Research Project: Genetic Improvement of Sugarcane for Adaptation to Temperate Climates

Location: Sugarcane Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Identification of QTLs for smut resistance in sugarcane using a bi-parental mapping population - (Peer Reviewed Journal)
Cortes, J.D., Gutierrez, A.F., Hoy, J.W., Hale, A.L., Baisakh, N. 2023. Identification of QTLs for smut resistance in sugarcane using a bi-parental mapping population. Gene. 2352-4073. https://doi.org/10.1016/j.plgene.2023.100445.

Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in Saccharum spp. and Tripidium spp. - (Peer Reviewed Journal)
Pan, Y., Todd, J.R., Lomax, L.E., White Jr, P.M., Simpson, S.A., Scheffler, B.E. 2023. Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in Saccharum spp. and Tripidium spp.. Agronomy Journal. https://doi.org/10.3390/agronomy13112728.

Registration of 'Ho 13-739' sugarcane - (Peer Reviewed Journal)
Todd, J.R., Hale, A.L., Pan, Y., Tew, T.L., William, W.H., Dufrene Jr, E.O., Grisham, M.P., Hoy, J., Penn, H., Wilson, B.E., Orgeron, A., Waguespack, H., Pontif, M.J., Gravois, K.A., Jackson, W.R., Duet Jr, M.J., Landry, C.J., Verdun, D.L. 2024. Registration of 'Ho 13-739' sugarcane. Journal of Plant Registrations. https://doi.org/10.1002/plr2.20355.

A genome-wide association study and genomic prediction for Phakopsora pachyrhizi resistance in soybean - (Peer Reviewed Journal)
Xiong, H., Chen, Y., Pan, Y.-B., Shi, A., Wang, J. 2023. A genome-wide association study and genomic prediction for Phakopsora pachyrhizi resistance in soybean. Frontiers in Plant Science. 14(1179357):1-12. https://doi.org/10.3389/fpls.2023.1179357.

2022 Louisiana “Ho” nursery variety trials - (Experiment Station)

2022 Louisiana variety development program infield trials - (Experiment Station)

A genome-wide association study and genomic prediction for fiber and sucrose contents in a mapping population of LCP 85-384 sugarcane - (Peer Reviewed Journal)
Xiong, H., Chen, Y.-B, Pan, Y., Shi, A. 2023. A genome-wide association study and genomic prediction for fiber and sucrose contents in a mapping population of LCP 85-384 sugarcane. Plants. 12(5):1041. https://doi.org/10.3390/plants12051041.

Identification of QTLs and critical genes related to sugarcane mosaic disease resistance - (Peer Reviewed Journal)
Lu, G., Wang, Z., Pan, Y.-B, Wu, Q., Cheng, W., Xu, F., Dai, S., Li, B., Que, Y., Xu, L. 2023. Identification of QTLs and critical genes related to sugarcane mosaic disease resistance. Frontiers in Plant Science. 14:1107314. https://doi.org/10.3389/fpls.2023.1107314.

Genome-wide characterization of sugarcane catalase gene family identifies a ScCAT1 gene associated disease resistance - (Peer Reviewed Journal)
Wu, Q., Chen, Y., Zou, W., Pan, Y.-B, Lin, P., Xu, L., Grisham, M.P., Ding, Q., Su, Y., Que, Y. 2023. Genome-wide characterization of sugarcane catalase gene family identifies a ScCAT1 gene associated disease resistance. International Journal of Biological Macromolecules. 232:123398. https://doi.org/10.1016/j.ijbiomac.2023.123398.

Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq - (Peer Reviewed Journal)
Wu, Q., Su, Y., Pan, Y.-B., Xu, F., Zou, W., Que, B., Lin, P., Sun, T., Grisham, M.P., Xu, L., Que, Y. 2022. Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq. Frontiers in Plant Science. 13:1035266. https://doi.org/10.3389/fpls.2022.1035266.

Registration of ‘L 14-267’ sugarcane - (Peer Reviewed Journal)
Pontif, M., Kimbeng, C., Gravois, K., Taylor, Z., Sexton, D., Blanchard, B., Daigle, M., Fontenot, D., Hawkins, G., Hoy, J., Baisakh, N., Wilson, B., Orgeron, A., Todd, J.R., Hale, A.L., Waguespack, H. 2023. Registration of ‘L 14-267’ sugarcane. Journal of Plant Registrations. pp. 1-16. https://doi.org./10.1002/plr2.20267.

