Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers

Djè, Y.; Heuertz, Myriam; Lefèbvre, Claude; Vekemans, Xavier

doi:10.1007/s001220051371

Cited by 126 publications

(46 citation statements)

References 36 publications

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“…Allelic discrimination of such a population appears to be difficult and showed by relatively low mean value of PIC (0.33). The structure of the population as observed in the present study, that is, the separation of the accessions according to the botanical race and morpho-physiological characteristics of the grains (colour, size and degree of bitterness of the grains) and particularly the separation of guinea race from others races (caudatum and durra precisely) was already reported in previous studies (Djè et al, 2000;Folkertsma et al, 2005;Barnaud et al, 2007;Deu et al, 2008;Barro-Kondombo et al, 2010;Bhosale et al, 2011).…”

Section: Overall Genetic Diversitysupporting

confidence: 83%

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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Section: Overall Genetic Diversitysupporting

confidence: 83%

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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“…However, Dj et al (1999) estimated a higher genetic diversity when analysing 25 sorghum landraces derived from a restricted area of North Western Morocco with three SSRs. The same holds true for the genetic diversity estimated on all accessions (Table 5) when compared to results of Dj et al (2000) based on five SSRs and to studies of Grenier et al (2000). However, in these studies sorghum accessions derived from different parts of the world were included and the SSRs used were more informative, for example, the five SSRs analysed by Dj et al (2000) generated between 14 and 24 different alleles -i.e.…”

Section: Discussionmentioning

confidence: 84%

“…The same holds true for the genetic diversity estimated on all accessions (Table 5) when compared to results of Dj et al (2000) based on five SSRs and to studies of Grenier et al (2000). However, in these studies sorghum accessions derived from different parts of the world were included and the SSRs used were more informative, for example, the five SSRs analysed by Dj et al (2000) generated between 14 and 24 different alleles -i.e. 19.2 on average on 25 accessions -while in our studies on average 8.68 alleles per SSR loci were detected.…”

Section: Discussionmentioning

confidence: 84%

Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs

et al. 2003

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In order to get an overview on the genetic relatedness of sorghum (Sorghum bicolor) landraces and cultivars grown in low-input conditions of small-scale farming systems, 46 sorghum accessions derived from Southern Africa were evaluated on the basis of amplified fragment length polymorphism (AFLPs), random amplified polymorphic DNAs (RAPDs) and simple sequence repeats (SSRs). By this approach all sorghum accessions were uniquely fingerprinted by all marker systems. Mean genetic similarity was estimated at 0.88 based on RAPDs, 0.85 using AFLPs and 0.31 based on SSRs. In addition to this, genetic distance based on SSR data was estimated at 57 according to a stepwise mutation model (Deltamu-SSR). All UPGMA-clusters showed a good fit to the similarity estimates (AFLPs: r = 0.92; RAPDs: r = 0.88; SSRs: r = 0.87; Deltamu-SSRs: r = 0.85). By UPGMA-clustering two main clusters were built on all marker systems comprising landraces on the one hand and newly developed varieties on the other hand. Further sub-groupings were not unequivocal. Genetic diversity (H, DI) was estimated on a similar level within landraces and breeding varieties. Comparing the three approaches to each other, RAPD and AFLP similarity indices were highly correlated (r = 0.81), while the Spearman's rank correlation coefficient between SSRs and AFLPs was r = 0.57 and r = 0.51 between RAPDs and SSRs. Applying a stepwise mutation model on the SSR data resulted in an intermediate correlation coefficient between Deltamu-SSRs and AFLPs (r = 0.66) and RAPDs ( r = 0.67), respectively, while SSRs and Deltamu-SSRs showed a lower correlation coefficient (r = 0.52). The highest bootstrap probabilities were found using AFLPs (56% on average) while SSR, Deltamu-SSR and RAPD-based similarity estimates had low mean bootstrap probabilities (24%, 27%, 30%, respectively). The coefficient of variation (CV) of the estimated genetic similarity decreased with an increasing number of bands and was lowest using AFLPs.

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“…bicolor), namely bicolor, caudatum, durra, guinea, and kafir, as well as 10 intermediate types. This species has been studied with various types of molecular markers (Ollitrault et al 1989;Aldrich et al 1992;Deu et al 1994Deu et al , 1995Cui et al 1995;De Oliveira et al 1996;Menkir et al 1997;Djè et al 2000;Grenier et al 2000;Casa et al 2005) and has recently undergone detailed sequence diversity analysis using small representative panels of diverse accessions (Hamblin et al 2004(Hamblin et al , 2006, which enabled investigation of linkage disequilibrium (LD) and patterns of selection among several hundred loci. This resulted in a fine understanding of ecogeographic patterns of variation in sorghum, in particular with reference to its geographic spreading out of the area of origin in the northeastern part of sub-Saharan Africa.…”

mentioning

confidence: 99%

Phylogeographic Evidence of Crop Neodiversity in Sorghum

et al. 2008

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Sorghum has shown the adaptability necessary to sustain its improvement during time and geographical extension despite a genetic foundation constricted by domestication bottlenecks. Initially domesticated in the northeastern part of sub-Saharan Africa several millenia ago, sorghum quickly spread throughout Africa, and to Asia. We performed phylogeographic analysis of sequence diversity for six candidate genes for grain quality (Shrunken2, Brittle2, Soluble starch synthaseI, Waxy, Amylose extender1, and Opaque2) in a representative sample of sorghum cultivars. Haplotypes along 1-kb segments appeared little affected by recombination. Sequence similarity enabled clustering of closely related alleles and discrimination of two or three distantly related groups depending on the gene. This scheme indicated that sorghum domestication involved structured founder populations, while confirming a specific status for the guinea margaritiferum subrace. Allele rooted genealogy revealed derivation relationships by mutation or, less frequently, by recombination. Comparison of germplasm compartments revealed contrasts between genes. Sh2, Bt2, and SssI displayed a loss of diversity outside the area of origin of sorghum, whereas O2 and, to some extent, Wx and Ae1 displayed novel variation, derived from postdomestication mutations. These are likely to have been conserved under the effect of human selection, thus releasing valuable neodiversity whose extent will influence germplasm management strategies.

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Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers

Cited by 126 publications

References 36 publications

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

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

Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs

Phylogeographic Evidence of Crop Neodiversity in Sorghum

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