High Resolution Genome Wide Association Studies Reveal Rich Genetic Architectures of Grain Zinc and Iron in Common Wheat (Triticum aestivum L.)

A novel, major, and validated QTL for grain zinc concentration independent of yield traits in tetraploid wheat

Zinc deficiency is a critical global health issue, with declining grain zinc concentration (GrZnc) over time. To address this, it is essential to explore and utilize genetic resources from wild relatives to enhance GrZnc in cultivated bread wheat (Triticum aestivum L.). This study aimed to identify quantitative trait loci (QTL) for GrZnc using a recombinant inbred line population (AM population), derived from a cross between the Sichuan-endemic tetraploid wheat Ailanmai and wild emmer accession LM001. A linkage map was constructed based on the wheat 55K single-nucleotide polymorphism array, and phenotypic data were collected from five different environments. Four QTL for GrZnc were identified, spanning three chromosomal regions. Notably, a novel and stable QTL, QGrZnc.sau-AM-4A, was detected in all environments and the best linear unbiased prediction dataset. This QTL, with LOD values ranging from 2.72 to 9.31, explained 12.31%-30.50% of the phenotypic variance and was mapped to chromosome arm 4AS (54.43-60.02 Mbp). Interestingly, this QTL had no significant effect on key agronomic traits such as spike length, 1000-kernel weight, kernel number per spikelet, spikelet number per spike, spike density, and plant height, indicating no dilution effects. A kompetitive allele-specific PCR (KASP) marker, KASP-AX-108829087, closely linked to this major QTL, was developed and validated in two different genetic populations. A candidate gene (TRIDC4AG008520) related to zinc absorption and transport was identified within the QGrZnc.sau-AM-4A interval. These findings provide insight into the genetic basis of GrZnc and establish a foundation for further fine mapping and map-based cloning of this locus.

Further studies on pyramiding of alien genes for high grain Fe and Zn in bread wheat

Wheat serves as the primary source of staple food for the global human population, thus also making it a significant portion of the calorie intake in our daily vegetarian diets. However, in most of the improved wheat cultivars used for food, the grain is deficient in iron (Fe) and zinc (Zn). Therefore, biofortification involving improvement of grain Fe and Zn has become an important area in the current wheat breeding programmes. For this purpose, efforts have been made to develop alien substitution lines and utilize them for transfer of desirable alien genes to improved wheat cultivars. In the present study, two such genotypes in the background of improved cultivar PBW343LrYr were utilized for pyramiding of the following six desirable genes for enrichment of grain Fe and Zn: IRT2, MTP3, IREG, FRO7, YSL15 and NAS2. A forward breeding strategy, involving crossing of the two genotypes followed by inbreeding was used. Marker-assisted selection (MAS) of the genes of interest associated with grain Fe/Zn and plant type was used following selfing of F1 hybrids. The grains of F6 lines that were derived in this programmes were rich in both Fe and Zn contents in the grain. Among the six best derived lines, the values of improved contents of grain Fe ranged from 47.3 to 60.4 ppm and that of Zn ranged from 39.35 to 47.85 ppm. There was no yield penalty in these improved lines, such that the yield was either equal or better than the checks used in field trials.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01566-0.

Micronutrient Biofortification in Wheat: QTLs, Candidate Genes and Molecular Mechanism

Micronutrient deficiency (hidden hunger) is one of the serious health problems globally, often due to diets dominated by staple foods. Genetic biofortification of a staple like wheat has surfaced as a promising, cost-efficient, and sustainable strategy. Significant genetic diversity exists in wheat and its wild relatives, but the nutritional profile in commercial wheat varieties has inadvertently declined over time, striving for better yield and disease resistance. Substantial efforts have been made to biofortify wheat using conventional and molecular breeding. QTL and genome-wide association studies were conducted, and some of the identified QTLs/marker-trait association (MTAs) for grain micronutrients like Fe have been exploited by MAS. The genetic mechanisms of micronutrient uptake, transport, and storage have also been investigated. Although wheat biofortified varieties are now commercially cultivated in selected regions worldwide, further improvements are needed. This review provides an overview of wheat biofortification, covering breeding efforts, nutritional evaluation methods, nutrient assimilation and bioavailability, and microbial involvement in wheat grain enrichment. Emerging technologies such as non-destructive hyperspectral imaging (HSI)/red, green, and blue (RGB) phenotyping; multi-omics integration; CRISPR-Cas9 alongside genomic selection; and microbial genetics hold promise for advancing biofortification.

