Molecular markers and their application in cotton breeding: progress and future perspectives
Keywords:
cotton, DNA markers, genome, MASAbstract
Cotton is the most important natural fiber plant worldwide and a valued cash crop. It is also a significant source of oil and protein. The conventional breeding for genetic improvement has its limitations due mostly to the lack of knowledge about polygenic traits such as yield productivity, fiber quality, resistance to diseases, and adverse growing conditions. The use of molecular markers is one of the significant developments in the field of genetics, allowing faster detection and exploitation of DNA polymorphisms. Recent developments, including the sequencing of the genome of G. raimondii, G. arboreum, G. hirsutum, and G. barbadense open new possibilities for selection of the best traits present in the genome of cotton. This article gives an overview of various DNA markers used in cotton. They play a crucial role in cotton improvement programs, like (a) Analysis of genetic diversity, (b) Construction of linkage maps, (c) QTL analysis of agronomic and fiber-related traits, (d) Marker-assisted selection (MAS). There is no molecular marker type developed up to now which can fulfill all the requirements of the plant breeders. The scientists should take a holistic approach and use all tools at their disposal to utilize the full genetic diversity present in Gossypium spp.
References
Abdurakhmonov, I. Y., Buriev, Z. T. & Shermatov, S. E. (2011). Marker-assisted selection for complex fiber traits in cotton. In: 5th World Cotton Research Conference, Special session of ICGI, Mumbai, India, 7-12.
Abdurakhmonov, I. Y., Saha, S., Jenkins, J. N., Buriev, Z. T., Shermatov, S. E., Scheffler, B. E., Pepper, A.E., John, Z.Y., Kohel, R.J., & Abdukarimov, A. (2009). Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica, 136(3), 401-417.
Adhikari, J., Das, S., Wang, Z., Khanal, S., Chandnani, R., Patel, J. D., Goff, V.H., Auckland, S., Rainville, L.K., Jones, D., & Paterson, A. H. (2017). Targeted identification of association between cotton fiber quality traits and microsatellite markers. Euphytica, 213(3), 65.
Badigannavar, A. & Myers, G. O. (2015). Construction of genetic linkage map and QTL analysis for fiber traits in diploid cotton (Gossypium arboreum x Gossypium herbaceum). J. Cotton Sci, 19, 15-26.
Baytar, A. A., Erdogan, O., Frary, A., Frary, A. & Doganlar, S. (2017). Molecular diversity and identification of alleles for Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm. Euphytica, 213(2), 31.
Bojinov, B. & Lacape, J. M. (2003). Molecular markers for DNA fingerprinting in cotton. In: Cotton production for the new millennium: Proc. World Cotton Res. Conf., 3rd, Cape Town, South Africa, 9-13.
Bozhanova, V., Todorovska, E., Hadzhiivanova, B., & Dechev, D. (2014). Obtaining of Interspecific Hybrids between Durum Wheat (2n=28) and Triticale (2n=42) and Molecular Evidence of Alien Introgressions in Advanced Backcross Line. Türk Tarım ve Doğa Bilimleri, 6(6), 868-874.
Byers, R. L., Harker, D. B., Yourstone, S. M., Maughan, P. J. & Udall, J. A. (2012). Development and mapping of SNP assays in allotetraploid cotton. Theortical and Applied Genetics, 124(7), 1201-1214.
Cao, Z., Wang, P., Zhu, X., Chen, H. & Zhang T. (2014). SSR marker assisted improvement of fiber qualities in Gossypium hirsutum using Gossypium barbadense introgression. Theoretical and Applied Genetics, 127(3), 587-594.
Chaudhary, L., Sindhu, A., Kumar, M., Kumar, R. & Saini, M. (2010). Estimation of genetic divergence among some cotton varieties by RAPD analysis. J. Plant Breed. Crop Sci., 2(3), 039-043.
Cuming, D. S., Altan, F., Akdemir, H., Tosun, M., Gurel,A. & Tanyolac, B. (2015). QTL analysis of fiber color and fiber quality in naturally green colored cotton (Gossypium hirsutum L.). Turkish Journal of Field Crops, 20(1), 49-58.
Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S. & Mitchell, S. E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS one, 6(5), e19379.
Fang, X., Liu, X., Wang, X., Wang, W., Liu, D., Zhang, J., Liu, D., Teng, Z., Tan, Z., Liu, F., & Zhang, F. (2017). Fine-mapping qFS07. 1 controlling fiber strength in upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics, 130(4), 795-806.
Feng, C. D., Stewart, J. M. D., & Zhang, J. F. (2005). STS markers linked to the Rf 1 fertility restorer gene of cotton. Theoretical and Applied Genetics, 110(2), 237-243.
Gallagher, J. P., Grover, C. E., Rex, K., Moran, M. & Wendel, J. F. (2017). A new species of cotton from Wake Atoll, Gossypium stephensii (Malvaceae). Systematic Botany, 42(1), 115-123.
Gore, M. A., Fang, D. D., Poland, J. A., Zhang, J., Percy, R. G., Cantrell, R. G., Thyssen, G., & Lipka, A. E. (2014). Linkage map construction and quantitative trait locus analysis of agronomic and fiber quality traits in cotton. The Plant Genome, 7(1).
Grover, C. E., Zhu, X., Grupp, K. K., Jareczek, J. J., Gallagher, J. P., Szadkowski, E., Seijo, J.G. & Wendel, J. F. (2015). Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum Wittmack. Genetic Resources and Crop Evolution, 62(1), 103-114.
Guo, W., Zhang, T., Shen, X., Yu, Z.J., & Kohel, R.J. (2003). Development of SCAR Marker Linked to a Major QTL for High Fiber Strength and Its Usage in Molecular-Marker Assisted Selection in Upland Cotton, Crop Science, 43(6), 2252-2256.
Hulse-Kemp, A. M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D. D., Frelichowski, J., Giband, M., Hague, S., Hinze, L.L., & Kochan, K. J. (2015). Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. G3: Genes, Genomes, Genetics, 5(6), 1187-1209.
Ince, A. G., Karaca, M. & Onus, A. N. (2010). CAPS-microsatellites: use of CAPS method to convert non-polymorphic microsatellites into useful markers. Molecular Breeding, 25(3), 491-499.
Ismail, S. E., Adawy, S. S., El-Din, A. K. Y. G. & Hussein, E. H. (2015). Linkage map construction and detection of QTLs associated with earliness, fiber quality and yield in an interspecific cross between Gossypium hirsutum L. and Gossypium barbadense L. International Journal, 3(3), 637-649.
Ivanova, B. & Bojinov, B. (2009). Identification of QTLs for fiber quality in Bulgarian cotton breeding collection. Genet. Breed., 38, 55-60.
Jenkins, J. N., McCarty, J. C., Wubben, M. J., Hayes, R., Gutierrez, O. A., Callahan, F. & Deng, D. (2012). SSR markers for marker assisted selection of root-knot nematode (Meloidogyne incognita) resistant plants in cotton (Gossypium hirsutum L). Euphytica, 183(1), 49-54.
John, Z. Y., Kohel, R. J., Fang, D. D., Cho, J., Van Deynze, A., Ulloa, M., Hoffman, S.M., Pepper, A.E., Stelly, D.M., Jenkins, J.N. & Saha, S. (2012). A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. G3: Genes, Genomes, Genetics, 2(1), 43-58.
Kalia, R. K., Rai, M. K., Kalia, S., Singh, R. & Dhawan, A. K. (2011). Microsatellite markers: an overview of the recent progress in plants, Euphytica, 177(3): 309-334.
Karaca, M. & Ince, A. G. (2011). New non-redundant microsatellite and CAPS-microsatellite markers for cotton (Gossypium L.). Turkish Journal of Field Crops, 16(2), 172-178.
Kumpatla, S. P., Buyyarapu, R., Abdurakhmonov, I. Y. & Mammadov, J. A. (2012). Genomics-assisted plant breeding in the 21st century: technological advances and progress. In: Plant breeding. Intechopen, Croatia, 131-184.
