Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs)

Kong, Li; Dong, Jiaqi; Hart, G. E.

doi:10.1007/s001220051501

Cited by 187 publications

(159 citation statements)

References 29 publications

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“…The average number of alleles, 15.1 per locus, for the seven SSR loci was higher than values reported in other studies on sorghum (Brown et al, 1996;Taramino et al, 1997;Dean et al, 1999;Kong et al, 2000;Deu et al, 2010;Weerasooriya et al, 2016). We used a higher number of landraces than previous authors, and this may account for some of these differences.…”

Section: Genetic Diversitycontrasting

confidence: 61%

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DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces

Desmae¹,

Jordan²,

Godwin³

2016

Afr. J. Biotechnol.

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North Eastern Ethiopia is a major sorghum-growing region. A total of 415 sorghum landraces were sampled to represent the range of agro-ecologies (three altitude ranges) as well as spatial heterogeneity, that is, 4 zones: North Welo, South Welo, Oromiya and North Shewa with each zone containing 2 to 5 districts. The landraces were genotyped with simple sequence repeats (SSR) and inter simple sequence repeats (ISSR) markers. High genetic diversity was observed among the landraces for both marker systems. STRUCTURE analysis revealed 4 clusters of genetically differentiated groups of landraces. Cluster analysis revealed a close relationship between landraces along geographic proximity with genetic distance between landraces increasing with an increase in geographic distance. The grouping of landraces based on districts was influenced by clinal trend and geographic proximity. The F ST statistics showed significant geographic differentiation among landraces at various levels of predefined geographic origin but a large portion of the variation was among landraces within rather than between predefined populations. The landraces from North Shewa were predominantly in one cluster, and landraces from this area also exhibited the greatest allelic diversity and the highest number of private alleles. There was low variation among the highland Zengada landraces, but these landraces were quite strongly differentiated and fell into one population cluster. The low to moderate genetic differentiation between landraces from various geographic origins could be attributed to gene flow across the region as a consequence of seed exchange among farmers.

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Section: Genetic Diversitycontrasting

confidence: 61%

“…Seven sorghum SSR markers (Brown et al, 1996;Taramino et al, 1997;Dean et al, 1999;Kong et al, 2000) were selected based on their polymorphism, amplified product size range and genome coverage. The M13 primer tailing system (Schuelke, 2000) was used to fluorescently label PCR products.…”

Section: Ssr Analysismentioning

confidence: 99%

DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces

Desmae¹,

Jordan²,

Godwin³

2016

Afr. J. Biotechnol.

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“…After drying, leaf samples were ground using a Geno-grinder (RETSCH) at 500 strokes per minute for 9 minutes and then DNA was extracted following a Mixed Alkyl Trimethyl Ammonium Bromide (MATAB) method (Frost et al, 2007 mSBCIR238,mSBCIR222,mSBCIR225,mSBCIR314,mSBCIR188,mSBCIR243,gpsb014,gpsb079,gpsb098,gpsb123,gpsb133,gpsb136,gpsb158,Sbagb02,gpsb032,Xcup011, used were part of sorghum SSR kit (http://sorghum.cirad.fr/SSR_kit) which provide good coverage of the sorghum nuclear genome (Billot et al, 2012). The remaining markers (Xcup043, Xtxp023, Xtxp003, Xtxp055, Xtxp072, Xtxp123, Xtxp225, Xtxp285) were developed by Bhattramakki et al (2000), Kong et al (2000) and Schloss et al (2002). The genotyping was performed at ''Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse'' (CERAAS) genotyping Platform of Thies (Senegal).…”

Section: Molecular Characterization Samples Collection and Dna Extracmentioning

confidence: 99%

Genetic diversity among sorghum landraces and polymorphism assessment of local improved varieties for stay-green trait

Ouédraogo¹,

Sanou²,

Traoré³

et al. 2017

Int. J. Bio. Chem. Sci

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Microsatellites or simple sequence repeats (SSR) are playing an important role in molecular breeding. This investigation was undertaken to study the genetic diversity among local sorghum accessions from two different agro-ecological zones of Burkina Faso and to assess the polymorphism within local improved varieties and a source (B35) exhibiting the stay-green trait. One hundred and eighty-six local and some exotic accessions were assessed using 26 SSR markers (including 14 markers linked to stay-green QTLs). DNA was extracted using Mixed Alkyl Trimethyl Ammonium Bromide method from dried sample after collection of leaves from three week old plantlets. The average number of alleles per locus was 4 with a medium value of gene diversity (He=0.45) across loci, indicating a low level of dissimilarity among local accessions. The genetic differentiation was significant between local and exotic materials and accessions were grouped according to their racial affiliation. The important finding was the presence of private alleles at markers linked to stay-green loci in the background of some local guinea accessions. The polymorphism between B35 and some local improved varieties for stay-green QTL indicates that most of the linked markers could be used in a breeding program through marker-assisted selection.

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“…Genomic sorghum SSR markers used in this study belonged to the linkage maps of sorghum published by Taramino et al (1997), Bhattramakki et al (2000) and Kong et al (2000) which were recently used by Shehzad et al (2009), Barro-Kondombo et al (2010 and Bhosale et al (2011). Thirty six (36) SSR primers were initially tested on four sorghum accessions and finally, 20 genomic sorghum SSR markers were selected based on their high polymorphic information content (PIC) value observed on the previous studies on African sorghum Landraces.…”

Section: Genomic Dna Extraction and Ssrs Genotypingmentioning

confidence: 99%

Genetic diversity of Sorghum bicolor (L.) Moench landraces from Northwestern Benin as revealed by microsatellite markers

Missihoun¹,

Adoukonou‐Sagbadja²,

Sédah³

et al. 2015

Afr. J. Biotechnol.

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The understanding of genetic diversity within local crop varieties constitutes an important step in the preservation of their genetic potential. The objective of this study was to assess the genetic diversity of sorghum (Sorghum bicolor (L.) Moench) cultivated in the Northwest of Benin and to reveal certain fundamental evolutionary mechanisms. A total of 61 accessions of sorghum landraces belonging to the four identified races in Benin were estimated using 20 microsatellite markers. For all the loci analyzed, 140 polymorphic alleles were detected with a mean value of 7.00 per locus and polymorphic information content (PIC) average value was 0.33 for all the 20 simple sequence repeats (SSRs), suggesting an important genetic diversity within the cultivated sorghum germplasm used. An unweighted pair group method arithmetic average (UPGMA) clustering and principal coordinate analysis (PCoA) based on DICE coefficient revealed three major genetic groups supported by two main components: the botanical race and the morpho-physiological characteristics of the grains (colour and degree of bitterness). It was thus recommended that further research on genetic diversity of sorghum should integrate these genetic parameters for a better preservation of the genetic resources of this important crop in Benin.

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Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs)

Cited by 187 publications

References 29 publications

DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces

DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces

Genetic diversity among sorghum landraces and polymorphism assessment of local improved varieties for stay-green trait

Genetic diversity of Sorghum bicolor (L.) Moench landraces from Northwestern Benin as revealed by microsatellite markers

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