Genetic gains in grain yield of a maize population improved through marker assisted recurrent selection under stress and non-stress conditions in west Africa

Open Access JournakMarker-assisted recurrent selection (MARS) is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S1 lines derived from the original (C0) and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS) and well-watered (WW) conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S1 lines each derived from the four cycles (C0, C1, C2, C3) were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga, improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S1 lines from 114 in C0 to 124 in C3. The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved maize inbred lines

Isolation, identification and in silico analysis of alpha-amylase gene of Aspergillus niger strain CSA35 obtained from cassava undergoing spoilage

In this investigation, a gene (CDF_Amyl) encoding extracellular α-amylase in Aspergillus niger strain CSA35 associated with cassava spoilage was amplified using specific primers and characterized in silico. The gene had a partial nucleotide sequence of 968 bp and encoded a protein of 222 aa residues with a molecular weight and isoelectric point of 25.13 kDa and 4.17, respectively. Its catalytic site was located in the active site domain. BLASTp analysis showed that the protein primary sequence of the α-amylase gene had 98% and 99% homologies with the α-amylase of A. niger and A. oryzae RIB40, respectively. The gene is more closely related to α-amylase genes from fungi than to bacterial, plant, or animal α-amylase genes. Restriction mapping of the gene showed it can be digested with restriction enzymes like NcoI, PstI, SmaI, and BcLI among others but not with EcoRI and EcoRV. Its protein product had a hydrophobicity score of − 0.43 but no transmembrane helix. The CDF_Amyl protein was subcellularly localized in the secretory pathway, an indication of its release into extracellular space after secretion. Also, the 3D structure of the CDF-Amyl protein was barrel-shaped with domains characteristic of α-amylases. The encoded α-amylase Vmax is 6.90 U/mg protein and Km is 6.70 mg/ml. It was concluded that the unique characteristics of the CDF_Amyl gene and its deduced protein could find applications in biotechnological, food and pharmaceutical industries where cloning and further modification of this gene would be required for product development and improvement

Contrasting Response Mechanisms of Maize Lines to Striga hermonthica

Strigahermonthica (Del.) Benth is a parasitic weed that devastates cereals in Sub-Saharan Africa. Several control measures have been proposed for the parasite, of these, host plant resistance is considered the most cost-effective for poor farmers. Some tolerant/resistant lines have been developed and these lines display tolerance/resistance mechanisms to the parasite. A series of studies was done to investigate some of the mechanisms through which a resistant (TZISTR1108) and a susceptible (5057) maize line responds to S. hermonthica infestation, as well as the effects of parasitism on these lines. In this study, TZISTR1108 stimulated the germination and attachment of fewer S. hermonthica plants than 5057, both in the laboratory and on the field. In TZISTR1108, the growth of the S. hermonthica plants, that successfully attached, was slowed. When compared to the un-infested plants, the infested resistant plants showed fewer effects of parasitism than the infested susceptible plants. The infested TZISTR1108 plants were more vigorous, taller and resembled their un-infected counterparts. There were substantial reductions in the stomatal conductance and nitrogen content of the 5057 upon infestation. The resistant inbred line showed multiple mechanisms of resistance to S. hermonthica infestation. It thrives better than the susceptible line by reducing the attachment of S. hermonthica and it delays the parasite’s development

Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids

Abstract Background The establishment of heterotic groups of inbred lines is crucial for hybrid maize breeding programs. Currently, there is no information on the heterotic patterns of the Provitamin A (PVA) inbred lines developed in the maize improvement program of the International Institute of Tropical Agriculture (IITA) to form productive PVA enriched hybrids for areas affected by vitamin A deficiency. This study assessed the feasibility of classifying PVA-enriched inbred lines into heterotic groups based on PVA content without compromising grain yield in hybrids. Sixty PVA inbred lines were crossed to two testers representing two existing heterotic groups. The resulting 120 testcrosses hybrids were evaluated for two years at four locations in Nigeria. Results The two testers effectively classified the inbred lines into two heterotic groups. The PVA-based general combining ability and specific combining ability (HSGCA) method assigned 31 and 27 PVA enriched maize inbred lines into HGB and HGA, respectively, leaving two inbred lines not assigned to any group. The yield-based HSGCA method classified 32 inbred lines into HGB and 28 inbred lines into HGA. Both PVA and yield-based heterotic grouping methods assigned more than 40% of the inbred lines into the same heterotic groups. Even though both PVA and yield-based heterotic grouping of the inbred lines differed from the clusters defined by the DArTag SNP markers, more than 40% of the inbred lines assigned to HGA were present in Cluster-1 and 60% of the inbred lines assigned to HGB were present in Cluster-3. Interestingly, the inbred lines assigned to the same heterotic groups based on PVA content and grain yield were distributed across the three Ward’s clusters. The PVA-based HSGCA was identified as the most effective heterotic grouping method for breeding programs working on PVA biofortification. Conclusions Selecting PVA enriched maize inbred lines with diverse genetic backgrounds from the three marker-based clusters may facilitate the development of productive hybrids with high PVA content and for generating source populations to develop more vigorous maize inbred lines with much higher concentrations of PVA

