Advances in Genetic Mapping of Cotton for Yield, Fiber Quality, and Stress Resistance

Ayesha Khawar; Muhammad Abu Bakar Ghalib; Asad Sultan; Jareer Abdullah; Waqas Mushtaq; Ashir Masroor; Ahsan Raza

Advances in Genetic Mapping of Cotton for Yield, Fiber Quality, and Stress Resistance

Authors

Ayesha Khawar Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan,
Muhammad Abu Bakar Ghalib University of Agriculture Faisalabad
Asad Sultan Department of Entomology, University of Agriculture, Faisalabad, Pakistan
Jareer Abdullah State Key Laboratory of High-Efficiency Production of Wheat-Maize Double Cropping / Agronomy College, Henan Agricultural University, Zhengzhou, China,
Waqas Mushtaq Affiliation key laboratory of crop physiology, Ecology, and Genetics, Ministry of education college of Agronomy Jiangxi Agriculture Nanchang china, 330045,china Department of crop Genetics and breeding Jiangxi Agriculture Nanchang china
Ashir Masroor Department of Plant Pathology, University of Agriculture, Faisalabad Sub campus Burewala, Pakistan,
Ahsan Raza Department of Plant Pathology, University of Agriculture, Faisalabad Sub campus Burewala, Pakistan

Keywords:

CRISPR/CAS9, Genomic Breeding, Stress Rsisitance, Fibre Quality, QTL

Abstract

Cotton (Gossypium spp.) is a major global cash crop providing natural fibre and supporting textile and agriculture industries. However, its productivity is negatively impacted by pests, diseases, and abiotic stresses, which are inadequately addressed by conventional breeding. Recent advances in genome sequencing and molecular breeding offer new opportunities to improve fibre quality and stress resistance. This review highlights the role of genetic mapping, quantitative trait locus (QTL) analysis, and marker-assisted selection (MAS) in uncovering genes linked to key traits. High-throughput sequencing and genome-editing approaches, particularly CRISPR/Cas9, enable precise improvement of cotton genomic characteristics. Integration of high-density molecular markers with genomic selection accelerates breeding program by enabling early trait identification. Studies demonstrate that combining traditional breeding with genomics reduces the limitations of polyploidy and genetic bottlenecks, while enhancing yield stability under stress. Future directions include wider adaptability of genome-assisted breeding, functional genomics, and high-throughput phenotyping to strengthen cotton resilience against climate variability and biotic challenges. This review concludes that genomics-integrated breeding can deliver long-term improvements in fibre quality, productivity, and stress tolerance, thereby supporting sustainable cotton production.

References

Abdelraheem, A., Liu, F., Song, M., & Zhang, J. F. (2017). A meta-analysis of quantitative trait loci for abiotic and biotic stress resistance in tetraploid cotton. Molecular Genetics and Genomics, 292(6), 1221–1235. https://doi.org/10.1007/s00438-017-1342-0

Abdelraheem, A., Thyssen, G. N., Fang, D. D., Jenkins, J. N., McCarty, J. C., Wedegaertner, T., & Zhang, J. (2021). GWAS reveals consistent QTL for drought and salt tolerance in a MAGIC population of 550 lines derived from intermating of 11 Upland cotton (Gossypium hirsutum) parents. Molecular Genetics and Genomics, 296(1), 119–129. https://doi.org/10.1007/s00438-020-01733-2

Adeleke, A. A. (2024). Technological advancements in cotton agronomy: a review and prospects. Technology in Agronomy, 4(1), 0–0. https://doi.org/10.48130/tia-0024-0005

Agarwal, M., Shrivastava, N., & Padh, H. (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports, 27(4), 617–631. https://doi.org/10.1007/s00299-008-0507-z

Ahmed, M., Iqbal, A., Latif, A., Din, S. Ud, Sarwar, M. B., Wang, X., Rao, A. Q., Husnain, T., & Ali Shahid, A. (2020). Overexpression of a Sucrose Synthase Gene Indirectly Improves Cotton Fibre Quality Through Sucrose Cleavage. Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.476251

