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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC IMPROVEMENT OF SUGARCANE BY CONVENTIONAL AND MOLECULAR APPROACHES Title: Genetic variability among the chloroplast genomes of sugarcane (Saccharum spp.) and its wild progenitor species Saccharum spontaneum L.

Authors
item Zhu, Jian -
item Zhou, Hui -
item Pan, Yong-Bao
item Lu, X -

Submitted to: Genetics and Molecular Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 11, 2013
Publication Date: January 24, 2014
Repository URL: http://handle.nal.usda.gov/10113/59003
Citation: Zhu, J.R., Zhou, H., Pan, Y.-B., Lu, X. 2014. Genetic variability among the chloroplast genomes of sugarcane (Saccharum spp.) and its wild progenitor species Saccharum spontaneum L. Genetics and Molecular Research. 13(2):3037-3047. DOI: 10.4238/2014.January.24.3.

Interpretive Summary: As interspecific hybrids between tropical sugarcane species (S. officinarum) and related wild species (S. spontaneum), the nuclear genomes of modern sugarcane cultivars consist of chromosomes from both ancestors. However, the cytoplasmic genomes of modern sugarcane cultivars, located in sub-cellular organs, called chloroplasts (cp) and mitochondria (mt), are derived only from the tropical sugarcane. In order to explore the potential value of S. spontaneum cytoplasm, a new line of sugarcane hybrids were produced at the USDA-ARS, Sugarcane Research Laboratory that contain cytoplasm from S. spontaneum. This study was conducted to analyze the genetic variability of cpDNA of four sugarcane cultivars, eight S. spontaneum clones, and three new hybrids that contain a S. spontaneum cytoplasm. We found from the public GenBank database complete cpDNA sequences of two sugarcane cultivars, NCo 310 and SP 80-3280, and five related grass species, namely barley, maize, rice, sorghum, and wheat. These cpDNA sequences were aligned and 19 cpDNA segments were identified as targets for PCR amplification and nucleotide sequencing. PCR primer pairs were designed targeting each of these 19 cpDNA segments. Ten of the 19 cpDNA segments showed variability among the 15 specimen harboring 14 mutation sites. The result of mutation analysis demonstrated for the first time that the cpDNA of S. spontaneum was maternally inherited. Furthermore, comparative sequence homology analysis put sugarcane cultivars into a distinct group, while the eight S. spontaneum specimen and the three new hybrids into another group. We also found three mutation sites with consistent, yet species-specific, nucleotide composition. The genetic variability among cpDNA of sugarcane cultivars and S. spontaneum will be useful information for the determination of maternal origin in Saccharum genus.

Technical Abstract: A striking characteristic of modern sugarcane is that all sugarcane cultivars (Saccharum spp.) share a common cytoplasm from S. officinarum. To explore the potential value of S. spontaneum cytoplasm, new Saccharum hybrids with a S. spontaneum cytoplasm were developed at the USDA-ARS, sugarcane research Laboratory through a combination of conventional and molecular breeding approaches. In this study, we analyzed the genetic variability among the chloroplast genomes of four sugarcane cultivars, eight S. spontaneum clones, and three F1 progeny containing a S. spontaneum cytoplasm. Based on the complete chloroplast genome sequence information of two sugarcane cultivars (NCo 310 and SP 80-3280) and five related grass species (barley, maize, rice, sorghum, and wheat), 19 PCR primer pairs were designed targeting various chloroplast DNA (cpDNA) segments with a total length varying from 4,781 to 4,791 bp. Ten of the 19 cpDNA segments were polymorphic harboring 14 mutation sites [a 15-nt indel, a 5-nt indel, two poly (T), and 10 single nucleotide polymorphisms (SNPs)]. We demonstrate for the first time that the chloroplast genome of S. spontaneum was maternally inherited. Comparative sequence homology analyses clustered sugarcane cultivars into a distinctive group away from S. spontaneum and its progeny. Three mutation sites with consistent, yet species-specific, nucleotide composition were found, namely, an A/C transversion and two indels. The genetic variability among cpDNA of sugarcane cultivars and S. spontaneum will be useful information for the determination of maternal origin in Saccharum genus.

Last Modified: 10/30/2014
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