EXPLORING THE GENETIC RESOURCES OF COTTON
Keywords:
Gossypium hirsutum, Diversity, Cultivated Species, QTL Map, Hybrid cotton, Structural genomic resources, DNA marker, RFLP, RAPD, SSRAbstract
Since its first use in 6000 BC, cotton (genus Gossypium) has become a major natural textile in the global market. Modern tools such as web databases, microsatellite databases, and comparative QTL resources have been developed to evaluate the consequences of human dispersal and selection on different strains of Gossypium. Out of the fifty species of Gossypium, only four have been domesticated, leading to significant changes in lint percentage (40%), fibre length (22%), and boll size. The biggest challenge with domestication is the lack of genetic variety. This is particularly evident in Gossypium hirsutum L. upland cotton cultivars compared to Pima and Egyptian cotton cultivars of Gossypium barbadense. The latter possess a higher degree of genetic diversity due to the introduction of G. hirsutum genes into G. barbadense cultivars. Including genes from all types of Gossypium in cultivated cotton species is very important. The use of genome-wide markers such as Simple Sequence Repeat (SSR), Restriction Fragment Length Polymorphism (RFLP), Amplified Fragment Length Polymorphism (AFLP), and Random Amplified Polymorphic DNA (RAPD) enabled the discovery of 16,162 public SSRs and 312 mapped RFLP sequences. These markers were further employed to study various plant traits reported in 26 mapping populations. These included qualitative traits such as fiber quality, yield, leaf and flower shape, trichome density and placement, disease protection, and quantitative traits such as quantitative trait loci (QTLs). After a suitable comparison of the mapped populations, 432 QTLs were associated with 3,475 loci within 11 mapping groups. Furthermore, a meta-analysis of over 1,000 QTLs derived from backcross and hybrid inbred line populations with the same parents revealed the most accurate meta-clusters for fiber color, fineness, and length. The cotton genome has undergone enrichment by incorporating genes obtained from distantly related organisms via diverse transformation techniques.
Downloads
References
Abbas, H. G., Mahmood, A., & Ali, Q. (2016). Zero tillage: a potential technology to improve cotton yield. Genetika, 48(2), 761-776.
Abbas, H. G., Mahmood, A., & Ali, Q. (2015). Genetic variability and correlation analysis for various yield traits of cotton (Gossypium hirsutum L.). Journal of Agricultural Research, 53(4), 481-491.
Abdurakhmonov, I. Y., Kohel, R. J., Yu, J. Z., Pepper, A. E., Abdullaev, A. A., Kushanov, F. N., ... & Abdukarimov, A. (2008). Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics, 92(6), 478-487.
Abelson, P. H. (1998). A third technological revolution. Science, 279(5359), 2019-2109.
Adkisson, P. L., Niles, G. A., Walker, J. K., Bird, L. S., & Scott, H. B. (1982). Controlling cotton's insect pests: a new system. Science, 216(4541), 19-22.
Asad, S., Mukhtar, Z., Nazir, F., Hashmi, J. A., Mansoor, S., Zafar, Y., & Arshad, M. (2008). Silicon carbide whisker-mediated embryogenic callus transformation of cotton (Gossypium hirsutum L.) and regeneration of salt tolerant plants. Molecular biotechnology, 40, 161-169.
Asif, M. (2010). Genomic analysis for quality traits in cotton (Gossypium hirsutum L.) by DNA fingerprinting technology (Doctoral dissertation, Bahauddin Zakariya University (BZU), Multan).
Batool, F., Hassan, S., Azam, S., Sher, Z., Ali, Q., & Rashid, B. (2023). Transformation and expressional studies of GaZnF gene to improve drought tolerance in Gossypium hirsutum. Scientific Reports, 13(1), 5064.
Bowers, J. E., Chapman, B. A., Rong, J., & Paterson, A. H. (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature, 422(6930), 433-438.
Brubaker, C. L., Paterson, A. H., & Wendel, J. F. (1999). Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome, 42(2), 184-203.
Brubaker, C. L., Paterson, A. H., & Wendel, J. F. (1999). Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome, 42(2), 184-203.
Buckler, E. S., Yu, J. I. A. N. M. I. N. G., Holland, J. B., & McMullen, M. D. (2008). Genome-wide complex trait dissection through nested association mapping. Genetics, 178, 539-551.
Cai, Y., Xie, Y., & Liu, J. (2010). Glandless seed and glanded plant research in cotton. A review. Agronomy for sustainable development, 30, 181-190.
Dong, J., Wu, F., Jin, Z., & Huang, Y. (2006). Heterosis for yield and some physiological traits in hybrid cotton Cikangza 1. Euphytica, 151, 71-77.
