Marker assisted selection of low phytic acid trait in maize (Zea maysL.)

NM, Jebakani K. S, Selvaraj S, Pramitha J. L, Selvaraj R, Petchiammal K. I, Kather Sheriff S, Thinakaran J, Rathinamoorthy S, Kumar P. R. Genetic manipulation of anti-nutritional factors in major crops for a sustainable diet in future

The consumption of healthy food, in order to strengthen the immune system, is now a major focus of people worldwide and is essential to tackle the emerging pandemic concerns. Moreover, research in this area paves the way for diversification of human diets by incorporating underutilized crops which are highly nutritious and climate-resilient in nature. However, although the consumption of healthy foods increases nutritional uptake, the bioavailability of nutrients and their absorption from foods also play an essential role in curbing malnutrition in developing countries. This has led to a focus on anti-nutrients that interfere with the digestion and absorption of nutrients and proteins from foods. Anti-nutritional factors in crops, such as phytic acid, gossypol, goitrogens, glucosinolates, lectins, oxalic acid, saponins, raffinose, tannins, enzyme inhibitors, alkaloids, β-N-oxalyl amino alanine (BOAA), and hydrogen cyanide (HCN), are synthesized in crop metabolic pathways and are interconnected with other essential growth regulation factors. Hence, breeding with the aim of completely eliminating anti-nutrition factors tends to compromise desirable features such as yield and seed size. However, advanced techniques, such as integrated multi-omics, RNAi, gene editing, and genomics-assisted breeding, aim to breed crops in which negative traits are minimized and to provide new strategies to handle these traits in crop improvement programs. There is also a need to emphasize individual crop-based approaches in upcoming research programs to achieve smart foods with minimum constraints in future. This review focuses on progress in molecular breeding and prospects for additional approaches to improve nutrient bioavailability in major crops.

Diverse role of phytic acid in plants and approaches to develop low-phytate grains to enhance bioavailability of micronutrients

Natural or synthetic compounds that interfere with the bioavailability of nutrients are called antinutrients. Phytic acid (PA) is one of the major antinutrients present in the grains and acts as a chelator of micronutrients. The presence of six reactive phosphate groups in PA hinders the absorption of micronutrients in the gut of non-ruminants. Consumption of PA-rich diet leads to deficiency of minerals such as iron and zinc among human population. On the contrary, PA is a natural antioxidant, and PA-derived molecules function in various signal transduction pathways. Therefore, optimal concentration of PA needs to be maintained in plants to avoid adverse pleiotropic effects, as well as to ensure micronutrient bioavailability in the diets. Given this, the chapter enumerates the structure, biosynthesis, and accumulation of PA in food grains followed by their roles in growth, development, and stress responses. Further, the chapter elaborates on the antinutritional properties of PA and explains the conventional breeding and transgene-based approaches deployed to develop low-PA varieties. Studies have shown that conventional breeding methods could develop low-PA lines; however, the pleiotropic effects of these methods viz. reduced yield, embryo abnormalities, and poor seed quality hinder the use of breeding strategies. Overexpression of phytase in the endosperm and RNAi-mediated silencing of genes involved in myo-inositol biosynthesis overcome these constraints. Next-generation genome editing approaches, including CRISPR-Cas9 enable the manipulation of more than one gene involved in PA biosynthesis pathway through multiplex editing, and scope exists to deploy such tools in developing varieties with optimal PA levels.

Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves

Alternative splicing (AS) is a post-transcriptional process common in plants and essential for regulation of environmental fitness of plants. In the present study, we focus on the AS events in poplar leaves to understand their effects on plant growth and development. The hybrid poplar (P.alba×P.glandulosa cv.84K) leaves were collected for RNA extraction. The extracted RNA was sequenced using on an Illumina HiSeq™ 2000 platform. Using the Populus trichocarpa genome as the reference, a total of 3810 AS genes were identified (9225 AS events), which accounted for 13.51% of all the expressed genes. Intron retention was the most common AS event, accounting for 43.86% of all the AS events, followed by alternative 3′ splice sites (23.75%), alternative 5′ splice sites (23.71%), and exon skipping (8.68%). Chromosomes 10 had the most condensed AS events (33.67 events/Mb) and chromosome 19 had the least (12.42 events/Mb). Association analysis showed that AS in the poplar leaves was positively correlated with intron length, exon number, exon length, and gene expression level, and was negatively correlated with GC content. AS genes in the poplar leaves were associated mainly with inositol phosphate metabolism and phosphatidylinositol signaling system pathways that would be significant on wooden plant production.