Aydoğdu, M. H., Doğan, H. P., & Küçük, N. (n.d.). Economic Analysis of Agricultural Water Usage Efficiency in the GAP-Harran Plain: Cotton Production Sampling, Sanliurfa-Turkey. www.kibanresearchpublications.com

Baghyalakshmi, K., Priyanka, R. A., Sarathapriya, G., Ramchander, S., & Prakash, A. H. (2024). Genetic improvement of fibre quality in tetraploid cotton: an overview of major QTLs and genes involved in and edited for the quality of cotton fibres. Journal of Cotton Research, 7(1), 33. https://doi.org/10.1186/s42397-024-00196-9

Bolouri, F., Kocoglu, Y., Pabuayon, I. L., Ritchie, G., & Sari-Sarraf, H. (2024). CottonSense: A high-throughput field phenotyping system for cotton fruit segmentation and enumeration on edge devices. Computers and Electronics in Agriculture, 216, 108531. https://doi.org/10.1016/j.compag.2023.108531

Chang, X., Guo, C., Pan, Z., Wu, Y., Shen, C., Chao, L., Shui, G., You, C., Xu, J., Lin, Z., & Nie, X. (2023). QTL Mapping for Fibre Quality Based on Introgression Lines Population from G. hirsutum × G. tomentosum. Agriculture (Switzerland), 13(3). https://doi.org/10.3390/agriculture13030579

Chen, X., Lu, X., Shu, N., Wang, S., Wang, J., Wang, D., Guo, L., & Ye, W. (2017). Targeted mutagenesis in cotton (Gossypium hirsutum L.) using the CRISPR/Cas9 system. Scientific Reports, 7(1), 44304. https://doi.org/10.1038/srep44304

Chen, Z. J., Scheffler, B. E., Dennis, E., Triplett, B. A., Zhang, T., Guo, W., Chen, X., Stelly, D. M., Rabinowicz, P. D., Town, C. D., Arioli, T., Brubaker, C., Cantrell, R. G., Lacape, J. M., Ulloa, M., Chee, P., Gingle, A. R., Haigler, C. H., Percy, R., … Paterson, A. H. (2007). Toward sequencing cotton (Gossypium) genomes. In Plant Physiology (Vol. 145, Issue 4, pp. 1303–1310). American Society of Plant Biologists. https://doi.org/10.1104/pp.107.107672

Chen, Z. J., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L. M., Hulse-Kemp, A. M., Ding, M., Ye, W., Kirkbride, R. C., Jenkins, J., Plott, C., Lovell, J., Lin, Y. M., Vaughn, R., Liu, B., Simpson, S., Scheffler, B. E., Wen, L., Saski, C. A., … Schmutz, J. (2020). Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nature Genetics, 52(5), 525–533. https://doi.org/10.1038/s41588-020-0614-5

Collard, B. C. Y., & Mackill, D. J. (2008a). Marker-assisted selection: An approach for precision plant breeding in the twenty-first century. In Philosophical Transactions of the Royal Society B: Biological Sciences (Vol. 363, Issue 1491, pp. 557–572). Royal Society. https://doi.org/10.1098/rstb.2007.2170

Collard, B. C. Y., & Mackill, D. J. (2008b). Marker-assisted selection: An approach for precision plant breeding in the twenty-first century. In Philosophical Transactions of the Royal Society B: Biological Sciences (Vol. 363, Issue 1491, pp. 557–572). Royal Society. https://doi.org/10.1098/rstb.2007.2170

Constable, Greg, Clement Koebernick, J., Llewelyn, Danny, & Walford, S. (2015). Cotton Breeding for Fibre Quality Improvement. In Industrial Crops: Breeding for Bioenergy and Bioproducts (pp. 191–232). https://doi.org/10.1007/978-1-4939-1447-0_10

