Identifying Candidate Genes for Enhancing Grain Zn Concentration in Wheat

Genome-wide association study of trace elements in maize kernels

Maize (Zea mays L.), a staple food and significant economic crop, is enriched with riboflavin, micronutrients and other compounds that are beneficial for human health. As emphasis on the nutritional quality of crops increases maize research has expanded to focus on both yield and quality. This study exploreed the genetic factors influencing micronutrient levels in maize kernels through a comprehensive genome-wide association study (GWAS). We utilized a diverse panel of 244 inbred maize lines and approximately 3 million single nucleotide polymorphisms (SNPs) to investigate the accumulation of essential and trace elements including cadmium (Cd), cobalt (Co), copper (Cu), nickel (Ni), selenium (Se) and zinc (Zn). Our analysis identified 842 quantitative trait loci (QTLs), with 12 QTLs shared across multiple elements and pinpointed 524 potential genes within a 100 kb radius of these QTLs. Notably ZmHMA3 has emerged as a key candidate gene previously reported to influence the Cd accumulation. We highlighted ten pivotal genes associated with trace element transport including those encoding heavy metal ATPases, MYB transcription factors, ABC transporters and other crucial proteins involved in metal handling. Additionally, haplotype analysis revealed that eight inbred linesaccumulated relatively high levels of beneficial elements while harmful elements were minimized. These findings elucidate the genetic mechanisms underlying trace element accumulation in maize kernels and provide a foundation for the breeding of nutritionally enhanced maize varieties.

Biofortification of Triticum species: a stepping stone to combat malnutrition

BACKGROUND

Biofortification represents a promising and sustainable strategy for mitigating global nutrient deficiencies. However, its successful implementation poses significant challenges. Among staple crops, wheat emerges as a prime candidate to address these nutritional gaps. Wheat biofortification offers a robust approach to enhance wheat cultivars by elevating the micronutrient levels in grains, addressing one of the most crucial global concerns in the present era.

MAIN TEXT

Biofortification is a promising, but complex avenue, with numerous limitations and challenges to face. Notably, micronutrients such as iron (Fe), zinc (Zn), selenium (Se), and copper (Cu) can significantly impact human health. Improving Fe, Zn, Se, and Cu contents in wheat could be therefore relevant to combat malnutrition. In this review, particular emphasis has been placed on understanding the extent of genetic variability of micronutrients in diverse Triticum species, along with their associated mechanisms of uptake, translocation, accumulation and different classical to advanced approaches for wheat biofortification.

CONCLUSIONS

By delving into micronutrient variability in Triticum species and their associated mechanisms, this review underscores the potential for targeted wheat biofortification. By integrating various approaches, from conventional breeding to modern biotechnological interventions, the path is paved towards enhancing the nutritional value of this vital crop, promising a brighter and healthier future for global food security and human well-being.

Alien introgression to wheat for food security: functional and nutritional quality for novel products under climate change

Crop yield and quality has increased globally during recent decades due to plant breeding, resulting in improved food security. However, climate change and shifts in human dietary habits and preferences display novel pressure on crop production to deliver enough quantity and quality to secure food for future generations. This review paper describes the current state-of-the-art and presents innovative approaches related to alien introgressions into wheat, focusing on aspects related to quality, functional characteristics, nutritional attributes, and development of novel food products. The benefits and opportunities that the novel and traditional plant breeding methods contribute to using alien germplasm in plant breeding are also discussed. In principle, gene introgressions from rye have been the most widely utilized alien gene source for wheat. Furthermore, the incorporation of novel resistance genes toward diseases and pests have been the most transferred type of genes into the wheat genome. The incorporation of novel resistance genes toward diseases and pests into the wheat genome is important in breeding for increased food security. Alien introgressions to wheat from e.g. rye and Aegilops spp. have also contributed to improved nutritional and functional quality. Recent studies have shown that introgressions to wheat of genes from chromosome 3 in rye have an impact on both yield, nutritional and functional quality, and quality stability during drought treatment, another character of high importance for food security under climate change scenarios. Additionally, the introgression of alien genes into wheat has the potential to improve the nutritional profiles of future food products, by contributing higher minerals levels or lower levels of anti-nutritional compounds into e.g., plant-based products substituting animal-based food alternatives. To conclude, the present review paper highlights great opportunities and shows a few examples of how food security and functional-nutritional quality in traditional and novel wheat products can be improved by the use of genes from alien sources, such as rye and other relatives to wheat. Novel and upcoming plant breeding methods such as genome-wide association studies, gene editing, genomic selection and speed breeding, have the potential to complement traditional technologies to keep pace with climate change and consumer eating habits.

Molecular characterization of QTL for grain zinc and iron concentrations in wheat landrace Chinese Spring

KEY MESSAGE

Three stable QTL for grain zinc concentration were identified in wheat landrace Chinese Spring. Favorable alleles were more frequent in landraces than in modern wheat cultivars. Wheat is a major source of dietary energy for the growing world population. Developing cultivars with enriched zinc and iron can potentially alleviate human micronutrient deficiency. In this study, a recombinant inbred line (RIL) population with 245 lines derived from cross Zhou 8425B/Chinese Spring was used to detect quantitative trait loci (QTL) for grain zinc concentration (GZnC) and grain iron concentration (GFeC) across four environments. Three stable QTL for GZnC with all favorable alleles from Chinese Spring were identified on chromosomes 3BL, 5AL, and 5BL. These QTL explaining maxima of 8.7%, 5.8%, and 7.1% of phenotypic variances were validated in 125 resequenced wheat accessions encompassing both landraces and modern cultivars using six kompetitive allele specific PCR (KASP) assays. The frequencies of favorable alleles for QGZnCzc.caas-3BL, QGZnCzc.caas-5AL and QGZnCzc.caas-5BL were higher in landraces (90.4%, 68.0%, and 100.0%, respectively) compared to modern cultivars (45.9%, 35.4%, and 40.9%), suggesting they were not selected in breeding programs. Candidate gene association studies on GZnC in the cultivar panel further delimited the QTL into 8.5 Mb, 4.1 Mb, and 47.8 Mb regions containing 46, 4, and 199 candidate genes, respectively. The 5BL QTL located in a region where recombination was suppressed. Two stable and three less stable QTL for GFeC with favorable alleles also from Chinese Spring were identified on chromosomes 4BS (Rht-B1a), 4DS (Rht-D1a), 1DS, 3AS, and 6DS. This study sheds light on the genetic basis of GZnC and GFeC in Chinese Spring and provides useful molecular markers for wheat biofortification.

Single- and multi-trait genomic prediction and genome-wide association analysis of grain yield and micronutrient-related traits in ICARDA wheat under drought environment

Globally, over 2 billion people suffer from malnutrition due to inadequate intake of micronutrients. Genomic-assisted breeding is identified as a valuable method to facilitate developing new improved plant varieties targeting grain yield and micronutrient-related traits. In this study, a genome-wide association study (GWAS) and single- and multi-trait-based genomic prediction (GP) analysis was conducted using a set of 252 elite wheat genotypes from the International Center for Agricultural Research in Dry Areas (ICARDA). The objective was to identify linked SNP markers, putative candidate genes and to evaluate the genomic estimated breeding values (GEBVs) of grain yield and micronutrient-related traits.. For this purpose, a field trial was conducted at a drought-prone station, Merchouch, Morocco for 2 consecutive years (2018 and 2019) followed by GWAS and genomic prediction analysis with 10,173 quality SNP markers. The studied genotypes exhibited a significant genotypic variation in grain yield and micronutrient-related traits. The GWAS analysis identified highly significantly associated markers and linked putative genes on chromosomes 1B and 2B for zinc (Zn) and iron (Fe) contents, respectively. The genomic predictive ability of selenium (Se) and Fe traits with the multi-trait-based GP GBLUP model was 0.161 and 0.259 improving by 6.62 and 4.44%, respectively, compared to the corresponding single-trait-based models. The identified significantly linked SNP markers, associated putative genes, and developed GP models could potentially facilitate breeding programs targeting to improve the overall genetic gain of wheat breeding for grain yield and biofortification of micronutrients via marker-assisted (MAS) and genomic selection (GS) methods.

