Hidden Pearls - Opportunities in Problems

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Views Read Edit View history. This page was last edited on 22 November , at For example, QTL mapping for phytate content has been accomplished in rice Stangoulis et al. It has also been proved that loci affecting phytate content are different than loci affecting grain micronutrient content, this suggests that the simultaneous increase of grain micronutrient content and a decrease in phytate content is possible White and Broadley, For example, in the case of Stangoulis et al. Since the QTLs of phytate are located on different chromosomal regions compared to those found for Fe and Zn, this suggests that they are genetically distinct and it should be possible to use molecular markers for breeding and selection purposes to modify the phytate concentration without affecting grain micronutrient content Stangoulis et al.

Following these studies, further population improvement should be implemented using recurrent selection to breed for low phytate content, whilst keeping yield and micronutrient uptake high. In recent decades, the potential of pearl millet and genetic variations associated with beneficial phenomic traits has been recognized. However, the use of molecular breeding technology for the genetic improvement of pearl millet is somewhat limited and progress is slow due to insufficient numbers of PCR compatible co-dominant markers Senthilvel et al.

Genetic maps enable a phenotypic trait to be linked to a gene or a region on a chromosome. Previously, genetic maps were highly dependent on morphological markers. However, recent advances in biotechnology have facilitated the creation of high-density maps that consist of thousands of molecular markers Hyten and Lee, Recently, the use of an F2 population of 93 progenies and 9 cultivated pearl millet crosses has facilitated the production of a genetic map with higher density and better uniformity of markers than previously published maps.

These efforts resulted in 3, SNPs generated for public use Moumouni et al.

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The availability of large numbers of SNP markers and high-density genetic maps will enhance the progress of gene and QTL mapping in biparental populations significantly, and facilitate association analyses on panels of unrelated lines. GWAS have expanded into a powerful tool for investigating the genetic architecture in many staple crops. GWAS exploits the natural diversity generated by multi-generational recombination events that occur in a population or germplasm panels Deschamps et al. This approach results in increased mapping resolution as compared to linkage mapping populations.

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Genetic sources of phenotypic variation are an essential component of plant genetics. Taking on the lessons learned from model species, such as rice and maize, future developments are being applied to staple crops as well as orphan crops. Comprehensive maps of genome variations will facilitate GWAS of complex agriculture benefitting traits in crops.

The result of which will greatly accelerate the improvement of crops via genomics-assisted breeding Huang and Han, Recent advances toward whole genome sequencing of the pearl millet genome together with resequencing of the entries of the various germplasm populations will certainly assist in such endeavors. Findings from GWAS will be the catalyst in the mining of candidate genes. These candidate genes can be verified through Transfer T -DNA mutants or genetic transformation, which will then facilitate the genetic modification or MAS for validated genes.

These steps will then lead to more nutrient rich, improved varieties Huang and Han, Synteny studies among the grass family sets the stage for a comparative study of millets and non-millet cereals to trace common genes associated with nutrition biosynthesis pathways Muthamilarasan et al. When these genes, alleles and QTLs are discovered, they can then be incorporated into elite lines through the use of molecular marker assisted breeding or transgene based methods. Synteny studies may also facilitate the introgression of these traits of interest from the major cereals into millets.

This will largely be achieved with the role of genomics, bioinformatics, transcriptomics, proteomics, metabolomics, and ionomics Muthamilarasan et al. The dearth of genomic resources that has characterized most major cereal crops is going to benefit pearl millet directly. The high throughput and low cost of NGS technologies has made it possible to sequence crops with lower economic value for the development of elite cultivars with desirable traits.

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The benefits of this include i improved analysis of cereal biodiversity and the identification of useful variants; ii MAS of alleles and allele combinations of interest; and iii cloning and efficient transfer of useful alleles among members of the cereal family Nelson et al. Resources from well sequenced species will enable functional definition of many key genes and pathways Chen et al. For example, Chen et al. It was found that distinct and overlapping aspects of genetic control of metabolism exist within and between species and the mGWAS analysis indicated that the rice and maize are likely to share common genetic control strategies for a variety of metabolites.

A search for homologous loci mapped by the same metabolites or metabolites with similar structures identified 42 loci underlying the 23 co-detected metabolic features between maize and rice. This data suggests that there is potential for the identification of genes associated with traits of interest between cereals using mGWAS and pGWAS and genetic analysis of the metabolome could improve what is currently known about these complex traits. Quantitative trait loci associated with increased Zn and Fe accumulation in pearl millet are an important asset to those targeting candidate genes associated with these traits and continue to drive biofortification research.

