Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane

Singh, Rameshwar; Jena, Satya Narayan; Khan, Mohammad Suhail; Yadav, S. K.; Banarjee, Nandita; Raghuvanshi, Saurabh; Bhardwaj, Vasudha; Dattamajumder, Sanjay K.; Kapur, Raman; Solomon, S.; Swapna, M.; Srivastava, Sangeeta; Tyagi, Akhilesh K.

doi:10.1016/j.gene.2013.03.125

Cited by 47 publications

(44 citation statements)

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“…EST-SSR markers have important implications for genetic analysis and exploitation of the genetic resources of sugarcane as they provide a more direct estimate of functional diversity (Oliveira et al 2009). Previous studies reported EST-SSR primers and their biological/functional annotation (Pinto et al 2004;Oliveira et al 2009;Marconi et al 2011;Singh et al 2013). The present study indicated the usefulness of EST-SSR markers and a few g-SSR markers selected from the earlier reports for AM in sugarcane.…”

Section: Discussionsupporting

confidence: 64%

“…Genotyping A set of 123 polymorphic SSR primers comprising 21 g-SSRs (Govindaraj et al 2005;Parida et al 2009), and 102 EST-SSRs (Pinto et al 2004;Oliveira et al 2009;Singh et al 2013) were used for genotyping (Table 1, S2). Amplification was carried out in a 10 ll reaction volume consisting of 19 PCR assay buffer, 200 mM of each dNTPs (Bangalore Genei Pvt.…”

Section: Crop Raising and Phenotypingmentioning

confidence: 99%

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Marker-trait association study for sucrose and yield contributing traits in sugarcane (Saccharum spp. hybrid)

et al. 2015

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Linkage disequilibrium (LD)-based marker-trait association (MTA) was used to identify markers for sucrose and yield contributing traits in a panel of 108 sugarcane genotypes from sub-tropical India. Population structure (Q), kinship (K), and MTA study exploited a set of 989 marker loci generated from 123 genomic-and expressed sequence tag-SSR primers. The mixed linear model (MLM) coupled with a modified algorithm for population structure (Q) analysis was able to control both type I and type II errors and provided a deeper understanding of the genetics, population stratification and its manifestations on LD in the sugarcane genome. Significant associations were identified for four markers with cane diameter, seven markers each with cane length and number of millable canes (NMCs), eleven markers with number of nodes, six with sucrose per cent, and five markers with average cane weight. A total of 15 markers stable for all the 3 years of study explained 57 % trait variation for NMCs, 34 % for cane width, 27 % for cane length, 20 % for sucrose content, and 19 % for number of nodes. The frequent deviation of structure-based profiles from pedigree-based grouping in this complex heterozygous system reinforced the importance of using genotypic data for selection and breeding. The results contribute to a deeper insight of the complex genome and the identified MTAs could be exploited to fine-tune marker-assisted breeding programmes in genetically complex sugarcane crop.

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Section: Discussionsupporting

confidence: 64%

Section: Crop Raising and Phenotypingmentioning

confidence: 99%

Marker-trait association study for sucrose and yield contributing traits in sugarcane (Saccharum spp. hybrid)

et al. 2015

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“…Such results are quite obvious in view of the fact that sugarcane possesses a mosaic genome which is a highly heterozygous Fig. 1 The STRUCTURE generated profiles of the 92 sugarcane varieties from subtropical India (Each one of the 92 Sugarcane varietal profiles is depicted as a vertical column and based on their similarity, grouped into seven sub clusters) and complex conglomerate of randomly segregating long stretches of genetic elements (Singh et al 2013). A very high average gene-flow value (0.59) between population sub-clusters also supports this theory and indicates a mixed ancestry for all the sugarcane varieties in current study.…”

