Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling intricate genotype–phenotype association across various species. Maize (Zea mays L.), renowned for its extensive genetic diversity and rapid linkage disequilibrium (LD), stands as an exemplary candidate for GWAS. In maize, GWAS has made significant advancements by pinpointing numerous genetic loci and potential genes associated with complex traits, including responses to both abiotic and biotic stress. These discoveries hold the promise of enhancing adaptability and yield through effective breeding strategies. Nevertheless, the impact of environmental stress on crop growth and yield is evident in various agronomic traits. Therefore, understanding the complex genetic basis of these traits becomes paramount. This review delves into current and future prospectives aimed at yield, quality, and environmental stress resilience in maize and also addresses the challenges encountered during genomic selection and molecular breeding, all facilitated by the utilization of GWAS. Furthermore, the integration of omics, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics has enriched our understanding of intricate traits in maize, thereby enhancing environmental stress tolerance and boosting maize production. Collectively, these insights not only advance our understanding of the genetic mechanism regulating complex traits but also propel the utilization of marker-assisted selection in maize molecular breeding programs, where GWAS plays a pivotal role. Therefore, GWAS provides robust support for delving into the genetic mechanism underlying complex traits in maize and enhancing breeding strategies.

Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize

Lactic acid bacteria (LAB) fermentation is commonly used to improve the nutritional, functional, and sensory characteristics of fruit juice. Here, we explore the effects of fermentation with Lactiplantibacillus plantarum and Lactiplantibacillus pentosus on the physicochemical properties, antioxidant activities, sensory properties, and metabolic profile of jackfruit juice. The colony counts of the two selected strains reached approximately 8.0 log CFU/mL at 48 h and the results showed significant increases in total phenolic, flavonoid content, antioxidant activities, and color parameters at the end of the LAB fermentation. Electronic tongue analysis revealed that LAB fermentation significantly altered the values of sourness, bitterness, astringency, aftertaste-B, aftertaste-A, umami, richness and saltiness. A total of 765 compounds were screened for discriminative pre- and post-fermentation differential metabolites by non-target metabolomics analysis in different fermentation groups. These findings highlight the great potential of using jackfruit pulp for LAB fermentation to develop bioactive probiotic juices. 

Insights into physicochemical and sensory properties and metabolomic changes of antioxidant-rich jackfruit juice fermented by lactic acid bacteria

The aim of this study was to create various formulations of yogurt enriched with freeze-dried adjuncts, namely (i) probiotic Lactobacillus plantarum ATCC 14917 culture, and (ii) L. plantarum ATCC 14917 fermented black chokeberry juice, along with a commercial starter culture. The goal was to enhance functionality and optimize the nutritional value of the products. These new yogurt-style formulations were subsequently compared with commercially produced yogurt. All products demonstrated favorable physicochemical properties, and the probiotic strain consistently maintained viable levels exceeding 7 log cfu/g throughout the entire storage period. The fermented milk produced with the adjunct-free L. plantarum cells, as well as the yogurt produced with the proposed lactobacilli-fermented chokeberry juice, exhibited the highest lactic acid production (1.44 g/100 g yogurt by the end of storage). Levels of syneresis were observed at lower values in yogurt produced with freeze-dried fermented chokeberry juice. Yogurts prepared with the lactobacilli-fermented freeze-dried chokeberry juice displayed elevated total phenolic content and antioxidant capacity (25.74 µg GAE/g and 69.05 µmol TE/100 g, respectively). Furthermore, sensory tests revealed a distinctive fruity flavor in samples incorporating fermented juice. The results demonstrate that probiotic L. plantarum-fermented chokeberry juice enhances both the antioxidant capacity and the viability of beneficial bacteria in yogurt while it can be readily applied and commercialized, especially in the form of a freeze-dried formulation.

Assessment of the Physicochemical, Antioxidant, Microbial, and Sensory Attributes of Yogurt-Style Products Enriched with Probiotic-Fermented Aronia melanocarpa Berry Juice