Nutritional Genomic Approach for Improving Grain Protein Content in Wheat

Grain protein content (GPC) is a key aspect of grain quality, a major determinant of the flour functional properties and grain nutritional value of bread wheat. Exploiting diverse germplasms to identify genes for improving crop performance and grain nutritional quality is needed to enhance food security. Here, we evaluated GPC in a panel of 255 Triticum aestivum L. accessions from 27 countries. GPC determined in seeds from three consecutive crop seasons varied from 8.6 to 16.4% (11.3% on average). Significant natural phenotypic variation in GPC among genotypes and seasons was detected. The population was evaluated for the presence of the trait-linked single nucleotide polymorphism (SNP) markers via a genome-wide association study (GWAS). GWAS analysis conducted with calculated best linear unbiased estimates (BLUEs) of phenotypic data and 90 K SNP array using the fixed and random model circulating probability unification (FarmCPU) model identified seven significant genomic regions harboring GPC-associated markers on chromosomes 1D, 3A, 3B, 3D, 4B and 5A, of which those on 3A and 3B shared associated SNPs with at least one crop season. The verified SNP-GPC associations provide new promising genomic signals on 3A (SNPs: Excalibur_c13709_2568 and wsnp_Ku_c7811_13387117) and 3B (SNP: BS00062734_51) underlying protein improvement in wheat. Based on the linkage disequilibrium for significant SNPs, the most relevant candidate genes within a 4 Mbp-window included genes encoding a subtilisin-like serine protease; amino acid transporters; transcription factors; proteins with post-translational regulatory functions; metabolic proteins involved in the starch, cellulose and fatty acid biosynthesis; protective and structural proteins, and proteins associated with metal ions transport or homeostasis. The availability of molecular markers within or adjacent to the sequences of the detected candidate genes might assist a breeding strategy based on functional markers to improve genetic gains for GPC and nutritional quality in wheat.

Antagonistic Strain Bacillus halotolerans Jk-25 Mediates the Biocontrol of Wheat Common Root Rot Caused by Bipolaris sorokiniana

Common root rot caused by Bipolaris sorokiniana infestation in wheat is one of the main reasons for yield reduction in wheat crops worldwide. The bacterium strain JK-25 used in the current investigation was isolated from wheat rhizosphere soil and was later identified as Bacillus halotolerans based on its morphological, physiological, biochemical, and molecular properties. The strain showed significant antagonism to B. sorokiniana, Fusarium oxysporum, Fusarium graminearum, and Rhizoctonia zeae. Inhibition of B. sorokiniana mycelial dry weight and spore germination rate by JK-25 fermentation supernatant reached 60% and 88%, respectively. The crude extract of JK-25 was found, by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), to contain the surfactin that exerted an inhibitory effect on B. sorokiniana. The disruption of mycelial cell membranes was observed under laser scanning confocal microscope (LSCM) after treatment of B. sorokiniana mycelium with the crude extract. The antioxidant enzyme activity of B. sorokiniana was significantly reduced and the oxidation product malondialdehyde (MDA) content increased after treatment with the crude extract. The incidence of root rot was significantly reduced in pot experiments with the addition of JK-25 culture fermentation supernatant, which had a significant biological control effect of 72.06%. Its ability to produce siderophores may help to promote wheat growth and the production of proteases and pectinases may also be part of the strain's role in suppressing pathogens. These results demonstrate the excellent antagonistic effect of JK-25 against B. sorokiniana and suggest that this strain has great potential as a resource for biological control of wheat root rot strains.

Genome wide association analysis for grain micronutrients and anti-nutritional traits in mungbean [Vigna radiata (L.) R. Wilczek] using SNP markers

Mungbean is an important food grain legume for human nutrition and nutritional food due to its nutrient-dense seed, liked palatability, and high digestibility. However, anti-nutritional factors pose a significant risk to improving nutritional quality for bio-fortification. In the present study, genetic architecture of grain micronutrients (grain iron and zinc concentration) and anti-nutritional factors (grain phytic acid and tannin content) in association mapping panel of 145 diverse mungbean were evaluated. Based on all four parameters genotypes PUSA 1333 and IPM 02-19 were observed as desired genotypes as they had high grain iron and zinc concentration but low grain phytic acid and tannin content. The next generation sequencing (NGS)-based genotyping by sequencing (GBS) identified 14,447 genome-wide SNPs in a diverse selected panel of 127 mungbean genotypes. Population admixture analysis revealed the presence of four different ancestries among the genotypes and LD decay of ∼57.6 kb kb physical distance was noted in mungbean chromosomes. Association mapping analysis revealed that a total of 20 significant SNPs were shared by both GLM and Blink models associated with grain micronutrient and anti-nutritional factor traits, with Blink model identifying 35 putative SNPs. Further, this study identified the 185 putative candidate genes. Including potential candidate genes Vradi07g30190, Vradi01g09630, and Vradi09g05450 were found to be associated with grain iron concentration, Vradi10g04830 with grain zinc concentration, Vradi08g09870 and Vradi01g11110 with grain phytic acid content and Vradi04g11580 and Vradi06g15090 with grain tannin content. Moreover, two genes Vradi07g15310 and Vradi09g05480 showed significant variation in protein structure between native and mutated versions. The identified SNPs and candidate genes are potential powerful tools to provide the essential information for genetic studies and marker-assisted breeding program for nutritional improvement in mungbean.

Biofortification to avoid malnutrition in humans in a changing climate: Enhancing micronutrient bioavailability in seed, tuber, and storage roots

Malnutrition results in enormous socio-economic costs to the individual, their community, and the nation's economy. The evidence suggests an overall negative impact of climate change on the agricultural productivity and nutritional quality of food crops. Producing more food with better nutritional quality, which is feasible, should be prioritized in crop improvement programs. Biofortification refers to developing micronutrient -dense cultivars through crossbreeding or genetic engineering. This review provides updates on nutrient acquisition, transport, and storage in plant organs; the cross-talk between macro- and micronutrients transport and signaling; nutrient profiling and spatial and temporal distribution; the putative and functionally characterized genes/single-nucleotide polymorphisms associated with Fe, Zn, and β-carotene; and global efforts to breed nutrient-dense crops and map adoption of such crops globally. This article also includes an overview on the bioavailability, bioaccessibility, and bioactivity of nutrients as well as the molecular basis of nutrient transport and absorption in human. Over 400 minerals (Fe, Zn) and provitamin A-rich cultivars have been released in the Global South. Approximately 4.6 million households currently cultivate Zn-rich rice and wheat, while ~3 million households in sub-Saharan Africa and Latin America benefit from Fe-rich beans, and 2.6 million people in sub-Saharan Africa and Brazil eat provitamin A-rich cassava. Furthermore, nutrient profiles can be improved through genetic engineering in an agronomically acceptable genetic background. The development of "Golden Rice" and provitamin A-rich dessert bananas and subsequent transfer of this trait into locally adapted cultivars are evident, with no significant change in nutritional profile, except for the trait incorporated. A greater understanding of nutrient transport and absorption may lead to the development of diet therapy for the betterment of human health.

Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat

Introduction

Wheat is grown and consumed worldwide, making it an important staple food crop for both its calorific and nutritional content. In places where wheat is used as a staple food, suboptimal micronutrient content levels, especially of grain iron (Fe) and zinc (Zn), can lead to malnutrition. Grain nutrient content is influenced by abiotic stresses, such as drought and heat stress. The best method for addressing micronutrient deficiencies is the biofortification of food crops. The prerequisites for marker-assisted varietal development are the identification of the genomic region responsible for high grain iron and zinc contents and an understanding of their genetics.

Methods

A total of 193 diverse wheat genotypes were evaluated under drought and heat stress conditions across the years at the Indian Agricultural Research Institute (IARI), New Delhi, under timely sown irrigated (IR), restricted irrigated (RI) and late sown (LS) conditions. Grain iron content (GFeC) and grain zinc content (GZnC) were estimated from both the control and treatment groups. Genotyping of all the lines under study was carried out with the single nucleotide polymorphisms (SNPs) from Breeder's 35K Axiom Array.

Result and Discussion

Three subgroups were observed in the association panel based on both principal component analysis (PCA) and dendrogram analysis. A large whole-genome linkage disequilibrium (LD) block size of 3.49 Mb was observed. A genome-wide association study identified 16 unique stringent marker trait associations for GFeC, GZnC, and 1000-grain weight (TGW). In silico analysis demonstrated the presence of 28 potential candidate genes in the flanking region of 16 linked SNPs, such as synaptotagmin-like mitochondrial-lipid-binding domain, HAUS augmin-like complex, di-copper center-containing domain, protein kinase, chaperonin Cpn60, zinc finger, NUDIX hydrolase, etc. Expression levels of these genes in vegetative tissues and grain were also found. Utilization of identified markers in marker-assisted breeding may lead to the rapid development of biofortified wheat genotypes to combat malnutrition.

Genome-wide association study for grain zinc concentration in bread wheat (Triticum aestivum L.)

Introduction

Zinc (Zn) deficiency causes serious diseases in people who rely on cereals as their main food source. However, the grain zinc concentration (GZnC) in wheat is low. Biofortification is a sustainable strategy for reducing human Zn deficiency.

Methods

In this study, we constructed a population of 382 wheat accessions and determined their GZnC in three field environments. Phenotype data was used for a genome-wide association study (GWAS) using a 660K single nucleotide polymorphism (SNP) array, and haplotype analysis identified an important candidate gene for GZnC.

Results

We found that GZnC of the wheat accessions showed an increasing trend with their released years, indicating that the dominant allele of GZnC was not lost during the breeding process. Nine stable quantitative trait loci (QTLs) for GZnC were identified on chromosomes 3A, 4A, 5B, 6D, and 7A. And an important candidate gene for GZnC, namely, TraesCS6D01G234600, and GZnC between the haplotypes of this gene showed, significant difference (P ≤ 0.05) in three environments.

Discussion

A novel QTL was first identified on chromosome 6D, this finding enriches our understanding of the genetic basis of GZnC in wheat. This study provides new insights into valuable markers and candidate genes for wheat biofortification to improve GZnC.

Genomic approaches for improving grain zinc and iron content in wheat

More than three billion people worldwide suffer from iron deficiency associated anemia and an equal number people suffer from zinc deficiency. These conditions are more prevalent in Sub-Saharan Africa and South Asia. In developing countries, children under the age of five with stunted growth and pregnant or lactating women were found to be at high risk of zinc and iron deficiencies. Biofortification, defined as breeding to develop varieties of staple food crops whose grain contains higher levels of micronutrients such as iron and zinc, are one of the most promising, cost-effective and sustainable ways to improve the health in resource-poor households, particularly in rural areas where families consume some part of what they grow. Biofortification through conventional breeding in wheat, particularly for grain zinc and iron, have made significant contributions, transferring important genes and quantitative trait loci (QTLs) from wild and related species into cultivated wheat. Nonetheless, the quantitative, genetically complex nature of iron and zinc levels in wheat grain limits progress through conventional breeding, making it difficult to attain genetic gain both for yield and grain mineral concentrations. Wheat biofortification can be achieved by enhancing mineral uptake, source-to-sink translocation of minerals and their deposition into grains, and the bioavailability of the minerals. A number of QTLs with major and minor effects for those traits have been detected in wheat; introducing the most effective into breeding lines will increase grain zinc and iron concentrations. New approaches to achieve this include marker assisted selection and genomic selection. Faster breeding approaches need to be combined to simultaneously increase grain mineral content and yield in wheat breeding lines.

Identification of genomic regions of wheat associated with grain Fe and Zn content under drought and heat stress using genome-wide association study

Wheat is the staple food crop of global importance for its grain nutrient quality. Grain iron and zinc content of the wheat grain is an important quantitatively inherited trait that is influenced by the environmental factors such as drought and heat stress. Phenotypic evaluation of 295 advanced breeding lines from the wheat stress breeding program of IARI was carried out under timely sown irrigated (IR), restricted irrigated, and late-sown conditions at New Delhi during the cropping season of 2020-21, and grain iron (GFeC) and zinc (GZnC) contents were estimated from both control and treatments. A statistically significant increase in GFeC and GZnC was observed under stress conditions compared to that of the control. Genotyping was carried out with the SNPs from the 35K Axiom Breeder's array, and marker-trait association was identified by GWAS analysis. Of the 23 MTAs identified, seven were linked with GFeC and sixteen were linked with GZnC. In silico analysis revealed a few important transcripts involved in various plant metabolism, growth, and development activities such as auxin response factor, root UVB sensitive proteins, potassium transporter, glycosyl transferase, COBRA, and F-box-like domain. The identified MTAs can be used for molecular breeding after validation and also for rapid development of micronutrient-rich varieties of wheat to mitigate hidden hunger.

Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study

Genetic biofortification is recognized as a cost-effective and sustainable strategy to reduce micronutrient malnutrition. Genomic regions governing grain iron concentration (GFeC), grain zinc concentration (GZnC), and thousand kernel weight (TKW) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using 35 K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 17 Bonferroni-corrected marker-trait associations (MTAs) in nine chromosomes representing all the three wheat subgenomes. The TKW showed the highest MTAs (7), followed by GZnC (5) and GFeC (5). Furthermore, 14 MTAs were identified with more than 10% phenotypic variation. One stable MTA i.e. AX-95025823 was identified for TKW in both E4 and E5 environments along with pooled data, which is located at 68.9 Mb on 6A chromosome. In silico analysis revealed that the SNPs were located on important putative candidate genes such as Multi antimicrobial extrusion protein, F-box domain, Late embryogenesis abundant protein, LEA-18, Leucine-rich repeat domain superfamily, and C3H4 type zinc finger protein, involved in iron translocation, iron and zinc homeostasis, and grain size modifications. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection. The identified SNPs will be valuable in the rapid development of biofortified wheat varieties to ameliorate the malnutrition problems.

