Project description:BackgroundInformation on population structure and genetic diversity of germplasm in a breeding programme is useful because it enhances judicious utilisation of genetic resources to achieve breeding objectives. Seventy early maturing provitamin A (PVA) quality protein maize (QPM) inbreds developed by the IITA- maize improvement programme were genotyped using 8171 DArTseq markers. Furthermore, 96 hybrids derived from 24 selected inbreds plus four checks were evaluated under low-N and optimal environments in Nigeria during 2016 and 2017. Genotypic and phenotypic data of inbreds and hybrids respectively, were analysed to (i) assess the level of genetic dissimilarities and population structure of the inbreds, and (ii) investigate the grain yield performance of derived hybrids under low-N, optimal and across environments.ResultsGenetic diversity among the seventy inbreds was high varying from 0.042 to 0.500 with an average of 0.357. Sixty-six inbred lines with probabilities ≥0.70 were assigned to a single group. The population structure analysis, the UPGMA phylogeny, and the principal Coordinate Analysis (PCoA) of the DArTseq markers revealed a clear separation of five groups and each followed pedigree records. Clustered inbreds displayed common characteristics including high PVA levels, and drought and low-N tolerance. The top performing hybrid, TZEIORQ 40 × TZEIORQ 26 out-yielded the best hybrid control, TZEIOR 127 × TZEIOR 57 by 8, 3, and 9% under low-N, optimal, and across environments, respectively. High repeatability estimates were detected for grain yield under each and across environments. Similarly, high breeding efficiency of 71, 70 and 72% were computed under low-N, optimal, and across environments, respectively.ConclusionsThe UPGMA clustering, the structure analysis, and the PCoA consistently revealed five groups which largely followed pedigree information indicating the existence of genetically distinct groups in the inbred lines. High repeatability and breeding efficiency values estimated for grain yield of hybrids under low-N, optimal and across environments demonstrated that high productive hybrids could be developed using inbreds from the opposing clusters identified by the DArTseq markers. The 15 top performing hybrids identified, particularly TZEIORQ 40 × TZEIORQ 26 and TZEIORQ 29 × TZEIORQ 43 should be further evaluated for release and commercialization in SSA.

Project description:BackgroundThe 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.ResultsThe 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.ConclusionsSelecting 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.

Project description:Vitamin A deficiency poses health risks for children, pregnant women, and nursing mothers in sub-Saharan Africa (SSA) and Southeast Asia. Provitamin A-biofortified maize varieties can contribute to minimizing the adverse effects of vitamin A deficiency in areas where maize is a staple food crop. Identifying suitable testers is important to breed provitamin A-biofortified hybrid maize. This study was therefore conducted to 1) assess the suitability of maize inbred lines with contrasting levels of provitamin A (one with high and one with low provitamin A concentration) to assess the combining ability of maize inbred lines in accumulating provitamin A and other carotenoids, and grain yield, 2) confirm the mode of inheritance of provitamin A and grain yield, and 3) identify promising inbred lines with desirable combining ability effects for use to develop high-yielding provitamin A-biofortified hybrids. The inbreds crossed to the two inbred testers were evaluated in four environments for the carotenoid content and eight environments for the agronomic performance. The combined analysis of variance revealed a significant genetic variation among the testcrosses for all carotenoids, grain yield, and other agronomic traits. The mode of inheritance for grain yield, other agronomic traits, provitamin A, and other carotenoids was regulated by both additive and non-additive gene effects with a prominence of additive gene effects. The high provitamin A tester that displayed positive GCA effects for β-carotene and provitamin A content, broader agronomic performance of testcrosses, and higher levels of provitamin A in testcrosses can be considered suitable for breeding programs developing provitamin A-biofortified hybrids. The inbred lines TZI2012, TZI2142, TZI2130, TZI2065-2, TZI2161, TZI2025, TZI1278, TZI1314, TZI1304, and TZI2032 with positive GCA effects for grain yield and provitamin A content could be used as parental lines to develop source population of new inbred lines and high-yielding hybrids with elevated levels of provitamin A. The best performing hybrids are promising for release as high-yielding provitamin A maize hybrids after further evaluations.

Project description:The phenomenon of heterosis describes the increased agronomic performance of heterozygous F1-plants compared to their homozygous parental inbred plants. Heterosis is already manifested during the early stages of root development in maize. The goal of this study was to identify non-additive gene expression in primary roots of maize hybrids compared to the average expression levels of their parental inbred lines. To achieve this goal a two step strategy was selected. First, a microarray preselection of non-additively expressed candidate genes was performed. Subsequently, gene expression levels in a subset of genes were determined via high throughput qRT-PCR experiments. Initial microarray experiments identified 1941 non-redundant genes which displayed non-additive gene expression in at least one of the twelve analyzed hybrids compared to the midparent value of their parental inbred lines. Comparison of these 1941 genes with non-additively expressed genes identified in maize shoot apical meristems via the same experimental procedure in the same genotypes revealed significantly less overlap than expected by pure chance supporting. This supports the notion of organ specific patterns of non-additively expressed genes. qRT-PCR analyses of 64 of the 1941 non-additively expressed genes in four different hybrids revealed that the majority of non-additively expressed genes were expressed between the high and low parent expression values and only a small fraction of genes was expressed below low or above high parent levels. Subsequently, 22 of the 64 genes that displayed non-additive expression in all four hybrids were analyzed in twelve hybrids that were generated from four inbred lines. Among those genes a superoxide dismutase 2 was expressed significantly above the midparent value in all twelve hybrids and might thus play a protective role in antioxidative defense in the primary root of maize hybrids. These findings are consistent with the hypothesis that global expression trends but also the consistent differential expression of key genes might be relevant during the organ-specific manifestation of heterosis. Keywords: Comparative genomic hybridization

