Transcriptional factor influence on OTA production and the quelling attribute of Sirna on the OTA producing strains of Aspergillus section Nigri

This study determined the influence of some transcriptional factors on ochratoxin A production as well as investigates the quelling attributes of some designed siRNA on the OTA producing Aspergillus section Nigri using standard recommended techniques. Results obtained following comparison of the pks gene promoter sequences from 15 isolates depicts differences in length and homology with the pks gene ranging from 218bp in a strain of the Aspergillus niger to 700bp in Aspergillus carbonarius. The alignment of the pks gene promoter region revealed that six and two of the aligned genes have Aba A binding site corresponding to CATTCT and CATTCC respectively while Brl A binding site was absent in all the isolates. Pac C binding site corresponding to CCTGGC and GCCAAG was also found in two and three of the pks gene promoter region respectively. The three designed siRNA shows significant impact on OTA inhibitions with no significant statistical differences (80.9, 74.4 and 75.3% for pks_Ia, pks_Ib and pks_Ic respectively) (F= 3.830, p>0.05). It can be concluded that Are A and Aba A are potential enhancers for ochratoxin A biosynthesis and none of the investigated transcriptional factors is enough for the activation of ochratoxin A production. However, pks gene was seen as a good target gene for inactivation in order to develop efficient means for ochratoxin A control using RNA silencing technology.Key words: Transcriptional factors, Ochratoxin A, siRNA, Quelling , Aspergillus section Nigr

Genetic diversity of ochratoxigenic Aspergillus section Nigri, using RAPD and VCG techniques

This study evaluates the genetic diversity of ochratoxigenic Aspergillus section Nigri using RAPD and VCG techniques. Results obtained revealed OPX 07 as the most informative of the tested RAPD markers generating 12 polymorphic bands while the least bands were generated by OPR 19. Of the 40 Aspergillus section Nigri (20 each of Aspergillus niger and Aspergillus carbonarius), 22 VCGs and 27 RAPD haplotypes were delineated. The two techniques demonstrated similar resolution except in few cases where the RAPD technique further sub divided some VCGs into simpler haplotypes. The average percentage of variable VCG and RAPD reactions were 25 and 50% in that order of sequence while 75 and 50% of the isolates were resolved as same isolates by these techniques respectively. It was also found that the Simpson index of genetic diversity approached one for the isolates from the four geopolitical zones of Ogun State, Nigeria with the mean genetic diversity within isolates (GL) contributing significantly approximately 89% of the total diversity observed within the isolates (F=22.23, p<0.05). The remaining 11% of variation could only be allotted to diversity among isolates (GS). On the whole, the total genetic diversity (HT) was found to be approximately 48%. In conclusion, RAPD markers provided better resolution than the classical VCG typing technique.Keywords; Genetic Diversity, Ochratoxigenic Aspergillus, RAPD and VC

Molecular characterization of Auricularia spp from south-western Nigeria using Random Amplified Polymorphic DNA (RAPD) markers

This study was conducted to investigate the genetic diversity in 48 samples of Auricularia species randomly collected from secondary forests in Osun (11), Oyo (10), Ondo (9), Ekiti (8), Ogun (8) and Lagos States (8) of Nigeria. Fourteen Random Amplified Polymorphic DNA (RAPD) markers were used for molecular characterization of Auricularia species. Phylogenetic relations were determined by cluster analysis and Polymorphic Information Content (PIC) and gene diversity determined using standard procedures. The Auricularia species were grouped into 6 distinct clusters based on morphological traits. The PIC value ranged from 0.5594 (OPH-15) to 0.7819 (OPB-12) and gene diversity from 0.5930 (OPH-15) to 0.7977 (OPB-12). Primer OPB-12 was the most informative for genetic diversity of Auricularia species. However, primer OPB-21 gave the highest number of alleles while OPB-12 showed the highest range of gene diversity and accounted for the diversity of the Auricularia species. The dendrogram and the principal coordinate analysis exhibited similar clustered patterns, revealing that all the tested strains could be divided into six distinct groups, each of which correlated with different geographical regions. Molecular characterisation is essential in genetic diversity studies and has proven useful in the classification of Auricularia spp.Keywords:  Auricularia spp, Cluster analysis, Genetic diversity, Mushroom cultivation, Principal coordinate analysis, Polymorphic information content, RAPD marker

Marker-trait association in selected Nigerian mini-core pigeonpea [Cajanus cajan (L.) Millsp.] accessions using SCoT markers

