A Meta-Analysis of Quantitative Trait Loci Associated with Stay-Green in Sorghum
DOI:
https://doi.org/10.29244/jtcs.9.01.39-46Keywords:
Meta-QTL, drought, genetic map, stress, QTL, clusteringAbstract
A strong association between stay-green and post-flowering drought tolerance in sorghum has been established previously. In this study, a meta-analysis was conducted to find relevant genetic intervals that regulate stay-green in sorghum and thereby affect drought resilience. Meta-QTL analysis was performed to combine 115 QTLs mapped in previous studies and locate regions where recurrent QTLs occurred across experiments. This approach overcomes the constraints of a single QTL association experiment by increasing heterogeneity in populations and environments. The analysis included the construction of consensus maps, QTL projection, and QTL clustering. We report 32 Meta-QTL for stay-green and their position relative to genetic markers on the sorghum genome. The results from this study will facilitate future attempts aiming to improve and understand drought tolerance in Sorghum by the use of fine mapping and marker-assisted selection.
References
Abebe, T., Belay, G., Tadesse, T., and Keneni, G. (2021). Stay-green genes contributed for drought adaptation and performance under post-flowering moisture stress on sorghum (Sorghum bicolor L. Moench). Journal of Plant Breeding and Crop Science 13,190-202. https://doi.org/10.5897/JPBCS2020.0894
Abreha, K. B., Enyew, M., Carlsson, A. S., Vetukuri, R. R., Feyissa, T., Motlhaodi, T., Ng’uni, D., and Geleta, M. (2022). Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress. Planta 255,1-23. https://doi.org/10.1007/s00425-021-03799-7
Amelework, B., Shimelis, H., Tongoona, P., and Laing, M. (2015). Physiological mechanisms of
drought tolerance in sorghum, genetic basis and breeding methods: a review. African Journal of
Agricultural Research 10, 3029-3040. https://doi.org/10.5897/AJAR2015.9595
Crasta, O. R., Xu, W. W., Rosenow, D. T., Mullet, J., and Nguyen, H. T. (1999). Mapping of post-flowering drought resistance traits in grain sorghum: association between QTLs influencing premature senescence and maturity. Molecular and General Genetics 262, 579-588. https://doi.org/10.1007/s004380051120
De Oliveira, Y., Sosnowski, O., Charcosset, A., and Joets, J. (2014). BioMercator 4: a complete framework to integrate QTL, meta-QTL, and genome annotation In European Conference on Computational Biology 2014.
Goffinet, B., and Gerber, S. (2000). Quantitative trait loci: a meta-analysis. Genetics 55, 463-473. https://doi.org/10.1093/genetics/155.1.463
Guo, B., Sleper, D. A., Lu, P., Shannon, J. G., Nguyen, H. T., and Arelli, P. R. (2006). QTLs associated with resistance to soybean cyst nematode in soybean: meta-analysis of QTL locations. Genomics, Molecular Genetics and Biotechnology 46, 595-602. https://doi.org/10.2135/cropsci2005.04-0036-2
Harris, K., Subudhi, P.K., Borrell, A., Jordan, D., Rosenow, D., Nguyen, H., Klein, P., Klein, R. and Mullet, J. (2007). Sorghum stay-green QTL individually reduce post-flowering drought-induced leaf senescence. Journal of Experimental Botany 58, 327-338. https://doi.org/10.1093/jxb/erl225
Haussmann, B., Mahalakshmi, V., Reddy, B., Seetharama, N., Hash, C., and Geiger, H. (2002). QTL mapping of stay-green in two sorghum recombinant inbred populations. Theoretical and Applied Genetics 106, 133-142. https://doi.org/10.1007/s00122-002-1012-3
Kebede, H., Subudhi, P. K., Rosenow, D. T., and Nguyen, H. T. (2001). Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L. Moench). Theoretical and Applied Genetics 103, 266-276. https://doi.org/10.1007/s001220100541