Focus should be made on what resources could provide potential candidates for the identification of QTLs. As discussed, there are several germplasm panels that hold lines associated with high micronutrient accumulation that cover global diversity. Potential candidates for QTL fine mapping exist within these germplasm banks. For example, in the Iniadi pearl millet germplasm, certain lines have been found to be particularly high in Fe and Zn, with a highly significant and high positive correlation between these two micronutrients.

One of these lines, ICTP has been released in India and in it was cultivated on more than 0. At present, ICTP is still cultivated on about 0. Simultaneous accumulation has been reported in a wide variety of crops, including pearl millet and these positive correlations could be due to common and overlapping QTLs for grain Fe and Zn densities Kumar, Research into identifying QTLs and candidate genes for elevated levels of Fe and Zn in pearl millet is limited at this time, perhaps due to resource constraints such as lack of a reference genome.

The fact that QTLs associated with the trait have been identified in other crops will benefit QTL fine mapping in pearl millet through synteny studies. These were located in 32 non-overlapping genomic regions. Research into DNA technology has been developed extensively in major cereal crops, more so than for pearl millet. Although recent advances for the improvement of pearl millet have been well established via traditional breeding methods and MAS, genetic engineering and in vitro culture allows the gene pool to be expanded further than previously thought possible.

In vitro culture and transformation of pearl millet is established and reliable protocols have been developed and can be further improved thanks to the progress of transformation in major crop species Oldach et al. For example, improved nutritional quality and better genetic engineering methods can be used to elevate levels of minerals and vitamins in the starchy endosperm of cereal seeds.

This has been accomplished in rice, where expression of soybean ferritin a Fe binding protein in developing seeds of rice has resulted in a threefold increase in endosperm Fe content compared to the non-transformant Qu et al. Similar findings were also reported by Goto et al. GluB-1 was used to facilitate the expression of the soybean gene in developing, self-pollinated seeds of transgenic plants.

Findings showed that the Fe content of seeds from the transgenic plants was up to three times greater than that of their untransformed counterparts Goto et al. The same techniques could be applied to pearl millet for the increased Fe accumulation. Harnessing tools that facilitate genetic engineering have also been established for anti-nutrient compounds such as phytate.

The pathway of phytate from myoinositol is also considered to be well understood and the screening of mutant populations for reduced phytate accumulation is now possible. For example the identification of low phytate mutants in maize, barley, wheat, soybean, and rice will assist in the selection of similar mutations millets and incorporated into breeding programs.

In barley, grains were mutagenised with sodium azide and screened for high levels of free phosphate for the identification of low-phytate mutants. Results showed that nine out of 27 mutants had an increased free phosphate content in the grain and this was correlated with a significant decrease in levels of phytate. Allelic testing of four out of the nine mutants showed that at least two distinct loci control the biosynthesis of grain phytin a calcium magnesium salt of phytic acid. It is therefore possible to screen for and isolate low phytate mutants through identification of genes involved in the biosynthetic pathway of phytin.

This contributes to the development of low-phytin crops with higher nutritional value Rasmussen and Hatzack, As previously discussed, NA, plays a key role in metal assimilation and homeostasis Morrissey and Guerinot, Therefore, manipulation of cellular NA concentrations should be considered for the improvement of Fe and Zn content pearl millet.

This has been achieved through the use of activation and knockout mutants in rice and tobacco. A study by Inoue et al. Activation and knockout mutants were used to examine the functioning of OsNAS3 in metal homeostasis in rice plants and it was found that there was an increase in NA by activation of OsNAS3 , causing increased levels of Fe and Zn in both leaves and seeds Lee et al. NAS genes could therefore be potential candidates for the improvement of Fe and Zn in rice. Constitutive overexpression of NAS genes also resulted in elevated levels of Fe and Zn in transgenic tobacco plants Douchkov et al.

This method is desirable in the field of crop science because it is highly efficient, robust, is associated with reduced risk and enables a wide variety of agricultural applications. Genetic transmission of edits has been reported in A. In Rice, large chromosomal segment deletions, the inheritance of genome mutations in multiple generations and the construction of a set of facile vectors for highly efficient, multiplex gene targeting has been reported. In a study by Zhou et al. Due to the orphan status of pearl millet, little work has been performed so far on the nutritional enhancement of their grains via genetic engineering — thus presenting a significant gap in the literature.