Section: Discussionmentioning

confidence: 99%

“…Genotyping was carried out using a set of 174 polymorphic SSR primers (Table S3) comprising of 43 genomic SSRs (Govindaraj et al 2005;Parida et al 2009), and 131 EST-SSRs (Pinto et al 2004;Oliveira et al 2009;Singh et al 2013). DNA amplification was carried out in a 15 lL reaction volume consisting of 1 9 PCR assay buffer, 200 mM of each dNTPs (Fermentas, USA), 12 ng (1.8 pmol) each of forward and reverse primers (Operon Biotechnologies, GmbH, Germany), 0.5 units of Taq DNA polymerase (Fermentas, USA) and 25 ng genomic DNA using a thermal cycler (MyCycler, Biorad, USA).…”

Section: Genotyping Using Ssr Markersmentioning

confidence: 99%

Identification of marker-trait associations for morphological descriptors and yield component traits in sugarcane

Siraree

Banerjee

Khan

et al. 2016

Physiol Mol Biol Plants

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Ninety two sugarcane varieties from sub-tropical India were subjected to molecular profiling with 174 simple sequence repeat markers and characterized for 23 qualitative (morphological descriptors) and nine quantitative traits that directly or indirectly contribute to yield and juice quality. Using STRUCTURE-based population stratification study and a mixed linear model for marker-trait association (MTA) analysis, a total of 60 MTAs were identified for 22 qualitative traits that were able to explain a significantly higher (up to 40%) proportion of the phenotypic variations compared to all the previous reports of MTA studies in sugarcane. In addition, 21 MTAs stable over the three years of study were also identified for nine quantitative traits that explained 16-37% of the total trait variation. It could be concluded that the qualitative traits that are governed mostly by one or a few genes are more responsive to MTA studies and hence have a better potential to be adopted in marker-assisted breeding programmes in sugarcane. The MTAs identified in this study could also find significant applications in upcoming more stringent IP regime, which may necessitate tracking of specific alleles integrated in breeding programmes.

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“…The binary data were used to calculate genetic parameters using PopGene v1.32. The polymorphism information content (PIC) value for each SSR marker was calculated as described previously (Huang, 2013;Singh et al, 2013). For C. chekangoleosa (diploid) and C. japonica (diploid), statistical analysis treated the SSRs as codominant markers.…”

Section: Discussionmentioning

confidence: 99%

Development and cross-species transferability of unigene-derived microsatellite markers in an edible oil woody plant, Camellia oleifera (Theaceae)

Jia¹,

Lin²,

Feng³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Camellia oleifera is an important edible oil woody plant in China. Lack of useful molecular markers hinders current genetic research on this tree species. Transcriptome sequencing of developing C. oleifera seeds generated 69,798 unigenes. A total of 6949 putative microsatellites were discovered among 6042 SSRcontaining unigenes. Then, 150 simple sequence repeats (SSRs) were evaluated in 20 varieties of C. oleifera. Of these, 52 SSRs revealed (2015) polymorphism, with the number of alleles per locus ranging from 2 to 15 and expected heterozygosity values from 0.269 to 0.888. The polymorphic information content varied from 0.32 to 0.897. Crossspecies transferability rates in Camellia chekangoleosa and Camellia japonica were 90.4 and 78.8%, respectively. The 52 polymorphic unigene-derived SSR markers serve to enrich existing microsatellite marker resources for C. oleifera and offer potential for applications in genetic diversity evaluation, molecular fingerprinting, and genetic mapping in C. oleifera, C. chekangoleosa, and C. japonica.

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Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane

Cited by 47 publications

References 58 publications

Marker-trait association study for sucrose and yield contributing traits in sugarcane (Saccharum spp. hybrid)

Marker-trait association study for sucrose and yield contributing traits in sugarcane (Saccharum spp. hybrid)

Identification of marker-trait associations for morphological descriptors and yield component traits in sugarcane

Development and cross-species transferability of unigene-derived microsatellite markers in an edible oil woody plant, Camellia oleifera (Theaceae)

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