Linkage Disequilibrium in Plant U-box Gene in Sugarcane (Saccharum spp.)
Article Sidebar
Main Article Content
Abstract
Understanding linkage disequilibrium (LD) is important for planning breeding strategies to target beneficial alleles for agronomic traits. In the present study, we analyzed the LD pattern of U-box domain-containing protein35 gene (SaPUB35) in 68 exotic sugarcane collections and 73 sugarcane breeding lines. PacBio single molecule, real-time (SMRT) sequencing was performed to identify 126 single nucleotide polymorphisms (SNPs) and 50 Insertion/deletions (InDels) in 5731 bp of SaPUB35. The exotic sugarcane population has more variants than the breeding line population. Pairwise LD analysis revealed that mean LD, at a threshold of squared allele frequency correlations (r2 ) = 0.1, extends to at least 1500 bp in the breeding line population but is eroded to 1400 bp in exotic sugarcane population. This implies a signature of a selective sweep for a beneficial mutation during the selection processes of sugarcane breeding. Uncovering allelic erosion and a diversity bottleneck due to modern sugarcane breeding will be useful for understanding sugarcane breeding targets and in devising future breeding strategies to target beneficial alleles currently not pursued.
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
บทความที่ได้รับการตีพิมพ์เป็นลิขสิทธิ์ของคณะวิทยาศาสตร์และเทคโนโลยี มหาวิทยาลัยธรรมศาสตร์ ข้อความที่ปรากฏในแต่ละเรื่องของวารสารเล่มนี้เป็นเพียงความเห็นส่วนตัวของผู้เขียน ไม่มีความเกี่ยวข้องกับคณะวิทยาศาสตร์และเทคโนโลยี หรือคณาจารย์ท่านอื่นในมหาวิทยาลัยธรรมศาสตร์ ผู้เขียนต้องยืนยันว่าความรับผิดชอบต่อทุกข้อความที่นำเสนอไว้ในบทความของตน หากมีข้อผิดพลาดหรือความไม่ถูกต้องใด ๆ
References
Abdel-Ghany, S.E., Hamilton, M., Jacobi, J.L., Ngam, P., Devitt, N., Schilkey, F., Ben-Hur, A., & Reddy, A. S. (2016). A survey of the sorghum transcriptome using single-molecule long reads. Nature communications, 7(1), 1-11.
Barrett, J.C., Fry, B., Maller, J., & Daly, M.J. (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265.
Breslauer, K.J., Frank, R., Blöcker, H., & Marky, L.A. (1986). Predicting DNA duplex stability from the base sequence. Proceedings of the National Academy of Sciences, 83(11), 3746-3750.
Caldwell, K.S., Russell, J., Langridge, P., & Powell, W. (2006). Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics, 172(1), 557-567.
Chen, L., Deng, R., Liu, G., Jin, J., Wu, J., & Liu, X. (2019). Cytological and transcriptome analyses reveal OsPUB73 defect affects the gene expression associated with tapetum or pollen exine abnormality in rice. BMC Plant Biology, 19(546), 1-19.
Cordeiro, G.M., Eliott, F., McIntyre, C.L., Casu, R.E., & Henry, R.J. (2006). Characterisation of single nucleotide polymorphisms in sugarcane ESTs. Theoretical and Applied Genetics, 113(2), 331-343.
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., & Bettman, B. (2009). Real-time DNA sequencing from single polymerase molecules. Science, 323(5910), 133-138.
Garsmeur, O., Droc, G., Antonise, R., Grimwood, J., Potier, B., Aitken, K., Jenkins, J., Martin, G., Charron, C., Catherine, H., Laurent, C., Nabila, Y., Adam, H., David, S., Yesesri, C., Avinash, S., Andrzej, K., Agnes, C., Marie-Anne Van, S., Kankshita, S., Christopher, T., Hélène, B., Blake, S., Jean Christophe, G., Edwin van der, V., Robert, H., Jeremy, S., & Angélique, D.H. (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature communications, 9(1), 1-10.
Gawel, N., & Jarret, R. (1991). A modified CTAB DNA extraction procedure for Musa and Ipomoea. Plant molecular biology reporter, 9(3), 262-266.
Hoang, N.V., Furtado, A., O’Keeffe, A.J., Botha, F.C., & Henry, R.J. (2017). Association of gene expression with biomass content and composition in sugarcane. PLoS One, 12(8), 1-31.
Inghelandt, D.V., Reif, J.C., Dhillon, B.S., Flament, P., & Melchinger, A.E. (2011). Extent and genome-wide distribution of linkage disequilibrium in commercial maize germplasm. Theoretical and Applied Genetics, 123(1), 11-20.
Jaikishan, I., Rajendrakumar, P., Madhusudhana, R., Elangovan, M., & Patil, J.V. (2015). Development and utility of PCR-based intron polymorphism markers in sorghum [Sorghum bicolor (L.) Moench]. Journal of crop science and biotechnology, 18(5), 309-318.
Jannoo , N., Grivet , L., Chantret , N., Garsmeur , O., Glaszmann , J.C., Arruda , P., & D’Hont , A. (2007). Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. The Plant Journal, 50(4), 574-585.
Khanbo, S. (2020). Association Mapping of Sugar Related Traits in Sugarcane (Saccharum spp.). (Doctoral of Philosophy’s Degree). Thammasat University, Pathum Thani.
