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

Full Length Research Article

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

Trinh Ngoc Ai1, Anh Phu Nam Bui2*

Adv. life sci., vol. 9, no. 4, pp. 462-466, December 2022
*Corresponding Author: Anh Phu Nam Bui (Email:
Authors' Affiliations

 1. Tra Vinh University, No. 126 Nguyen Thien Thanh Street, Ward 5, Tra Vinh City – Viet Nam
2. Institute of Applied Technology, Thu Dau Mot University, Binh Duong Provincen – Vietnam 
[Date Received: 07/05/2021; Date Revised: 24/08/2022; Date Published: 31/12/2022]

Abstractaa download_button



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     

Introduction6th button-01

Diseases exhibit an adverse impact on cotton (Gossypium spp.) production. The yield loss is projected at approximately 60% of the annual potential production [1,2]. Black root rot (BRR) is a seedling disease caused by Thielaviopsis basicola, a soil-borne pathogen fungal with a broad infection spectrum of crops. Since its first reported case on cotton in Arizona in 1922 [3], it has become one of the significant threats in cotton industry.

Because of the susceptibility to BRR of the two commercially important tetraploid cotton genome AADD species G. barbadense and G. hirsutum, tremendous efforts have been made toward developing BRR resistance germplasm. However, BRR partial resistance has only been demonstrated in several studies conducted in uncommercial AA genome specie G. arboretum (variance PI1415) and G. herbaceum (variance A20) [4,5]. Most recently, by employing crossbreeding from these two cultivars, followed by genetic analysis with simple sequence repeats (SSR) markers, three quantitative trait loci (QTL) BRR5.1, BRR9.1, BRR13.1 were demonstrated to improve BRR resistance [6]. Nevertheless, there is a limited number of reports on how cotton DD genome, which is the progenitor of the cotton genome AADD species, confer BRR tolerance. 

The importance of comparative mapping is the establishment of the syntenic relationships between genomes from different species [7-9]. Mountain of evidences have accumulated in comparative mapping analysis in many species of great economic importance, such as Pinaceae, soybean (Glycine max), barrel medic (Medicago truncatula), cabbage (Brassica oleracea), potato (Solanum tuberosum), and Arabidopsis thaliana [10-14] By using a standard set of frequently applied markers such as SSR and RFLP, comparative mapping assists the translation and transferring the information from one genomic map to another, such as verification of QTL, obtaining better knowledge of genome evolution, and identification of candidate genes underlying QTL [15].  Specifically, the idea of transferring map information to improve disease resistance has been conducted in coffee (Psilanthus). Molecular markers were used to isolate the new resistance genes which were subsequently introduced novel more robust sources into commercially elite coffee varieties [16].

The purpose of this study is to physically map the published SSRs from three QTL conferring BRR resistance on AA genome to DD genome in cotton. By utilizing CottonGen and Phytozome database, our findings suggested that there was a correlation between the genetic map in AA genome and physical map in DD genome. A comparative map was constructed, illustrating the conserved order of SSR markers from the genetic mapping results in diploid AA genome and in DD genome [6]. These results will shed new lights in understanding of shared synteny of QTL conferring black root rot disease between two diploid genomes in cotton, which could also pave the way to isolate the resistance gene against BRR in DD genome.

Methods6th button-01

The study was carried out at Department of Plant and Soil Science, Texas Tech University, USA from January 2014 to May 2014.


CottonGen is an online mapping database for cotton [17]. CottonGen contains information on genomic, genetics, breeding, and molecular genetic markers. It also incorporates genomic sequences of different cotton genomes, markers, and traits. Additionally, various platforms such as BLAST, JBrowse, MapViewer, Primer3 are also included on the website.

Retrieving AA genome-derived SSR markers sequence

1.      Go to the CottonGen website ( Along the Tools Quick Start, go to ‘Search Markers’ (Figure 1).

2.      In the ‘Marker Name’ section, click on ‘contains’ in the first box and then type the name of the marker in the second box (Figure 2). Use the marker name in the publication of Niu et al. [6], page 1318, Figure 3.

3.      In the ‘Marker Type’ section, click on ‘SSR’. Then hit ‘Search’.

4.      In the resulting search table, click any of the records that showed in the table.

In the ‘Marker Overview’, click on the ‘Source Sequence’ to get the sequence of the markers (Figure 3). Copy the sequence of the marker in Notepad program of Microsoft Windows.


Since its development from 2008, Phytozome has become a connective platform for much research on plant genome. Besides its easily and friendly accessible database, which contains 25 plant genomes including cotton, Phytozome is also equipped with tools for comparative analysis so that scientists can compare every plant genes at the various level of sequences [18].

Localizing AA genome derived SSR markers to DD genome

1.      Go the Phytozome website ( Along the top menu header, go to ‘Species’ and choose ‘Gossypium raimondii v2.1’ (Figure 4).

2.      In the new resulting page, along the menu under the title ‘Gossypium raimondii v2.1 (Cotton), click on ‘BLAST search’ (Figure 5).

3.      In the second column ‘2. Build your query’, paste the copied marker’s sequence into the box the says ‘Enter a single sequence…’. Then hit ‘Go’.

