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Analysis of Flavonoids Structural Genes in Between Chalaza and Microphyll a Mutant Natural Green Cotton Fiber

Year 2025, Volume: 28 Issue: 1, 191 - 204, 12.02.2025

Öner Canavar , Hatice Kübra Gören

https://doi.org/10.18016/ksutarimdoga.vi.1575961

Abstract

Undesirable coloring pigments in naturally colored fibers can affect their aesthetic and commercial value in the textile industry. In our green cotton breeding program, we identified a gene mutation that causes different colored fibers to form on a single seed. We investigated the expression patterns of flavonoid biosynthesis structural genes to understand the formation of these different colors between the chalazal and microphyll parts of the seed. Significant variations in gene expression levels were observed among the examined flavonoid genes, highlighting the complexity of flavonoid biosynthesis pathways in cotton seeds. In the green fibers on the microphyll part, lower expression levels of enzymes such as 4Cl (4-coumarate: CoA ligase), C4h (cinnamate 4-hydroxylase), F3h (flavone 3-hydroxylase), F3′5′h (flavonoid 3′5′-hydroxylase), Ans (anthocyanidin synthase), Anr (anthocyanidin reductase), and Ufgt (UDP-glucose: flavonoid 3-O-glucosyltransferase) were identified as potential factors influencing fiber coloration. Conversely, in the white fibers on the chalazal part, the expression levels of Chs (chalcone synthase) and Chı (chalcone isomerase) genes were lower than those in the microphyll part. This low expression is thought to be due to a mutation at the beginning of the phenylalanine pathway, preventing the formation of a green color in the white fibers on the chalazal part together with the low synthesis of the Chı gene. Understanding the molecular mechanisms behind these mutations is crucial for developing strategies to mitigate their effects and sustain the textile industry. The findings can inform cotton breeding programs to address unwanted coloration issues through genetic interventions, potentially enhancing the aesthetic and commercial value of naturally colored cotton fibers.

Keywords

Natural colored cotton (Gossypium hirsutum L.) Mutation Flavonoid Pigmentation

References

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  • Lv, L. M., Zuo, D. Y., Wang, X. F., Cheng, H. L., Zhang, Y. P., Wang, Q. L., Ma, Z. Y. (2020). Genome-wide identification of the expansin gene family reveals that expansin genes are involved in fibre cell growth in cotton. BMC plant biology, 20, 1-13.
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  • Mercier, R., Mézard, C., Jenczewski, E., Macaisne, N., & Grelon, M. (2015). The molecular biology of meiosis in plants. Annual Review of Plant Biology, 66(1), 297-327. https://doi.org/10.1146/annurev-arplant-050213-035923
  • Moire, L., Schmutz, A., Buchala, A., Yan, B., Stark, R. E., & Ryser, U. (1999). Glycerol is a suberin monomer. New experimental evidence for an old hypothesis. Plant Physiology, 119(3), 1137-1146.
  • Ookawa, T., Hobo, T., Yano, M., Murata, K., Ando, T., Miura, H., & Matsuoka, M. (2010). New approach for rice improvement using a pleiotropic qtl gene for lodging resistance and yield. Nature Communications, 1(1),132. https://doi.org/10.1038/ncomms1132.
  • Peng, Z., Gao, Q., Luo, C., Gong, W., Tang, S., Zhang, X., & Liu, H. (2020). Flavonoid biosynthetic and starch and sucrose metabolic pathways are involved in the pigmentation of naturally brown-colored cotton fibers. Industrial Crops and Products, 158, 113045.
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  • Schmutz A, Jenny T, Amrhein N, Ryser U. (1993). Caffeic acid and glycerol are constituents of the suberin layers in green cotton fibres. Planta, 189(1), 453–460.
  • Schmutz, A., Buchala, A. J., & Ryser, U. (1996). Changing the dimensions of suberin lamellae of green cotton fibers with a specific inhibitor of the endoplasmic reticulum-associated fatty acid elongases. Plant Physiology, 110(2), 403-411.
  • Song, Q., Gao, W., Du, C., Sun, W., Wang, J., & Zuo, K. (2023). Ghxb38d represses cotton fibre elongation through ubiquitination of ethylene biosynthesis enzymes ghacs4 and ghaco1. Plant Biotechnology Journal, 21(11), 2374-2388. https://doi.org/10.1111/pbi.14138.
  • Sun, S., Xiong, X. P., Zhu, Q., Li, Y. J., & Sun, J. (2019). Transcriptome sequencing and metabolome analysis reveal genes involved in pigmentation of green-colored cotton fibers. International Journal of Molecular Sciences, 20(19), 4838.
  • Sun, S., Xiong, X. P., Zhu, Q., Li, Y. J., & Sun, J. (2019). Transcriptome sequencing and metabolome analysis reveal genes involved in pigmentation of green-colored cotton fibers. International Journal of Molecular Sciences, 20 (19), 4838.
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Mutant Doğal Yeşil Pamuk Lifinde Chalaza ve Microphyll Arasındaki Flavonoid Yapısal Genlerı̇n Analizi