Molecular mapping and validation of quantitative trait loci for content of micronutrients in wheat grain

Manganese (Mn), iron (Fe), copper (Cu), zinc (Zn), and selenium (Se) are essential micronutrients for human health. However, the genetic basis for the content of Mn, Fe, Cu, Zn, and Se in wheat grains remains unclear. A recombinant inbred lines (RIL) population derived from Yangmai 4/Yanzhan 1 (YM4/YZ1) with wheat 55K single nucleotide polymorphism (SNP) arrays and micronutrient content of two environments was used to construct a genetic linkage map and dissect the quantitative trait loci (QTL) for the content of Mn, Fe, Cu, Zn, and Se in wheat. A total of 8 QTL were detected and located on chromosomes 1A, 1B, 2D, 4D, 7A, and 7D, respectively. Among them, QFe.yaas-2D and QSe.yaas-2D were co-located on chromosome 2D, while QMn.yaas-4D and QZn.yaas-4D were co-located on chromosome 4D, which were in the dwarfing locus of Rht-D1 region. The positive alleles of QCu.yaas-1A, QMn.yaas-1B, and QZn.yaas-7D were contributed by YZ1 and explained 7.66-19.92% of the phenotypic variances, while the positive alleles of QFe.yaas-2D, QSe.yaas-2D, QMn.yaas-4D, QZn.yaas-4D, and QCu.yaas-7A were contributed by YM4 and explained 5.77-20.11% of the phenotypic variances. The positive alleles of QCu.yaas-1A, QMn.yaas-1B, and QMn/Zn.yaas-4D increased TGW by 3.52%, 3.45%, and 7.51% respectively, while the positive alleles of QFe/Se.yaas-2D decreased TGW by 6.45%. Six SNP markers flanked the target QTL were converted into Kompetitive allele specific PCR (KASP) markers, and their effects were validated in a panel of one hundred and forty-nine wheat advanced lines. Twenty-five advanced lines harboring at least five positive alleles were identified in the validation populations. A total of 60 and 51 high-confidence annotated genes for QFe/Se.yaas-2D and QMn/Zn.yaas-4D were identified using the International Wheat Genome Sequencing Consortium Reference Sequence v2.1 (IWGSC RefSeq v2.1), respectively. Some genes in these two regions were involved in stress tolerance, growth development, Zn synthesis in plants. These results provide the basis for fine-mapping the target QTL of micronutrient content and marker-assisted selection in grain quality breeding programs.

Simulation of Daily Iron Intake by Actual Diet Considering Future Trends in Wheat and Rice Biofortification, Environmental, and Dietary Factors: An Italian Case Study

BACKGROUND AND AIM

Cereals' iron content is a major contributor to dietary iron intake in Europe and a potential for biofortification. A simulation of daily iron intake from wheat and rice over the next 20 years will be quantified.

METHODS

Food items, and energy and iron intake by age classes are estimated using the Italian dietary survey (IV SCAI). Iron intake and adequacy estimation trends were categorized in four scenarios compared to a baseline (basic scenario; only climate change effects): over wheat and rice biofortification effects (scenario 1); over the shift in whole wheat consumption of up to 50% of the total amount of wheat-based foods (scenario 2); over the shift in brown rice consumption up to 100% of the total amount of rice (scenario 3); over the cumulative effects of biofortifications and whole wheat and brown rice consumption (scenario 4).

RESULTS

Increasing the iron intake from wheat and rice biofortification and the shift in whole wheat consumption is similar and sufficient to recover the baseline iron depletion effect due to climate change. The shift in brown rice consumption produces a negligible increment in iron intake. The cumulative effects of the corrective actions considered in the scenarios can significantly reduce the iron intake inadequacy, despite not reaching the recommended levels.