Improving Zinc and Iron Biofortification in Wheat through Genomics Approaches

Globally, about 20% of calories (energy) come from wheat. In some countries, it is more than 70%. More than 2 billion people are at risk for zinc deficiency and even more, people are at risk of iron deficiency, nearly a quarter of all children underage group of 5 are physically and cognitively stunted, and lack of dietary zinc is a major contributing factor. Biofortified wheat with elevated levels of zinc and iron has several potential advantages as a delivery vehicle for micronutrients in the diets of resource-poor consumers who depend on cereal-based diets. The conventional breeding strategies have been successful in the introduction of novel alleles for grain Zn and Fe that led to the release of competitive Zn enriched wheat varieties in South Asia. The major challenge over the next few decades will be to maintain the rates of genetic gains for grain yield along with increased grain Zn/Fe concentration to meet the food and nutritional security challenges. Therefore, to remain competitive, the performance of Zn-enhanced lines/varieties must be equal or superior to that of current non-biofortified elite lines/varieties. Since both yield and Zn content are invisible and quantitatively inherited traits except few intermediate effect QTL regions identified for grain Zn, increased breeding efforts and new approaches are required to combine them at high frequency, ensuring that Zn levels are steadily increased to the required levels across the breeding pipelines. The current review article provides a comprehensive list of genomic regions for enhancing grain Zn and Fe concentrations in wheat including key candidate gene families such NAS, ZIP, VLT, ZIFL, and YSL. Implementing forward breeding by taking advantage of the rapid cycling trait pipeline approaches would simultaneously introgress high Zn and Fe QTL into the high Zn and normal elite lines, further increasing Zn and Fe concentrations.

Genomic and Phenotypic Insights into the Potential of Bacillus subtilis YB-15 Isolated from Rhizosphere to Biocontrol against Crown Rot and Promote Growth of Wheat

Simple Summary

Biological control of plant diseases caused by fungal pathogens using antagonistic microorganisms including Bacilli has been considered to be an effective and safe alternative to chemical fungicides. Fusarium crown rot of wheat is a serious fungal disease affecting yield and grain quality. In this study, a newly isolated strain of Bacillus subtilis YB-15 from soil of wheat rhizosphere significantly inhibited Fusarium crown rot as well as improved growth of wheat seedlings. Multiple potential biocontrol and growth-promoting attributes of Bacillus subtilis YB-15 were determined in vitro and according to the whole genome sequencing analysis. Overall, the results demonstrated that Bacillus subtilis YB-15 has great potential for practical application in controlling plant fungal diseases and improving plant growth.

Abstract

Fusarium crown rot caused by Fusarium pseudograminearum is one of the most devastating diseases of wheat worldwide causing major yield and economic losses. In this study, strain YB-15 was isolated from soil of wheat rhizosphere and classified as Bacillus subtilis by average nucleotide identity analysis. It significantly reduced Fusarium crown rot with a control efficacy of 81.50% and significantly improved the growth of wheat seedlings by increasing root and shoot fresh weight by 11.4% and 4.2%, respectively. Reduced Fusarium crown rot may have been due to direct antagonism by the production of β-1, 3-glucanase, amylase, protease and cellulase, or by the ability of B. subtilis YB-15 to induce defense-related enzyme activities of wheat seedlings, both alone and in seedlings infected with F. pseudograminearum. Improved plant growth may be related to the ability of B. subtilis YB-15 to secrete indole acetic acid and siderophores, as well as to solubilize phosphorus. In addition, the genome of strain YB-15 was determined, resulting in a complete assembled circular genome of 4,233,040 bp with GC content of 43.52% consisting of 4207 protein-encoding genes. Sequencing the B. subtilis YB-15 genome further revealed genes for encoding carbohydrate-active enzymes, biosynthesis of various secondary metabolites, nutrient acquisition, phytohormone production, chemotaxis and motility, which could explain the potential of strain YB-15 to be plant growth-promoting bacteria and biological control agent. B. subtilis YB-15 appears to be a promising biocontrol agent against Fusarium crown rot as well as for wheat growth promotion.

Genome-wide association study identifies loci and candidate genes for grain micronutrients and quality traits in wheat (Triticum aestivum L.)

Malnutrition due to micronutrients and protein deficiency is recognized among the major global health issues. Genetic biofortification of wheat is a cost-effective and sustainable strategy to mitigate the global micronutrient and protein malnutrition. Genomic regions governing grain zinc concentration (GZnC), grain iron concentration (GFeC), grain protein content (GPC), test weight (TW), and thousand kernel weight (TKW) were investigated in a set of 184 diverse bread wheat genotypes through genome-wide association study (GWAS). The GWAS panel was genotyped using Breeders' 35 K Axiom Array and phenotyped in three different environments during 2019-2020. A total of 55 marker-trait associations (MTAs) were identified representing all three sub-genomes of wheat. The highest number of MTAs were identified for GPC (23), followed by TKW (15), TW (11), GFeC (4), and GZnC (2). Further, a stable SNP was identified for TKW, and also pleiotropic regions were identified for GPC and TKW. In silico analysis revealed important putative candidate genes underlying the identified genomic regions such as F-box-like domain superfamily, Zinc finger CCCH-type proteins, Serine-threonine/tyrosine-protein kinase, Histone deacetylase domain superfamily, and SANT/Myb domain superfamily proteins, etc. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection.

Genetic analysis toward more nutritious barley grains for a food secure world

BACKGROUND

Understanding the relationships between nutrition, human health and plant food source is among the highest priorities for public health. Therefore, enhancing the minerals content such as iron (Fe), zinc (Zn) and selenium (Se) in barley (Hordeum vulgare L.) grains is an urgent need to improve the nutritive value of barley grains in overcoming malnutrition and its potential consequencing. This study aimed to expedite biofortification of barley grains by elucidating the genetic basis of Zn, Fe, and Se accumulation in the grains, which will contribute to improved barley nutritional quality.

RESULTS

A genome-wide association study (GWAS) was conducted to detect the genetic architecture for grain Zn, Fe, and Se accumulations in 216 spring barley accessions across two years. All the accessions were genotyped by single nucleotide polymorphisms (SNPs) molecular markers. Mineral heritability values ranging from moderate to high were revealed in both environments. Remarkably, there was a high natural phenotypic variation for all micronutrient accumulation in the used population. High-LD SNP markers (222 SNPs) were detected to be associated with all micronutrients in barley grains across the two environments plus BLUEs. Three genomic regions were detected based on LD, which were identified for the most effective markers that had associations with more than one trait. The strongest SNP-trait associations were found to be physically located within genes that may be involved in grain Zn and Fe homeostasis. Two putative candidate genes were annotated as Basic helix loop helix (BHLH) family transcription factor and Squamosa promoter binding-like protein, respectively, and have been suggested as candidates for increased grain Zn, Fe, and Se accumulation.

CONCLUSIONS

These findings shed a light on the genetic basis of Zn, Fe, and Se accumulation in barley grains and have the potential to assist plant breeders in selecting accessions with high micronutrient concentrations to enhance grain quality and, ultimately human health.

Genome-Wide Association Study Reveals Genomic Regions Associated With Molybdenum Accumulation in Wheat Grains

Molybdenum (Mo) is an essential micronutrient for almost all organisms. Wheat, a major staple crop worldwide, is one of the main dietary sources of Mo. However, the genetic basis for the variation of Mo content in wheat grains remains largely unknown. Here, a genome-wide association study (GWAS) was performed on the Mo concentration in the grains of 207 wheat accessions to dissect the genetic basis of Mo accumulation in wheat grains. As a result, 77 SNPs were found to be significantly associated with Mo concentration in wheat grains, among which 52 were detected in at least two sets of data and distributed on chromosome 2A, 7B, and 7D. Moreover, 48 out of the 52 common SNPs were distributed in the 726,761,412-728,132,521 bp genomic region of chromosome 2A. Three putative candidate genes, including molybdate transporter 1;2 (TraesCS2A02G496200), molybdate transporter 1;1 (TraesCS2A02G496700), and molybdopterin biosynthesis protein CNX1 (TraesCS2A02G497200), were identified in this region. These findings provide new insights into the genetic basis for Mo accumulation in wheat grains and important information for further functional characterization and breeding to improve wheat grain quality.