The pigeonpea [Cajanus cajan (L.) Millsp.] is a popular leguminous plant in the Fabaceae family. Its low yield is a major challenge in Nigeria with no improved varieties developed. The identification of markers linked to agronomical traits will accelerate agronomic yield improvements in pigeonpea. Hence, the study was conducted to identify SCoT markers associated with important agronomic traits within selected Nigerian pigeonpea lines. A total of 52 Nigerian pigeonpea were phenotyped for vegetative and yield traits. DNA was extracted from sampled accessions and evaluated with SCoT markers. Marker performance and association to agronomic traits were evaluated. The coefficient of variation (CoV) varied with agronomical traits, ranging from leaflet length (CoV = 15.77) to tertiary branches (CoV = 155.23). Broad sense heritability was high for all traits (H2 > 75%) except for the number of seeds per pod (H2 = 9.13%). Genetic advances ranged from 0.65 in leaflet width to 106.65 in pod number. Only seeds per pod showed more environmental variance than the genetic variance. SCoT markers showed 100% polymorphism with average Polymorphic Information Content values > 0.6. The effective marker ratio also ranged between 1.50 in SCoT-3 to 45.38 in SCoT-2. The cumulated phenotypic variance explained by associated markers ranged between 9.11% in 100 seed weight to 44.7% in leaflet width. Some markers were associated with more than one agronomic trait. These markers can be harnessed for their potential application in pigeonpea improvement programmes

Assessment of Bruchid (Callosobruchus maculatus) Tolerance of Some Elite Cowpea (Vigna unguiculata) Varieties

The resistance of cowpea to bruchid infestation has been a major concern to plant breeders as some elite cowpea varieties become susceptible to the polymorphic nature of this storage insect pest. The current status of ten bruchid resistant varieties collected from the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria was evaluated for bruchid tolerance. Each of the varieties was infested with two pairs of bruchids and comparative data was taken for 60 days. Results showed a delay in bruchid emergence with mean development period for successful adult emergence ranging from 32-47 days. Nine of the varieties studied showed percentage seed damage above 80% and percentage pest tolerance below 50%. Susceptibility index indicates that seven of the studied varieties to be moderately resistant and the remaining three to be resistance to the bruchid infestation with TVu 11953 being the most resistant of all with index 1.78. Analysis of seed coat resistance indicated no significant difference in number of eggs laid, mean bruchid development time, percentage bruchid emergence, percentage seed damage and susceptibility index between the smooth and rough seed coats. The study indicates other factors, not seed coat nature to be responsible for bruchid resistance in cowpea

Molecular characterization of cultivated cowpea (Vigna unguiculata L. Walp) using simple sequence repeats markers

Forty eight accessions of cultivated cowpea were assessed using 12 simple sequence repeat (SSR) markers. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram constructed revealed three main clusters when truncated at 65% similarity coefficient. All accessions showed high genetic variation except four which are genetically similar at 100% similarity coefficient. A two dimensional principal coordinate analysis (PCA) also revealed high genetic relationships among the accessions used. The polymorphism information content (PIC) revealed that the number of alleles per locus ranged from 2 to 5 with a total of 37 alleles generated from the SSR primers. The PIC value ranged from 0.075 to 0.603 with a mean value of 0.344 from a total of 4.467. There was no significant correlation between the repeat number and the allele numbers (r=0.21) so also between repeat numbers and PIC (r=0.11). The PIC also revealed the comparative genetic diversity from three sub-regions in Africa; West Africa, North East and Central Africa and Southern Africa with thirteen accessions each. West African accessions were the most diverse with a PIC value of 4.4310, showing the greatest genetic diversity and most likely the center of origin of cultivated cowpea

Genetic diversity in wild relatives of cowpea (Vigna unguiculata) as revealed by simple sequence repeats (SSR) markers

The genetic diversity in wild cowpea was assessed using cowpea derived simple sequence repeat (SSR) markers. A total of forty eight wild cowpea lines collected from diverse geographical locations in Africa were used for the study. Twelve SSR markers were selected for amplification of DNA of the test lines and these produced a total of ninety polymorphic bands. A dendrogram constructed using unweighted pair group using mathematical averages (UPGMA) analysis distinguished forty three accessions out of a total of forty eight accessions used for the study implying that a great diversity in wild cowpea. Accessions from Southern part of Africa have the highest polymorphism information content (PIC) values suggesting a high level of diversity from that region and is likely to be center of diversity of wild cowpea. The allele number per primer varied from 4 to 13 with an average of 7.5 alleles. The SSR, VM 36 showed the highest number of alleles with the PIC value of 0.870. This analysis revealed that SSR markers are useful tools in assessing the level of genetic diversity in wild cowpea