Kim, Y., & Nielsen, R. (2004). Linkage disequilibrium as a signature of selective sweeps. Genetics, 167(3), 1513-1524.
Lu, Y., Shah, T., Hao, Z., Taba, S., Zhang, S., Gao, S., Liu, J., Cao, M., Wang, J., & Prakash, A.B. (2011). Comparative SNP and haplotype analysis reveals a higher genetic diversity and rapider LD decay in tropical than temperate germplasm in maize. PLoS One, 6(9), e24861.
McIntyre , C.L., Jackson, M., Cordeiro, G.M., Amouyal, O., Hermann, S., Aitken, F.S., Eliott, F., Henry, R.J., Casu, R.E., & Bonnett, G.D. (2006). The identification and characterisation of alleles of sucrose phosphate synthase gene family III in sugarcane. Molecular breeding, 18(1), 39-50.
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., & Daly, M. (2010). The Genome Analysis Toolkit: a Map Reduce framework for analyzing next-generation DNA sequencing data. Genome research, 20(9), 1297-1303.
Nimmakayala, P., Levi, A., Abburi, L., Abburi, V.L., Tomason, Y.R., Saminathan, T., Vajja, V.G., Malkaram, S., Reddy, R., & Wehner, T.C. (2014). Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC genomics, 15(1), 767.
Piriyapongsa, J., Kaewprommal, P., Vaiwsri, S., Anuntakarun, S., Wirojsirasak, W., Punpee, P., Klomsa-ard, P., Shaw, P.J., Pootakham, W., & Yoocha, T. (2018). Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing. PeerJ, 6(5818), 1-23.
Qian, L., Qian, W., & Snowdon, R.J. (2014). Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome. BMC genomics, 15(1), 1170.
Qin, Q., Wang, Y., Huang, L., Du, F., Zhao, X., Li, Z., Wang, W., & Fu, B. (2020). A U-box E3 ubiquitin ligase OsPUB67 is positively involved in drought tolerance in rice. Plant molecular biology, 102(1-2), 89-107.
Raboin , L.M., Pauquet , J., Butterfield , M., D’Hont , A., & Glaszmann , J.C. (2008). Analysis of genome-wide linkage disequilibrium in the highly polyploid sugarcane. Theoretical and Applied Genetics, 116(5), 701-714.
Rozen, S., & Skaletsky, H. (2000). Primer3 on the WWW for general users and for biologist programmers pp. 365-386. Bioinformatics methods and protocols.
Ryu, M.Y., Cho, S.K., Hong, Y., Kim, J., Kim, J.H., Kim, G.M., Chen, Y.-J., Knoch, E., Møller, B.L., & Kim, W.T. (2019). Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses. BMC genomics, 20(326), 1-15.
Sela, H., Loutre, C., Keller, B., Schulman, A., Nevo, E., Korol, A., & Fahima, T. (2011). Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations. Theoretical and Applied Genetics, 122(1), 175-187.
Shearman, J.R., Sonthirod, C., Naktang, C., Pootakham, W., Yoocha, T., Sangsrakru, D., Jomchai, N., Tragoonrung, S., & Tangphatsornruang, S. (2016). The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads. Scientific reports, 6(1), 1-7.
Song , J., Yang , X., Resende Jr , M.F., Neves , L.G., Todd , J., Zhang , J., Comstock , J.C., & Wang , J. (2016). Natural allelic variations in highly polyploidy Saccharum complex. Frontiers in plant science, 7(804), 1-18.
Stephan, W. (2019). Selective sweeps. Genetics, 211(1), 5-13.
Wang, B., Tseng, E., Regulski, M., Clark, T.A., Hon, T., Jiao, Y., Lu, Z., Olson, A., Stein, J.C., & Ware, D. (2016). Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nature communications, 7(1), 1-13.
Wang, W., Wang, W., Wu, Y., Li, Q., Zhang, G., Shi, R., Yang, J., Wang, Y., & Wang, W. (2020). The involvement of wheat U‐box E3 ubiquitin ligase TaPUB1 in salt stress tolerance. Journal of Integrative Plant Biology, 62(5), 631-651.
Wang, Y.-H., Upadhyaya, H.D., Burrell, A.M., Sahraeian, S.M.E., Klein, R.R., & Klein, P.E. (2013). Genetic structure and linkage disequilibrium in a diverse, representative collection of the C4 model plant, Sorghum bicolor, G3: Genes, Genomes. Genetics, 3(5), 783-793.
Zhang , W., Wang, L., Wang, Y., Wang, Y., & Gao, Q. (2020). Cloning and characterization of TaPUB4, a U-box gene from common wheat (Triticum aestivum L.) involved in regulation of pollen development by influencing sucrose-starch pathway in anther. Molecular breeding, 40(6), 1-18.
Zhao, J., Zhao, L., Zhang, M., Zafar, S.A., Fang, J., Li, M., Zhang, W., & Li, X. (2017). Arabidopsis E3 ubiquitin ligases PUB22 and PUB23 negatively regulate drought tolerance by targeting ABA receptor PYL9 for degradation. International journal of molecular sciences, 18(9), 1841.
Zhu, C., Gore, M., Buckler, E.S., & Yu, J. (2008). Status and prospects of association mapping in plants. The Plant Genome, 1(1), 5-20.
Zia, M.A.B., Demirel, U., Nadeem, M.A., & Caliskan, M.E. (2020). Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel. Physiology and Molecular Biology of Plants, 26, 1003-1020.