Identification of genomic regions conferring rust resistance and enhanced mineral accumulation in a HarvestPlus Association Mapping Panel of wheat

New genomic regions for high accumulation of 10 minerals were identified. The 1B:1R and 2NS translocations enhanced concentrations of four and two minerals, respectively, in addition to disease resistance. Puccinia species, the causal agents of rust diseases of wheat, have the potential to cause total crop failures due their high evolutionary ability to acquire virulence for resistance genes deployed in commercial cultivars. Hence, the discovery of genetically diverse sources of rust resistance is essential. On the other hand, biofortification of wheat for essential nutrients, such as zinc (Zn) and iron (Fe), is also an objective in wheat improvement programs to tackle micronutrient deficiency. The development of rust-resistant and nutrient-concentrated wheat cultivars would be important for sustainable production and the fight against malnutrition. The HarvestPlus association mapping panel (HPAMP) that included nutrient-dense sources from diverse genetic backgrounds was genotyped using a 90 K Infinium SNP array and 13 markers linked with rust resistance genes. The HPAMP was used for genome-wide association mapping to identify genomic regions underpinning rust resistance and mineral accumulation. Twelve QTL for rust resistance and 53 for concentrations of 10 minerals were identified. Comparison of results from this study with the published QTL information revealed the detection of already known and some putatively new genes/QTL underpinning stripe rust and leaf rust resistance in this panel. Thirty-six new QTL for mineral concentration were identified on 17 chromosomes. Accessions carrying the 1B:1R translocation accumulated higher concentrations of Zn, Fe, Copper (Cu) and sulphur (S). The 2NS segment showed enhanced accumulation of grain Fe and Cu. Fifteen rust-resistant and biofortified accessions were identified for use as donor sources in breeding programs.

Meta-QTLs, ortho-MetaQTLs and candidate genes for grain Fe and Zn contents in wheat (Triticum aestivum L.)

Majority of cereals are deficient in essential micronutrients including grain iron (GFe) and grain zinc (GZn), which are therefore the subject of research involving biofortification. In the present study, 11 meta-QTLs (MQTLs) including nine novel MQTLs for GFe and GZn contents were identified in wheat. Eight of these 11 MQTLs controlled both GFe and GZn. The confidence intervals of the MQTLs were narrower (0.51-15.75 cM) relative to those of the corresponding QTLs (0.6 to 55.1 cM). Two ortho-MQTLs involving three cereals (wheat, rice and maize) were also identified. Results of MQTLs were also compared with the results of earlier genome wide association studies (GWAS). As many as 101 candidate genes (CGs) underlying MQTLs were also identified. Twelve of these CGs were prioritized; these CGs encoded proteins with important domains (zinc finger, RING/FYVE/PHD type, flavin adenine dinucleotide linked oxidase, etc.) that are involved in metal ion binding, heme binding, iron binding, etc. qRT-PCR analysis was conducted for four of these 12 prioritized CGs using genotypes which have differed for GFe and GZn. Significant differential expression in these genotypes was observed at 14 and 28 days after anthesis. The MQTLs/CGs identified in the present study may be utilized in marker-assisted selection (MAS) for improvement of GFe/GZn contents and also for understanding the molecular basis of GFe/GZn homeostasis in wheat.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01149-9.

Zinc in plants: Integrating homeostasis and biofortification

Zinc plays many essential roles in life. As a strong Lewis acid that lacks redox activity under environmental and cellular conditions, the Zn²⁺ cation is central in determining protein structure and catalytic function of nearly 10% of most eukaryotic proteomes. While specific functions of zinc have been elucidated at a molecular level in a number of plant proteins, wider issues abound with respect to the acquisition and distribution of zinc by plants. An important challenge is to understand how plants balance between Zn supply in soil and their own nutritional requirement for zinc, particularly where edaphic factors lead to a lack of bioavailable zinc or, conversely, an excess of zinc that bears a major risk of phytotoxicity. Plants are the ultimate source of zinc in the human diet, and human Zn deficiency accounts for over 400 000 deaths annually. Here, we review the current understanding of zinc homeostasis in plants from the molecular and physiological perspectives. We provide an overview of approaches pursued so far in Zn biofortification of crops. Finally, we outline a "push-pull" model of zinc nutrition in plants as a simplifying concept. In summary, this review discusses avenues that can potentially deliver wider benefits for both plant and human Zn nutrition.

Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies

Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.

Genetic biofortification of wheat with zinc: Opportunities to fine-tune zinc uptake, transport and grain loading

Zinc (Zn) is an important micronutrient in the human body, and health complications associated with insufficient dietary intake of Zn can be overcome by increasing the bioavailable concentrations in edible parts of crops (biofortification). Wheat (Triticum aestivum L) is the most consumed cereal crop in the world; therefore, it is an excellent target for Zn biofortification programs. Knowledge of the physiological and molecular processes that regulate Zn concentration in the wheat grain is restricted, inhibiting the success of genetic Zn biofortification programs. This review helps break this nexus by advancing understanding of those processes, including speciation regulated uptake, root to shoot transport, remobilisation, grain loading and distribution of Zn in wheat grain. Furthermore, new insights to genetic Zn biofortification of wheat are discussed, and where data are limited, we draw upon information for other cereals and Fe distribution. We identify the loading and distribution of Zn in grain as major bottlenecks for biofortification, recognising anatomical barriers in the vascular region at the base of the grain, and physiological and molecular restrictions localised in the crease region as major limitations. Movement of Zn from the endosperm cavity into the modified aleurone, aleurone and then to the endosperm is mainly regulated by ZIP and YSL transporters. Zn complexation with phytic acid in the aleurone limits Zn mobility into the endosperm. These insights, together with synchrotron-X-ray-fluorescence microscopy, support the hypothesis that a focus on the mechanisms of Zn loading into the grain will provide new opportunities for Zn biofortification of wheat.

Omics Technologies to Enhance Plant Based Functional Foods: An Overview

Functional foods are natural products of plants that have health benefits beyond necessary nutrition. Functional foods are abundant in fruits, vegetables, spices, beverages and some are found in cereals, millets, pulses and oilseeds. Efforts to identify functional foods in our diet and their beneficial aspects are limited to few crops. Advances in sequencing and availability of different omics technologies have given opportunity to utilize these tools to enhance the functional components of the foods, thus ensuring the nutritional security. Integrated omics approaches including genomics, transcriptomics, proteomics, metabolomics coupled with artificial intelligence and machine learning approaches can be used to improve the crops. This review provides insights into omics studies that are carried out to find the active components and crop improvement by enhancing the functional compounds in different plants including cereals, millets, pulses, oilseeds, fruits, vegetables, spices, beverages and medicinal plants. There is a need to characterize functional foods that are being used in traditional medicines, as well as utilization of this knowledge to improve the staple foods in order to tackle malnutrition and hunger more effectively.

Potato biofortification: an effective way to fight global hidden hunger

Hidden hunger is leading to extensive health problems in the developing world. Several strategies could be used to reduce the micronutrient deficiencies by increasing the dietary uptake of essential micronutrients. These include diet diversification, pharmaceutical supplementation, food fortification and crop biofortification. Among all, crop biofortification is the most sustainable and acceptable strategy to overcome the global issue of hidden hunger. Since most of the people suffering from micronutrient deficiencies, have monetary issues and are dependent on staple crops to fulfil their recommended daily requirements of various essential micronutrients. Therefore, increasing the micronutrient concentrations in cost effective staple crops seems to be an effective solution. Potato being the world's most consumed non-grain staple crop with enormous industrial demand appears to be an ideal candidate for biofortification. It can be grown in different climatic conditions, provide high yield, nutrition and dry matter in lesser time. In addition, huge potato germplasm have natural variations related to micronutrient concentrations, which can be utilized for its biofortification. This review discuss the current scenario of micronutrient malnutrition and various strategies that could be used to overcome it. The review also shed a light on the genetic variations present in potato germplasm and suggest effective ways to incorporate them into modern high yielding potato varieties.