WGCNA identifies a comprehensive and dynamic gene co-expression network that associates with smut resistance in sugarcane - (Peer Reviewed Journal)
Wu, Q., Pan, Y.-B., Su, Y., Zou, W., Xu, F., Yang, S., Grisham, M.P., Sun, T., Xu, L., Que, Y. 2022. WGCNA identifies a comprehensive and dynamic gene co-expression network that associates with smut resistance in sugarcane. International Journal of Molecular Sciences. 23:1-23. https://doi.org/10.3390/ijms231810770.

Identification of selection preferences and predicting tield related traits in sugarcane seedling families using RGB spectral indices - (Peer Reviewed Journal)
Todd, J.R., Johnson, R.M., Verdun, D.L., Richard, K.A. 2022. Identification of selection preferences and predicting tield related traits in sugarcane seedling families using RGB spectral indices. Agriculture. 12(9):1313. https://doi.org/10.3390/agriculture12091313.

Long non-coding RNAs: new players in plants - (Peer Reviewed Journal)
Zhao, Z., Zang, S., Zou, W., Pan, Y.-B., Yao, W., You, C., Que, Y. 2022. Long non-coding RNAs: new players in plants. International Journal of Molecular Sciences. 12(9301):1-18. https://doi.org/10.3390/ijms23169301.

Selection preferences of sugarcane seedling families related to yield traits and RGB spectral indices - (Abstract Only)

A genomic wide association study of yield-related traits in sugarcane - (Abstract Only)
Phiri, T.M., Bhattarai, G., Shi, A., Pan, Y.-B. 2022. A genomic wide association study of yield-related traits in sugarcane [abstract]. 2022 ASHS annual conference July 30–August 3, Chicago, IL. Proceedings American Society of Horticultural Sciences. Article 37572. https://ashs.confex.com/ashs/2022/meetingapp.cgi/Paper/37572.

A genome-wide association study and genomic prediction for fiber and sucrose contents in sugarcane - (Abstract Only)
Xiong, H., Chen, Y., Shi, A., Pan, Y.-B. 2022. A genome-wide association study and genomic prediction for fiber and sucrose contents in sugarcane [abstract]. 2022 ASHS annual conference July 30–August 3, Chicago, IL. Proceedings American Society of Horticultural Sciences. Article 37890. https://ashs.confex.com/ashs/2022/meetingapp.cgi/Paper/37890.

Population structure and genetic diversity analysis in sugarcane (Saccharum spp. hybrids) and six related Saccharum species - (Peer Reviewed Journal)
Xiong, H., Chen, Y., Gao, S., Pan, Y.-B., Shi, A. 2022. Population structure and genetic diversity analysis in sugarcane (Saccharum spp. hybrids) and six related Saccharum species. Agronomy. 12(2):412. https://doi.org/10.3390/agronomy12020412.

SSR-based molecular identification and population structure analysis for the Yunrui-series sugarcane (Saccharum spp. hybrids) genotypes - (Peer Reviewed Journal)
Tian, C., Zhu, J., Pan, Y.-B., Lu, X., Dong, L., Burner, D.M., Tao, L., Wu, C., Jing, Y. 2022. SSR-based molecular identification and population structure analysis for the Yunrui-series sugarcane (Saccharum spp. hybrids) genotypes. Sugar Tech. 24(5):1391–1403. https://doi.org/10.1007/s12355-021-01099-8.

Utilization of a sugarcane100K single nucleotide polymorphisms microarray-derived high-density genetic map in quantitative trait loci mapping and function role prediction of genes related to chlorophyll content in sugarcane - (Peer Reviewed Journal)
Lu, G., Pan, Y., Wang, Z., Xu, F., Cheng, W., Huang, X., Ren, H., Pang, C., Que, Y., Xu, L. 2021. Utilization of a sugarcane100K single nucleotide polymorphisms microarray-derived high-density genetic map in quantitative trait loci mapping and function role prediction of genes related to chlorophyll content in sugarcane. Frontiers in Plant Science. 12. Article 817875. https://doi.org/10.3389/fpls.2021.817875.

Analysis of sugarcane genotype by environment yield in the Rio Grande Valley of Texas - (Abstract Only)

Sugarcane mosaic disease: characteristics, identification and control - (Peer Reviewed Journal)
Lu, G., Wang, Z., Xu, F., Pan, Y., Grisham, M.P., Xu, L. 2021. Sugarcane mosaic disease: characteristics, identification and control. Microorganisms. 9(9):1984. https://doi.org/10.3390/microorganisms9091984.