Breeding cowpea for resistance to striga gesnerioides in the Nigerian dry savannas using marker-assisted selection

Published online:10 April 2017Historically, conventional breeding has been the primary strategy used to develop a number of Striga-resistant varieties currently grown in the Sahel of Western Africa. In this study, we have successfully developed and applied a marker-assisted selection strategy that employs a single backcross programme to introgress Striga resistance into farmer preferred varieties of cowpea for the Nigeria savannas. In this strategy, we have introduced the Striga resistance gene from the donor parent IT97K-499-35 into an elite farmer preferred cowpea cultivar ‘Borno Brown’. The selected 47 BC1F2 populations confirmed the recombinants with desirable progeny having Striga resistance gene(s). The 28 lines selected in the BC1F2:4 generation with large seed size, brown seed coat colour and carrying marker alleles were evaluated in the field for resistance to Striga resistance. This led to the selection of a number of desirable improved lines that were immune to Striga having local genetic background with higher yield than those of their parents and standard varieties

Genetic diversity in yardlongbean (Vigna unguiculata subspecies unguiculata cvgr sesquipedalis) as revealed by simple sequence repeat (SSR) markers

Genetic diversity was investigated among fifty accessions of yard-long-bean (Vigna unguiculatasubspecies unguiculatacultivar group sesquipedalis) using simple sequence repeat (SSR) markers. Sixteen SSR primers were used to amplify DNA of the 50 accessions. A total of 63 polymorphic bands were detected and these were used for cluster analysis. A dendrogram generated following unweighted pair group using mathematical average (UPGMA) cluster analysis isolated one of the accessions from the others at a similarity coefficient of 0.68. However, at 0.76 similarity coefficient, nine clusters were formed with the eighth and ninth clusters containing more than two-thirds of the total accessions used. There were four accessions that paired at 1.0 similarity coefficient. The members of each pair could not be separated from each other on the dendrogram suggesting very close relationships be-tween each pair. The distribution of the yard-long-bean accessions along the axes of the first two principal components showed to a very large extent similar grouping as were identified on the den-drogram. Accessions of yard-long-bean from India showed the highest level of genetic diversity, as revealed by SSR markers, compared with those from other countries thereby providing further evidence in support of the suggestion that India may be the center of diversity for the crop. Thus SSR markers are useful in assessing the genetic diversity among individuals of yard-long-bean

Genome-wide association analysis reveals genetic architecture and candidate genes associated with grain yield and other traits under low soil nitrogen in early-maturing white quality protein maize inbred lines

Open Access Journal; Published online: 05 May 2022Maize production in the savannas of sub-Saharan Africa (SSA) is constrained by the low nitrogen in the soils. The identification of quantitative trait loci (QTL) conferring tolerance to low soil nitrogen (low-N) is crucial for the successful breeding of high-yielding QPM maize genotypes under low-N conditions. The objective of this study was to identify QTLs significantly associated with grain yield and other low-N tolerance-related traits under low-N. The phenotypic data of 140 early-maturing white quality protein maize (QPM) inbred lines were evaluated under low-N. The inbred lines were genotyped using 49,185 DArTseq markers, from which 7599 markers were filtered for population structure analysis and genome-wide association study (GWAS). The inbred lines were grouped into two major clusters based on the population structure analysis. The GWAS identified 24, 3, 10, and 3 significant SNPs respectively associated with grain yield, stay-green characteristic, and plant and ear aspects, under low-N. Sixteen SNP markers were physically located in proximity to 32 putative genes associated with grain yield, stay-green characteristic, and plant and ear aspects. The putative genes GRMZM2G127139, GRMZM5G848945, GRMZM2G031331, GRMZM2G003493, GRMZM2G067964, GRMZM2G180254, on chromosomes 1, 2, 8, and 10 were involved in cellular nitrogen assimilation and biosynthesis, normal plant growth and development, nitrogen assimilation, and disease resistance. Following the validation of the markers, the putative candidate genes and SNPs could be used as genomic markers for marker-assisted selection, to facilitate genetic gains for low-N tolerance in maize production