Year 2025, Volume: 28 Issue: 1, 191 - 204, 12.02.2025

Öner Canavar , Hatice Kübra Gören

https://doi.org/10.18016/ksutarimdoga.vi.1575961

Abstract

Doğal renkli liflerdeki istenmeyen farklı renk pigmentleri, tekstil endüstrisindeki estetik ve ticari değerlerini etkileyebilir. Yeşil pamuk ıslah programımızda, tek bir tohumunda farklı renkli liflerin oluşmasına neden olan bir gen mutasyonu tespit ettik. Tohumun şalazal ve mikrofil kısımları arasındaki bu farklı renklerin oluşumunu anlamak için flavonoid biyosentez yapısal genlerinin ifade modellerini araştırdık. İncelenen flavonoid genleri arasında gen ekspresyon seviyelerinde önemli farklılıklar gözlenmiş, bu da pamuk tohumlarındaki flavonoid biyosentez yollarının karmaşıklığını vurgulamıştır. Mikrofil kısmındaki yeşil liflerde, 4Cl (4-coumarate: CoA ligaz), C4h (sinamat 4-hidroksilaz), F3h (flavon 3-hidroksilaz), F3′5′h (flavonoid 3′5′-hidroksilaz), Ans (antosiyanidin sentaz), Anr (antosiyanidin redüktaz) ve Ufgt (UDP-glukoz: flavonoid 3-O-glukosiltransferaz) lif renklenmesini etkileyen potansiyel faktörler olarak tanımlanmıştır. Buna karşılık, şalazal kısımdaki beyaz liflerde, Chs (chalcone synthase) ve Chı (chalcone isomerase) genlerinin ifade seviyeleri mikrofil kısımdakilerden daha düşüktü. Bu düşük ifadenin, şalazal kısımdaki beyaz liflerde yeşil renk oluşumunu engelleyen fenilalanin yolunun başlangıcındaki bir mutasyondan kaynaklandığı düşünülmektedir. Bu mutasyonların arkasındaki moleküler mekanizmaları anlamak, etkilerini azaltmak ve tekstil endüstrisini sürdürmek için stratejiler geliştirmek açısından çok önemlidir. Bulgular, genetik müdahaleler yoluyla istenmeyen renklenme sorunlarını ele almak için pamuk ıslah programlarını bilgilendirebilir ve potansiyel olarak doğal renkli pamuk liflerinin estetik ve ticari değerini artırabilir.