Diouf, L., Pan, Z., He, S. P., Gong, W. F., Jia, Y. H., Magwanga, R. O., Romy, K. R. E., Rashid, H. O., Kirungu, J. N., & Du, X. (2017). High-density linkage map construction and mapping of salt-tolerant QTLs at the seedling stage in upland cotton using genotyping by sequencing (GBS). International Journal of Molecular Sciences, 18(12). https://doi.org/10.3390/ijms18122622

Du, X., Huang, G., He, S., Yang, Z., Sun, G., Ma, X., Li, N., Zhang, X., Sun, J., Liu, M., Jia, Y., Pan, Z., Gong, W., Liu, Z., Zhu, H., Ma, L., Liu, F., Yang, D., Wang, F., … Li, F. (2018). Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature Genetics, 50(6), 796–802. https://doi.org/10.1038/s41588-018-0116-x

Gao, W., Long, L., Tian, X., Xu, F., Liu, J., Singh, P. K., Botella, J. R., & Song, C. (2017a). Genome editing in cotton with the CRISPR/Cas9 system. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.01364

Gao, W., Long, L., Tian, X., Xu, F., Liu, J., Singh, P. K., Botella, J. R., & Song, C. (2017b). Genome editing in cotton with the CRISPR/Cas9 system. Frontiers in Plant Science, 8. https://doi.org/10.3389/fpls.2017.01364

He, D., Lin, Z.-X., Zhang, X., Nie, Y.-C., Guo, X.-P., Zhang, Y.-X., & Li, W. (2007). QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica, 153, 181–197. https://doi.org/10.1007/s10681-006-9254-9

He, D.-H., Lin, Z.-X., Zhang, X.-L., Nie, Y.-C., Guo, X.-P., Zhang, Y.-X., & Li, W. (2007). QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica, 153(1), 181–197. https://doi.org/10.1007/s10681-006-9254-9

HE, W., ZHAO, H., YANG, X., ZHANG, R., & WANG, J. (2019). Patent analysis provides insights into the history of cotton molecular breeding worldwide over the last 50 years. Journal of Integrative Agriculture, 18(3), 539–552. https://doi.org/https://doi.org/10.1016/S2095-3119(18)62012-X

Hu, Y., Chen, J., Fang, L., Zhang, Z., Ma, W., Niu, Y., Ju, L., Deng, J., Zhao, T., Lian, J., Baruch, K., Fang, D., Liu, X., Ruan, Y. ling, Rahman, M. ur, Han, J., Wang, K., Wang, Q., Wu, H., … Zhang, T. (2019). Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nature Genetics, 51(4), 739–748. https://doi.org/10.1038/s41588-019-0371-5

Huang, G., Wu, Z., Percy, R. G., Bai, M., Li, Y., Frelichowski, J. E., Hu, J., Wang, K., Yu, J. Z., & Zhu, Y. (2020). Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics, 52(5), 516–524. https://doi.org/10.1038/s41588-020-0607-4

Ijaz, B., Zhao, N., Kong, J., & Hua, J. (2019). Fibre Quality Improvement in Upland Cotton (Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker-Assisted Selection Application. In Frontiers in Plant Science (Vol. 10). Frontiers Media S.A. https://doi.org/10.3389/fpls.2019.01585

Iqbal, M. J., Reddy, O. U. K., El-Zik, K. M., & Pepper, A. E. (2001). A genetic bottleneck in the “evolution under domestication” of upland cotton Gossypium hirsutum L. was examined using DNA fingerprinting. Theoretical and Applied Genetics, 103(4), 547–554. https://doi.org/10.1007/PL00002908

Jans, Y., Von Bloh, W., Schaphoff, S., & Müller, C. (2021). Global cotton production under climate change – Implications for yield and water consumption. Hydrology and Earth System Sciences, 25, 2027–2044. https://doi.org/10.5194/hess-25-2027-2021

JIA, Y., SUN, J., WANG, X., ZHOU, Z., PAN, Z., HE, S., PANG, B., WANG, L., & DU, X. (2014). Molecular Diversity and Association Analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm. Journal of Integrative Agriculture, 13(9), 1845–1853. https://doi.org/https://doi.org/10.1016/S2095-3119(13)60668-1