Development and validation of breeder-friendly gene-based markers for lpa1-1 and lpa2-1 genes conferring low phytic acid in maize kernel

Based on C (wild) to T (mutant) transition at amino acid position 1432 bp of lpa1-1 gene, two dominant markers each specific to wild type (LPA1) and mutant (lpa1-1) allele were developed and validated across seven F₂ populations. Joint segregation of these markers behaved in co-dominant fashion, clearly distinguishing heterozygote from two other homozygote genotypes. Full length sequence alignment between wild type (LPA2) and mutant (lpa2-1) allele revealed one transition mutation (A to G) and a co-dominant CAPS marker was developed which differentiated all three types of segregants across seven F₂ populations. Across populations, segregants with lpa1-1/lpa1-1 (1.77 mg/g) and lpa2-1/lpa2-1 (1.85 mg/g) possessed significantly lower phytic acid compared to LPA1/LPA1 (2.58 mg/g) and LPA2/LPA2 (2.53 mg/g). Inorganic phosphorus was however higher in recessive homozygotes (lpa1-1/lpa1-1: 0.77 mg/g, lpa2-1/lpa2-1: 0.53 mg/g) than the dominant homozygotes (LPA1/LPA1: 0.33 mg/g, LPA2/LPA2: 0.19 mg/g). Overall, homozygous segregants of lpa1-1 and lpa2-1 showed 31% and 27% reduction of phytic acid, respectively. Analysis of phytate and inorganic phosphorous in the maize kernel in these segregating populations confirmed co-segregation of trait and markers specific to lpa1-1 and lpa2-1. This is the first report of the development of breeder-friendly gene-based markers for lpa1-1 and lpa2-1; and it holds great significance for maize biofortification.

Molecular Breeding for Nutritionally Enriched Maize: Status and Prospects

Maize is a major source of food security and economic development in sub-Saharan Africa (SSA), Latin America, and the Caribbean, and is among the top three cereal crops in Asia. Yet, maize is deficient in certain essential amino acids, vitamins, and minerals. Biofortified maize cultivars enriched with essential minerals and vitamins could be particularly impactful in rural areas with limited access to diversified diet, dietary supplements, and fortified foods. Significant progress has been made in developing, testing, and deploying maize cultivars biofortified with quality protein maize (QPM), provitamin A, and kernel zinc. In this review, we outline the status and prospects of developing nutritionally enriched maize by successfully harnessing conventional and molecular marker-assisted breeding, highlighting the need for intensification of efforts to create greater impacts on malnutrition in maize-consuming populations, especially in the low- and middle-income countries. Molecular marker-assisted selection methods are particularly useful for improving nutritional traits since conventional breeding methods are relatively constrained by the cost and throughput of nutritional trait phenotyping.

Enumerating the phytic acid content in maize germplasm and formulation of reference set to enhance the breeding for low phytic acid