Endrizzi, J. E., & Ramsay, G. (1979). Monosomes and telosomes for 18 of the 26 chromosomes of Gossypium hirsutum. Canadian Journal of Genetics and Cytology, 21(4), 531-536.
Feng, C. D., Stewart, J. M. D., & Zhang, J. F. (2005). STS markers linked to the Rf<? A3B2 show $132#?> 1 fertility restorer gene of cotton. Theoretical and applied genetics, 110, 237-243.
Fryxell, P. A. (1979). The natural history of the cotton tribe (Malvaceae, tribe Gossypieae). Texas A & M University Press..
Fryxell, P. A., Craven, L. A., & McD, J. (1992). A revision of Gossypium sect. Grandicalyx (Malvaceae), including the description of six new species. Systematic Botany, 91-114.
Guo, W., Cai, C., Wang, C., Han, Z., Song, X., Wang, K., ... & Zhang, T. (2007). A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics, 176(1), 527-541.
Gur, A., & Zamir, D. (2004). Unused natural variation can lift yield barriers in plant breeding. PLoS biology, 2(10), e245.
Hafeez, M. N., Khan, M. A., Sarwar, B., Hassan, S., Ali, Q., Husnain, T., & Rashid, B. (2021). Mutant Gossypium universal stress protein-2 (GUSP-2) gene confers resistance to various abiotic stresses in E. coli BL-21 and CIM-496-Gossypium hirsutum. Scientific reports, 11(1), 20466.
Hao, J. J., Yu, S. X., Dong, Z. D., Fan, S. L., Ma, Q. X., Song, M. Z., & Yu, J. W. (2008). Quantitative inheritance of leaf morphological traits in upland cotton. The Journal of Agricultural Science, 146(5), 561-569.
Hsu, C. Y., Jenkins, J. N., Saha, S., & Ma, D. P. (2005). Transcriptional regulation of the lipid transfer protein gene LTP3 in cotton fibers by a novel MYB protein. Plant Science, 168(1), 167-181.
http://chibba.agtec.uga.edu/cgi-bin/cmap/viewer.
Iqbal, A., Aslam, S., Ahmed, M., Khan, F., Ali, Q., & Han, S. (2023a). Role of actin dynamics and GhACTIN1 gene in cotton fiber development: A prototypical cell for study. Genes, 14(8), 1642.
Iqbal, A., Aslam, S., Akhtar, S., Ali, Q., Rao, A. Q., & Husnain, T. (2023b). Over-expression of GhACTIN1 under the control of GhSCFP promoter improves cotton fiber and yield. Scientific Reports, 13(1), 18377.
Jakoby, M. J., Falkenhan, D., Mader, M. T., Brininstool, G., Wischnitzki, E., Platz, N., ... & Schnittger, A. (2008). Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106. Plant Physiology, 148(3), 1583-1602.
Jiang, C. X., Chee, P. W., Draye, X., Morrell, P. L., Smith, C. W., & Paterson, A. H. (2000). Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton). Evolution, 54(3), 798-814.
Kohel, R. J., Richmond, T. R., & Lewis, C. F. (1974). Genetics of Flowering Response in Cotton. VI. Flowering Behavior of Gossypium hirsutum L. and G. barbadense L. Hybrids 1. Crop science, 14(5), 696-699.
Lacape, J. M., Dessauw, D., Rajab, M., Noyer, J. L., & Hau, B. (2007). Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs. Molecular Breeding, 19, 45-58.
Lacape, J. M., Gawrysiak, G., Cao, T. V., Viot, C., Llewellyn, D., Liu, S., ... & Giband, M. (2013). Mapping QTLs for traits related to phenology, morphology and yield components in an inter-specific Gossypium hirsutum× G. barbadense cotton RIL population. Field Crops Research, 144, 256-267.
Lacape, J. M., Nguyen, T. B., Thibivilliers, S., Bojinov, B., Courtois, B., Cantrell, R. G., ... & Hau, B. (2003). A combined RFLP SSR AFLP map of tetraploid cotton based on a Gossypium hirsutum× Gossypium barbadense backcross population. Genome, 46(4), 612-626.
Lan, T. H., Cook, C. G., & Paterson, A. H. (1999). Identification of a RAPD marker linked to a male fertility restoration gene in cotton (Gossypium hirsutum L.). J Agric genomics, 4, 1-5.
Liu, S., Cantrell, R. G., McCarty Jr, J. C., & Stewart, J. M. (2000). Simple sequence repeat–based assessment of genetic diversity in cotton race stock accessions. Crop Science, 40(5), 1459-1469.