CONCLUSIONS

Corrective actions including biofortification and whole grain consumption are still far from ensuring the full recovery in children and females of fertile age as at-risk groups of iron deficiency. Further actions are needed considering other biofortified food sources, fortified foods, and/or dietary food diversification.

Identification of Genomic Regions Conferring Enhanced Zn and Fe Concentration in Wheat Varieties and Introgression Lines Derived from Wild Relatives

Wild and cultivated relatives of wheat are an important source of genetic factors for improving the mineral composition of wheat. In this work, a wheat panel consisting of modern bread wheat varieties, landraces, and introgression lines with genetic material of the wheat species Triticum timopheevii, T. durum, T. dicoccum, and T. dicoccoides and the synthetic line T. kiharae was used to identify loci associated with the grain zinc (GZnC) and iron (GFeC) content. Using a BLINK model, we identified 31 and 73 marker-trait associations (MTAs) for GZnC and GFeC, respectively, of which 19 were novel. Twelve MTAs distributed on chromosomes 1B, 2A, 2B, 5A, and 5B were significantly associated with GZnC, five MTAs on 2A, 2B, and 5D chromosomes were significantly associated with GFeC, and two SNPs located on 2A and 2B were related to the grain concentration of both trace elements. Meanwhile, most of these MTAs were inherited from At and G genomes of T. timopheevii and T. kiharae and positively affected GZnC and GFeC. Eight genes related to iron or zinc transporters, representing diverse gene families, were proposed as the best candidates. Our findings provide an understanding of the genetic basis of grain Zn and Fe accumulation in species of the Timopheevi group and could help in selecting new genotypes containing valuable loci.

Improving wheat grain composition for human health by constructing a QTL atlas for essential minerals

Wheat is an important source of minerals for human nutrition and increasing grain mineral content can contribute to reducing mineral deficiencies. Here, we identify QTLs for mineral micronutrients in grain of wheat by determining the contents of six minerals in a total of eleven sample sets of three biparental populations from crosses between A.E. Watkins landraces and cv. Paragon. Twenty-three of the QTLs are mapped in two or more sample sets, with LOD scores above five in at least one set with the increasing alleles for sixteen of the QTLs being present in the landraces and seven in Paragon. Of these QTLs, the number for each mineral varies between three and five and they are located on 14 of the 21 chromosomes, with clusters on chromosomes 5A (four), 6A (three), and 7A (three). The gene content within 5 megabases of DNA on either side of the marker for the QTL with the highest LOD score is determined and the gene responsible for the strongest QTL (chromosome 5A for Ca) identified as an ATPase transporter gene (TraesCS5A02G543300) using mutagenesis. The identification of these QTLs, together with associated SNP markers and candidate genes, will facilitate the improvement of grain nutritional quality.

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.

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.

Molecular characterization of stable QTL and putative candidate genes for grain zinc and iron concentrations in two related wheat populations

KEY MESSAGE

Major QTL for grain zinc and iron concentrations were identified on the long arm of chromosomes 2D and 6D. Gene-based KASP markers were developed for putative candidate genes TaIPK1-2D and TaNAS10-6D. Micronutrient malnutrition is one of the most common public health problems in the world. Biofortification, the most attractive and sustainable solution to surmount malnutrition requires the development of micronutrient enriched new crop cultivars. In this study, two recombinant inbred line (RIL) populations, ZM175/XY60 and ZM175/LX987, were used to identify QTL for grain zinc concentration (GZnC), grain iron concentration (GFeC) and thousand grain weight (TGW). Eight QTL for GZnC, six QTL for GFeC and five QTL for TGW were detected. Three QTL on chromosomes 2DL and 4BS and chromosome 6A showed pleiotropic effects on all three traits. The 4BS and 6A QTL also increased plant height and might be Rht-B1a and Rht25a, respectively. The 2DL locus within a suppressed recombination region was identified in both RIL populations and the favorable allele simultaneously increasing GZnC, GFeC and TGW was contributed by XY60 and LX987. A QTL on chromosome 6DL associated only with GZnC was detected in ZM175/XY60 and was validated in JD8/AK58 RILs using kompetitive allele-specific PCR (KASP) marker K_AX-110119937. Both the 2DL and 6DL QTL were new loci for GZnC. Based on gene annotations, sequence variations and expression profiles, the phytic acid biosynthesis gene TaIPK1-2D and nicotianamine synthase gene TaNAS10-6D were predicted as candidate genes. Their gene-based KASP markers were developed and validated in a cultivar panel of 343 wheat accessions. This study investigated the genetic basis of GZnC and GFeC and provided valuable candidate genes and markers for breeding Zn- and Fe-enriched wheat.

