Development and integration of an SSR marker-based molecular identity database into Louisiana sugarcane breeding program

Authors: Pan, Yong-Bao; Todd, James; Hale, Anna; White, Paul; Lomax, Lionel; Simpson, Sheron

Submitted to: International Society of Sugar Cane Technologists Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 4/22/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: It takes 12 to 14 years to develop a new sugarcane cultivar for commercial production. Clone mis-identification and mix-up often occur during vegetative propagation and germplasm exchange. To help the breeders deal with the potential problem, a simple sequence repeats (SSR)-based molecular identity database has been developed by the USDA-ARS in 2005 and annually updated by fingerprinting of newly designated varieties, parental clones, and germplasm accessions. DNA fingerprints are amplified by PCR using 21 pairs of fluorescence-labeled polymorphic ICSB (International Consortium of Sugarcane Biotechnologists) SSR primers, which are separated through capillary electrophoresis with fluorescence-labeled DNA size markers and visualized by GeneMapper™ or GeneMarker® software. A total of 144 SSR fingerprints are manually scored as “A” for presence or “C” for absence and recorded in a DNA sequence of fixed order based on the name of SSR primer pair and the size of fingerprint. The DNA sequence is saved as a <.seq> file to represent the SSR-based molecular identity of the sugarcane clone being fingerprinted to allow future analysis by the DNAMAN® software. As of 2024, about 7,200 molecular identities have been deposited into the database for cultivars, breeding lines, and related Saccharum species from Argentina, Australia, Bangladesh, Brazil, China, Colombia, India, Japan, Mexico, Pakistan, Philippines, South Africa, Thailand, USA (Louisiana, Florida, Texas, and Hawaii), and Venezuela. Multiple molecular identities have been constructed for certain Louisiana sugarcane cultivars and breeding lines across years and locations due to quality control. The molecular identity database has been successfully integrated into the Louisiana Sugarcane Breeding Program to help improve the overall efficacy of cultivar development and commercialization in the following areas: (1) provide molecular descriptors to newly registered cultivars; (2) identify in a timely fashion any mislabeled or unidentifiable clones from the cross parents and field evaluation plots; (3) assist in breeding energy cane varieties with a S. spontaneum cytoplasm; (4) assess cross fidelity and paternity of polycross; (5) determine genetic relatedness of parental clones; (6) select F1 hybrids from (elite x wild) or (wild x elite) crosses; and (7) investigate the inheritance of SSR markers in sugarcane.

Technical Abstract: It takes 12 to 14 years to develop a new sugarcane cultivar for commercial production. Clone mis-identification and mix-up often occur during vegetative propagation and germplasm exchange. To help the breeders deal with the potential problem, a simple sequence repeats (SSR)-based molecular identity database has been developed by the USDA-ARS in 2005 and annually updated by fingerprinting of newly designated varieties, parental clones, and germplasm accessions. DNA fingerprints are amplified by PCR using 21 pairs of fluorescence-labeled polymorphic ICSB (International Consortium of Sugarcane Biotechnologists) SSR primers, which are separated through capillary electrophoresis with fluorescence-labeled DNA size markers and visualized by GeneMapper™ or GeneMarker® software. A total of 144 SSR fingerprints are manually scored as “A” for presence or “C” for absence and recorded in a DNA sequence of fixed order based on the name of SSR primer pair and the size of fingerprint. The DNA sequence is saved as a <.seq> file to represent the SSR-based molecular identity of the sugarcane clone being fingerprinted to allow future analysis by the DNAMAN® software. As of 2024, about 7,200 molecular identities have been deposited into the database for cultivars, breeding lines, and related Saccharum species from Argentina, Australia, Bangladesh, Brazil, China, Colombia, India, Japan, Mexico, Pakistan, Philippines, South Africa, Thailand, USA (Louisiana, Florida, Texas, and Hawaii), and Venezuela. Multiple molecular identities have been constructed for certain Louisiana sugarcane cultivars and breeding lines across years and locations due to quality control. The molecular identity database has been successfully integrated into the Louisiana Sugarcane Breeding Program to help improve the overall efficacy of cultivar development and commercialization in the following areas: (1) provide molecular descriptors to newly registered cultivars; (2) identify in a timely fashion any mislabeled or unidentifiable clones from the cross parents and field evaluation plots; (3) assist in breeding energy cane varieties with a S. spontaneum cytoplasm; (4) assess cross fidelity and paternity of polycross; (5) determine genetic relatedness of parental clones; (6) select F1 hybrids from (elite x wild) or (wild x elite) crosses; and (7) investigate the inheritance of SSR markers in sugarcane.