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In order to employ recombinant DNA technology methods, there needs to be an increase in knowledge about the Zn and Fe pathways in pearl millet and it is also important to consider factors such as cost, consumer acceptability and socioeconomics to small holder farmers. The current state biofortification research in pearl millet for nutritional purposes is still limited at this time, as compared to major crop species Shivran, In light of this, combined efforts are needed from all fields relating to agriculture, medicine, nutrition and genetics to drive this research in a safe and consumer friendly way Rahal and Shivay, To facilitate this research, Fe and Zn pathways in pearl millet must be better understood.

A better understanding would increase the safety of transgenic techniques and biotechnological applications, thus making the end-product more reliable and consumer friendly. The mechanisms behind efficient Fe and Zn uptake for improved health and productivity could be better understood by research into the root rhizosphere, dissecting the complex biological and ecological processes within the soil microbiome, elucidating the mechanisms behind cation selectivity and investigation into potential downsides such as enhanced accumulation of antinutrients and toxic metals.

Since pearl millet is commonly grown in infertile soils, which are lacking in Fe and Zn, any potential technologies should also be evaluated under real conditions. This could be greatly facilitated by transcriptomics and metabolomics. As demonstrated, the molecular mechanisms of Zn and Fe homeostasis in nutrient rich and nutrient lacking soils have been researched extensively in A. The well-established theories and protocols from model species could be applied specifically to pearl millet, allowing further improvement and increased efficiency of Zn and Fe biofortification.

Biofortified pearl millet with increased Zn and Fe content may be achieved either through conventional plant breeding methods or through the use of transgenic techniques. Genetic improvement of pearl millet results from the use of available genetic and bioinformatic resources coupled with extensive phenotyping of diverse germplasm collections. The usefulness of the available germplasm collections is not disputed, although extensive GEI analysis is needed for accurate predictions of how genotypes will suit different environments for efficient nutrient uptake, this can be achieved through real time multi environmental trials to verify the stability of phenotypic data.

Traditional breeding methods highly depend on the existence of genetic variation for the target traits in the gene pool. However, whilst there are a number of studies that show this for Fe and Zn, there are a variety of other complex factors to a consider such as; maintaining high yield and good end use quality, which can be affected by a variety of factors such as levels of phytate and certain methods of processing. In light of this, biofortification should encompass a wide range of factors and not be solely focused on increasing Fe and Zn content.

Advances in DNA-based molecular markers have already contributed to the identification and tagging of some agronomically important genes and QTLs for agricultural applications.

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The availability of large-scale genome-wide markers in pearl millet will further improve the tagging of nutrition relevant genes and QTLs in pearl millet, and it is hoped that as the awareness of capturing genetic variations for micronutrients in the genome increases, this will facilitate the discovery and validation of genes associated with high micronutrient uptake Kumar et al. Even though nutritional enhancement of pearl millet grains via genetic engineering should be considered as an important area of research for nutrition security, little work has been performed on pearl millet so far.

This research should be employed when the Zn and Fe pathways in pearl millet are better understood whilst considering socioeconomic factors such as consumer acceptability and feasibility to small holder farmers. It is well documented that there are severe health limiting consequences as a result of Fe and Zn deficiencies. Prevention of these deficiencies is therefore perceived as a desirable worldwide goal. The tragic loss of human potential predominantly applies to people living in poverty stricken areas, who depend on grain from staple crops that they eat on a daily basis.

The lack of nutritious food has forced many people to depend on food fortification, supplements and agronomic practices as interventions. However, these are not sustainable and suffer major drawbacks. Biofortification of staple crops, such as pearl millet, is considered to be the most sustainable method of intervention and is largely facilitated by traditional plant breeding and transgenic techniques.

Due to the potential role of pearl millet in addressing the challenges associated with MNDs, efforts are being made to target genes responsible to efficient Zn and Fe uptake to be bred into elite varieties. This will have a snowball effect as well-nourished children grow up to be stronger adults. Any attempt to increase Fe and Zn levels via traditional breeding or genetic engineering must first consider the mechanisms behind Fe and Zn uptake, distribution and storage. Genetics and functional genomic platforms have driven research that enhances the productivity, sustainability and nutritional quality of food production systems for a number of years Asins, and it is now possible identify QTLs and candidate genes that warrant further investigation to determine if these are accountable for beneficial traits, despite the lack of a reference genome.