Löffler, M., Schön, C. C., and Miedaner, T. (2009). Revealing the genetic architecture of FHB resistance in hexaploid wheat (Triticum aestivum L.) by QTL meta-analysis. Molecular Breeding, 23, 473-488. https://doi.org/10.1007/s11032-008-9250-y
Mace, E. S., and Jordan, D. R. (2011). Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement. Theoretical and Applied Genetics 123, 169-191. https://doi.org/10.1007/s00122-011-1575-y
Menz, M. A., Klein, R. R., Unruh, N. C., Rooney, W. L., Klein, P. E., and Mullet, J. E. (2004). Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers. https://doi.org/10.2135/cropsci2004.1236
Reddy, N. R. R., Ragimasalawada, M., Sabbavarapu, M. M., Nadoor, S., and Patil, J. V. (2014). Detection and validation of stay-green QTL in post-rainy sorghum involving widely adapted cultivar, M35-1 and a popular stay-green genotype B35. BMC Genomics 15, 1-16. https://doi.org/10.1186/1471-2164-15-909
Sabadin, P.K., Malosetti, M., Boer, M.P., Tardin, F.D., Santos, F.G., Guimaraes, C.T., Gomide, R.L., Andrade, C.L.T., Albuquerque, P.E.P., Caniato, F.F. and Mollinari, M. (2012). Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences. Theoretical and Applied Genetics 124, 1389-1402. https://doi.org/10.1007/s00122-012-1795-9
Srinivas, G., Satish, K., Madhusudhana, R., Reddy, R. N., Mohan, S. M., and Seetharama, N. (2009). Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum. Theoretical and Applied Genetics 118, 1439-1454. https://doi.org/10.1007/s00122-009-0993-6
Subudhi, P. K., Rosenow, D. T., and Nguyen, H. T. (2000). Quantitative trait loci for the stay green trait in sorghum (Sorghum bicolor L. Moench): consistency across genetic backgrounds and environments. Theoretical and Applied Genetics 101, 733-741. https://doi.org/10.1007/s001220051538
Tao, Y. Z., Henzell, R. G., Jordan, D. R., Butler, D. G., Kelly, A. M., and McIntyre, C. L. (2000). Identification of genomic regions associated with stay green in sorghum by testing RILs in multiple environments. Theoretical and Applied Genetics 100, 1225-1232. https://doi.org/10.1007/s001220051428
Tello-Ruiz, M.K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B.,
Chougule, K., Garg, P. and Elser, J.(2021). Gramene 2021: harnessing the power of comparative
genomics and pathways for plant research. Nucleic Acids Research 49, D1452-D1463. https://doi.org/10.1093/nar/gkaa979
Veyrieras, J. B., Goffinet, B., and Charcosset, A. (2007). MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BMC Bioinformatics 8, 1-16. https://doi.org/10.1186/1471-2105-8-49
Xu, W., Subudhi, P. K., Crasta, O. R., Rosenow, D. T., Mullet, J. E., and Nguyen, H. T. (2000). Molecular mapping of QTLs conferring stay-green in grain sorghum (Sorghum bicolor L. Moench). Genome, 43, 461-469. https://doi.org/10.1139/g00-003
Abreha, K. B., Enyew, M., Carlsson, A. S., Vetukuri, R. R., Feyissa, T., Motlhaodi, T., Ng’uni, D., and Geleta, M. (2022). Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress. Planta 255,1-23. https://doi.org/10.1007/s00425-021-03799-7
Amelework, B., Shimelis, H., Tongoona, P., and Laing, M. (2015). Physiological mechanisms of
drought tolerance in sorghum, genetic basis and breeding methods: a review. African Journal of
Agricultural Research 10, 3029-3040. https://doi.org/10.5897/AJAR2015.9595
Crasta, O. R., Xu, W. W., Rosenow, D. T., Mullet, J., and Nguyen, H. T. (1999). Mapping of post-flowering drought resistance traits in grain sorghum: association between QTLs influencing premature senescence and maturity. Molecular and General Genetics 262, 579-588. https://doi.org/10.1007/s004380051120
De Oliveira, Y., Sosnowski, O., Charcosset, A., and Joets, J. (2014). BioMercator 4: a complete framework to integrate QTL, meta-QTL, and genome annotation In European Conference on Computational Biology 2014.