Registration of ‘L 12-201’ Sugarcane - (Peer Reviewed Journal)
Pontif, M., Kimbeng, C., Gravois, K.A., Bishoff, K.P., Sexton, D.R., Laborde, C.M., Hawkins, G., Hoy, J., Baisakh, N., Wilson, B.E., Orgeron, A., Todd, J.R., Waguespack, H.L. 2022. Registration of ‘L 12-201’ Sugarcane. Journal of Plant Registrations. 16(2):363-377. https://doi.org/10.1002/plr2.20185.

Prediction of ratoon sugarcane family yield and selection using remote imagery - (Peer Reviewed Journal)
Todd, J.R., Johnson, R.M. 2021. Prediction of ratoon sugarcane family yield and selection using remote imagery. Agronomy. 11(7):Article 1273. https://doi.org/10.3390/agronomy11071273.

Release of ‘HoCP 14-885’ sugarcane - (Abstract Only)

Analysis of sugarcane genotype by environment yield in the Rio Grande Valley of Texas using GGE biplot - (Abstract Only)

A report on the 2019 outfield variety trials - (Trade Journal)

Registration of ‘Ho 07-613’ sugarcane - (Peer Reviewed Journal)
Hale, A.L., Todd, J.R., Pan, Y., Tew, T.L., Veremis, J.C., White, W.H., Dufrene Jr, E.O., Grisham, M.P., Gravois, K.A., Jackson, W.R., Dalley, C.D., Spaunhorst, D.J., Duet Jr, M.J., Landry, C.J., Verdun, D.L. 2022. Registration of ‘Ho 07-613’ sugarcane. Journal of Plant Registrations. 16(2):351-362. https://doi.org/10.1002/plr2.20163.

Occurrence of two races of Puccinia kuehnii causing orange rust of sugarcane in Florida - (Peer Reviewed Journal)
Sanjel, S., Hincapie, M., Wang, Y., Todd, J.R., Chaulagain, B., Sood, S.G., Comstock, J.C., Raid, R.N., Rott, P. 2021. Occurrence of two races of Puccinia kuehnii causing orange rust of sugarcane in Florida. Plant Pathology. 00:1-10. https://doi.org/10.1111/ppa.13405.

Registration of ‘Ho 11-573’ sugarcane - (Peer Reviewed Journal)
Todd, J.R., Hale, A.L., Pan, Y., Tew, T.L., Dufrene Jr, E.O., Duet Jr, M.J., Verdun, D.L., Landry, C.J., Grisham, M.P., Kimbeng, C., Gravois, K.A., Bischoff, K.P., Pontif, M.J., Jackson, W.R., Waguespack Jr, H.L., Davidson, W., Scott Jr, A.W., Hernandez, E., Klostermann, M., Nuessly, G.S., White, W.H., Richard, R.T. 2021. Registration of ‘Ho 11-573’ sugarcane. Journal of Plant Registrations. 15:463-470. https://doi.org/10.1002/plr2.20153.

2020 Louisiana variety development program infield trials - (Experiment Station)

2020 Louisiana variety development program infield trials - (Experiment Station)

Sugarcane breeding programs in the USA - (Peer Reviewed Journal)
Hale, A.L., Todd, J.R., Gravois, K.A., Mollov, D.S., Malapi-Wight, M., Momotaz, A., Laborde, C., Goenaga, R.J., Solis, A., Waguespack, H. 2021. Sugarcane breeding programs in the USA. Sugar Tech. 24(1):97-111. https://doi.org/10.1007/s12355-021-01018-x.

Data mining sugarcane breeding yield data for ratoon yield prediction - (Peer Reviewed Journal)
Todd, J.R., Dufrene Jr, E.O., Waguespack, H., Kimbeng, C., Pontif, M., Boykin, D.L. 2021. Data mining sugarcane breeding yield data for ratoon yield prediction. Euphytica. 217:54. https://doi.org/10.1007/s10681-021-02786-z.

Identification of quantitative trait loci (QTL) controlling fiber content of sugarcane (Saccharum hybrids spp.) - (Peer Reviewed Journal)
Islam, M.S., Pan, Y.-B., Lomax, L.E., Grisham, M.P. 2021. Identification of quantitative trait loci (QTL) controlling fiber content of sugarcane (Saccharum hybrids spp.). Plant Breeding. 140(2):360-366. https://doi.org/10.1111/pbr.12912.