Phytic acid (Myoinositol 1, 2, 3, 4, 5, 6 hexakisphosphate) is a ubiquitous compound present in plants. It is an important constituent in seed reducing the bioavailability of phosphorous and mineral nutrients when fed to monogastric animals like swine, poultry, fish etc. Hence, identification of maize germplasm with reduced phytic acid content is imperative to formulate the breeding programs to evolve low phytate lines. Towards this, three hundred and thirty-eight maize germplasm accessions available at Department of Millets, TNAU, were raised and screened for phytic acid content which varied from 2.77 to 16.70 mg/g of seed. Based on the variability present, a reference set with fifty-eight genotypes for phytic acid was formulated. The reference set was formed with random genotypes selected from the base population to follow a normal distribution (skewness; 0.17, kurtosis; 0.61 and K-S test for normality D_n = 0.70) for phytic acid. The non-significant difference between the means of the base and the reference ensured the entire representation of the base in the formulated reference for phytic acid. Among all the lines in the reference set, the lowest phytic acid content were observed in the lines UMI-113 (2.77 mg/g) followed by UMI-300-1 (3.17 mg/g), UMI-467 (5.50 mg/g) and UMI-158 (6.58 mg/g) could be used as donors for low phytic acid in breeding programs. The principal component analysis for studying the extent of variability in the reference, revealed six major principal components that exhibited 80.40% of variation with flowering traits, ear height and phytic acid as a major contributor for variability. The characters namely plant stand, germination percentage, kernel yield, ear length, ear diameter and number of kernels per row were found to be positively correlated with the phytic acid and this emphasizes the negative pleiotropic effects of low phytic acid lines in germination and seed set. Thus this formulated reference set enables the breeders to handle minimum population for further grouping the genotypes to analyse their heterotic potential combined with low phytic acid.

MRP Transporters and Low Phytic Acid Mutants in Major Crops: Main Pleiotropic Effects and Future Perspectives

Phytic acid (PA) represents the major storage form of seed phosphate (P). During seed maturation, it accumulates as phytate salts chelating various mineral cations, therefore reducing their bioavailability. During germination, phytase dephosphorylates PA releasing both P and cations which in turn can be used for the nutrition of the growing seedling. Animals do not possess phytase, thus monogastric animals assimilate only 10% of the phytate ingested with feed, whilst 90% is excreted and may contribute to cause P pollution of the environment. To overcome this double problem, nutritional and environmental, in the last four decades, many low phytic acid (lpa) mutants (most of which affect the PA-MRP transporters) have been isolated and characterized in all major crops, showing that the lpa trait can increase the nutritional quality of foods and feeds and improve P management in agriculture. Nevertheless, these mutations are frequently accompanied by negative pleiotropic effects leading to agronomic defects which may affect either seed viability and germination or plant development or in some cases even increase the resistance to cooking, thus limiting the interest of breeders. Therefore, although some significant results have been reached, the isolation of lpa mutants improved for their nutritional quality and with a good field performance remains a goal so far not fully achieved for many crops. Here, we will summarize the main pleiotropic effects that have been reported to date in lpa mutants affected in PA-MRP transporters in five productive agronomic species, as well as addressing some of the possible challenges to overcome these hurdles and improve the breeding efforts for lpa mutants.

lpa1-5525: A New lpa1 Mutant Isolated in a Mutagenized Population by a Novel Non-Disrupting Screening Method

Phytic acid, or myo-inositol 1,2,3,4,5,6-hexakisphosphate, is the main storage form of phosphorus in plants. It is localized in seeds, deposited as mixed salts of mineral cations in protein storage vacuoles; during germination, it is hydrolyzed by phytases to make available P together with all the other cations needed for seed germination. When seeds are used as food or feed, phytic acid and the bound cations are poorly bioavailable for human and monogastric livestock due to their lack of phytase activity. Therefore, reducing the amount of phytic acid is one strategy in breeding programs aimed to improve the nutritional properties of major crops. In this work, we present data on the isolation of a new maize (Zea mays L.) low phytic acid 1 (lpa1) mutant allele obtained by transposon tagging mutagenesis with the Ac element. We describe the generation of the mutagenized population and the screening to isolate new lpa1 mutants. In particular, we developed a fast, cheap and non-disrupting screening method based on the different density of lpa1 seed compared to the wild type. This assay allowed the isolation of the lpa1-5525 mutant characterized by a new mutation in the lpa1 locus associated with a lower amount of phytic phosphorus in the seeds in comparison with the wild type.

A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia

Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species.