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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #327769

Research Project: Genetic Improvement of Sugarcane for Temperate Climates

Location: Sugarcane Research

Title: SSR-CE/FD assessment of Guizhou approved sugarcane cultivars and regional materials

Author
item Fu, Yu-hua - Collaborator
item Pan, Yong-bao
item Lei, Chao-yun - Collaborator
item Xie, Hui-jue - Collaborator
item Lei, Shi-fu - Collaborator
item Lu, Jia-ju - Collaborator

Submitted to: Chinese Science Bulletin
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2016
Publication Date: 4/26/2017
Citation: Fu, Y.-H, Pan, Y.-B., Lei, C.-Y., Xie, H.-J., Lei, S.-F., Lu, J.-J. 2017. SSR-CE/FD assessment of Guizhou approved sugarcane cultivars and regional materials. Chinese Agricultural Science Bulletin. 33(8):5-12.

Interpretive Summary: Sugar- or chewing cane clones developed from the Karst region in Guizhou Province, China provide unique genetic resource to the sugarcane germplasm. Characterization of these clones has been limited to morphological traits, which often are not stable due to extreme level of gene x environment interaction. Molecular fingerprints from a cultivar’s whole DNA are stable and not influenced by time and environment changes. This study aimed to construct DNA fingerprints for 12 sugar- or chewing cane clones from the Karst region using the SSR-CE/FD DNA fingerprinting technique developed by the USDA-ARS. A total of 131 fluorescence-labeled DNA fragments were identified, of which 118 fragments showed variable distribution among the 12 clones. Eleven DNA fragments were clone-specific; each SSR-DNA fragment could be used to distinguish the fragment-bearing clone from the other clones. The SMC31CUQ primer pair was the most efficient marker that could distinguish all the 12 clones from one another. The presence (coded as 1) or absence (coded as 0) of each of the 131 DNA fragments in a clone was recorded a sequential order to represent the molecular fingerprints or identity of that clone. Pairwise similarity values among these 12 molecular fingerprints varied from 64% to 92%, an indication of a narrow genetic base. The sugarcane breeders from the Karst region can use these molecular identities to barcode their sugar- or chewing cane cultivars, thereby safeguarding germplasm evaluation and exchange activities between different regions and breeding institutions.

Technical Abstract: Twelve sugarcane genotypes (three cultivars and nine clones involved in regional tests) from Guizhou Province, China were analyzed using SSR-capillary electrophoresis/fluorescence detection (SSR-CE/FD) technology to construct the SSR fingerprints and assess the genetic diversity. A total of 131 DNA fragments or alleles were amplified through PCR by 21 pairs of highly polymorphic SSR primers with an average of 6.2 alleles per primer pair. One hundred and eighteen alleles (90.1%) were polymorphic. Eleven alleles from seven genotypes were genotype-specific; each was able to identify the allele-bearing genotype from the other genotypes. The SMC31CUQ primer pair was the most efficient marker that could distinguish all the 12 genotypes from one another. The molecular identity of each genotype was constructed by the presence or absence of these 131 SSR alleles following a sequential order. Using the UPGMA program of NTSys software, pairwise similarity coefficients among the 12 molecular identities varied from 0.64 to 0.92, indicating a narrow genetic base for these sugarcane genotypes.