Registration of ‘L 11-183’ sugarcane - (Peer Reviewed Journal)
Pontif, M.J., Kimbeng, C.A., Bischoff, K.P., Gravois, K.A., LaBorde, C.M., Hawkins, G.L., Sexton, D.R., Hoy, J.W., Baisakh, N.E., Wilson, B.E., Orgeron, A., Todd, J.R., Waguespack, H.L. 2021. Registration of ‘L 11-183’ sugarcane. Journal of Plant Registrations. 15:447-462. https://doi.org/10.1002/plr2.20136.

Ratoon family selection using remote sensing - (Abstract Only)

Registration of ‘Ho 05-961’ sugarcane - (Peer Reviewed Journal)
Todd, J.R., Hale, A.L., Pan, Y., Tew, T.L., White, W.H., Dufrene Jr, E.O., Duet Jr, M.J., Verdun, D.L., Spaunhorst, D.J., Dalley, C., Grisham, M.P., Wilson, B.E., Gravois, K.A., Jackson, W.R. 2022. Registration of ‘Ho 05-961’ sugarcane. Journal of Plant Registrations. 16(2):341-350. https://doi.org/10.1002/plr2.20100.

Subcellular localization of the D27 protein in sugarcane (Saccharum hybrids spp.) using an optimized protoplast isolation, purification, and transient gene expression protocol - (Peer Reviewed Journal)
Wu, Z., Hu, X., Zan, F., Pan, Y.-B., Burner, D.M., Luo, Z., Liu, J., Zhao, L., Yao, L., Zhao, Y., Liu, X., Xia, H., Yang, K., Zhao, J., Zhao, P., Qin, W., Chen, X., Wu, C. 2020. Subcellular localization of the D27 protein in sugarcane (Saccharum hybrids spp.) using an optimized protoplast isolation, purification, and transient gene expression protocol. Sugar Tech. 23(2):316-325. https://doi.org/10.1007/s12355-020-00879-y.

An enriched sugarcane diversity panel for utilization in genetic improvement of sugarcane - (Peer Reviewed Journal)
Ficket, N., Ebrahimi, L., Parco, A., Hale, A.L., Gutierrez, A.V., Pontif, M.J., Todd, J.R., Kimbeng, C.A., Hoy, J.W., Ayala Silva, T., Gravois, K.A., Baisakh, N. 2020. An enriched sugarcane diversity panel for utilization in genetic improvement of sugarcane. Scientific Reports. 10:1-13. https://doi.org/10.1038/s41598-020-70292-8.

Measurement of the variability of brix along sugarcane stalk - (Abstract Only)

Cultivar-specific SSR markers as revealed through fluorescence- labeling and capillary electrophoresis in sugarcane (Saccharum hybrids spp.) - (Peer Reviewed Journal)
Luzaran, R.T., Pan, Y.-B. 2020. Cultivar-specific SSR markers as revealed through fluorescence- labeling and capillary electrophoresis in sugarcane (Saccharum hybrids spp.). Philippine Journal of Crop Science. 45(2):47-57.

Genome-wide analysis of the trehalose-6-phosphate synthase (TPS) gene family and expression profiling of ScTPS genes in sugarcane - (Peer Reviewed Journal)
Hu, X., Wu, Z., Luo, Z., Burner, D., Pan, Y.-B., Wu, C. 2020. Genome-wide analysis of the trehalose-6-phosphate synthase (TPS) gene family and expression profiling of ScTPS genes in sugarcane. Agronomy Journal. 10(7):969. https://doi.org/10.3390/agronomy10070969.

Multivariate analysis of 31 phenotypic traits among major parental lines of sugarcane breeding programs in China - (Peer Reviewed Journal)
Wu, J., Wang, Q., Pan, Y., Zie, J., Zhou, F., Xu, H., Qiu, Y., Liu, Z. 2021. Multivariate analysis of 31 phenotypic traits among major parental lines of sugarcane breeding programs in China. The Journal of Animal and Plant Sciences. 31(3):719-732. https://doi.org/10.36899/JAPS.2021.3.0262.

Genetic variation within and among lowland switchgrass cultivars as revealed with AFLP polymorphisms - (Peer Reviewed Journal)
Makaju, S.O., Wu, Y., Anderson, M.P., Kakani, V.G., Smith, M., Todd, J.R., Adhikari, L. 2020. Genetic variation within and among lowland switchgrass cultivars as revealed with AFLP polymorphisms. Global Journal of Agricultural and Allied Sciences. 2(1):11-17. https://doi.org/10.35251/gjaas.2020.002.

