Marker-trait association analysis of functional gene markers for provitamin A levels across diverse tropical yellow maize inbred lines

Background: Biofortification of staple crops is a cost effective and sustainable approach that can help combat vitamin A and other micronutrient deficiencies in developing countries. PCR -based DNA markers distinguishing alleles of three key genes of maize endosperm carotenoid biosynthesis (PSY1, lcyE and crtRB1) have been developed to facilitate maize provitamin A biofortification via marker assisted selection. Previous studies of these functional DNA markers revealed inconsistent effects. The germplasm previously employed for discovering and validating these functional markers was mainly of temperate origin containing low frequencies of the favourable allele of the most significant polymorphism, crtRB1-5'TE. Here, we investigate the vitamin A biofortification potential of these DNA markers in a germplasm panel of diverse tropical yellow maize inbred lines, with mixed genetic backgrounds of temperate and tropical germplasm to identify the most effective diagnostic markers for vitamin A biofortification. Results: The functional DNA markers crtRB1-5'TE and crtRB1-3'TE were consistently and strongly associated with provitamin A content across the tropical maize inbred lines tested. The alleles detected by these two functional markers were in high linkage disequilibrium (R-2 = 0.75) and occurred in relatively high frequency (18%). Genotypes combining the favourable alleles at the two loci (N = 20) displayed a 3.22 fold average increase in beta-carotene content compared to those genotypes lacking the favourable alleles (N = 106). The PSY1 markers were monomorphic across all of the inbred lines. The functional DNA markers for lcyE were associated with lutein, and with the ratio of carotenoids in the alpha and beta branches, but not with provitamin A levels. However, the combined effects of the two genes were stronger than their individual effects on all carotenoids. Conclusions: Tropical maize inbred lines harbouring the favourable alleles of the crtRB1-5'TE and 3'TE functional markers produce higher levels of provitamin A. Such maize lines can be used as donor parents to speed up the development of provitamin A biofortified tropical maize varieties adapted to growing conditions and consumer preferences, providing a route towards mitigation of vitamin A malnutrition in Sub-Saharan Africa

Marker-trait association analysis of functional gene markers for provitamin a levels across diverse tropical yellow maize inbred lines

Background: Biofortification of staple crops is a cost effective and sustainable approach that can help combat vitamin A and other micronutrient deficiencies in developing countries. PCR -based DNA markers distinguishing alleles of three key genes of maize endosperm carotenoid biosynthesis (PSY1, lcyE and crtRB1) have been developed to facilitate maize provitamin A biofortification via marker assisted selection. Previous studies of these functional DNA markers revealed inconsistent effects. The germplasm previously employed for discovering and validating these functional markers was mainly of temperate origin containing low frequencies of the favourable allele of the most significant polymorphism, crtRB1-5\u27TE. Here, we investigate the vitamin A biofortification potential of these DNA markers in a germplasm panel of diverse tropical yellow maize inbred lines, with mixed genetic backgrounds of temperate and tropical germplasm to identify the most effective diagnostic markers for vitamin A biofortification. Results: The functional DNA markers crtRB1-5\u27TE and crtRB1-3\u27TE were consistently and strongly associated with provitamin A content across the tropical maize inbred lines tested. The alleles detected by these two functional markers were in high linkage disequilibrium (R-2 = 0.75) and occurred in relatively high frequency (18%). Genotypes combining the favourable alleles at the two loci (N = 20) displayed a 3.22 fold average increase in beta-carotene content compared to those genotypes lacking the favourable alleles (N = 106). The PSY1 markers were monomorphic across all of the inbred lines. The functional DNA markers for lcyE were associated with lutein, and with the ratio of carotenoids in the alpha and beta branches, but not with provitamin A levels. However, the combined effects of the two genes were stronger than their individual effects on all carotenoids. Conclusions: Tropical maize inbred lines harbouring the favourable alleles of the crtRB1-5\u27TE and 3\u27TE functional markers produce higher levels of provitamin A. Such maize lines can be used as donor parents to speed up the development of provitamin A biofortified tropical maize varieties adapted to growing conditions and consumer preferences, providing a route towards mitigation of vitamin A malnutrition in Sub-Saharan Africa