Joshi, B., Singh, S., Tiwari, G. J., Kumar, H., Boopathi, N. M., Jaiswal, S., Adhikari, D., Kumar, D., Sawant, S. V., Iquebal, M. A., & Jena, S. N. (2023). Genome-wide association study of fibre yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.). Frontiers in Plant Science, 14. https://doi.org/10.3389/fpls.2023.1252746

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. https://doi.org/10.1007/s10681-010-0286-9

Kamburova, V., & Abdurakhmonov, I. (2018). Overview of the Biosafety and Risk Assessment Steps for Insect-Resistant Biotech Crops. https://doi.org/10.1201/9781315119571-9

Khan, Z., Khan, S. H., Ahmed, A., Iqbal, M. U., Mubarik, M. S., Ghouri, M. Z., Ahmad, F., Yaseen, S., Ali, Z., Khan, A. A., & Azhar, M. T. (2023). Genome editing in cotton: challenges and opportunities. In Journal of Cotton Research (Vol. 6, Issue 1). BioMed Central Ltd. https://doi.org/10.1186/s42397-023-00140-3

Kun, W., Shoupu, H., & Yuxian, Z. (2025). Cotton2035: From genomics research to optimized breeding. Molecular Plant, 18(2), 298–312. https://doi.org/https://doi.org/10.1016/j.molp.2025.01.010

Kushanov, F. N., Turaev, O. S., Ernazarova, D. K., Gapparov, B. M., Oripova, B. B., Kudratova, M. K., Rafieva, F. U., Khalikov, K. K., Erjigitov, D. S., Khidirov, M. T., Kholova, M. D., Khusenov, N. N., Amanboyeva, R. S., Saha, S., Yu, J. Z., & Abdurakhmonov, I. Y. (2021a). Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.). In Frontiers in Plant Science (Vol. 12). Frontiers Media S.A. https://doi.org/10.3389/fpls.2021.779386

Kushanov, F. N., Turaev, O. S., Ernazarova, D. K., Gapparov, B. M., Oripova, B. B., Kudratova, M. K., Rafieva, F. U., Khalikov, K. K., Erjigitov, D. S., Khidirov, M. T., Kholova, M. D., Khusenov, N. N., Amanboyeva, R. S., Saha, S., Yu, J. Z., & Abdurakhmonov, I. Y. (2021b). Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.). In Frontiers in Plant Science (Vol. 12). Frontiers Media S.A. https://doi.org/10.3389/fpls.2021.779386

Kushanov, F. N., Turaev, O. S., Ernazarova, D. K., Gapparov, B. M., Oripova, B. B., Kudratova, M. K., Rafieva, F. U., Khalikov, K. K., Erjigitov, D. S., Khidirov, M. T., Kholova, M. D., Khusenov, N. N., Amanboyeva, R. S., Saha, S., Yu, J. Z., & Abdurakhmonov, I. Y. (2021c). Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.). In Frontiers in Plant Science (Vol. 12). Frontiers Media S.A. https://doi.org/10.3389/fpls.2021.779386

Kushanov, F. N., Turaev, O. S., Ernazarova, D. K., Gapparov, B. M., Oripova, B. B., Kudratova, M. K., Rafieva, F. U., Khalikov, K. K., Erjigitov, D. S., Khidirov, M. T., Kholova, M. D., Khusenov, N. N., Amanboyeva, R. S., Saha, S., Yu, J. Z., & Abdurakhmonov, I. Y. (2021d). Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.). In Frontiers in Plant Science (Vol. 12). Frontiers Media S.A. https://doi.org/10.3389/fpls.2021.779386

Li, C., Unver, T., & Zhang, B. (2017). A high-efficiency CRISPR/Cas9 system for targeted mutagenesis in Cotton (Gossypium hirsutum L.). Scientific Reports, 7(1), 43902. https://doi.org/10.1038/srep43902

