Genetic Diversity of Populations of Saccharum spontaneum with Different Ploidy Levels Using SSR Molecular Markers

Liu, X. L.; Li, X. J.; Xu, Chaohua; Lin, Xiuqin; Deng, Zuhu

doi:10.1007/s12355-015-0399-5

Cited by 13 publications

(3 citation statements)

References 21 publications

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“…Later on a number of reports focused on the analysis of genetic diversity and population structure among commercial Saccharum spp. hybrids varieties 7,21–25 and among S. spontaneum populations with different ploidy levels in China 26 . Therefore, there has been an increasing interest among sugarcane breeders to investigate the genetic diversity of parental resources and to broaden the genetic base by tapping into the gene pools of the wild relatives 27–29 .…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Ali

Pan

Wang³

et al. 2019

Sci Rep

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In order to understand the genetic diversity and structure within and between the genera of Saccharum and Erianthus, 79 accessions from five species (S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense), six accessions of E. arundinaceus, and 30 Saccharum spp. hybrids were analyzed using 21 pairs of fluorescence-labeled highly poloymorphic SSR primers and a capillary electrophoresis (CE) detection system. A total of 167 polymorphic SSR alleles were identified by CE with a mean value of polymorphic information content (PIC) of 0.92. Genetic diversity parameters among these 115 accessions revealed that Saccharum spp. hybrids were more diverse than those of Saccharum and Erianthus species. Based on the SSR data, the 115 accessions were classified into seven main phylogenetic groups, which corresponded to the Saccharum and Erianthus genera through phylogenetic analysis and principle component analysis (PCA). We propose that seven core SSR primer pairs, namely, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, SMC24DUQ, mSSCIR3, and mSSCIR43, may have a wide appicability in genotype identification of Saccharum species and Saccharum spp. hybrids. Thus, the information from this study contibites to manage sugarcane genetic resources.

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Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Ali

Pan

Wang³

et al. 2019

Sci Rep

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“…According to (Liu et al, 2016), the study of genetic diversity is very important for understanding the evolution of different populations at the ploidy level that exists among them, for planning and implementing new crosses, and for better utilizing the broad genetic base of sugarcane to create new cultivars in breeding programs. Therefore, to assess genetic diversity in sugarcane cultivars, molecular markers such as Simple Sequence Repeats (SSR) loci, formed by simple repeated DNA sequences, also known as microsatellite loci, and EST-SSR (Expressed Sequence Tag-SSR) loci, which correspond to SSR loci contained within expressed DNA sequences, have been successfully used (Ali et al, 2017(Ali et al, , 2019Augusto et al, 2015;Maranho et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Selection of families obtained from caryopsis in a polyploid species (Saccharum spp.) using multicategory model

Borsuk,

Montini,

Neto

et al. 2023

Preprint

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Genetic diversity analysis is essential for sugarcane (Saccharum spp.) breeding programs. Crossbreeding based on genetic distances between the parental plants is one of the tools to increase genetic variability and enhance plant selection. The present study aimed to evaluate diversity within and between twelve families (A, B, C, D, E, F, G, H, I, J, K, and L) of sugarcane, derived from caryopses, using primers for sixteen microsatellite loci, five SSR (Simple Sequence Repeats) loci, and eleven EST-SSR (Expressed Sequence Tag-SSR) loci. Similarity calculations used the Bruvo`s distances among individuals and RST distances among families. The analysis of molecular variance (AMOVA) indicated that the majority of genetic variability is within families (72%), with only 28% found between families. The highest genetic similarity was observed between families E and I, while the lowest genetic similarity was between families K and D. Despite the high genetic similarity observed among the twelve sugarcane families in this study, the percentage of genetic variation within families in the 16 SSR and EST-SSR loci was high (72%), showing promise for exploitation in breeding programs to expand or restrict genetic variability in the selection of desirable morpho-agronomic traits in the crop. Furthermore, the study highlights the importance of using appropriate distances for diversity studies with co-dominant markers such as microsatellites in polyploid species.

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“…Since the late 1980s, the molecular markers including amplified fragment length polymorphisms (AFLP) [7][8][9], restriction fragment length polymorphisms (RFLP) [10], random amplification of polymorphic DNAs (RAPD) [11], single nucleotide polymorphism (SNP) [12], simple sequence repeats (SSRs) [13,14], inter simple sequence repeat (ISSRs) [15], and expressed sequence tag-simple sequence repeat (EST-SSRs) [16][17][18] were being developed by breeders and geneticists and applied in many sugarcane studies. Due to its co-dominant, multi-allelic characteristics, relative abundance, and high genome coverage, SSR primers are one of the most effective markers in plant genetics and breeding [19,20] and have been widely used to study sugarcane genetic diversity, genetic mapping, cross-transferability, paternity analysis, segregation analysis, and marker-assisted selection [21].…”

Section: Introductionmentioning

confidence: 99%

Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species

et al. 2022

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Sugarcane (Saccharum spp. hybrids) is one of the most important commercial crops for sugar, ethanol, and other byproducts production; therefore, it is of great significance to carry out genetic research. Assessing the genetic population structure and diversity plays a vital role in managing genetic resources and gene mapping. In this study, we assessed the genetic diversity and population structure among 196 Saccharum accessions, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 Saccharum spp. hybrids. A total of 624 polymorphic SSR alleles were amplified by PCR with 22 pairs of fluorescence-labeled highly polymorphic SSR primers and identified on a capillary electrophoresis (CE) detection system including 109 new alleles. Three approaches (model-based clustering, principal component analysis, and phylogenetic analysis) were conducted for population structure and genetic diversity analyses. The results showed that the 196 accessions could be grouped into either three (Q) or eight (q) sub-populations. Phylogenetic analysis indicated that most accessions from each species merged. The species S. barberi and S. sinense formed one group. The species S. robustum, S. barberi, S. spontaneum, S. edule, and sugarcane hybrids merged into the second group. The S. officinarum accessions formed the third group located between the other two groups. Two-way chi-square tests derived a total of 24 species-specific or species-associated SSR alleles, including four alleles each for S. officinarum, S. spontaneum, S. barberi, and S. sinense, five alleles for S. robustum. and three alleles for Saccharum spp. hybrids. These species-specific or species-associated SSR alleles will have a wide application value in sugarcane breeding and species identification. The overall results provide useful information for future genetic study of the Saccharum genus and efficient utilization of sugarcane germplasm resources in sugarcane breeding.

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Genetic Diversity of Populations of Saccharum spontaneum with Different Ploidy Levels Using SSR Molecular Markers

Cited by 13 publications

References 21 publications

Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Selection of families obtained from caryopsis in a polyploid species (Saccharum spp.) using multicategory model

Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species

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