Ma, X. X., Zhou, B. L., Lü, Y. H., Guo, W. Z., & Zhang, T. Z. (2008). Simple sequence repeat genetic linkage maps of a‐genome diploid cotton (Gossypium arboreum). Journal of Integrative Plant Biology, 50(4), 491-502.
May, O. L. (2001). Registration of PD 94045 germplasm line of upland cotton. Crop science, 41(1), 279-279.
May, O. L., Bowman, D. T., & Calhoun, D. S. (1995). Genetic diversity of US upland cotton cultivars released between 1980 and 1990. Crop Science, 35(6), 1570-1574.
May, O. L., Chee, P. W., & Sakhanokho, H. (2004). Registration of GA98033 upland cotton germplasm line. Crop science, 44(6), 2278-2280.
McCarty Jr, J. C., & Jenkins, J. N. (1992). Cotton germplasm: characteristics of 79 day-neutral primitive race accessions. Technical bulletin-Mississippi Agricultural and Forestry Experiment Station (USA).
McCarty Jr, J. C., & Jenkins, J. N. (1992). Cotton germplasm: characteristics of 79 day-neutral primitive race accessions. Technical bulletin-Mississippi Agricultural and Forestry Experiment Station (USA).
Mumtaz, H. (2007). Identification of structural and functional genomic markers for fiber quality traits in cotton using interspecific population (G. hirsutum x G. barbadense) (Doctoral dissertation, MPhil Thesis, QA Univ Islamabad Pakistan).
Perlak, F. J., Oppenhuizen, M., Gustafson, K., Voth, R., Sivasupramaniam, S., Heering, D., ... & Roberts, J. K. (2001). Development and commercial use of Bollgard® cotton in the USA–early promises versus today's reality. The Plant Journal, 27(6), 489-501.
Pflieger, S., Lefebvre, V., & Causse, M. (2001). The candidate gene approach in plant genetics: a review. Molecular breeding, 7(4), 275-291.
Plett, J. M., Mathur, J., & Regan, S. (2009). Ethylene receptor ETR2 controls trichome branching by regulating microtubule assembly in Arabidopsis thaliana. Journal of experimental botany, 60(13), 3923-3933.
Puspito, A. N., Rao, A. Q., Hafeez, M. N., Iqbal, M. S., Bajwa, K. S., Ali, Q., ... & Husnain, T. (2015). Transformation and evaluation of Cry1Ac+ Cry2A and GTGene in Gossypium hirsutum L. Frontiers in plant science, 6, 943.
Quisenberry, J. E. (1975). Inheritance of Fiber Properties Among Crosses of Acala and High Plains Cultivars of Upland Cotton 1. Crop Science, 15(2), 202-204.
Rahman, M., Hussain, D., & Zafar, Y. (2002). Estimation of genetic divergence among elite cotton cultivars–genotypes by DNA fingerprinting technology. Crop Science, 42(6), 2137-2144.
Rahman, M., Hussain, D., Malik, T. A., & Zafar, Y. (2005). Genetics of resistance to cotton leaf curl disease in Gossypium hirsutum. Plant pathology, 54(6), 764-772.
Rahman, M., Yasmin, T., Tabbasam, N., Ullah, I., Asif, M., & Zafar, Y. (2008). Studying the extent of genetic diversity among Gossypium arboreum L. genotypes/cultivars using DNA fingerprinting. Genetic Resources and Crop Evolution, 55, 331-339.
Rehman, I., Aftab, B., Bilal, S. M., Rashid, B., Ali, Q., Umair, M. M., ... & Husnain, T. (2017). Gene expression in response to Cotton Leaf Curl Virus Infection In Gossypium hirsutum under variable environmental conditions. Genetika, 49(3), 1115-1126.
Rong, J., Pierce, G. J., Waghmare, V. N., Rogers, C. J., Desai, A., Chee, P. W., ... & Paterson, A. H. (2005). Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton. Theoretical and applied genetics, 111, 1137-1146.
Rosenow, D. T., Quisenberry, J. E., Wendt, C. W., & Clark, L. E. (1983). Drought tolerant sorghum and cotton germplasm. Agricultural Water Management, 7(1-3), 207-222.
Saha, S., Raska, D. A., & Stelly, D. M. (2006). Upland Cotton (Gossypium hirsutum L.) x Hawaiian Cotton (G. tomentosum Nutt. Ex. Seem.) F1 hybrid hypoaneuploid chromosome substitution series.