Keywords

Doğal renkli pamuk (Gossypium hirsutum L.) Mutasyon Flavonoid Pigmentasyon

References

  • Balasubramanian, V. K., Rai, K. M., Thu, S. W., Hii, M. M., & Mendu, V. (2016). Genome-wide identification of Balasubramanian fiber development. Scientific Reports, 6(1), 34309. https://doi.org/10.1038/srep34309. Boerma, H. R. and Walker, D. (2005). Discovery and utilization of QTLs for insect resistance in soybean. Genetica, 123(1-2), 181-189. https://doi.org/10.1007/s10709-004-2741-9
  • Canavar, Ö., & Rausher, M. D. (2021). Differences of flavonoid structural genes preferentially expressed in brown and green natural colored cotton. Turkish Journal of Agriculture and Forestry, 45(3), 266-272.
  • Canavar, Ö., & Rausher, M. D. (2021). Molecular analysis of structural genes involved in flavonoids biosynthesis in naturally colored cotton. Crop Science, 61(2), 1117-1126.
  • Didelot, X., Lawson, D. J., Darling, A. E., & Falush, D. (2010). Inference of homologous recombination in bacteria using whole-genome sequences. Genetics, 186(4), 1435-1449. https://doi.org/10.1534/genetics.110.120121
  • Feng, H., Guo, L., Wang, G., Sun, J., Pan, Z., He, S., & Du, X. (2015). The negative correlation between fiber color and quality traits revealed by QTL analysis. Plos One, 10(6), e0129490.
  • Feng, H., Tian, X., Liu, Y., Li, Y., Zhang, X., Jones, B. J., & Sun, J. (2013). Analysis of flavonoids and the flavonoid structural genes in brown fiber of upland cotton. Plos One, 8(3), e58820.
  • Fernandes, J. B., Séguéla-Arnaud, M., Larchevêque, C., Lloyd, A. B., & Mercier, R. (2017). Unleashing meiotic crossovers in hybrid plants. Proceedings of the National Academy of Sciences, 115(10), 2431-2436. https://doi.org/10.1073/pnas.1713078114
  • Gao, J., Shi, Y., Wang, W., Wang, Y. H., Yang, H., Shi, Q. H., & Cai, L. W. (2021). Genome sequencing identified novel mechanisms underlying virescent mutation in upland cotton Gossypium hirsutum L. BMC genomics, 22(1), 498-524.
  • Gao, W., Long, L., Tian, X., Xu, F., Liu, J., Singh, P. K., & Song, C. (2017). Genome editing in cotton with the CRISPR/Cas9 system. Frontiers in plant science, 8, 290219.
  • Gilbert, M. K., Turley, R. B., Kim, H. J., Li, P., Thyssen, G. N., Tang, Y., & Fang, D. D. (2013). Transcript profiling by microarray and marker analysis of the short cotton (Gossypium hirsutum L.) fiber mutant ligon lintless-1 (li1 ). BMC Genomics, 14(1): 1-18.. https://doi.org/10.1186/1471-2164-14-403.
  • Gong, W., He, S., Tian, J., Sun, J., Pan, Z., Jia, Y., & Du, X. (2014). Comparison of the transcriptome between two cotton lines of different fiber color and quality. PLoS ONE, 9(11), e112966. https://doi.org/10.1371/journal.pone.0112966.
  • Graça, J. (2015). Suberin: the biopolyester at the frontier of plants. Frontiers in Chemistry, 3: 62 -78. https://doi.org/10.3389/fchem.2015.00062.
  • Gürel, A., Akdemir, H., & Karadayı, HB. (2001). Doğal Renkli Elyaflı Pamukların Ege Bölgesi Koşullarında Üretilme Olanakları. Anadolu Ege Tarımsal Araştırma Enstitüsü Dergisi, 11(1):56-70.
  • Jia, C., Guo, B., Wang, B., Li, X., Yang, T., Li, N., & Yu, Q. (2022). Integrated metabolomic and transcriptomic analysis reveals the role of phenylpropanoid biosynthesis pathway in tomato roots during salt stress. Frontiers in Plant Science, 13, 1023696.
  • Khatodia, S., Bhatotia, K., Passricha, N., Khurana, S. M. P., & Tuteja, N. (2016). The crispr/cas genome-editing tool: application in improvement of crops. Frontiers in Plant Science, 7, 506. https://doi.org/10.3389/fpls.2016.00506.
  • Kim, H. J., & Triplett, B. A. (2001). Cotton fiber growth in planta and in vitro: Models for plant cell elongation and cell wall biogenesis. Plant Physiology, 127, 1361–1366. https://doi.org/10.1104/pp.010724.
  • Lacape, J., Claverie, M., Vidal, R., Carazzolle, M. F., Pereira, G. A. G., Ruiz, M., & Lanaud, C. (2012). Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PLoS ONE, 7(11), e48855. https://doi.org/10.1371/journal.pone.0048855.
  • Li, X., Fridman, E., Tesso, T., & Yu, J. (2015). Dissecting repulsion linkage in the dwarfing gene dw3 region for sorghum plant height provides insights into heterosis. Proceedings of the National Academy of Sciences, 112(38), 11823-11828. https://doi.org/10.1073/pnas.1509229112
  • Li, Z., Su, Q., Xu, M., You, J., Khan, A. Q., Li, J., & You, C. (2020). Phenylpropanoid metabolism and pigmentation show divergent patterns between brown color and green color cottons as revealed by metabolic and gene expression analyses. Journal of Cotton Research, 3, 1-11.
