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

Ali, Ahmad; Pan, Yong‐Bao; Wang, Qinnan; Wang, Jinda; Chen, Jun-Lü; Gao, San‐Ji

doi:10.1038/s41598-018-36630-7

Cited by 52 publications

(41 citation statements)

References 35 publications

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“…In the first PCA ( Fig 1A), into A group, the Erianthus accessions were clearly divergent from the Saccharum accessions, supporting the taxonomic evidence which assigned each of them to a separate genus [77]. Our result agrees with other studies that used AFLP [78,79], cpSSR [80], TRAP [21,30,59], SRAP [55] and SSR [3,81] markers. The introgression of alleles of the Erianthus genus in sugarcane breeding programs, mainly from E. arundinaceus, has been evaluated in recent years to increase adaptability, disease resistance, drought resistance and biomass production [82,83].…”

Section: Discussionsupporting

confidence: 89%

“…According to marker nature, is expected that genomic markers, such as AFLP and SSR markers, show higher polymorphism content than functional markers, since in transcribed regions the DNA sequences are more conserved [26,29]. However, PIC and DP averages values obtained in our study by functional TRAP markers were higher than related by other works in sugarcane [21,29,30,59,60] even when these values were compared with genomic markers [3,23]. Moreover, functional markers are more efficient for gene tagging than genomic markers and, consequently, facilitate the introgression of alleles that potentially control agronomic traits of interest by breeding programs [21,28,32,57].…”

Section: Discussioncontrasting

confidence: 58%

“…Sugarcane, a high efficiency photosynthetic grass, is important for economy of many countries in the tropics and subtropics, playing a central role as a primary sugar-producing crop and has major potential as a bioenergy crop [1][2][3]. The modern sugarcane cultivars originate from the Saccharum complex, which gathers two wild Saccharum species (S. spontaneum and S. robustusm), four cultivated species (S. officinarum, S. sinense, S. barberi and S. edule) and four related interbreeding genera (Erianthus, Miscanthus, Narenga and Sclerostachya) [4][5][6][7].…”

Section: Introductionmentioning

confidence: 99%

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Molecular diversity and genetic structure of Saccharum complex accessions

Balsalobre

Carneiro

2020

PLoS ONE

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Sugarcane is an important crop for food and energy security, providing sucrose and bioethanol from sugar content and bioelectricity from lignocellulosic bagasse. In order to evaluate the diversity and genetic structure of the Brazilian Panel of Sugarcane Genotypes (BPSG), a core collection composed by 254 accessions of the Saccharum complex, eight TRAP markers anchored in sucrose and lignin metabolism genes were evaluated. A total of 584 polymorphic fragments were identified and used to investigate the genetic structure of BPSG through analysis of molecular variance (AMOVA), principal components analysis (PCA), a Bayesian method using STRUCTURE software, genetic dissimilarity and phylogenetic tree. AMOVA showed a moderate genetic differentiation between ancestors and improved accessions, 0.14, and the molecular variance was higher within populations than among populations, with values of 86%, 95% and 97% when constrasting improved with ancestors, foreign with ancestors and improved with foreign, respectively. The PCA approach suggests clustering in according with evolutionary and Brazilian breeding sugarcane history, since improved accessions from older generations were positioned closer to ancestors than improved accessions from recent generations. This result was also confirmed by STRUCTURE analysis and phylogenetic tree. The Bayesian method was able to separate ancestors of the improved accessions while the phylogenetic tree showed clusters considering the family relatedness within three major clades; the first being composed mainly by ancestors and the other two mainly by improved accessions. This work can contribute to better management of the crosses considering functional regions of the sugarcane genome.

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Section: Discussionsupporting

confidence: 89%

Section: Discussioncontrasting

confidence: 58%

Section: Introductionmentioning

confidence: 99%

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Molecular diversity and genetic structure of Saccharum complex accessions

Balsalobre

Carneiro

2020

PLoS ONE

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“…Among PCR-based markers, SSR (microsatellite) markers are considered one of the most efficient markers for plant breeding due to large quantity, low dosage, co-dominant, reliability and multi-allelic detecting [22]. SSR markers have been used widely to study sugarcane genetic diversity and population structure [22][23][24], variety identity [25], genetic map [26,27], and genetic association [28][29][30].…”

Section: Introductionmentioning

confidence: 99%

“…SSR markers have been used widely to study sugarcane genetic diversity and population structure [22][23][24], variety identity [25], genetic map [26,27], and genetic association [28][29][30]. Furthermore, fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) have manifested better performance in genotyping of polyploid sugarcane, due to higher accuracy and better detection power [22][23][24][31][32][33][34][35][36][37]. Now, this paper reports a study that was designed to manage the parental germplasm of the sugarcane breeding programs in China through the microsatellite (SSR) DNA fingerprinting using fluorescence-labeled SSR primers and the high-performance capillary electrophoresis (HPCE) system.…”

Section: Introductionmentioning

confidence: 99%

SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

Jiantao¹,

Wang²,

Xie³

et al. 2019

Agronomy

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Sugarcane (Saccharum spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improvement through breeding. In order to understand genetic characteristics of parental lines used in sugarcane breeding programs in China, 150 of the most popular accessions were analyzed with 21 fluorescence-labeled simple sequence repeats (SSR) markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among the series obtained from different origins, the YC-series, which contained eight unique alleles, had the highest genetic diversity. Based on the population structure analysis, the principal coordinate analysis (PCoA) and phylogenetic analysis, the 150 accessions were clustered into two distinct sub-populations (Pop1 and Pop2). Pop1 contained the majority of clones introduced to China (including 28/29 CP-series accessions) while accessions native to China clustered in Pop2. The analysis of molecular variance (AMOVA), fixation index (Fst) value and gene flow (Nm) value all indicated the very low genetic differentiation between the two groups. This study illustrated that fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) could be a very useful tool for genotyping of the polyploidy sugarcane. The results provided valuable information for sugarcane breeders to better manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar(s).

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A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data

Wang

Gao

Liu

et al. 2022

Ecology and Evolution

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Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next‐generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi‐sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared‐pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high‐quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies.

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

Cited by 52 publications

References 35 publications

Molecular diversity and genetic structure of Saccharum complex accessions

Molecular diversity and genetic structure of Saccharum complex accessions

SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data

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