Toward identification of a putative candidate gene for nutrient mineral accumulation in wheat grains for human nutrition purposes

A multilocus genome-wide association study of a panel of 369 diverse wheat (Triticum aestivum) genotypes was carried out in order to examine the genetic basis of variations in nutrient mineral concentrations in the grains. The panel was grown under field conditions for three consecutive years and the concentrations of Ca, K, Mg, Mn, P, and S were determined. Wide ranges of natural variation were detected among the genotypes. Strong positive correlations were found among the minerals except for K, which showed negative correlation trends with the other minerals. Genetic association analysis detected 86 significant marker-trait associations (MTAs) underlying the natural variations in mineral concentrations in grains. The major MTA was detected on the long arm of chromosome 5A and showed a pleiotropic effect on Ca, K, Mg, Mn, and S. Further significant MTAs were distributed among the whole genome except for chromosomes 3D and 6D. We identified putative candidate genes that are potentially involved in metal uptake, transport, and assimilation, including TraesCS5A02G542600 on chromosome 5A, which was annotated as a Major Facilitator Superfamily transporter and acted on all the minerals except K. TraesCS5A02G542600 was highly expressed in seed coat, and to a lesser extent in the peduncle, awns, and lemma. Our results provide important insights into the genetic basis of enhancement of nutrient mineral concentrations that can help to inform future breeding studies in order to improve human nutrition.

A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica

This study presents a comprehensive study of the genetic bases controlling variation in the rice ionome employing genome-wide association studies (GWAS) with a diverse panel of indica accessions, each genotyped with 5.2 million markers. GWAS was performed for twelve elements including B, Ca, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, and Zn and four agronomic traits including days to 50% flowering, grain yield, plant height and thousand grain weight. GWAS identified 128 loci associated with the grain elements and 57 associated with the agronomic traits. There were sixteen co-localization regions containing QTL for two or more traits. Fourteen grain element quantitative trait loci were stable across growing environments, which can be strong candidates to be used in marker-assisted selection to improve the concentrations of nutritive elements in rice grain. Potential candidate genes were revealed including OsNAS3 linked to the locus that controls the variation of Zn and Co concentrations. The effects of starch synthesis and grain filling on multiple grain elements were elucidated through the likely involvement of OsSUS1 and OsGSSB1 genes. Overall, our study provides crucial insights into the genetic basis of ionomic variations in rice and will facilitate improvement in breeding for trace mineral content.

Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.

Identification of novel genomic regions associated with nine mineral elements in Chinese winter wheat grain

BACKGROUND

Mineral elements are important for maintaining good human health besides heavy metals. Mining genes that control mineral elements are paramount for improving their accumulation in the wheat grain. Although previous studies have reported some loci for beneficial trace elements, they have mainly focused on Zn and Fe content. However, little information is available regarding the genetic loci differences in dissecting synchronous accumulation of multiple mineral elements in wheat grains, including beneficial and heavy elements. Therefore, a genome-wide association study (GWAS) was conducted on 205 wheat accessions with 24,355 single nucleotide polymorphisms (SNPs) to identify important loci and candidate genes for controlling Ca, Fe, Zn, Se, Cu, Mn, Cd, As, and Pb accumulation in wheat grains.

RESULTS

A total of 101 marker-trait associations (MTAs) (P < 10^-5) loci affecting the content of nine mineral elements was identified on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 3D, 4A, 4B, 5A, 5B, 5D, 6B, 7A, 7B, and 7D. Among these, 17 major MTAs loci for the nine mineral elements were located, and four MTAs loci (P < 10^-5) were found on chromosomes 1B, 6B, 7B, and 7D. Eight multi-effect MTAs loci were detected that are responsible for the control of more than one trait, mainly distributed on chromosomes 3B, 7B, and 5A. Furthermore, sixteen candidate genes controlling Ca, Fe, Zn, Se, Cd, and Pb were predicted, whose functions were primarily related to ion binding, including metals, Fe, Ca, Cu, Mg, and Zn, ATP binding, ATPase activity, DNA binding, RNA binding, and protein kinase activity.

CONCLUSIONS

Our study indicated the existence of gene interactions among mineral elements based on multi-effect MTAs loci and candidate genes. Meanwhile this study provided new insights into the genetic control of mineral element concentrations, and the important loci and genes identified may contribute to the rapid development of beneficial mineral elements and a reduced content of harmful heavy metals in wheat grain.

Identification of a 193 bp promoter region of TaNRX1-D gene from common wheat that contributes to osmotic or ABA stress inducibility in transgenic Arabidopsis

BACKGROUND

Cloning and characterizing the drought-inducible promoters is essential for their use in crop resistance's genetic improvement. Previous studies have shown that the TaNRX1-D gene participates in regulating the response of wheat to drought stress. However, its promoter has not yet been identified.

OBJECTIVE

In this study, we aimed to characterize the promoter of the TaNRX1-D gene.

METHODS

The promoter of TaNRX1-D (named P0, 2081 bp) was isolated from common wheat with several cis-acting elements that regulate in response to abiotic stresses and some core cis-acting elements. Functional verification of the promoter, eight 5'-deletion fragments of TaNRX1-D promoter, was fused to the β-glucuronidase (GUS) gene P0::GUS ~ P7::GUS and transformed into Arabidopsis, respectively. Agrobacterium-mediated GUS transient assay the P6a and P6b promoter regions in tobacco leaves under normal, osmotic or ABA stress.

RESULTS

Activity analysis of the full-length promoter (P0) showed that the intensity of stronger β-glucuronidase (GUS) staining in the roots and leaves was obtained during the growth of transgenic Arabidopsis. P0::GUS displayed the GUS activity was much higher in the roots and leaves than in other parts of the transgenic plant under normal conditions, which was similarly within wheat. Analysis of the 5'-deletion fragments revealed that P0::GUS ~ P6::GUS responded well upon exposure to osmotic (polyethylene glycol-6000, PEG6000) and abscisic acid (ABA) stress treatments and expressed significantly higher GUS activity than the CaMV35S promoter (35S::GUS), while P7::GUS did not. GUS transient assay in tobacco leaves showed that the GUS activities of P6a and P6b were lower than P6 in the PEG6000 and ABA stresses.

CONCLUSION

The 193 bp (P6) segment was considered the core region of TaNRX1-D responding to PEG6000 or ABA treatment. GUS activity assay in transgenic Arabidopsis showed that this segment was sufficient for the PEG6000 or ABA stress response. The identified 193 bp promoter of TaNRX1-D in this study will help breed osmotic or ABA tolerant crops. The 36 bp segment between P6 and P6b (-193 to -157 bp) was considered the critical sequence for the TaNRX1-D gene responding to PEG6000 or ABA treatment.