Genetic Characterization Of Early Generation Lines Using SNPS Makers And Agronomic Traits For Resistance To Striga Improvement In Maize

The characterization of a greater number of lines hence potentially increase the efficiency of maize breeding programs. This study aims to assess the genetic variation and relationships existing within a population of 177 lines and the two parental lines, using 8,883 SNPs markers obtained from sequencing genotyping (GBS) and four agronomic traits. Two hundred S1 lines and four checks including the two parents have been evaluated under Striga hermonthica infestation in Benin Republic and Nigeria for two years during 2018 and 2019 growing seasons using 51 x 4 lattice design with two replicates. The UPGMA phylogeny, was used to group the progenies based on their genetic similarity. The tested lines have displayed high genetic variability for all the agronomic traits. Analysis molecular revealed that the polymorphism information content has been varied from 0.047 to 0.50, with average of 0.37, and 63% of the SNP makers were highly polymorphic. The population has displayed a moderate diversity with average genetic diversity of 0.44. The estimated genetic distance has been varied from 0.01 to 0.79 and the highest distance has been observed between the two parental lines. UPGMA clustering based on the Gower dissimilarity matrix grouped the 177 lines into two clusters (I and II) at 30% genetic similarity threshold. The estimated genetic distances between lines showed that all the progenies were genetically related to the two parental lines; and have the potential to provide new favorable alleles for the development of high-performing, Striga-resistant and/or Striga-tolerant maize populations

Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers

Striga hermonthica is a serious biotic stress limiting maize production in sub-Saharan Africa. The limited information on the patterns of genetic diversity among maize inbred lines derived from source germplasm with mixed genetic backgrounds limits the development of inbred lines, hybrids, and synthetics with durable resistance to S. hermonthica. This study was conducted to assess the level of genetic diversity in a panel of 150 diverse maize inbred lines using agronomic and molecular data and also to infer the population structure among the inbred lines. Ten Striga-resistance-related traits were used for the phenotypic characterization, and 16,735 high-quality single-nucleotide polymorphisms (SNPs), identified by genotyping-by-sequencing (GBS), were used for molecular diversity. The phenotypic and molecular hierarchical cluster analyses grouped the inbred lines into five clusters, respectively. However, the grouping patterns between the phenotypic and molecular hierarchical cluster analyses were inconsistent due to non-overlapping information between the phenotypic and molecular data. The correlation between the phenotypic and molecular diversity matrices was very low (0.001), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and molecular diversity analyses. The joint phenotypic and genotypic diversity matrices grouped the inbred lines into three groups based on their reaction patterns to S. hermonthica, and this was able to exploit a broad estimate of the actual diversity among the inbred lines. The joint analysis shows an invaluable insight for measuring genetic diversity in the evaluated materials. The result indicates that wide genetic variability exists among the inbred lines and that the joint diversity analysis can be utilized to reliably assign the inbred lines into heterotic groups and also to enhance the level of resistance to Striga in new maize varieties

Additional file 4 of Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids

Additional file 4: Fig. S1. Summary statistics of 1879 markers used to assess the genetic diversity among the inbred lines

Additional file 1 of Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids

Additional file 1: Table S1. Provitamin A-based classification of 60 PVA enriched maize inbred lines into heterotic groups

Additional file 3 of Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids

Additional file 3: Table S3. Provitamin A and yield-based separation of the lines into heterotic groups coupled with marker-based grouping of the PVA enriched maize inbred lines into clusters

Additional file 2 of Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids

Additional file 2: Table S2. Yield-based classification of 60 PVA enriched maize inbred lines into heterotic groups