Li, F., Fan, G., Lu, C., Xiao, G., Zou, C., Kohel, R. J., Ma, Z., Shang, H., Ma, X., Wu, J., Liang, X., Huang, G., Percy, R. G., Liu, K., Yang, W., Chen, W., Du, X., Shi, C., Yuan, Y., … Yu, S. (2015). Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nature Biotechnology, 33(5), 524–530. https://doi.org/10.1038/nbt.3208

Liu, K., & Muse, S. V. (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 21(9), 2128–2129. https://doi.org/10.1093/bioinformatics/bti282

Lübberstedt, T., Beavis, W., & Suza, W. (n.d.). Chapter 7: Marker-Assisted Selection and Genomic Selection. https://iastate.pressbooks.pub/molecularplantbreeding/chapter/marker-assisted-selection-and-genomic-selection/

MA, L., SU, Y., NIE, H., CUI, Y., CHENG, C., IJAZ, B., & HUA, J. (2020). QTL and genetic analysis controlling fibre quality traits using paternal backcross population in upland cotton. Journal of Cotton Research, 3(1), 22. https://doi.org/10.1186/s42397-020-00060-6

Ma, X., Zhang, Q., Zhu, Q., Liu, W., Chen, Y., Qiu, R., Wang, B., Yang, Z., Li, H., Lin, Y., Xie, Y., Shen, R., Chen, S., Wang, Z., Chen, Y., Guo, J., Chen, L., Zhao, X., Dong, Z., & Liu, Y.-G. (2015). A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants. Molecular Plant, 8(8), 1274–1284. https://doi.org/10.1016/j.molp.2015.04.007

Ma, X., Zhu, Q., Chen, Y., & Liu, Y.-G. (2016). CRISPR/Cas9 Platforms for Genome Editing in Plants: Developments and Applications. Molecular Plant, 9(7), 961–974. https://doi.org/10.1016/j.molp.2016.04.009

MA, Z. (2020). Unravelling the puzzle of the origin and evolution of cotton A-genome. Journal of Cotton Research, 3(1), 17. https://doi.org/10.1186/s42397-020-00056-2

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 prospects. In Scientific World Journal (Vol. 2014). Hindawi Publishing Corporation. https://doi.org/10.1155/2014/607091

Maqbool, A., Abbas, W., Rao, A. Q., Irfan, M., Zahur, M., Bakhsh, A., Riazuddin, S., & Husnain, T. (2010). Gossypium arboreum GHSP26 enhances drought tolerance in Gossypium hirsutum. Biotechnology Progress, 26(1), 21–25. https://doi.org/10.1002/btpr.306

Mei, M., Syed, N. H., Gao, W., Thaxton, P. M., Smith, C. W., Stelly, D. M., & Chen, Z. J. (2004a). Genetic mapping and QTL analysis of fibre-related traits in cotton (Gossypium). Theoretical and Applied Genetics, 108(2), 280–291. https://doi.org/10.1007/s00122-003-1433-7

Mei, M., Syed, N. H., Gao, W., Thaxton, P. M., Smith, C. W., Stelly, D. M., & Chen, Z. J. (2004b). Genetic mapping and QTL analysis of fibre-related traits in cotton (Gossypium). Theoretical and Applied Genetics, 108(2), 280–291. https://doi.org/10.1007/s00122-003-1433-7

Mollaee, M., Mobli, A., Mutti, N. K., Manalil, S., & Chauhan, B. S. (2019). Challenges and Opportunities in Cotton Production. In Cotton Production (pp. 371–390). Wiley. https://doi.org/10.1002/9781119385523.ch18

Morales-Aranibar, L., Rivera, M. Y. N., Gonzales, H. H. S., Aranibar, C. G. M., Gutiérrez, N. L., Gomez, F. G., Zuffo, A. M., Aguilera, J. G., & Steiner, F. (2024). Comparative analysis of key fibre characteristics in white Pima cotton (Gossypium barbadense L.): Native accessions from the Peruvian Amazon. Agrosystems, Geosciences and Environment, 7(2). https://doi.org/10.1002/agg2.20517