  • Liu, H. F., Luo, C., Song, W., Shen, H., Li, G., He, Z. G., & Liu, H. (2018). Flavonoid biosynthesis controls fiber color in naturally colored cotton. Peerj, 6, e4537.
  • Lv, L. M., Zuo, D. Y., Wang, X. F., Cheng, H. L., Zhang, Y. P., Wang, Q. L., Ma, Z. Y. (2020). Genome-wide identification of the expansin gene family reveals that expansin genes are involved in fibre cell growth in cotton. BMC plant biology, 20, 1-13.
  • Lv, Y. P., Zhao, G., Xie, Y. F., Owusu, A. G., Wu, Y., & Gao, J. S. (2023). Transcriptome and metabolome profiling unveil pigment formation variations in brown cotton lines (Gossypium hirsutum L.). International Journal of Molecular Sciences, 24(6), 5249.
  • Mackay, I., Cockram, J., Howell, P., & Powell, W. (2020). Understanding the classics: the unifying concepts of transgressive segregation, inbreeding depression and heterosis and their central relevance for crop breeding. Plant Biotechnology Journal, 19(1), 26-34. https://doi.org/10.1111/pbi.13481.
  • Majeed, S., Rana, I. A., Mubarik, M. S., Atif, R. M., Yang, S. H., Chung, G., ... & Azhar, M. T. (2021). Heat stress in cotton: a review on predicted and unpredicted growth-yield anomalies and mitigating breeding strategies. Agronomy, 11(9), 1825.
  • Mercier, R., Mézard, C., Jenczewski, E., Macaisne, N., & Grelon, M. (2015). The molecular biology of meiosis in plants. Annual Review of Plant Biology, 66(1), 297-327. https://doi.org/10.1146/annurev-arplant-050213-035923
  • Moire, L., Schmutz, A., Buchala, A., Yan, B., Stark, R. E., & Ryser, U. (1999). Glycerol is a suberin monomer. New experimental evidence for an old hypothesis. Plant Physiology, 119(3), 1137-1146.
  • Ookawa, T., Hobo, T., Yano, M., Murata, K., Ando, T., Miura, H., & Matsuoka, M. (2010). New approach for rice improvement using a pleiotropic qtl gene for lodging resistance and yield. Nature Communications, 1(1),132. https://doi.org/10.1038/ncomms1132.
  • Peng, Z., Gao, Q., Luo, C., Gong, W., Tang, S., Zhang, X., & Liu, H. (2020). Flavonoid biosynthetic and starch and sucrose metabolic pathways are involved in the pigmentation of naturally brown-colored cotton fibers. Industrial Crops and Products, 158, 113045.
  • Rehman, A., Almas, H. I., Qayyum, A., Li, H., Peng, Z., Qin, G., & Du, X. (2023). Mutation Breeding in Cotton. In Biotechnologies and Genetics in Plant Mutation Breeding (pp. 23-51). Apple Academic Press.
  • Schmutz A, Jenny T, Amrhein N, Ryser U. (1993). Caffeic acid and glycerol are constituents of the suberin layers in green cotton fibres. Planta, 189(1), 453–460.
  • Schmutz, A., Buchala, A. J., & Ryser, U. (1996). Changing the dimensions of suberin lamellae of green cotton fibers with a specific inhibitor of the endoplasmic reticulum-associated fatty acid elongases. Plant Physiology, 110(2), 403-411.
  • Song, Q., Gao, W., Du, C., Sun, W., Wang, J., & Zuo, K. (2023). Ghxb38d represses cotton fibre elongation through ubiquitination of ethylene biosynthesis enzymes ghacs4 and ghaco1. Plant Biotechnology Journal, 21(11), 2374-2388. https://doi.org/10.1111/pbi.14138.
  • Sun, S., Xiong, X. P., Zhu, Q., Li, Y. J., & Sun, J. (2019). Transcriptome sequencing and metabolome analysis reveal genes involved in pigmentation of green-colored cotton fibers. International Journal of Molecular Sciences, 20(19), 4838.
  • Sun, S., Xiong, X. P., Zhu, Q., Li, Y. J., & Sun, J. (2019). Transcriptome sequencing and metabolome analysis reveal genes involved in pigmentation of green-colored cotton fibers. International Journal of Molecular Sciences, 20 (19), 4838.
  • Tan J, Tu L, Deng F, Hu H, Nie Y et al. (2013). A genetic and metabolic analysis revealed that cotton fiber cell development was retarded by flavonoid naringenin1[W][OA]. Plant Physiology 162: 86-95. Doi: 10.1104/pp.112.212142.
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There are 49 citations in total.

Details

Primary Language English
Subjects Industrial Crops
Journal Section RESEARCH ARTICLE
Authors

Öner Canavar 0000-0003-4168-953X

Hatice Kübra Gören 0000-0001-7654-1450

Early Pub Date January 31, 2025
Publication Date February 12, 2025
Submission Date October 30, 2024
Acceptance Date December 30, 2024
Published in Issue Year 2025 Volume: 28 Issue: 1

Cite

APA Canavar, Ö., & Gören, H. K. (2025). Analysis of Flavonoids Structural Genes in Between Chalaza and Microphyll a Mutant Natural Green Cotton Fiber. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 28(1), 191-204. https://doi.org/10.18016/ksutarimdoga.vi.1575961
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