Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility

Background: Cassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. Results: A total of 846 putative microsatellites were identified in silico from an 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species as well as two other important taxa in the Euphorbiaceae, leafy spurge (Euphorbia esula) and castor bean (Ricinus communis). Of 168 markers with clean amplification products, 124 (73.8%) displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1%) amplified alleles from one or more wild species (M epruinosa, M glaziovii, M brachyandra, M tripartita) whereas 13 (15.3%) amplified alleles from castor bean and 9 (10.6%) amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC) from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes. Conclusion: A set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for cultivar identification, taxonomic studies, and genetic mapping. The study further shows that mining ESTs is a highly efficient strategy for polymorphism detection within the cultivated cassava gene pool

Characterization of mutant cowpea [Vigna unguiculata (L) Walp] lines using random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphism (AFLP) markers

Phylogenetic relationship and polymorphism was detected in 10 cowpea lines comprising of leaf, flower and stem mutants, their putative parents and an exotic accession using 10 random amplified polymorphic DNAs (RAPDs) and three primer combinations of amplified fragment length polymorphism (AFLP) markers. These mutants were earlier obtained through the probable activities of transposable elements. The RAPD and AFLP markers revealed a genetic diversity of 47 and 31%, respectively, within the cowpea lines used. Genetic distance ranged from 0.05 to 0.30 based on AFLP markers, while it ranged between 0.13 and 0.44 for RAPD markers. Cluster analysis indicated that there are differences in RAPD markers between the various mutants and it grouped an exotic genotype separately. OPC-14 primer had the highest discriminatory capacity (11 polymorphic fragments). The AFLP analysis was able to group two of the flower mutants, leaf mutants and wild types separately. A combined analysis of the two markers gave a similar grouping as was obtained from the AFLP analysis. AFLP was more discriminatory in grouping the plant samples and the exotic line was distinguished based on both markers. Useful heterotic prediction can be done based on the genetic distance between the mutants and their parents. This will further broaden the genetic base of cowpea and enhance the use of these mutants which have some evolutionary significance. In addition, unique allele RAPD_OPC15-500bp can be harnessed in genetic identification of reduced petal mutant. This study further corroborates the discriminatory power of AFLP over RAPDs.Key words: Vigna unguiculata, amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), mutants, transposable elements

Genetic relationships between interspecific lines derived from Oryza glaberrima and Oryza sativa crosses using microsatellites and agro-morphological markers

New Rice(s) for Africa (NERICA) are high yielding rice varieties mostly cultivated in Sub-Saharan Africa and developed by the Africa Rice Center. This study is aimed at investigating the proportion of introgression of parental genomic contribution of 60 lowland NERICA varieties and establishment of molecular profiling. Agro-morphological data from 17 characteristics was recorded and significant (p<0.05) to high significant (p<0.0001) differences were obtained with leaf length and width, plant height at maturity, days to heading, maturity, primary and secondary branching of panicles, and grain width and grain thickness. A total of 114 microsatellite polymorphic markers covering 2183.13 cM of the rice genome showed the proportions of alleles introgressed from the donor parent (Oryza glaberrima) into 52 lowland NERICA lines (TOG5681 and IR64) as follows: 11% for BC2, 6.07% for BC3, and 7.55% for BC4. The introgression proportions for the eight remaining lowland NERICA lines derived from other crosses ranged from 5.5 to 11.3%. The proportion recorded with the recurrent parent was 83.99%. The highest introgression proportions of the O. glaberrima allele for all 60 lowland NERICA lines were found on chromosomes 2, 6 and 12 (TOG5681/IR64) and on chromosome 3 with NERIC-L-29 (TOG5681/IR1529-680-3-2). Multivariate analyses performed using an association of agro-morphological and molecular data revealed two major groups according to the distribution of the lowland NERICAs including the lowland NERICAs released were found in cluster 1 of the dendrogram. Genetic and genomic studies, QTL identification and analysis using agro-morphologically significant traits revealed should be used to develop mega-varieties adapted in rice growth conditions in Sub-Saharan Africa

Gene-based microsatellites for cassava (<it>Manihot esculenta </it>Crantz): prevalence, polymorphisms, and cross-taxa utility

Abstract Background Cassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. Results A total of 846 putative microsatellites were identified in silico from an 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species as well as two other important taxa in the Euphorbiaceae, leafy spurge (Euphorbia esula) and castor bean (Ricinus communis). Of 168 markers with clean amplification products, 124 (73.8%) displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1%) amplified alleles from one or more wild species (M epruinosa, M glaziovii, M brachyandra, M tripartita) whereas 13 (15.3%) amplified alleles from castor bean and 9 (10.6%) amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC) from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes. Conclusion A set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for cultivar identification, taxonomic studies, and genetic mapping. The study further shows that mining ESTs is a highly efficient strategy for polymorphism detection within the cultivated cassava gene pool.</p

Fine mapping of RYMV3: a new resistance gene to Rice yellow mottle virus from Oryza glaberrima

International audienc

Identification of QTLs Controlling Resistance to Anthracnose Disease in Water Yam (<i>Dioscorea alata</i>)

Anthracnose disease caused by a fungus Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Resistance to yam anthracnose disease (YAD) is a prime target in breeding initiatives to develop durable-resistant cultivars for sustainable management of the disease in water yam cultivation. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata. Parent genotypes and their recombinant progenies were genotyped using the Genotyping by Sequencing (GBS) platform and phenotyped in two crop cycles for two years. A high-density genetic linkage map was built with 3184 polymorphic Single Nucleotide Polymorphism (NSP) markers well distributed across the genome, covering 1460.94 cM total length. On average, 163 SNP markers were mapped per chromosome with 0.58 genetic distances between SNPs. Four QTL regions related to yam anthracnose disease resistance were identified on three chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 29.54 to 39.40%. The QTL regions identified showed genes that code for known plant defense responses such as GDSL-like Lipase/Acylhydrolase, Protein kinase domain, and F-box protein. The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers identified herewith form a relevant resource to apply marker-assisted selection as an alternative to a conventional labor-intensive screening for anthracnose resistance in water yam

The positions of the 28 QTLs associated with African gall midge incidence (<i>qPI</i>) and severity (<i>qAfRGM</i>) in the ITA306xTOG7106 (black font), ITA306xBW348-1 (pink font) and ITA306xTOS14519 (blue font) populations.

<p>The vertical ruler on the left shows map position in centiMorgan. QTL are shown on the left side of each chromosome, with vertical bars indicating their 95% confidence interval. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160749#pone.0160749.t001" target="_blank">Table 1</a> for details on each QTL and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160749#pone.0160749.s002" target="_blank">S1 Table</a> for details on marker positions.</p

Summary of the number of SNPs used for QTL mapping for each of the three populations and combined across all populations.

<p>Summary of the number of SNPs used for QTL mapping for each of the three populations and combined across all populations.</p