Genetic loci controlling carotenoid biosynthesis in diverse tropical maize lines

The discovery and use of genetic markers associated with carotenoid levels can help to exploit the genetic potential of maize for provitamin A accumulation more effectively. Provitamin A carotenoids are classes of carotenoids that are precursors of vitamin A, an essential micronutrient in humans. Vitamin A deficiency is a global public health problem affecting millions of people, especially in developing countries. Maize is one of the most important staple crops targeted for provitamin A biofortification to help alleviate vitamin A deficiency in developing countries. A genome-wide association study (GWAS) of maize endosperm carotenoids was conducted using a panel of 130 diverse yellow maize tropical inbred lines genotyped with Genotyping by Sequencing (GBS) SNP markers. Numerous significant association signals co-localizing with the known carotenoid biosynthesis genes crtRB1, lcyE and ZEP1 were identified. The GWAS confirmed previously reported large effects of the two major carotenoid biosynthesis genes lcyE and crtRB1. In addition, significant novel associations were detected for several transcription factors (e.g., RING zinc finger domain and HLH DNA-binding domain super family proteins) that may be involved in regulation of carotenoid biosynthesis in maize. When the GWAS was re-conducted by including the major effects of lcyE and crtRB1 genes as covariates, a SNP in a gene coding for an auxin response factor 20 transcription factor was identified which displayed an association with -carotene and provitamin A levels. Our study provides a foundation for design and implementation of genomics-assisted selection strategies for provitamin A maize breeding in tropical regions, and advances efforts toward identification of additional genes (and allelic variants) involved in the regulation of carotenoid biosynthesis in plants

Performance of Variety Cross Hybrids of Maize (Zea Mays L.) in the Mid-Altitude and Highland Transition Areas of Ethiopia

Improved open-pollinated varieties (OPVs) have been developed and released for commercial production in maize growing areas of Ethiopia. However, the dissemination of these improved varieties is limited because of a low level of interest of seed producers in the production and marketing of OPV seed. The dissemination of broad based improved varieties could be increased by the development and release of adapted commercial high yielding variety cross hybrids. This study was conducted in 2002 at seven locations in the mid-altitude (1000 – 1800 meter above sea level, masl) and highland transition areas (1800 – 2000 masl) of Ethiopia to evaluate the performance of variety cross hybrids. Twenty-nine variety cross hybrids and nine parental OPVs/populations along two checks were tested in randomized complete block design with three replications at each location. Analysis of variance revealed significant difference (P<0.01) among the entries. The mean grain yield ranged from 3.9 to 8.3 t ha-1. Some variety cross hybrids gave a better performance than the improved OPVs. Kuleni (Pool-9A) x Abo-Bako outyielded the high parent (Kuleni) by 29.7% and Gibe-1 x Kuleni outyielded the best OPV and high parent (Gibe-1) by 14.7%. Gibe-1 x Kuleni also had a more stable performance across the testing locations than the parental OPVs. This implied that moving from OPVs to variety cross hybrids, particularly under small scale farmers’ conditions, could increase the productivity of maize

Fast-Tracking the Development and Dissemination of a Drought-Tolerant Maize Variety in Ethiopia in Response to the Risks of Climate Change

Climate change projections suggest increased frequency of drought in many parts of sub-Saharan Africa (SSA). The replacement of old varieties of maize with new drought-tolerant (DT) varieties will be crucial to respond to the future risk of drought, as it already is today. The first group of locally developed maize hybrids in Ethiopia—BH140, BH660 and BH540—were commercialised between 1988 and 1995, but were not selected for drought tolerance. Among these, BH660 remained the most popular and widely grown maize variety in the Ethiopian maize belt between 2000 and 2010, accounting for nearly 50% of maize area under improved seed. A new DT hybrid, BH661, with better agronomic performances under optimum and random drought than BH660, was identified and released in 2011. In 2016, 9000 tonnes of certified seed—enough to plant 360,000 ha—was produced and marketed. The concerted effort of breeders and seed producers as well as governmental and non-governmental extension workers drove the development, release and rapid adoption of BH661 contributing to food and income security of more than 300,000 households by mitigating the effects of climate change in Ethiopia. The success of BH661 is a valuable and timely case study for breeders, seed companies, extension agents, regulatory bodies and policy-makers striving to develop and disseminate new DT varieties in sub-Saharan Africa

Additional file 4: of Genetic variation and population structure of maize inbred lines adapted to the mid-altitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers

Heat map of the 265 inbred lines based on relative kinship matrix estimated from 220,878 polymorphic SNPs. (DOCX 211 kb

Additional file 1: of Genetic variation and population structure of maize inbred lines adapted to the mid-altitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers

Summary of the 265 inbred lines and population structure. (XLSX 47 kb