Nabi, G., Shokat, S., Azhar, M. T., & Azhar, F. M. (2015). GENETIC BASIS OF ION UPTAKE AND PROLINE ACCUMULATION IN GOSSYPIUM HIRSUTUM L. of relative frequency of dominance and recessive alleles in the parents; (H 1 /D) 0.5-average degree of dominance; H 1 and H 2-dominance effects of genes; H 2 /4H 1-proportion of gene with positive and negative effects in the parents; h2-overall dominance effect; h 2-heritability in narrow sense; NaCl-sodium chloride; K-Potassium; TSS-total soluble salts.842 Agricultural Academy. In Bulgarian Journal of Agricultural Science (Vol. 21, Issue 4).

Pabuayon, I. L. B., Sun, Y., Guo, W., & Ritchie, G. L. (2019). High-throughput phenotyping in cotton: a review. In Journal of Cotton Research (Vol. 2, Issue 1). BioMed Central Ltd. https://doi.org/10.1186/s42397-019-0035-0

Pan, Y., Jiang, F., Shaw, R. K., Sun, J., Li, L., Yin, X., Bi, Y., Kong, J., Zong, H., Gong, X., Ijaz, B., & Fan, X. (2024). QTL mapping and genome-wide association analysis reveal genetic loci and candidate genes for resistance to gray leaf spot in tropical and subtropical maize germplasm. Theoretical and Applied Genetics, 137(12). https://doi.org/10.1007/s00122-024-04764-0

Paterson, A. H., Wendel, J. F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K. C., Shu, S., Udall, J., Yoo, M. J., Byers, R., Chen, W., Doron-Faigenboim, A., Duke, M. V., Gong, L., Grimwood, J., Grover, C., Grupp, K., … Schmutz, J. (2012). Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 492(7429), 423–427. https://doi.org/10.1038/nature11798

Razzaq, A., Zafar, M. M., Ali, A., Hafeez, A., Sharif, F., Guan, X., Deng, X., Pengtao, L., Shi, Y., Haroon, M., Gong, W., Ren, M., & Yuan, Y. (2022). The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fibre Quality Traits of Cotton. In Frontiers in Genetics (Vol. 12). Frontiers Media S.A. https://doi.org/10.3389/fgene.2021.642595

Rodgers, J., Zumba, J., & Fortier, C. (2017). Measurement comparison of cotton fibre micronaire and its components by portable near infrared spectroscopy instruments. Textile Research Journal, 87(1), 57–69. https://doi.org/10.1177/0040517515622153

Saski, C. A., Scheffler, B. E., Hulse-Kemp, A. M., Liu, B., Song, Q., Ando, A., Stelly, D. M., Scheffler, J. A., Grimwood, J., Jones, D. C., Peterson, D. G., Schmutz, J., & Chen, Z. J. (2017). Sub-genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-14885-w

Saud, S., & Wang, L. (2022). Mechanism of cotton resistance to abiotic stress, and recent research advances in the osmoregulation-related genes. In Frontiers in Plant Science (Vol. 13). Frontiers Media S.A. https://doi.org/10.3389/fpls.2022.972635

Schoonmaker, A. N., Hulse-Kemp, A. M., Youngblood, R. C., Rahmat, Z., Atif Iqbal, M., Rahman, M. U., Kochan, K. J., Scheffler, B. E., & Scheffler, J. A. (2023). Detecting Cotton Leaf Curl Virus Resistance Quantitative Trait Loci in Gossypium hirsutum and iCottonQTL: a New R/Shiny App to Streamline Genetic Mapping. Plants, 12(5). https://doi.org/10.3390/plants12051153

Shahzad, K., Mubeen, I., Zhang, M., Zhang, X., Wu, J., & Xing, C. (2022). Progress and perspective on cotton breeding in Pakistan. Journal of Cotton Research, 5(1), 29. https://doi.org/10.1186/s42397-022-00137-4