The use of available genetic resources and diverse germplasm collections will facilitate this research. A positive and highly significant correlation between Fe and Zn has been demonstrated extensively, therefore there are good prospects for increasing levels of both micronutrients simultaneously, which can be achieved without compromising yield Velu et al.

Therefore, methods of processing should be considered to suitably benefit those suffering from Fe and Zn deficiencies Eyzaguirre et al. The potentially toxic side-effects of increasing levels of Fe and Zn have also been evaluated. For example, the simultaneous uptake of Zn and Cd should be accounted for and levels antinutrient compounds such as phytate should be reduced.

In light of this efforts have been made to develop low phytate lines in pearl millet. There are a variety of platforms that aid the development of nutrient rich pearl millet, including the use of genetic maps, GWAS, synteny studies, QTL fine mapping for targeting candidate genes and genetic engineering technology. Using existing genomic resources from other important crops and synteny among the cereal family, common genes associated with nutrition biosynthesis pathways can be identified among millets and non-millets and the introgression of these pathways can be incorporated into pearl millet through either transgene based techniques or traditional breeding methods.

Although transgene technologies have been established in many major crop species, methods of gene editing CRISPR , in vitro culture systems, activation and knockout mutants are still being developed in pearl millet. Author of the manuscript, wrote and designed manuscript, implemented and revised during this process. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

National Center for Biotechnology Information , U. Journal List Front Plant Sci v. Published online Dec Author information Article notes Copyright and License information Disclaimer. Received Oct 17; Accepted Dec 7. The use, distribution or reproduction in other forums is permitted, provided the original author s or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. This article has been cited by other articles in PMC.

Abstract Deficiencies of essential micronutrients such as iron and zinc are the cause of extensive health problems in developing countries. Open in a separate window. Drawbacks in Current Strategies to Manage and Prevent Micronutrient Deficiencies Nutritional dietary supplementation is intended to provide nutrients that may otherwise not be consumed in sufficient quantities through diet alone. Biofortified Pearl Millet — Human Trials The literature reports a large number of studies that have had success from biofortified crops.

Understanding Iron and Zinc Uptake- From Root to Seed Any attempt to increase Fe and Zn concentrations in pearl millet grains using traditional breeding methods or genetic engineering must first consider how Fe and Zn are obtained from the environment, distributed and stored see Morrissey and Guerinot, for a comprehensive review. Biofortification of Pearl Millet Traditional Plant Breeding and Genetic Modification Biofortified pearl millet with elevated Zn and Fe levels may be achieved either through conventional plant breeding methods or through the use of transgenic techniques Bouis and Welch, Germplasm Collections — A Good Place to Start Managed germplasm collections are available for pearl millet, and characterisation of genetic diversity within these collections is a necessary prelude to their efficient use Varshney et al.

Traditional Breeding Methods Traditional breeding methods involve the selection of two parental lines with high Fe and Zn content and crossing them to create a hybrid that expresses the traits of interest. A Stable Phenotype and Maintaining Yield Many pearl millet studies have identified potential high Fe and Zn lines with stable phenotypes, including one by Velu et al. End Use Quality End-use quality is an important factor to consider when improving any grain crop quality trait.

Toxic Effects Any potential products of biofortification should be carefully evaluated under real conditions.

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The Effect of Phytate on Mineral Bioavailability The improvement of Fe and Zn levels in plants would also need to include the reduction of antinutrient compounds such as phytate. Tools that Harness the Potential of Pearl Millet in the Field of Genetics and Genomics In recent decades, the potential of pearl millet and genetic variations associated with beneficial phenomic traits has been recognized.

Genetic Maps Genetic maps enable a phenotypic trait to be linked to a gene or a region on a chromosome. Synteny Studies and Resources From Major Crop Species Synteny studies among the grass family sets the stage for a comparative study of millets and non-millet cereals to trace common genes associated with nutrition biosynthesis pathways Muthamilarasan et al.

QTL Fine Mapping Quantitative trait loci associated with increased Zn and Fe accumulation in pearl millet are an important asset to those targeting candidate genes associated with these traits and continue to drive biofortification research. There are also areas that aren't actually affected one way or the other based on which route you take.

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