Genetic variability among the chloroplast genomes of sugarcane (Saccharum spp) and its wild progenitor species Saccharum spontaneum L.

Zhu, J.-R.; Zhou, Hui; Pan, Yong‐Bao; Lü, Xin

doi:10.4238/2014.january.24.3

Cited by 9 publications

(4 citation statements)

References 20 publications

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“…Variability in the chloroplast genome had been widely used to investigate phylogenetic relationships and genetic variation among the different species of Saccharum complex (D'Hont et al 1993;Al-Janabi et al 1994;Sobral et al 1994;Takahashi et al 2005;Zhu et al 2014). The present study in chloroplast genetic variation in the Saccharum complex based on cpSSR proved useful in establishing the cytoplasmic variability existing in the Saccharum complex.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers

et al. 2015

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A basic understanding of the cytoplasmic diversity of Saccharum complex comprising of Saccharum species and related genera is essential for broadening the cytoplasmic base of sugarcane cultivars. In the present study markers generated by nine chloroplast microsatellite primer pairs designed from sugarcane chloroplast genome were used to establish the genetic relationship and phylogeny among 43 accessions belonging to different species of Saccharum and related genera representing the Saccharum complex. The polymorphic primer pairs amplified an average of six alleles per loci and possess relatively high polymorphism information content. Molecular diversity was estimated using 54 polymorphic markers. The overall chloroplast genetic diversity in the Saccharum complex was found to be 53 %. The genetic diversity among Saccharum species was 22 %. Among the Saccharum species S. spontaneum was found to be distinct from other species of Saccharum and cpSSR markers could efficiently distinguish S. spontaneum from rest of the Saccharum spcies. Ripidium, one of the most primitive among the Saccharum complex showed the highest genetic diversity (90 %) with Saccharum. Miscanthus, another primitive genus of Saccharum complex was found to be more closely related to Saccharum than Erianthus. In view of the high genetic diversity, the present study supports the utilization of different species of Erianthus in the sugarcane breeding programmes for broadening the cytoplasmic base of the sugarcane varieties.

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Section: Discussionmentioning

confidence: 99%

Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers

et al. 2015

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“…Chloroplasts (cp) are inherited maternally in most plants, and each of these organelles contains a quadripartite circular molecule of double-stranded DNA that comprises two inverted repeats (IRs), and single-copy regions, the large and small single-copy regions (LSC and SSC). Like most angiosperms, the chloroplasts of sugarcane are inherited maternally [ 6 ]. As a result of their relatively small size, simple structure, and conserved gene content, cpDNA sequences have been widely used for phylogenetic studies, and complete cp genome sequences could provide valuable datasets for resolving taxonomical complexes and/or DNA barcoding (e.g., matK and rbcL ) [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of ‘Saccharum Complex’

WeiXing

Zhao

et al. 2022

IJMS

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High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ‘Saccharum Complex’, and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species.

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“…With the recent advances in molecular markers and genomics-based techniques, the evolutionary aspects of the Saccharum complex and its related genera are beginning to be explored without any ambiguities. Chloroplast DNA, mitochondrial and nuclear ribosomal gene markers were applied to establish the probable polyphyletic origins of Saccharum with sorghum, Erianthus, Miscanthus , and other related genera ( D’Hont et al, 1993 , 1995 ; Selvi et al, 2005 ; Tambarussi et al, 2009 ; Singh et al, 2010 ; Viola et al, 2011 ; Zhu et al, 2014 ; Raj et al, 2016 ). It was found that the closest sugarcane diploid relative that could be identified till date, is Narenga porphyrocoma ( Al-Janabi et al, 1993 ), which had diverged from sugarcane at 2.5 MYA, while S. spontaneum and S. officinarum diverged at 1.5–2 MYA ( Garsmeur et al, 2011 ).…”

Section: Comparative Genomicsmentioning

confidence: 99%

The Challenge of Analyzing the Sugarcane Genome

2018

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Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.

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Genetic variability among the chloroplast genomes of sugarcane (Saccharum spp) and its wild progenitor species Saccharum spontaneum L.

Cited by 9 publications

References 20 publications

Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers

Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers

Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of ‘Saccharum Complex’

The Challenge of Analyzing the Sugarcane Genome

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