QTL Mapping for Grain Zinc and Iron Concentrations in Bread Wheat

Deficiency of micronutrient elements, such as zinc (Zn) and iron (Fe), is called “hidden hunger,” and bio-fortification is the most effective way to overcome the problem. In this study, a high-density Affymetrix 50K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for grain Zn (GZn) and grain Fe (GFe) concentrations in 254 recombinant inbred lines (RILs) from a cross Jingdong 8/Bainong AK58 in nine environments. There was a wide range of variation in GZn and GFe concentrations among the RILs, with the largest effect contributed by the line × environment interaction, followed by line and environmental effects. The broad sense heritabilities of GZn and GFe were 0.36 ± 0.03 and 0.39 ± 0.03, respectively. Seven QTL for GZn on chromosomes 1DS, 2AS, 3BS, 4DS, 6AS, 6DL, and 7BL accounted for 2.2–25.1% of the phenotypic variances, and four QTL for GFe on chromosomes 3BL, 4DS, 6AS, and 7BL explained 2.3–30.4% of the phenotypic variances. QTL on chromosomes 4DS, 6AS, and 7BL might have pleiotropic effects on both GZn and GFe that were validated on a germplasm panel. Closely linked SNP markers were converted to high-throughput KASP markers, providing valuable tools for selection of improved Zn and Fe bio-fortification in breeding.

Genome-Wide Association Study for Grain Micronutrient Concentrations in Wheat Advanced Lines Derived From Wild Emmer

Wheat is one of the important staple crops as the resources of both food and micronutrient for most people of the world. However, the levels of micronutrients (especially Fe and Zn) in common wheat are inherently low. Biofortification is an effective way to increase the micronutrient concentration of wheat. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, AABB, 2n = 4x = 28) is an important germplasm resource for wheat micronutrients improvement. In the present study, a genome-wide association study (GWAS) was performed to characterize grain iron, zinc, and manganese concentration (GFeC, GZnC, and GMnC) in 161 advanced lines derived from wild emmer. Using both the general linear model and mixed linear model, we identified 14 high-confidence significant marker-trait associations (MTAs) that were associated with GFeC, GZnC, and GMnC of which nine MTAs were novel. Six MTAs distributed on chromosomes 3B, 4A, 4B, 5A, and 7B were significantly associated with GFeC. Three MTAs on 1A and 2A were significantly associated with GZnC and five MTAs on 1B were significantly associated with GMnC. These MTAs show no negative effects on thousand kernel weight (TKW), implying the potential value for simultaneous improvement of micronutrient concentrations and TKW in breeding. Meanwhile, the GFeC, GZnC and GMnC are positively correlated, suggesting that these traits could be simultaneously improved. Genotypes containing high-confidence MTAs and 61 top genotypes with a higher concentration of grain micronutrients were recommended for wheat biofortification breeding. A total of 38 candidate genes related to micronutrient concentrations were identified. These candidates can be classified into four main groups: enzymes, transporter proteins, MYB transcription factor, and plant defense responses proteins. The MTAs and associated candidate genes provide essential information for wheat biofortification breeding through marker-assisted selection (MAS).

Biofortification and bioavailability of Zn, Fe and Se in wheat: present status and future prospects

Knowledge of genetic variation, genetics, physiology/molecular basis and breeding (including biotechnological approaches) for biofortification and bioavailability for Zn, Fe and Se will help in developing nutritionally improved wheat. Biofortification of wheat cultivars for micronutrients is a priority research area for wheat geneticists and breeders. It is known that during breeding of wheat cultivars for productivity and quality, a loss of grain micronutrient contents occurred, leading to decline in nutritional quality of wheat grain. Keeping this in view, major efforts have been made during the last two decades for achieving biofortification and bioavailability of wheat grain for micronutrients including Zn, Fe and Se. The studies conducted so far included evaluation of gene pools for contents of not only grain micronutrients as above, but also for phytic acid (PA) or phytate and phytase, so that, while breeding for the micronutrients, bioavailability is also improved. For this purpose, QTL interval mapping and GWAS were carried out to identify QTLs/genes and associated markers that were subsequently used for marker-assisted selection (MAS) during breeding for biofortification. Studies have also been conducted to understand the physiology and molecular basis of biofortification, which also allowed identification of genes for uptake, transport and storage of micronutrients. Transgenics using transgenes have also been produced. The breeding efforts led to the development of at least a dozen cultivars with improved contents of grain micronutrients, although land area occupied by these biofortified cultivars is still marginal. In this review, the available information on different aspects of biofortification and bioavailability of micronutrients including Zn, Fe and Se in wheat has been reviewed for the benefit of those, who plan to start work or already conducting research in this area.

Dissection of Molecular Processes and Genetic Architecture Underlying Iron and Zinc Homeostasis for Biofortification: From Model Plants to Common Wheat

The micronutrients iron (Fe) and zinc (Zn) are not only essential for plant survival and proliferation but are crucial for human health. Increasing Fe and Zn levels in edible parts of plants, known as biofortification, is seen a sustainable approach to alleviate micronutrient deficiency in humans. Wheat, as one of the leading staple foods worldwide, is recognized as a prioritized choice for Fe and Zn biofortification. However, to date, limited molecular and physiological mechanisms have been elucidated for Fe and Zn homeostasis in wheat. The expanding molecular understanding of Fe and Zn homeostasis in model plants is providing invaluable resources to biofortify wheat. Recent advancements in NGS (next generation sequencing) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms have initiated a revolution in resources and approaches for wheat genetic investigations and breeding. Here, we summarize molecular processes and genes involved in Fe and Zn homeostasis in the model plants Arabidopsis and rice, identify their orthologs in the wheat genome, and relate them to known wheat Fe/Zn QTL (quantitative trait locus/loci) based on physical positions. The current study provides the first inventory of the genes regulating grain Fe and Zn homeostasis in wheat, which will benefit gene discovery and breeding, and thereby accelerate the release of Fe- and Zn-enriched wheats.

MAPK Enzymes: a ROS Activated Signaling Sensors Involved in Modulating Heat Stress Response, Tolerance and Grain Stability of Wheat under Heat Stress

Mitogen-activated protein kinase (MAPK) signaling cascade is highly conserved across the species triggering the self-adjustment of the cells by transmitting the external signals to the nucleus. The cascade consists of MAPK kinase kinases (MAPKKKs), MAPK kinases (MAPKKs) and MAPKs. These kinases are functionally interrelated through activation by sequential phosphorylation. MAPK cascade is involved in modulating the tolerance and regulating the growth and developmental processes in plants through transcriptional programming. The cascade has been well characterized in Arabidopsis, Tobacco and rice, but limited information is available in wheat due to complexity of genome. MAPK-based sensors have been reported to be highly specific for the external or intracellular stimuli activating specific TF, stress-associated genes (SAGs) and stress-associated proteins (SAPs) linked with heat-stress tolerance and other biological functions especially size, number and quality of grains. Even, MAPKs have been reported to influence the activity of ATP-binding cassette (ABC) transporter superfamily involved in stabilizing the quality of the grains under adverse conditions. Wheat has also diverse network of MAPKs involved in transcriptional reprogramming upon sensing the terminal HS and in turn protect the plants. Current review mainly focuses on the role of MAPKs as signaling sensor and modulator of defense mechanism for mitigating the effect of heat on plants with focus on wheat. It also indirectly protects the nutrient depletion from the grains under heat stress. MAPKs, lying at pivotal positions, can be utilized for manipulating the heat-stress response (HSR) of wheat to develop plant for future (P4F).

Genetics of yield, abiotic stress tolerance and biofortification in wheat (Triticum aestivum L.)