Salentijn, E. M., Pereira, A., Angenent, G. C., van der Linden, C. G., Krens, F., Smulders, M. J., & Vosman, B. (2007). Plant translational genomics: from model species to crops. Molecular Breeding, 20, 1-13.
SARANGA, Y. E., Jiang, C. X., Wright, R. J., Yakir, D., & Paterson, A. H. (2004). Genetic dissection of cotton physiological responses to arid conditions and their inter‐relationships with productivity. Plant, Cell & Environment, 27(3), 263-277.
Saranga, Y., Menz, M., Jiang, C. X., Wright, R. J., Yakir, D., & Paterson, A. H. (2001). Genomic dissection of genotype× environment interactions conferring adaptation of cotton to arid conditions. Genome research, 11(12), 1988-1995.
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, 419-432.
Song, X. L., & Zhang, T. Z. (2007). Identification of quantitative trait loci controlling seed physical and nutrient traits in cotton. Seed Science Research, 17(4), 243-251.
SONG, X. L., GUO, W. Z., HAN, Z. G., & ZHANG, T. Z. (2005). Quantitative trait loci mapping of leaf morphological traits and chlorophyll content in cultivated tetraploid cotton. Journal of Integrative Plant Biology, 47(11), 1382-1390.
Tester, M., & Davenport, R. (2003). Na+ tolerance and Na+ transport in higher plants. Annals of botany, 91(5), 503-527.
Ullah, I. (2009). Molecular genetic studies for drought tolerance in cotton. Ph. D thesis Quaid-i-Azam University.
Van Esbroeck, G. A., Bowman, D. T., Calhoun, D. S., & May, O. L. (1998). Changes in the genetic diversity of cotton in the USA from 1970 to 1995. Crop Science, 38(1), 33-37.
Wada, T., Kurata, T., Tominaga, R., Koshino-Kimura, Y., Tachibana, T., Goto, K., ... & Okada, K. (2002). Role of a positive regulator of root hair development, CAPRICE, in Arabidopsis root epidermal cell differentiation.
Waghmare, V. N., Rong, J., Rogers, C. J., Pierce, G. J., Wendel, J. F., & Paterson, A. H. (2005). Genetic mapping of a cross between Gossypium hirsutum (cotton) and the Hawaiian endemic, Gossypium tomentosum. Theoretical and Applied Genetics, 111, 665-676.
Walker, A. R., Davison, P. A., Bolognesi-Winfield, A. C., James, C. M., Srinivasan, N., Blundell, T. L., ... & Gray, J. C. (1999). The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein. The Plant Cell, 11(7), 1337-1349.
Wang, B., Wu, Y., Guo, W., Zhu, X., Huang, N., & Zhang, T. (2007). QTL analysis and epistasis effects dissection of fiber qualities in an elite cotton hybrid grown in second generation. Crop science, 47(4), 1384-1392.
Wendel, J. F. (1989). New World tetraploid cottons contain Old World cytoplasm. Proceedings of the National Academy of Sciences, 86(11), 4132-4136.
Wright, R. J., Thaxton, P. M., El-Zik, K. M., & Paterson, A. H. (1998). D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel avenues for evolution. Genetics, 149(4), 1987-1996.
Yu, J., Yu, S., Lu, C., Wang, W., Fan, S., Song, M., ... & Zhang, J. (2007). High‐density linkage map of cultivated allotetraploid cotton based on SSR, TRAP, SRAP and AFLP markers. Journal of Integrative Plant Biology, 49(5), 716-724.
Zafar, M. M., Mustafa, G., Shoukat, F., Idrees, A., Ali, A., Sharif, F., ... & Li, F. (2022). Heterologous expression of cry3Bb1 and cry3 genes for enhanced resistance against insect pests in cotton. Scientific Reports, 12(1), 10878.
Zafar, Y., & Paterson, A. H. (2009). Gossypium DNA markers: types, numbers, and uses. Genetics and genomics of cotton, 101-139.
ZAFAR, Y., ASIF, M., KAUSAR, A., RIAZ, S., NIAZ, M., WAHID, A., & ABBAS, S. Q. (2009). Development of genetic linkage map of leaf red colour in cotton (Gossypium hirsutum) using DNA markers. Pak. J. Bot, 41(3), 1127-1136.
Zhu, W., Liu, K., & Wang, X. D. (2008). Heterosis in yield, fiber quality, and photosynthesis of okra leaf oriented hybrid cotton (Gossypium hirsutum L.). Euphytica, 164, 283-291.
Downloads
Published
Issue
Section
Categories
License
Copyright (c) 2022 A ABBAS, AU REHMAN, MS BUKHARI, MZ ABBAS (Author)
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
