Genetic Diversity and Population Structure Analysis of Saccharum and Erianthus Genera Using Microsatellite (SSR) Markers

Overview

Journal Sci Rep

Specialty Science

Date 2019 Jan 25

PMID 30674931

Citations 18

Authors

Ahmad Ali

Yong-Bao Pan

Qin-Nan Wang

Jin-da Wang

Jun-Lu Chen

San-Ji Gao

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Genetic association analysis in sugarcane (Saccharum spp.) for sucrose accumulation in humid environments in Colombia.

Saavedra-Diaz C, Trujillo-Montenegro J, Jaimes H, Londono A, Villareal F, Lopez L BMC Plant Biol. 2024; 24(1):570.

PMID: 38886648 PMC: 11184777. DOI: 10.1186/s12870-024-05233-y.

Genetic diversity and population structure of sugarcane introgressed hybrids by SSR markers.

Elumalai K, Srinivasan A 3 Biotech. 2023; 13(12):399.

PMID: 37974927 PMC: 10645997. DOI: 10.1007/s13205-023-03823-5.

De novo assembly of Iron-Heart Cunninghamia lanceolata transcriptome and EST-SSR marker development for genetic diversity analysis.

Liu S, He G, Xie G, Gong Y, Zhu N, Xiao C PLoS One. 2023; 18(11):e0293245.

PMID: 37917740 PMC: 10621985. DOI: 10.1371/journal.pone.0293245.

Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors.

Li A, Liao F, Wang M, Chen Z, Qin C, Huang R Int J Mol Sci. 2023; 24(10).

PMID: 37240257 PMC: 10219567. DOI: 10.3390/ijms24108913.

Small cardamom genome: development and utilization of microsatellite markers from a draft genome sequence of Maton.

Gaikwad A, Kumari R, Yadav S, Rangan P, Wankhede D, Bhat K Front Plant Sci. 2023; 14:1161499.

PMID: 37235027 PMC: 10206324. DOI: 10.3389/fpls.2023.1161499.

References

Cordeiro , Taylor , Henry . Characterisation of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploid species. Plant Sci. 2000; 155(2):161-168. DOI: 10.1016/s0168-9452(00)00208-9. View

Pan Y, Burner D, Legendre B . An assessment of the phylogenetic relationship among sugarcane and related taxa based on the nucleotide sequence of 5S rRNA intergenic spacers. Genetica. 2001; 108(3):285-95. DOI: 10.1023/a:1004191625603. View

DHont A, Paulet F, Glaszmann J . Oligoclonal interspecific origin of 'North Indian' and 'Chinese' sugarcanes. Chromosome Res. 2002; 10(3):253-62. DOI: 10.1023/a:1015204424287. View

Selvi A, Nair N, Balasundaram N, Mohapatra T . Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane. Genome. 2003; 46(3):394-403. DOI: 10.1139/g03-018. View

Schenck S, Crepeau M, Wu K, Moore P, Yu Q, Ming R . Genetic diversity and relationships in native Hawaiian Saccharum officinarum sugarcane. J Hered. 2004; 95(4):327-31. DOI: 10.1093/jhered/esh052. View

Aitken K, Jackson P, McIntyre C . A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar. Theor Appl Genet. 2005; 110(5):789-801. DOI: 10.1007/s00122-004-1813-7. View

Dillon S, Shapter F, Henry R, Cordeiro G, Izquierdo L, Lee L . Domestication to crop improvement: genetic resources for Sorghum and Saccharum (Andropogoneae). Ann Bot. 2007; 100(5):975-89. PMC: 2759214. DOI: 10.1093/aob/mcm192. View

Parida S, Kalia S, Kaul S, Dalal V, Hemaprabha G, Selvi A . Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet. 2008; 118(2):327-38. DOI: 10.1007/s00122-008-0902-4. View

Waclawovsky A, Sato P, Lembke C, Moore P, Souza G . Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnol J. 2010; 8(3):263-76. DOI: 10.1111/j.1467-7652.2009.00491.x. View

10.

Schliep K . phangorn: phylogenetic analysis in R. Bioinformatics. 2010; 27(4):592-3. PMC: 3035803. DOI: 10.1093/bioinformatics/btq706. View

11.

Singh R, Jena S, Khan S, Yadav S, Banarjee N, Raghuvanshi S . Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene. 2013; 524(2):309-29. DOI: 10.1016/j.gene.2013.03.125. View

12.

You Q, Xu L, Zheng Y, Que Y . Genetic diversity analysis of sugarcane parents in Chinese breeding programmes using gSSR markers. ScientificWorldJournal. 2013; 2013:613062. PMC: 3749591. DOI: 10.1155/2013/613062. View

13.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S . MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013; 30(12):2725-9. PMC: 3840312. DOI: 10.1093/molbev/mst197. View

14.

Nayak S, Song J, Villa A, Pathak B, Ayala-Silva T, Yang X . Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction. PLoS One. 2014; 9(10):e110856. PMC: 4205016. DOI: 10.1371/journal.pone.0110856. View

15.

Galili T . dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics. 2015; 31(22):3718-20. PMC: 4817050. DOI: 10.1093/bioinformatics/btv428. View

16.

Lu X, Zhou H, Pan Y, Chen C, Zhu J, Chen P . Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids. Genet Mol Res. 2016; 14(4):18384-95. DOI: 10.4238/2015.December.23.26. View

17.

Singh R, Banerjee N, Khan M, Yadav S, Kumar S, Duttamajumder S . Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping. Mol Genet Genomics. 2016; 291(3):1363-77. DOI: 10.1007/s00438-016-1190-3. View

18.

Yan J, Zhang J, Sun K, Chang D, Bai S, Shen Y . Ploidy Level and DNA Content of Erianthus arundinaceus as Determined by Flow Cytometry and the Association with Biological Characteristics. PLoS One. 2016; 11(3):e0151948. PMC: 4806844. DOI: 10.1371/journal.pone.0151948. View