Multivariate Genome-Wide Association Study of Concentrations of Seven Elements in Seeds Reveals Four New Loci in Russian Wheat Lines

Wheat is a cereal grain that plays an important role in the world's food industry. The identification of the loci that change the concentration of elements in wheat seeds is an important challenge nowadays especially for genomic selection and breeding of novel varieties. In this study, we performed a multivariate genome-wide association study (GWAS) of the seven traits-concentrations of Zn, Mg, Mn, Ca, Cu, Fe, and K in grain-of the Russian collection of common wheat Triticum aestivum (N = 149 measured in two years in two different fields). We replicated one known locus associated with the concentration of Zn (IAAV1375). We identified four novel loci-BS00022069_51 (associated with concentrations of Ca and K), RFL_Contig6053_3082 (associated with concentrations of Fe and Mn), Kukri_rep_c70864_329 (associated with concentrations of all elements), and IAAV8416 (associated with concentrations of Fe and Mn)-three of them were located near the genes TraesCS6A02G375400, TraesCS7A02G094800, and TraesCS5B02G325400. Our result adds novel information on the loci involved in wheat grain element contents and may be further used in genomic selection.

Genome-wide association study reveals the genetic variation and candidate gene for grain calcium content in bread wheat

KEY MESSAGE

This study provides important information on the genetic basis of GCaC in wheat, thus contributing to breeding efforts to improve the nutrient quality of wheat. Calcium (Ca) plays important roles in the human body. Wheat grain provides the main diet for billions of people worldwide but is low in Ca content. Here, grain Ca content (GCaC) of 471 wheat accessions was determined in four field environments. A genome-wide association study (GWAS) was performed to reveal the genetic basis of GCaC using the phenotypic data form four environments and a wheat 660 K single nucleotide polymorphism (SNP) array. Twelve quantitative trait locus (QTLs) for GCaC were identified on chromosomes 1A, 1D, 2A, 3B, 6A, 6D, 7A, and 7D, which was significant in at least two environments. Haplotype analysis revealed that the phenotypic difference between the haplotypes of TraesCS6D01G399100 was significant (P ≤ 0.05) across four environments, suggesting it as an important candidate gene for GCaC. This research enhances our understanding of the genetic architecture of GCaC for further improving the nutrient quality of wheat.

Linking genetic markers with an eco-physiological model to pyramid favourable alleles and design wheat ideotypes

Genetic markers can be linked with eco-physiological crop models to accurately predict genotype performance and individual markers' contributions in target environments, exploring interactions between genotype and environment. Here, wheat (Triticum aestivum L.) yield was dissected into seven traits corresponding to cultivar genetic coefficients in an eco-physiological model. Loci for these traits were discovered through the genome-wide association studies (GWAS). The cultivar genetic coefficients were derived from the loci using multiple linear regression or random forest, building a marker-based eco-physiological model. It is then applied to simulate wheat yields and design virtual ideotypes. The results indicated that the loci identified through GWAS explained 46%-75% variations in cultivar genetic coefficients. Using the marker-based model, the normalized root mean square error (nRMSE) between the simulated yield and observed yield was 13.95% by multiple linear regression and 13.62% by random forest. The nRMSE between the simulated and observed maturity dates was 1.24% by multiple linear regression and 1.11% by random forest, respectively. Structural equation modelling indicated that variations in grain yield could be well explained by cultivar genetic coefficients and phenological data. In addition, 24 pleiotropic loci in this study were detected on 15 chromosomes. More significant loci were detected by the model-based dissection method than considering yield per se. Ideotypes were identified by higher yield and more favourable alleles of cultivar genetic traits. This study proposes a genotype-to-phenotype approach and demonstrates novel ideas and tools to support the effective breeding of new cultivars with high yield through pyramiding favourable alleles and designing crop ideotypes.

