was conserved orders among mapped simple sequence repeats markers on AA genome and the physical map of these simple sequence repeats markers on DD genome.

Conclusion: It was suggested that the syntenic loci on chromosome 2, 7 and 11 on DD genome could harbor the resistance gene against the black root rot disease. This study could serve as a fundamental step in isolating and introducing the resistance gene against black root rot into elite cotton cultivars.

Keywords: Comparative mapping; Resistance gene; Phytozome; Simple sequence repeats; Quantitative trait loci     


Full Text:

PDF

References


Rothrock CS. Prevalence and distribution of Thielaviopsis basicola. In: Proceedings of the beltwide cotton conference, New Orleans, LA, (1997); (National Cotton Council of America, Memphis): 55-57.

Blasingame D. Cotton disease loss estimate. In: Proceedings of the beltwide Cotton Conference, San Antonio, TX, (2005); (National Cotton Council of America, Memphis): 155-157.

King CJ, Presley JT. A root rot of Cotton caused by Thielaviopsis basicola. Phytopathology, (1942); 32(9): 752-761 pp.

Wheeler TA, Gannaway JR, Keating K. Identification of Resistance to Thielaviopsis basicola in Diploid Cotton. Plant Disease, (1999); 83(9): 831-833.

Wheeler TA, Hake KD, Dever JK. Survey of Meloidogyne incognita and Thielaviopsis basicola: Their Impact on Cotton Fruiting and Producers' Management Choices in Infested Fields. Journal of nematology, (2000); 32(4S): 576-583.

Niu C, Lister HE, Nguyen B, Wheeler TA, Wright RJ. Resistance to Thielaviopsis basicola in the cultivated A genome cotton. Theoretical and Applied Genetics, (2008); 117(8): 1313.

Kliebenstein DJ, Gershenzon J, Mitchell-Olds T. Comparative Quantitative Trait Loci Mapping of Aliphatic, Indolic and Benzylic Glucosinolate Production in Arabidopsis thaliana Leaves and Seeds. Genetics, (2001); 159(1): 359-370.

Murphy WJ, Stanyon R, O'Brien SJ. Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biology, (2001); 2(6): reviews0005.0001.

Schmidt R (2002) Plant genome evolution: lessons from comparative genomics at the DNA level. In: Town C, editor. Functional Genomics. Dordrecht: Springer Netherlands. pp. 21-37.

Babula D, Kaczmarek M, Barakat A, Delseny M, Quiros CF, et al. Chromosomal mapping of Brassica oleracea based on ESTs from Arabidopsis thaliana: complexity of the comparative map. Molecular Genetics and Genomics, (2003); 268(5): 656-665.

Gebhardt C, Walkemeier B, Henselewski H, Barakat A, Delseny M, et al. Comparative mapping between potato (Solanum tuberosum) and Arabidopsis thaliana reveals structurally conserved domains and ancient duplications in the potato genome. The Plant Journal, (2003); 34(4): 529-541.

Grant D, Cregan P, Shoemaker RC. Genome organization in dicots: Genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proceedings of the National Academy of Sciences, (2000); 97(8): 4168-4173.

Lukens L, Zou F, Lydiate D, Parkin I, Osborn T. Comparison of a Brassica oleracea Genetic Map With the Genome of Arabidopsis thaliana. Genetics, (2003); 164(1): 359-372.

Zhu H, Kim D-J, Baek J-M, Choi H-K, Ellis LC, et al. Syntenic Relationships between Medicago truncatula and Arabidopsis Reveal Extensive Divergence of Genome Organization. Plant Physiology, (2003); 131(3): 1018-1026.

Duran C, Edwards D, Batley J (2009) Genetic Maps and the Use of Synteny. In: Gustafson JP, Langridge P, Somers DJ, editors. Plant Genomics: Methods and Protocols. Totowa, NJ: Humana Press. pp. 41-55.

Hendre PS, Bhat PR, Krishnakumar V, Aggarwal RK. Isolation and characterization of resistance gene analogues from Psilanthus species that represent wild relatives of cultivated coffee endemic to India. Genome, (2011); 54(5): 377-390.

Yu J, Jung S, Cheng C-H, Ficklin SP, Lee T, et al. CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic acids research, (2014); 42(Database issue): D1229-D1236.

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, et al. Phytozome: a comparative platform for green plant genomics. Nucleic acids research, (2012);

(Database issue): D1178-D1186.

Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, et al. A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium). Genetics, (2004); 166(1): 389-417.

O'Rourke JA (2014) Genetic and Physical Map Correlation. eLS: In: eLS. John Wiley & Sons, Ltd: Chichester.

Wendel JF. New World tetraploid cottons contain Old World cytoplasm. Proceedings of the National Academy of Sciences, (1989); 86(11): 4132.

Wendel JF, Schnabel A, Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences, (1995); 92(1): 280.

Grover CE, Gallagher JP, Jareczek JJ, Page JT, Udall JA, et al. Re-evaluating the phylogeny of allopolyploid Gossypium L. Molecular Phylogenetics and Evolution, (2015); 9245-52.

Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape J-M, et al. CMD: a Cotton Microsatellite Database resource for Gossypium genomics. BMC genomics, (2006); 7132-132.

Khan MKR, Chen H, Zhou Z, Ilyas MK, Wang X, et al. Genome Wide SSR High Density Genetic Map Construction from an Interspecific Cross of Gossypium hirsutum × Gossypium tomentosum. Frontiers in Plant Science, (2016); 7(436).

Kirungu JN, Deng Y, Cai X, Magwanga RO, Zhou Z, et al. Simple Sequence Repeat (SSR) Genetic Linkage Map of D Genome Diploid Cotton Derived from an Interspecific Cross between Gossypium davidsonii and Gossypium klotzschianum. International Journal of Molecular Sciences, (2018); 19(1): 204.

Tabbasam N, Zafar Y, Mehboob-ur-Rahman. Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium. Plant Systematics and Evolution, (2014); 300(3): 559-575.

Yu JZ, Fang DD, Kohel RJ, Ulloa M, Hinze LL, et al. Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica, (2012); 187(2): 203-213.

Yu Y, Yuan D, Liang S, Li X, Wang X, et al. 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, (2011); 12(1): 15.




DOI: http://dx.doi.org/10.62940/als.v9i4.1200

Refbacks

  • There are currently no refbacks.