4.      The BLAST results page shows the most significant hits. You will choose the first hit with the darkest color arrow bar. In the ‘Target View’ section, Click on that arrow bar in the ‘Feature scale” column.

In the close-up viewing mode in JBrowse, copy the information of the chromosome in the first box and the physical position of the marker in that chromosome in the second box (Figure 6). 

Results6th button-01

We showed here that after anchoring the SSR markers from the results of Niu et al. [6] on DD genome, there was collinearity between the genetic map of SSR markers associated three QTL conferring BRR on AA genome and the physical position of these SSR markers on DD genome (Table 1). We still observed some minor SRR markers inversions, especially in the chromosomal regions on DD genome which corresponds to the linkage group A9. The same observation was also portrayed in study by Rong et al., [19]. These inversions could be explained by the rearrangement of the chromosomal segments during evolution of AA and DD genomes after separating from the first common ancestor [19]. One more explanation could be the order of SSR markers were calculated based on the recombination frequency which could be utilized to measure the genetic distance between two loci, whereas the physical map was based on the number of nucleotides between two loci [20]. Overall, this result confirmed the accuracy of the genetic map in previous study [6].



Figures & Tables






Discussion6th button-01

Evolutionary evidence has suggested that from the origin of a common ancestor, diploid cotton species continued evolving and subsequently dividing into eight current monophyletic groups denoted as A–G, and K. A hybridization occurred approximately 1 to 2 million years ago between two diploid cotton species (2n = 2x = 26): G. raimondii (D5) and G. arboreum (A2) or G. herbaceum (A1). This event introduced the emergence of allotetraploid species (2n = 4x = 52) [21,22]. After undergoing the polyploidization and following independent evolution processes, these tetraploid cottons differentiate into six present tetraploid species including G. hirsutum (AD)1, G. barbadense (AD)2, G.tomentosum (AD)3, G. mustelinum (AD)4, G. darwinii (AD)5 and G. ekmanianum (AD)6 [23].

Owing to its information, versatility and easy detection in genetic experiments, SSR markers have been widely employed in QTL mapping and saturating in many plant genomes [24,25]. In cotton, mountain of evidence has been gathered in data mining to discover and characterize new SSR marker to narrow down the QTL regions. The ultimate purpose of this process is to isolate the candidate genes responsible for desired agricultural traits, including disease tolerance [24,26-29]. However, the susceptibility to BRR of two commercial tetraploid cotton species Gossypium hirsutum, Gossypium barbadense or crosses generated from these two species with other tetraploid species have hindered the development cotton cultivars conferring resistance to this disease. As a result, researches mainly focused on elaborating how cotton diploid genomes contribute to improving BRR resistance.

In this study, we presented a Phytozome-based comparative mapping between two cotton diploid genomes revealing conserved markers order in quantitative trait loci conferring resistance against black root rot disease. We report here a new method that could physically map AA genome-SSR markers in D genome by using Phytozome database. Given the collinearity between regions of AA and DD genomes in this study, we suggested that the syntenic regions on DD genome could also confer the BRR resistance. These regions were on chromosome 2 from position 7879824 to position 59691832, chromosome 7 from position 3320225 to position 58206145, chromosome 11 from position 5509175 to position 57112593. More research should be done to increase the density of SRR markers in these regions to isolate candidate R-genes.

Conclusively, our study revealed that three QTL regions conferring BRR resistance in AA genome exhibited a significant collinearity with DD genome. While the orders of SSR markers on linkage group A13 on AA genome and on its counterpart region of DD genome are conserved, there were some minor inversions among of SSR markers on linkage group A7 and A5 on two genomic regions that could be explicable by the rearrangement of the chromosomal segments or recombination frequency. The results from this paper could be further used for fine mapping resistance genes against BRR in DD genome in the future.

Author Contributions

All authors of this study participated in experimentation, data mining, analysis and drafting of the manuscript.

6th button-01

Conflict of Interest

The authors declare that there is no conflict of interest.

6th button-01


  1. 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.
  2. 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.
  3. King CJ, Presley JT. A root rot of Cotton caused by Thielaviopsis basicola. Phytopathology, (1942); 32(9): 752-761 pp.
  4. Wheeler TA, Gannaway JR, Keating K. Identification of Resistance to Thielaviopsis basicola in Diploid Cotton. Plant Disease, (1999); 83(9): 831-833.
  5. 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.
  6. 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.
  7. 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.
  8. Murphy WJ, Stanyon R, O'Brien SJ. Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biology, (2001); 2(6): reviews0005.0001.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, et al. Phytozome: a comparative platform for green plant genomics. Nucleic acids research, (2012); 40(Database issue): D1178-D1186.
  19. 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.
  20. O'Rourke JA (2014) Genetic and Physical Map Correlation. eLS: In: eLS. John Wiley & Sons, Ltd: Chichester.
  21. Wendel JF. New World tetraploid cottons contain Old World cytoplasm. Proceedings of the National Academy of Sciences, (1989); 86(11): 4132.
  22. 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.
  23. 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.
  24. 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.
  25. 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).
  26. 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.
  27. 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.
  28. 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.
  29. 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.

This work is licensed under a Creative Commons Attribution-Non Commercial 4.0 International License. To read the copy of this license please visit:

6th button-01