Project description:Maize karyotype variability has been extensively investigated. The identification of maize somatic and pachytene chromosomes has improved with the development of fluorescence in situ hybridization (FISH) using tandemly repeated DNA sequences as probes. We identified the somatic chromosomes of sister inbred lines that were derived from a tropical flint maize population (Jac Duro [JD]), and hybrids between them, using FISH probes for the 180-bp knob repeat, centromeric satellite (CentC), centromeric satellite 4 (Cent4), subtelomeric clone 4-12-1, 5S ribosomal DNA and nucleolus organizing region DNA sequences. The observations were integrated with data based on C-banded mitotic metaphases and conventional analysis of pachytene chromosomes. Heterochromatic knobs visible at pachynema were coincident with C-bands and 180-bp FISH signals on somatic chromosomes, and most of them were large. Variation in the presence of some knobs was observed among lines. Small 180-bp knob signals were invariant on the short arms of chromosomes 1, 6, and 9. The subtelomeric 4-12-1 signal was also invariant and useful for identifying some chromosomes. The centromere location of chromosomes 2 and 4 differed from previous reports on standard maize lines. Somatic chromosomes of a JD line and the commonly used KYS line were compared by FISH in a hybrid of these lines. The pairing behavior of chromosomes 2 and 4 at pachytene stage in this hybrid was investigated using FISH with chromosome-specific probes. The homologues were fully synapsed, including the 5S rDNA and CentC sites on chromosome 2, and Cent4 and subtelomeric 4-12-1 sites on chromosome 4. This suggests that homologous chromosomes could pair through differential degrees of chromatin packaging in homologous arms differing in size. The results contribute to current knowledge of maize global diversity and also raise questions concerning the meiotic pairing of homologous chromosomes possibly differing in their amounts of repetitive DNA.

Project description:The phenomenon of heterosis describes the increased agronomic performance of heterozygous F1-plants compared to their homozygous parental inbred plants. Heterosis is already manifested during the early stages of root development in maize. The goal of this study was to identify non-additive gene expression in primary roots of maize hybrids compared to the average expression levels of their parental inbred lines. To achieve this goal a two step strategy was selected. First, a microarray preselection of non-additively expressed candidate genes was performed. Subsequently, gene expression levels in a subset of genes were determined via high throughput qRT-PCR experiments. Initial microarray experiments identified 1941 non-redundant genes which displayed non-additive gene expression in at least one of the twelve analyzed hybrids compared to the midparent value of their parental inbred lines. Comparison of these 1941 genes with non-additively expressed genes identified in maize shoot apical meristems via the same experimental procedure in the same genotypes revealed significantly less overlap than expected by pure chance supporting. This supports the notion of organ specific patterns of non-additively expressed genes. qRT-PCR analyses of 64 of the 1941 non-additively expressed genes in four different hybrids revealed that the majority of non-additively expressed genes were expressed between the high and low parent expression values and only a small fraction of genes was expressed below low or above high parent levels. Subsequently, 22 of the 64 genes that displayed non-additive expression in all four hybrids were analyzed in twelve hybrids that were generated from four inbred lines. Among those genes a superoxide dismutase 2 was expressed significantly above the midparent value in all twelve hybrids and might thus play a protective role in antioxidative defense in the primary root of maize hybrids. These findings are consistent with the hypothesis that global expression trends but also the consistent differential expression of key genes might be relevant during the organ-specific manifestation of heterosis. Keywords: Comparative genomic hybridization Comparison of four inbred lines and the resulting twelve reciprocal hybrids. Samples from all 16 genotypes were paired on 85 arrays following a hybridization scheme including a dye-swap according to Keller et al. (2005). A tailor-made design was developed for this purpose using simulated annealing that was optimized for estimating non-additive effects while at the same time allowing estimation of additive effects with comparable precision. Optimizing precision for estimation of non-additivity required the design to be unbalanced with respect to the number of genotype pairings and the number of replications per genotype. Hence, two RNA samples were hybridized to each of the 85 microarray chips. Each RNA sample represented an independent biological replicate

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Genetic studies of extra-early provitamin-A maize inbred lines and their hybrids in multiple environments.

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Genetic studies of extra-early provitamin-A maize inbred lines and their hybrids in multiple environments.

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