Phenotypic characterization and validation of provitamin A functional genes in early maturing provitamin A-quality protein maize (Zea mays) inbred lines

Status of carotenoids in elite and landrace maize genotypes: Implications for provitamin A biofortification in Tanzania

Maize is among the crops containing carotenoids that are easily converted to vitamin A and have an enormous influence on consumers' health. Principally maize has high calories and proteins but has less number of other micronutrients such as vitamin A. Societies that use maize as their main and sole staple food are likely to be affected by vitamin A deficiency. Thus, development and production of maize varieties rich in micronutrients and vitamin A are important for improved health. This study characterized 5 carotenoid components in maize genotypes grown in Tanzania as a strategy for improving vitamin A content in maize. The study involved maize landraces, commercial or elite varieties, and inbred lines in determining their potential for provitamin A breeding programs for nutrition improvement. The study found that mean concentration of important carotenoid components, i.e., alpha carotene (AC), beta-carotene (BC), beta-cryptoxanthin (BCX), lutein (LU), zeaxanthin (ZX), provitamin A (ProVA), non-provitamin A (Non-ProVA), and total carotenoids (TC) varied significantly (P < 0.001) among maize genotypes. The 3 maize groups studied (landraces, commercial varieties, and breeding materials (BMs) varied significantly. For maize landraces, the concentration (µg/g) of studied carotenoids were AC (0.13-2.67), BC (0.60-3.72), BCX (0.36-1.01), ProVA (0.89-5.29), Retinol (0.25-0.87), LU (2.37-16.97). ZX (0.16-4.41), Non-ProVA (2.4-19.01), and TC (3.68-25.27); in commercial or elite maize varieties were (in µg/g): AC (0.31-3.84), BC (0.56-6.5), BCX (0.46-2.58), ProVA (0.92-11.80), Retinol (0.15-1.82), LU (3.28-22.39). ZX (0.05-11.31), Non-ProVA (2.56-28.81), and TC (4.23-37.84); and for maize BMs AC (0.53-6.64), BC (1.92-13.87), BCX (0.65-6.51), ProVA (2.69-18.62), Retinol (0.5-3.1), LU (4.86-34.99), ZX (0.06-18.58), Non-ProVA (4.8-53.57), and TC (9.86-76.94). Furthermore, the study found that the concentration of studied carotenoids was higher in pigmented (yellow or red) maize genotypes than in white maize genotypes. The current study found an appreciable amount of ProVA in studied materials, including maize landraces, commercial yellow varieties, and CIMMYT lines. The concentration of ProVA and retinol determined in studied maize genotypes were below 15 µg/g a daily vitamin A requirement, thus based on the current ProVA and retinol status it is difficult to meet Vitamin A requirement. Therefore, these maize genotypes with promising levels of carotenoid components are potential breeding materials that can be used in maize provitamin A biofortification program for improved food nutrition and livelihoods in Tanzania.

Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

BACKGROUND

Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines.

RESULTS

A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic.

CONCLUSIONS

These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.

Assessing inbred-hybrid relationships for developing drought-tolerant provitamin A-quality protein maize hybrids

Drought-tolerant early-maturing maize (Zea mays L.) inbred lines with high levels of provitamin A (PVA) and quality protein (QPM) are urgently needed for development of superior hybrids to mitigate malnutrition and to intensify maize production and productivity in sub-Saharan Africa (SSA). This study was designed to identify early-maturing inbred lines with combined tolerance to drought, elevated tryptophan, and PVA contents; to examine inbred-hybrid relationships for tryptophan and PVA accumulation; and to select hybrids with outstanding grain yield (GY) performance. A total of 64 inbred lines and six checks, plus 96 hybrids and four checks, were evaluated under drought and well-watered environments in Nigeria for 2 yr. Eighteen parental lines and 54 derived hybrids were assayed for tryptophan and PVA contents. Ten drought-tolerant inbred lines with high tryptophan and elevated PVA levels were identified in the top 10 hybrid combinations across managed drought and well-watered conditions. The inbred-hybrid relationship was significant for GY under each and across the two contrasting environments. Significant average heterosis was found for tryptophan and PVA under well-watered conditions. This indicated that the selected inbred lines could be used for developing high-yielding PVA-QPM hybrids tolerant to drought stress in SSA. The 10 top-performing PVA-QPM hybrids identified are being extensively evaluated in different locations and subsequently in on-farm trials for commercialization throughout SSA.

Genetic diversity among early provitamin A quality protein maize inbred lines and the performance of derived hybrids under contrasting nitrogen environments

BACKGROUND

Information 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.

RESULTS

Genetic 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.

CONCLUSIONS

The 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.

Functional Markers for Precision Plant Breeding

Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.