Lan, T. H., Cook, C. G. & Paterson, A. H. (1999). Identification of a RAPD marker linked to male fertility restoration gene in cotton (Gossypium hirsutum L.). J. Agri. Genom., 4, 1-5.
Li, F., Fan, G., Wang, K., Sun, F., Yuan, Y., Song, G., Li, Q., Ma, Z., Lu, C., Zou, C., & Chen, W. (2014). Genome sequence of the cultivated cotton Gossypium arboreum. Nature Genetics, 46(6), 567.
Li, X., Wu, M., Liu, G., Pei, W., Zhai, H., Yu, J., Zhang, J. & Yu, S. (2017). Identification of candidate genes for fiber length quantitative trait loci through RNA-Seq and linkage and physical mapping in cotton. BMC Genomics, 18(1), 427.
Liu, R., Wang, B., Guo, W., Qin, Y., Wang, L., Zhang, Y. & Zhang, T. (2012). Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L. Molecular Breeding, 29(2), 297-311.
Liu, X., Teng, Z., Wang, J., Wu, T., Zhang, Z., Deng, X., Fang, X., Tan, Z., Ali, I., Liu, D., & Zhang, J. (2017). Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.). Molecular Genetics and Genomics, 292(6), 1281-1306.
Lin, Z., He, D., Zhang, X., Nie, Y., Guo, X., Feng, C. & Stewart, JMCD. (2005). Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPD. Plant Breeding, 124, 180-187.
Lin, Z., Zhang, Y., Zhang, X. & Guo, X. (2009). A high-density integrative linkage map for Gossypium hirsutum. Euphytica, 166(1), 35-45.
Malik, W., Ashraf, J., Iqbal, M. Z., Ali Khan, A., Qayyum, A., Ali Abid, M., Noor, E., Qadir Ahmad, M., & Hasan Abbasi, G. (2014). Molecular markers and cotton genetic improvement: current status and future prospects. The Scientific World Journal, 2014.
Mishra, K. K., Fougat, R. S., Ballani, A., Thakur, V., Yachana, J. & Bora, M. (2014). Potential and application of molecular markers techniques for plant genome analysis. Int. J. Pure App. Biosci., 2(1), 169-188.
Noormohammadi, Z., Hasheminejad-Ahangarani, Y. F., Sheidai, M., Ghasemzadeh-Baraki, S. & Alishah, O. (2013). Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers. Genetics and Molecular Research: GMR, 12(1), 256-269.
Noormohammadi, Z., Shojaei-Jesvaghani, F., Sheidai, M., Farahani, F. & Alishah, O. (2011). Inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) analyses of genetic diversity in Mehr cotton cultivar and its crossing progenies. African Journal of Biotechnology, 10(56), 11839-11847.
Pham, A. T., Shannon, J. G. & Bilyeu, K. D. (2012). Combinations of mutant FAD2 and FAD3 genes to produce high oleic acid and low linolenic acid soybean oil. Theoretical and Applied Genetics, 125(3), 503-515.
Poland, J. A., Brown, P. J., Sorrells, M. E. & Jannink, J. L. (2012). Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PloS one, 7(2), e32253.
Qin, H., Chen, M., Yi, X., Bie, S., Zhang, C., Zhang, Y., Lan, J., Meng, Y., Yuan, Y., & Jiao, C. (2015). Identification of associated SSR markers for yield component and fiber quality traits based on frame map and upland cotton collections. PLoS One, 10(1), e0118073.
Rakshit, A., Rakshit, S., Singh, J., Chopra, S. K., Balyan, H. S., Gupta, P. K. & Bhat, S. R. (2010). Association of AFLP and SSR markers with agronomic and fibre quality traits in Gossypium hirsutum L. Journal of Genetics, 89(2), 155-162.
Ronin, Y. I., Mester, D. I., Minkov, D. G., Akhunov, E. & Korol, A. B. (2017). Building ultra-high-density linkage maps based on efficient filtering of trustable markers. Genetics, 206(3), 1285-1295.
