An enriched sugarcane diversity panel for utilization in genetic improvement of sugarcane

Authors: FICKET, NATHANAEL - LSU Agcenter; EBRAHIMI, LEILA - LSU Agcenter; PARCO, ARNOLD - LSU Agcenter; GUTIERREZ, ANDRES - LSU Agcenter; Hale, Anna; PONTIF, MICHAEL - LSU Agcenter; Todd, James; KIMBENG, COLLINS - LSU Agcenter; HOY, JEFFREY - LSU Agcenter; Ayala Silva, Tomas; GRAVOIS, KENNETH - LSU Agcenter; BAISAKH, NIRANJAN - LSU Agcenter

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/26/2020
Publication Date: 8/7/2020
Citation: 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.
DOI: https://doi.org/10.1038/s41598-020-70292-8

Interpretive Summary: Sugarcane crops are important for both sugar and biofuels; However sugarcane is a genetically complex crop and breeding new varieties requires many years. The crop is derived from six different species in the Saccharum genus, and germplasm banks containing sugarcane and releated species possess a large number of clones with overlapping genes of interest. To efficiently characterize the World Collection of Sugarcane and Related Grasses housed at the USDA-ARS in Miami Florida as well as the Louisiana sugarcane breeding population, a subset of clones was identified. This population (SDP1) was selected based on the analysis of molecular markers, and captures the maximum amount of genetic diversity with only 309 clones as opposed to the ~1500 originally analyzed. Including the Louisiana clones in the population ensures that the subset includes genetic material adapted to subtropical and temperate climates that can be used in the development of well adapted parents for Louisiana. Furthermore, a smaller subset of varieties will enable scientists to more efficiently screen the population for traits of interest and to identify molecular markers for use in marker assisted breeding. Marker assisted breeding could hasten the development of high-yielding cultivars and ultimately increase profits for U.S. sugarcane farmers.

Technical Abstract: Sugarcane crops are important for both sugar and biofuels. A world collection of sugarcane and related grasses (WCSRG) maintained at Miami, FL contains >1,200 non-redundant clones of different species and genera within the Saccharum complex. However, linkage of undesirable alleles with useful genes in wild species has hindered efficient utilization of exotic Saccharum material in sugarcane breeding. A core collection developed previously with smaller number of clones representing WCSRG did not take into account >120 wild/exotic clones maintained at the USDA-ARS Sugarcane Research Unit in Houma, Louisiana. Moreover, the genome complexity and sub-tropical to temperate growing climate of Louisiana warrant a region-specific core collection that can be used for base-broadening breeding aimed at efficient introgression of desirable alleles. A 309-clone diversity panel (SDP1) was developed that captured the genetic diversity among clones within WCSRG and Louisiana (commercials, wild/exotic). The breadth of the genetic variation of SDP1 was exemplified by the intra- and inter-specific diversity for known cold-responsive genes. SDP1 will facilitate genome-wide association studies for identification of trait-specific markers for use in marker-assisted breeding in Louisiana and elsewhere.