Shukla, R. P., Tiwari, G. J., Joshi, B., Song-Beng, K., Tamta, S., Boopathi, N. M., & Jena, S. N. (2021). GBS-SNP and SSR-based genetic mapping and QTL analysis for drought tolerance in upland cotton. Physiology and Molecular Biology of Plants, 27(8), 1731–1745. https://doi.org/10.1007/s12298-021-01041-y

Sun, H., Meng, M., Yan, Z., Lin, Z., Nie, X., & Yang, X. (2019). Genome-wide association mapping of stress-tolerance traits in cotton. The Crop Journal, 7(1), 77–88. https://doi.org/https://doi.org/10.1016/j.cj.2018.11.002

Sun, S., Li, C., Paterson, A. H., Jiang, Y., Xu, R., Robertson, J. S., Snider, J. L., & Chee, P. W. (2018). In-field high-throughput phenotyping and cotton plant growth analysis using LiDAR. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.00016

Syed, M. M. , & Gao, N. (2010). Publication Overview Title: Genetic mapping and QTL analysis of fibre-related traits in cotton (Gossypium). https://www.cottongen.org/pub/10143

Tan, Z., Fang, X., Tang, S., Zhang, J., Liu, D., Teng, Z., Li, L., Ni, H., Zheng, F., Liu, D., Zhang, T., Paterson, A. H., & Zhang, Z. (2015). Genetic map and QTL controlling fibre quality traits in upland cotton (Gossypium hirsutum L.). Euphytica, 203(3), 615–628. https://doi.org/10.1007/s10681-014-1288-9

Tan, Z., Zhang, Z., Sun, X., Li, Q., Sun, Y., Yang, P., Wang, W., Liu, X., Chen, C., Liu, D., Teng, Z., Guo, K., Zhang, J., Liu, D., & Zhang, Z. (2018). Genetic map construction and fibre quality QTL mapping using the cottonSNP80K array in upland cotton. Frontiers in Plant Science, 9. https://doi.org/10.3389/fpls.2018.00225

Thangaraj, A., Kaul, R., Sharda, S., & Kaul, T. (2025). Revolutionizing cotton cultivation: A comprehensive review of genome editing technologies and their impact on breeding and production. Biochemical and Biophysical Research Communications, 742, 151084. https://doi.org/https://doi.org/10.1016/j.bbrc.2024.151084

Udall, J. A., Long, E., Hanson, C., Yuan, D., Ramaraj, T., Conover, J. L., Gong, L., Arick, M. A., Grover, C. E., Peterson, D. G., & Wendel, J. F. (2019). De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri. G3: Genes, Genomes, Genetics, 9(10), 3079–3085. https://doi.org/10.1534/g3.119.400392

Walford, S. A., Wu, Y., Llewellyn, D. J., & Dennis, E. S. (2011). GhMYB25-like: A key factor in early cotton fibre development. Plant Journal, 65(5), 785–797. https://doi.org/10.1111/j.1365-313X.2010.04464.x

Wang, C., Ulloa, M., Duong, T., & Roberts, P. A. (2018a). Quantitative trait loci mapping of multiple independent loci for resistance to Fusarium oxysporum f. sp. vasinfectum Races 1 and 4 in an interspecific cotton population. Phytopathology, 108(6), 759–767. https://doi.org/10.1094/PHYTO-06-17-0208-R

Wang, C., Ulloa, M., Duong, T., & Roberts, P. A. (2018b). Quantitative trait loci mapping of multiple independent loci for resistance to Fusarium oxysporum f. sp. vasinfectum Races 1 and 4 in an interspecific cotton population. Phytopathology, 108(6), 759–767. https://doi.org/10.1094/PHYTO-06-17-0208-R

Wang, J., Yuan, J., Yu, J., Meng, F., Sun, P., Li, Y., Yang, N., Wang, Z., Pan, Y., Ge, W., Wang, L., Li, J., Liu, C., Zhao, Y., Luo, S., Ge, D., Cui, X., Feng, G., Wang, Z., … Xi, Z. (2019). Recursive paleohexaploidization shaped the durian genome. Plant Physiology, 179(1), 209–219. https://doi.org/10.1104/pp.18.00921

