Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines

The development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompting the use of marker-assisted selection. Presently, two types of genotyping with PVA trait-linked functional markers have been developed and extensively used in breeding programs. The two systems are low throughput gel-based genotyping and genotyping with Kompetitive Allele-Specific PCR (KASP) single nucleotide polymorphism (SNPs) markers. Although the KASP SNPs genotyping was developed to replace the gel-based genotyping, studies have not been conducted to compare the effectiveness of the KASP SNPs markers with the gel-based markers. This study was conducted to assess the carotenoid content of 64 tropical PVA biofortified maize inbred lines containing temperate germplasm in their genetic backgrounds and screen them with both gel-based and KASP markers of PSY1, LCYE and crtRB1 genes. Many of the 64 inbred lines had PVA concentrations surpassing the 15 µg/g provitamin A breeding target set by the HarvestPlus Challenge Program. Favorable alleles of crtRB1, crtRB1 and the KASP SNPs markers were detected in 25 inbred lines with high PVA concentrations. Inbred lines with the favorable alleles of LCYE had the highest concentrations of non-PVA carotenoids, whereas those with the favorable alleles of crtRB1 had high levels of PVA carotenoids. Data from the sequenced region of LCYE revealed one SNP in the first intron that clearly differentiated the high and low β-carotene maize inbred lines. The results of our study demonstrate that the automated KASP SNPs markers can replace the gel-based genotyping for screening a large number of early generation maize inbred lines for PVA content

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

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

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

Additional file 5: Fig. S2. Determination of the most appropriate K-value in structure analysis using Evanno’s Delta K

Additional file 6 of Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids

Additional file 6: table S5. Genotypic data for maize Provitamin A inbred lines for diversity assessment and heterotic grouping

Additional file 7 of Heterotic grouping of provitamin A-enriched maize inbred lines for increased provitamin A content in hybrids

Additional file 7: table S4. Maize inbred lines used in the present study

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 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