Roychowdhury, R., Taoutaou, A., Hakeem, K. R., Gawwad, M. R. A. & Tah, J. (2013). Molecular marker-assisted technologies for crop improvement. Crop Improvement in the Era of Climate Change, 241-58.
Said, J. I., Lin, Z., Zhang, X., Song, M. & Zhang, J. (2013). A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton. BMC Genomics, 14(1), 776.
Schuster, I. (2011). Marker-assisted selection for quantitative traits. Crop Breeding and Applied Biotechnology, 11(SPE), 50-55.
Sethi, K., Siwach, P., Verma, S. K. & Sihag, M. (2015). Assessing genetic diversity among Gossypium arboreum L. genotypes using ISSR markers. International Journal of Pharma and Bio Sciences. 6(1), 201-208.
Shaheen, T. & Zafar, Y. (2010). Detection of single nucleotide polymorphisms in the conserved ESTs regions of Gossypium arboreum. Electronic Journal of Biotechnology, 13(5), 3-4.
Shaheen, T., Tabbasam, N., Iqbal, M. A., Ashraf, M., Zafar, Y. & Paterson, A. H. (2012). Cotton genetic resources. A review. Agronomy for Sustainable Development, 32(2), 419-432.
Sharma, R., Joshi, A., Maloo, S. R. & Rajaman, G. (2012). Assessment of genetic finger printing using molecular marker in plants: A Review. Sci Res Impact, 1, 29-36.
Stewart, J. M., Craven, L. A., Brubaker, C. & Wendel, J. F. (2015). Gossypium anapoides (Malvaceae), a new species from Western Australia. Novon: A Journal for Botanical Nomenclature, 23(4), 447-451.
Stoilova, A. (2011). Breeding of Bulgarian cotton varieties with improved fiber quality. Vavilov Journal of Genetics and Breeding, 15, 550-553.
Stoilova, A., Valkova, N., Hadzhiivanova, B., Koleva, M. & Nedyalkova, S. (2014). The cotton breeding in Bulgaria. Türk Tarım ve Doğa Bilimleri Dergisi, 1 (Özel Sayı-1), 992-999.
Su, J., Fan, S., Li, L., Wei, H., Wang, C., Wang, H., Song, M., Zhang, C., Gu, L., Zhao, S., & Mao, G. (2016). Detection of favorable QTL alleles and candidate genes for lint percentage by GWAS in Chinese upland cotton. Frontiers in Plant Science, 7, 1576.
Sun, Z., Wang. X., Liu, Z., Gu, Q., Zhang, Y., Li, Z., Ke, H., Yang, J., Wu, J., Wu, L., Zhang, G., Zhang C., Ma Z. (2017). Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L. Plant Biotechnol J., 15(8), 982-996.
Sundar, R., Patil, S. S., Ranganath, H. M., Srivalli, P., Manjula, S. M. & Pranesh, K. J. (2014). Genetic diversity analysis in cotton (Gossypium hirsutum L.) based on morphological traits and microsatellite markers. Int. J. Basic and Applied Biol., 1(1), 19-22.
Tang, S., Teng, Z., Zhai, T., Fang, X., Liu, F., Liu, D., Wang, S., Zhang, K., & Shao, Q. (2015). Construction of genetic map and QTL analysis of fiber quality traits for Upland cotton (Gossypium hirsutum L.). Euphytica, 201(2), 195-213.
Todorovska, E., Hadjiivanova, B., Bozhanova, V., Dechev, D., Muhovski, Y., Panchev, I., Abu-Mhadi, N., Peycheva, V., & Ivanova, A. (2013). Molecular and phenotypic characterization of advanced backcross lines derived from interspecific hybridization of durum wheat. Biotechnology & Biotechnological Equipment, 27(3), 3760-3771.