Wang, M., Tu, L., Yuan, D., Zhu, D., Shen, C., Li, J., Liu, F., Pei, L., Wang, P., Zhao, G., Ye, Z., Huang, H., Yan, F., Ma, Y., Zhang, L., Liu, M., You, J., Yang, Y., Liu, Z., … Zhang, X. (2019). Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature Genetics, 51(2), 224–229. https://doi.org/10.1038/s41588-018-0282-x

Wang, P., Abbas, M., He, J., Zhou, L., Cheng, H., & Guo, H. (2024). Advances in genome sequencing and artificially induced mutation provide new avenues for cotton breeding. In Frontiers in Plant Science (Vol. 15). Frontiers Media SA. https://doi.org/10.3389/fpls.2024.1400201

Wang, X.-Y., Li, C.-Q., Xia, Z., Dong, N., & Wang, Q.-L. (2012). [QTL mapping for “pre-summer boll, summer boll and autumn boll” traits in cotton]. Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji, 34, 757–764. https://doi.org/10.3724/SP.J.1005.2012.00757

Wendel, J. F., Brubaker, C. L., & Seelanan, T. (2010). The Origin and Evolution of Gossypium. In J. McD. Stewart, D. M., Oosterhuis, J. J., Heitholt, & J. R. Mauney (Eds.), Physiology of Cotton (pp. 1–18). Springer Netherlands. https://doi.org/10.1007/978-90-481-3195-2_1

Wendel, J. F., & Cronn, R. C. (2003). POLYPLOIDY AND THE EVOLUTIONARY HISTORY OF COTTON.

Yang, X., Wang, Y., Zhang, G., Wang, X., Wu, L., Ke, H., Liu, H., & Ma, Z. (2016). Detection and validation of one stable fibre strength QTL on c9 in tetraploid cotton. Molecular Genetics and Genomics, 291(4), 1625–1638. https://doi.org/10.1007/s00438-016-1206-z

Yang, Z., Qanmber, G., Wang, Z., Yang, Z., & Li, F. (2020). Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement. Trends in Plant Science, 25(5), 488–500. https://doi.org/10.1016/j.tplants.2019.12.011

Zhai, D. (2023). Application of Various Genomic Selection Models in Cotton Fibre Quality. https://doi.org/10.20944/preprints202311.0677.v1

Zhang, H. Bin, Li, Y., Wang, B., & Chee, P. W. (2008a). Recent advances in cotton genomics. In International Journal of Plant Genomics (Vol. 2008). https://doi.org/10.1155/2008/742304

Zhang, H. Bin, Li, Y., Wang, B., & Chee, P. W. (2008b). Recent advances in cotton genomics. In International Journal of Plant Genomics (Vol. 2008). https://doi.org/10.1155/2008/742304

Zhang, J., Fang, H., Zhou, H., Sanogo, S., & Ma, Z. (2014). Genetics, Breeding, and Marker-Assisted Selection for Verticillium Wilt Resistance in Cotton. Crop Science, 54, 1289–1303. https://doi.org/10.2135/cropsci2013.08.0550

Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C. A., Scheffler, B. E., Stelly, D. M., Hulse-Kemp, A. M., Wan, Q., Liu, B., Liu, C., Wang, S., Pan, M., Wang, Y., Wang, D., Ye, W., … Chen, Z. J. (2015). Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fibre improvement. Nature Biotechnology, 33(5), 531–537. https://doi.org/10.1038/nbt.3207

Zhang, Y.-M., & Gai, J. (2009). Methodologies for segregation analysis and QTL mapping in plants. Genetica, 136(2), 311–318. https://doi.org/10.1007/s10709-008-9313-3

Zhang, Z.-S., Hu, M.-C., Zhang, J., Liu, D.-J., Zheng, J., Zhang, K., Wang, W., & Wan, Q. (2009). Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fibre quality traits in upland cotton (Gossypium hirsutum L.). Molecular Breeding, 24(1), 49–61. https://doi.org/10.1007/s11032-009-9271-1

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