Goffinet, B., and Gerber, S. (2000). Quantitative trait loci: a meta-analysis. Genetics 55, 463-473. https://doi.org/10.1093/genetics/155.1.463
Guo, B., Sleper, D. A., Lu, P., Shannon, J. G., Nguyen, H. T., and Arelli, P. R. (2006). QTLs associated with resistance to soybean cyst nematode in soybean: meta-analysis of QTL locations. Genomics, Molecular Genetics and Biotechnology 46, 595-602. https://doi.org/10.2135/cropsci2005.04-0036-2
Harris, K., Subudhi, P.K., Borrell, A., Jordan, D., Rosenow, D., Nguyen, H., Klein, P., Klein, R. and Mullet, J. (2007). Sorghum stay-green QTL individually reduce post-flowering drought-induced leaf senescence. Journal of Experimental Botany 58, 327-338. https://doi.org/10.1093/jxb/erl225
Haussmann, B., Mahalakshmi, V., Reddy, B., Seetharama, N., Hash, C., and Geiger, H. (2002). QTL mapping of stay-green in two sorghum recombinant inbred populations. Theoretical and Applied Genetics 106, 133-142. https://doi.org/10.1007/s00122-002-1012-3
Kebede, H., Subudhi, P. K., Rosenow, D. T., and Nguyen, H. T. (2001). Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L. Moench). Theoretical and Applied Genetics 103, 266-276. https://doi.org/10.1007/s001220100541
Löffler, M., Schön, C. C., and Miedaner, T. (2009). Revealing the genetic architecture of FHB resistance in hexaploid wheat (Triticum aestivum L.) by QTL meta-analysis. Molecular Breeding, 23, 473-488. https://doi.org/10.1007/s11032-008-9250-y
Mace, E. S., and Jordan, D. R. (2011). Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement. Theoretical and Applied Genetics 123, 169-191. https://doi.org/10.1007/s00122-011-1575-y
Menz, M. A., Klein, R. R., Unruh, N. C., Rooney, W. L., Klein, P. E., and Mullet, J. E. (2004). Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers. https://doi.org/10.2135/cropsci2004.1236
Reddy, N. R. R., Ragimasalawada, M., Sabbavarapu, M. M., Nadoor, S., and Patil, J. V. (2014). Detection and validation of stay-green QTL in post-rainy sorghum involving widely adapted cultivar, M35-1 and a popular stay-green genotype B35. BMC Genomics 15, 1-16. https://doi.org/10.1186/1471-2164-15-909
Sabadin, P.K., Malosetti, M., Boer, M.P., Tardin, F.D., Santos, F.G., Guimaraes, C.T., Gomide, R.L., Andrade, C.L.T., Albuquerque, P.E.P., Caniato, F.F. and Mollinari, M. (2012). Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences. Theoretical and Applied Genetics 124, 1389-1402. https://doi.org/10.1007/s00122-012-1795-9
Srinivas, G., Satish, K., Madhusudhana, R., Reddy, R. N., Mohan, S. M., and Seetharama, N. (2009). Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum. Theoretical and Applied Genetics 118, 1439-1454. https://doi.org/10.1007/s00122-009-0993-6
Subudhi, P. K., Rosenow, D. T., and Nguyen, H. T. (2000). Quantitative trait loci for the stay green trait in sorghum (Sorghum bicolor L. Moench): consistency across genetic backgrounds and environments. Theoretical and Applied Genetics 101, 733-741. https://doi.org/10.1007/s001220051538
Tao, Y. Z., Henzell, R. G., Jordan, D. R., Butler, D. G., Kelly, A. M., and McIntyre, C. L. (2000). Identification of genomic regions associated with stay green in sorghum by testing RILs in multiple environments. Theoretical and Applied Genetics 100, 1225-1232. https://doi.org/10.1007/s001220051428
Tello-Ruiz, M.K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B.,
Chougule, K., Garg, P. and Elser, J.(2021). Gramene 2021: harnessing the power of comparative
genomics and pathways for plant research. Nucleic Acids Research 49, D1452-D1463. https://doi.org/10.1093/nar/gkaa979
Veyrieras, J. B., Goffinet, B., and Charcosset, A. (2007). MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BMC Bioinformatics 8, 1-16. https://doi.org/10.1186/1471-2105-8-49
Xu, W., Subudhi, P. K., Crasta, O. R., Rosenow, D. T., Mullet, J. E., and Nguyen, H. T. (2000). Molecular mapping of QTLs conferring stay-green in grain sorghum (Sorghum bicolor L. Moench). Genome, 43, 461-469. https://doi.org/10.1139/g00-003
Downloads
Published
2022-02-09
How to Cite
Aquib, A., & Nafis, S. (2022). A Meta-Analysis of Quantitative Trait Loci Associated with Stay-Green in Sorghum. Journal of Tropical Crop Science, 9(01), 39–46. https://doi.org/10.29244/jtcs.9.01.39-46
Issue
Section
Articles
License
All publications by Journal of Tropical Crop Science is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