Todorovska, E., Ivanova, A., Ganeva, D., Pevicharova, G., Molle, E., Bojinov, B., Radkova, M., & Danailov, Z. (2014). Assessment of genetic variation in Bulgarian tomato (Solanum lycopersicum L.) genotypes, using fluorescent SSR genotyping platform. Biotechnology & Biotechnological Equipment, 28(1), 68-76.
Todorovska, E. G., Kolev, S., Christov, N. K., Balint, A., Kocsy, G., Vágújfalvi, A. & Galiba, G. (2014). The expression of CBF genes at Fr-2 locus is associated with the level of frost tolerance in Bulgarian winter wheat cultivars. Biotechnology & Biotechnological Equipment, 28(3), 392-401.
Valkova, N. (2009). Helius and Trakia new cotton varieties. Field Crops Studies, 1, 131-137 (Bg).
Valkova, N. & Bozhinov, M. (2010). Boyana cotton variety. Field Crops Studies, VI-3, 395-403 (Bg).
Valkova, N. & Dechev, D. 2004. Breeding evaluation of some traits and mutagenic cotton lines. Field Crops Studies, I-3, 402-406 (Bg).
Wang, B., Draye, X., Zhuang, Z., Zhang, Z., Liu, M., Lubbers, E. L., Jones, D., May, O.L., Paterson, A.H., & Chee, P. W. (2017). QTL analysis of cotton fiber length in advanced backcross populations derived from a cross between Gossypium hirsutum and G. mustelinum. Theoretical and Applied Genetics, 130(6), 1297-1308.
Wang, Q., Fang, L., Chen, J., Hu, Y., Si, Z., Wang, S., Chang, L., Guo, W., & Zhang, T. (2015). Genome-wide mining, characterization, and development of microsatellite markers in Gossypium species. Scientific Reports, 5, 10638.
Wang, X., Lu, X., Wang, J., Wang, D., Yin, Z., Fan, W., Wang, S., & Ye, W. (2016). Mining and analysis of SNP in response to salinity stress in upland cotton (Gossypium hirsutum L.). PloS one, 11(6), e0158142.
Wang, Z., Zhang, D., Wang, X., Tan, X., Guo, H. & Paterson, A. H. (2013). A whole-genome DNA marker map for cotton based on the D-genome sequence of Gossypium raimondii L. G3: Genes, Genomes, Genetics, 3(10), 1759-1767.
Xiao, J., Fang, D. D., Bhatti, M., Hendrix, B. & Cantrell, R. (2010). A SNP haplotype associated with a gene resistant to Xanthomonas axonopodis pv. malvacearum in upland cotton (Gossypium hirsutum L.). Molecular Breeding, 25(4), 593-602.
Zhang, Z., Hu, M., Zhang, J., Liu, D., Zheng, J., Zhang, K., Wang, W., & Wan, Q. (2009). Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.) Molecular Breed., 24, 49-61
Zhang, K., Zhang, J., Ma, J., Tang, S., Liu, D., Teng, Z., Liu, D., & Zhang, Z. (2012). Genetic mapping and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton (Gossypium hirsutum L.). Molecular Breeding, 29(2), 335-348.
Zhang, T., Qian, N., Zhu, X., Chen, H., Wang, S., Mei, H., & Zhang, Y. (2013). Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China. PLoS One, 8(2), e57220.
Zhang, Y., Wang, X. F., Li, Z. K., Zhang, G. Y. & Ma, Z. Y. (2011). Assessing genetic diversity of cotton cultivars using genomic and newly developed expressed sequence tag-derived microsatellite markers. Genet. Mol. Res., 10, 1462-1470.
Zhang, Z., Ge, Q., Liu, A., Li, J., Gong, J., Shang, H., Shi, Y., Chen, T., Wang, Y., Palanga, K.K., & Muhammad, J. (2017). Construction of a high-density genetic map and its application to QTL identification for fiber strength in Upland cotton. Crop Science, 57(2), 774-788.
Zhao, Y., Wang, H., Chen, W. & Li, Y. (2014). Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PloS One, 9(1), e86308.
Downloads
Published
Issue
Section
License
Copyright (c) 2020 Bulgarian Journal of Agricultural Science
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