2019 Louisiana variety development program infield trials - (Experiment Station)

2019 Louisiana “Ho” nursery variety trials - (Experiment Station)

Fidelity of sugarcane crosses assessed with SSR markers - (Peer Reviewed Journal)
Todd, J.R., Pan, Y.-B., Boykin, D.L. 2020. Fidelity of sugarcane crosses assessed with SSR markers. Agronomy. 10(3):1-18. http://doi.org/10.3390/agronomy10030386.

SSR-based genetic identity of sugarcane clones and its potential application in breeding and variety extension - (Peer Reviewed Journal)
Wang, Z., Pan, Y.-B., Luo, J., You, Q., Xu, L., Zhang, H., Que, Y. 2020. SSR-based genetic identity of sugarcane clones and its potential application in breeding and variety extension. Sugar Tech. 22(3):367-378. https://doi.org/10.1007/s12355-019-00788-9.

Genomic selection: A new marker-assisted breeding tool to facilitate Louisiana sugarcane variety development - (Trade Journal)
Baisakh, N., Kimbeng, C., Pontiff, M., Hoy, J., Gravois, K., Hale, A.L., Todd, J.R. 2020. Genomic selection: A new marker-assisted breeding tool to facilitate Louisiana sugarcane variety development. Sugar Bulletin. 98(4):23-25.

Evaluation of susceptibility to mosaic in Louisiana's sugarcane breeding program - (Peer Reviewed Journal)
Rice, J.L., Hoy, J.W., Hale, A.L., Todd, J.R., Grisham, M.P., Kimbeng, C.A., Pontif, M.J. 2019. Evaluation of susceptibility to mosaic in Louisiana's sugarcane breeding program. Journal of the American Society of Sugar Cane Technologists. 39:1-11.

Phenotypic and molecular characterization of a core collection of Saccharum spontaneum L. in China - (Peer Reviewed Journal)
Xu, C., Liu, X., Burner, D.M., Abbas, Z., Pan, Y.-B., Elgamal, I.S., Lu, X., Su, H. 2020. Phenotypic and molecular characterization of a core collection of Saccharum spontaneum L. in China. Sugar Tech. 22(1):76–88. https://doi.org/10.1007/s12355-019-00761-6.

SSR marker-assisted management of parental germplasm in sugarcane (Saccharum spp. hybrids) breeding programs - (Peer Reviewed Journal)
Wu, J., Wang, Q., Xie, J., Pan, Y.-B., Zhou, F., Guo, Y., Chang, H., Xu, H., Zhang, W., Zhang, C., Qiu, Y. 2019. SSR marker-assisted management of parental germplasm in sugarcane (Saccharum spp. hybrids) breeding programs. Agronomy Journal. 9(8):449. https://doi.org/10.3390/agronomy9080449.

A report on the 2019 outfield variety trials - (Trade Journal)

Notice of release of sugarcane variety Ho 12-615 - (Trade Journal)
Todd, J.R., Hale, A.L., Dufrene Jr, E.O., White, W.H., Tew, T.L., Grisham, M.P., Kimbeng, C., Duet Jr, M.J., Verdun, D.L., Waguespack, H., Pan, Y.-B., Gravois, K.A. 2019. Notice of release of sugarcane variety Ho 12-615. Sugar Bulletin. 97(8):17-18.

Prediction of sugarcane yield by machine learning - (Abstract Only)
Todd, J.R., Dufrene Jr, E.O., Pontiff, M. 2019. Prediction of sugarcane yield by machine learning [abstract]. Journal American Society of Sugar Cane Technologists. 39:43.

Identifying loci controlling fiber composition in polyploid sugarcane (Saccharum spp.) through genome-wide association study - (Peer Reviewed Journal)
Yang, X., Todd, J.R., Arundale, R., Binder, J., Luo, Z., Islam, M.S., Sood, S.G., Wang, J. 2019. Identifying loci controlling fiber composition in polyploid sugarcane (Saccharum spp.) through genome-wide association study. Industrial Crops and Products. 130:598-605. https://doi.org/10.1016/j.indcrop.2019.01.023.

Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection - (Peer Reviewed Journal)
Fickett, N., Gutierrez, A., Verma, M., Pontif, M., Hale, A.L., Kimbeng, C., Baisakh, N. 2018. Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection. Genomics. Available: https://doi.org/10.1016/j.ygeno.2018.12.002.