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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #351501
Title: Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Author
item ALI, AHMAD - Fujian Agricultural & Forestry University
item Pan, Yong-Bao
item WANG, QIN-NAN - Collaborator
item WANG, JIN-DA - Fujian Agricultural & Forestry University
item CHEN, JUN-LU - Collaborator
item GAO, SAN-JI - Fujian Agricultural & Forestry University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/26/2018
Publication Date: 1/23/2019
Citation: Ali, A., Pan, Y.-B. Wang, Q., Wang, J., Chen, J., Gao, S. 2019. Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers. Scientific Reports. 9:1-10. https://doi.org/10.1038/s41598-018-36630-7.
DOI: https://doi.org/10.1038/s41598-018-36630-7

Interpretive Summary: Sugarcane has a complex nuclear genome with each of the chromosomes in multiple copies, therefore, it requires a large number of highly informative DNA markers for genetics breeding research. In this study, highly polymorphic microsatellite (SSR) DNA markers were used to reveal the genetic structure and diversity within and among six species of the Saccharum genus. Forty-five Saccharum accessions along with eight sugarcane cultivars were involved, from which SSR DNA fragments were amplified through PCR with 21 pairs of fluorescence-labeled, highly poloymorphic SSR primers. The amplified SSR fragments were detected by two platforms, i.e., capillary electrophoresis (CE) and polyacrylamid gel electrophoresis (PAGE). While 167 SSR fragments were identified by CE, only 120 were identified by PAGE. The average polymorphic information content (PIC) value was 0.94 for CE and 0.92 for PAGE. Genetic diversity analysis showed that sugarcane cultivars weres more diverse than the six Saccharum species, while phylogenetic and principle component analyses clustered the 45 Saccharum accessions into seven groups corresponding to the Saccharum species. Based on the results, it is proposed that six primer pairs, namely, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, mSSCIR3, and mSSCIR43, are very useful in the identification of Saccharum species and sugarcane cultivars. The information from this study can be used to effectively manage the genetic resource in sugarcane breeding process.

Technical Abstract: Simple Sequence Repeat (SSR) markers are capable of revealing a high degree of polymorphism. Having a complex allopolyploid genome, Saccharum spp. requires a higher number of highly informative markers for various applications in genetics and breeding. In order to understand the genetic structure and diversity within and among species of the highly complex polyploid genus Saccharum, 45 accessions from six species (S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense, and S. arundinaceus) along with eight Saccharum spp. hybrids were analyzed with 21 pairs of fluorescence-labeled highly poloymorphic SSR primers utilizing two detections systems; i.e., capillary electrophoresis (CE) and polyacrylamid gel electrophoresis (PAGE). A total of 167 polymorphic SSR alleles including 38 new alleles identified by CE, and 120 alleles by PAGE. The mean value of polymorphic information content (PIC) was 0.94 for CE and 0.92 for PAGE, respectively. Genetic diversity parameters among the Saccharum species revealed that, Saccharum spp. hybrids weres more diverse than the six Saccharum species. Using 21 SSR primer pairs, the 45 accessions were classified into seven groups which corresponded to the Saccharum species based on phylogenetic analysis and principle component analysis (PCA). We also proposed that six core SSR primer pairs (SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, mSSCIR3 and mSSCIR43) could be widely used in genotype identification of Saccharum species and Saccharum spp. hybirds. Thus, the information from this study can be used in genetic resource management.