A review of the available literature on genetics of yield and its component traits, tolerance to abiotic stresses and biofortification should prove useful for future research in wheat in the genomics era. The work reviewed in this article mainly covers the available information on genetics of some important quantitative traits including yield and its components, tolerance to abiotic stresses (heat, drought, salinity and pre-harvest sprouting = PHS) and biofortification (Fe/Zn and phytate contents with HarvestPlus Program) in wheat. Major emphasis is laid on the recent literature on QTL interval mapping and genome-wide association studies, giving lists of known QTL and marker-trait associations. Candidate genes for different traits and the cloned and characterized genes for yield traits along with the molecular mechanism are also described. For each trait, an account of the present status of marker-assisted selection has also been included. The details of available results have largely been presented in the form of tables; some of these tables are included as supplementary files.

Identification of Novel Genomic Regions and Superior Alleles Associated with Zn Accumulation in Wheat Using a Genome-Wide Association Analysis Method

Micronutrient deficiencies, and especially zinc (Zn) deficiency, pose serious health problems to people who mainly depend on cereal-based diets. Here, we performed a genome-wide association study (GWAS) to detect the genetic basis of the Zn accumulation in wheat (Triticum aestivum L.) grains with a diversity panel of 207 bread wheat varieties. To uncover authentic quantitative trait loci (QTL) controlling Zn accumulation, the varieties were planted in three locations. In total, 29 unique loci associated with Zn grain accumulation were identified. Notably, seven non-redundant loci located on chromosomes 1B, 3B, 3D, 4A, 5A, 5B, and 7A, were detected at least in two environments. Of these quantitative trait loci (QTL), six coincided with known QTL or genes, whereas the highest effect QTL on chromosome 3D identified in this study was not reported previously. Searches of public databases revealed that the seven identified QTL coincided with seven putative candidate genes linked to Zn accumulation. Among these seven genes, NAC domain-containing protein gene (TraesCS3D02G078500) linked with the most significant single nucleotide polymorphism (SNP) AX-94729264 on chromosome 3D was relevant to metal accumulation in wheat grains. Results of this study provide new insights into the genetic architecture of Zn accumulation in wheat grains.

GWAS: Fast-forwarding gene identification and characterization in temperate Cereals: lessons from Barley - A review

Understanding the genetic complexity of traits is an important objective of small grain temperate cereals yield and adaptation improvements. Bi-parental quantitative trait loci (QTL) linkage mapping is a powerful method to identify genetic regions that co-segregate in the trait of interest within the research population. However, recently, association or linkage disequilibrium (LD) mapping using a genome-wide association study (GWAS) became an approach for unraveling the molecular genetic basis underlying the natural phenotypic variation. Many causative allele(s)/loci have been identified using the power of this approach which had not been detected in QTL mapping populations. In barley (Hordeum vulgare L.), GWAS has been successfully applied to define the causative allele(s)/loci which can be used in the breeding crop for adaptation and yield improvement. This promising approach represents a tremendous step forward in genetic analysis and undoubtedly proved it is a valuable tool in the identification of candidate genes. In this review, we describe the recently used approach for genetic analyses (linkage mapping or association mapping), and then provide the basic genetic and statistical concepts of GWAS, and subsequently highlight the genetic discoveries using GWAS. The review explained how the candidate gene(s) can be detected using state-of-art bioinformatic tools.

Genome-wide and SNP network analyses reveal genetic control of spikelet sterility and yield-related traits in wheat

Revealing the genetic factors underlying yield and agronomic traits in wheat are an imperative need for covering the global food demand. Yield boosting requires a deep understanding of the genetic basis of grain yield-related traits (e.g., spikelet fertility and sterility). Here, we have detected much natural variation among ancient hexaploid wheat accessions in twenty-two agronomic traits collected over eight years of field experiments. A genome-wide association study (GWAS) using 15 K single nucleotide polymorphisms (SNPs) was applied to detect the genetic basis of studied traits. Subsequently, the GWAS output was reinforced via other statistical and bioinformatics analyses to detect putative candidate genes. Applying the genome-wide SNP-phenotype network defined the most decisive SNPs underlying the traits. Six pivotal SNPs, co-located physically within the genes encoding enzymes, hormone response, metal ion transport, and response to oxidative stress have been identified. Of these, metal ion transport and Gibberellin 2-oxidases (GA2oxs) genes showed strong involvement in controlling the spikelet sterility, which had not been reported previously in wheat. SNP-gene haplotype analysis confirmed that these SNPs influence spikelet sterility, especially the SNP co-located on the exon of the GA2ox gene. Interestingly, these genes were highly expressed in the grain and spike, demonstrating their pivotal role in controlling the trait. The integrative analysis strategy applied in this study, including GWAS, SNP-phenotype network, SNP-gene haplotype, expression analysis, and genome-wide prediction (GP), empower the identification of functional SNPs and causal genes. GP outputs obtained in this study are encouraging for the implementation of the traits to accelerate yield improvement by making an early prediction of complex yield-related traits in wheat. Our findings demonstrate the usefulness of the ancient wheat material as a valuable resource for yield-boosting. This is the first comprehensive genome-wide analysis for spikelet sterility in wheat, and the results provide insights into yield improvement.

Genetic dissection of zinc, iron, copper, manganese and phosphorus in wheat (Triticum aestivum L.) grain and rachis at two developmental stages

The development of high-yielding wheat genotypes containing micronutrient-dense grains are the main priorities of biofortification programs. At the International Maize and Wheat Improvement Center, breeders have successfully crossed high zinc progenitors including synthetic hexaploid wheat, T. dicoccum, T. spelta and landraces to generate high-zinc varieties. In this study, we report a genome-wide association using a wheat diversity panel to dissect the genetics controlling zinc, iron, copper, manganese and phosphorus concentrations in the grain and rachis during grain development and at physiological maturity. Significant marker-trait associations (MTAs) were identified for each nutrient using multi-locus mixed model methodologies. For mature grain, markers that showed significant pleiotropic effects were found on chromosomes 1A, 3B and 5B, of which those on chromosome 5B at ∼95.5 cM were consistent over two growing seasons. Co-located MTAs were identified for the nutrient concentrations in developing grain, rachis and mature grain on multiple chromosomes. The identified genomic regions included putative candidate genes involved in metal uptake and transport and storage protein processing. These findings add to our understanding of the genetics of the five important nutrients in wheat grain and provide information on genetic markers for selecting high micronutrient genotypes.

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.

Whole-Genome Association Mapping and Genomic Prediction for Iron Concentration in Wheat Grains

Malnutrition of iron (Fe) affects two billion people worldwide. Therefore, enhancing grain Fe concentration (GFeC) in wheat (Triticum aestivum L.) is an important goal for breeding. Here we study the genetic factors underlying GFeC trait by genome-wide association studies (GWAS) and the prediction abilities using genomic prediction (GP) in a panel of 369 European elite wheat varieties which was genotyped with 15,523 mapped single-nucleotide polymorphism markers (SNP) and a subpanel of 183 genotypes with 44,233 SNP markers. The resulting means of GFeC from three field experiments ranged from 24.42 to 52.42 μg·g⁻¹ with a broad-sense heritability (H²) equaling 0.59 over the years. GWAS revealed 41 and 137 significant SNPs in the whole and subpanel, respectively, including significant marker-trait associations (MTAs) for best linear unbiased estimates (BLUEs) of GFeC on chromosomes 2A, 3B and 5A. Putative candidate genes such as NAC transcription factors and transmembrane proteins were present on chromosome 2A (763,689,738–765,710,113 bp). The GP for a GFeC trait ranged from low to moderate values. The current study reported GWAS of GFeC for the first time in hexaploid wheat varieties. These findings confirm the utility of GWAS and GP to explore the genetic architecture of GFeC for breeding programs aiming at the improvement of wheat grain quality.