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.

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.

Identification of quantitative trait loci (QTL) and meta-QTL analysis for kernel size-related traits in wheat (Triticum aestivum L.)

BACKGROUND

Kernel size-related traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR) and kernel thickness (KT), are critical determinants for wheat kernel weight and yield and highly governed by a type of quantitative genetic basis. Genome-wide identification of major and stable quantitative trait loci (QTLs) and functional genes are urgently required for genetic improvement in wheat kernel yield. A hexaploid wheat population consisting of 120 recombinant inbred lines was developed to identify QTLs for kernel size-related traits under different water environments. The meta-analysis and transcriptome evaluation were further integrated to identify major genomic regions and putative candidate genes.

RESULTS

The analysis of variance (ANOVA) revealed more significant genotypic effects for kernel size-related traits, indicating the moderate to high heritability of 0.61-0.89. Thirty-two QTLs for kernel size-related traits were identified, explaining 3.06%-14.2% of the phenotypic variation. Eleven stable QTLs were detected in more than three water environments. The 1103 original QTLs from the 34 previous studies and the present study were employed for the MQTL analysis and refined into 58 MQTLs. The average confidence interval of the MQTLs was 3.26-fold less than that of the original QTLs. The 1864 putative candidate genes were mined within the regions of 12 core MQTLs, where 70 candidate genes were highly expressed in spikes and kernels by comprehensive analysis of wheat transcriptome data. They were involved in various metabolic pathways, such as carbon fixation in photosynthetic organisms, carbon metabolism, mRNA surveillance pathway, RNA transport and biosynthesis of secondary metabolites.

CONCLUSIONS

Major genomic regions and putative candidate genes for kernel size-related traits in wheat have been revealed by an integrative strategy with QTL linkage mapping, meta-analysis and transcriptomic assessment. The findings provide a novel insight into understanding the genetic determinants of kernel size-related traits and will be useful for the marker-assisted selection of high yield in wheat breeding.

Genome-Wide Association Mapping Identifies Key Genomic Regions for Grain Zinc and Iron Biofortification in Bread Wheat

Accelerating breeding efforts for developing biofortified bread wheat varieties necessitates understanding the genetic control of grain zinc concentration (GZnC) and grain iron concentration (GFeC). Hence, the major objective of this study was to perform genome-wide association mapping to identify consistently significant genotyping-by-sequencing markers associated with GZnC and GFeC using a large panel of 5,585 breeding lines from the International Maize and Wheat Improvement Center. These lines were grown between 2018 and 2021 in an optimally irrigated environment at Obregon, Mexico, while some of them were also grown in a water-limiting drought-stressed environment and a space-limiting small plot environment and evaluated for GZnC and GFeC. The lines showed a large and continuous variation for GZnC ranging from 27 to 74.5 ppm and GFeC ranging from 27 to 53.4 ppm. We performed 742,113 marker-traits association tests in 73 datasets and identified 141 markers consistently associated with GZnC and GFeC in three or more datasets, which were located on all wheat chromosomes except 3A and 7D. Among them, 29 markers were associated with both GZnC and GFeC, indicating a shared genetic basis for these micronutrients and the possibility of simultaneously improving both. In addition, several significant GZnC and GFeC associated markers were common across the irrigated, water-limiting drought-stressed, and space-limiting small plots environments, thereby indicating the feasibility of indirect selection for these micronutrients in either of these environments. Moreover, the many significant markers identified had minor effects on GZnC and GFeC, suggesting a quantitative genetic control of these traits. Our findings provide important insights into the complex genetic basis of GZnC and GFeC in bread wheat while implying limited prospects for marker-assisted selection and the need for using genomic selection.