Kernel number per row (KNR) is an essential component of maize (Zea mays L.) grain yield (GY), and understanding its genetic mechanism is crucial to improve GY. In this study, two F7 recombinant inbred line (RIL) populations were created using a temperate–tropical introgression line TML418 and a tropical inbred line CML312 as female parents and a backbone maize inbred line Ye107 as the common male parent. Bi-parental quantitative trait locus (QTL) mapping and genome-wide association analysis (GWAS) were then performed on 399 lines of the two maize RIL populations for KNR in two different environments using 4118 validated single nucleotide polymorphism (SNP) markers. This study aimed to: (1) detect molecular markers and/or the genomic regions associated with KNR; (2) identify the candidate genes controlling KNR; and (3) analyze whether the candidate genes are useful in improving GY. The authors reported a total of 7 QTLs tightly linked to KNR through bi-parental QTL mapping and identified 21 SNPs significantly associated with KNR through GWAS. Among these, a highly confident locus qKNR7-1 was detected at two locations, Dehong and Baoshan, with both mapping approaches. At this locus, three novel candidate genes (Zm00001d022202, Zm00001d022168, Zm00001d022169) were identified to be associated with KNR. These candidate genes were primarily involved in the processes related to compound metabolism, biosynthesis, protein modification, degradation, and denaturation, all of which were related to the inflorescence development affecting KNR. These three candidate genes were not reported previously and are considered new candidate genes for KNR. The progeny of the hybrid Ye107 × TML418 exhibited strong heterosis for KNR, which the authors believe might be related to qKNR7-1. This study provides a theoretical foundation for future research on the genetic mechanism underlying KNR in maize and the use of heterotic patterns to develop high-yielding hybrids.

/pdf/mapping-and-functional-analysis-of-qtl-for-kernel-number-per-14t6qend.pdf

Mapping and Functional Analysis of QTL for Kernel Number per Row in Tropical and Temperate–Tropical Introgression Lines of Maize (Zea mays L.)

The assessment of 1000-kernel weight holds significant importance in determining maize grain yield, and elucidating its underlying genetic mechanisms is imperative for enhancing its overall performance. The material for the study consisted of 26 doubled-haploid (DH) maize lines obtained from crossing two cultivars with flint kernels. Lines were planted in the northern part of the Lower Silesia voivodship in Poland over ten years (2013–2022). The 1000-kernel weight was assessed. The purposes of the research were as follows: (1) to assess genotype by environment interaction (GEI by the additive main effects and multiplicative interaction (AMMI) model; (2) the selection of stable DH lines and environment-specific lines; and (3) the estimation of parameters related to additive and additive–additive gene interaction (epistasis). The results indicate the significant effects of genotype and environment, as well as the GEI, on the 1000-kernel weight. Estimates of additive gene action effects were statistically significant in every year of the study, except 2022. Estimates of epistasis (total additive-by-additive interaction) effects for 1000-kernel weight were statistically significant in 2013, 2015, and 2017 (positive effects), as well as in 2018 and 2020 (negative effects). The lines KN07 and KN10 are recommended for further inclusion in the breeding program due to their stability and highest average of 1000-kernel weight.

Analysis of Linkage on Interaction of Main Aspects (Genotype by Environment Interaction, Stability and Genetic Parameters) of 1000 Kernels in Maize (Zea mays L.)

A novel strategy for improving the antioxidant, iridoid, and flavor properties of Noni (Morinda citrifolia L.) fruit juice by lactic acid bacteria fermentation

Vitamin C (VC) can greatly enhance the quality properties of dough and steamed bread in the food field. However, there are few studies on the interaction between VC and gluten, and the mechanism of VC influencing the foaming capacity, emulsifiablity, and dynamic viscosity of gluten is not clear. In this study, different content of VC (0, 1%, 2%, 3%, 4% and 5%) was added to gluten to obtain VC-gluten dough samples (CK, GV1, GV2, GV3, GV4 and GV5), and the properties of the VC-gluten dough were determined. Results showed that the increasing VC content lead to increase in the content of high-, medium- and low-molecular weight gluten, suggesting that VC improved the protein solubility of gluten. The G ' and G " values of dough containing VC were higher than those of the control with the increase of scanning frequency. The foaming ability of gluten increased with the increase of VC content. Emulsibility of the dough of GV1 to GV 5 were significantly lower than that of the CK. Furthermore, VC could reduce the number of bubbles in gluten protein, when the VC content was less than 3%. In conclusion, VC might reduce the emulsifying characteristic and emulsifying stability of gluten, increase the solubility of gluten, and improve the dynamic viscosity of gluten dough by changing the content of disulfide bond in gluten. This study hopes to not only improve the functional characteristics of gluten protein, but also provide the basis for future development and improvement of VC-enriched health foods. 

Effects of vitamin C on the structural and functional characteristics of wheat gluten

https://doi.org/10.1016/j.fochx.2022.100548

Insights into the effects of extractable phenolic compounds and Maillard reaction products on the antioxidant activity of roasted wheat flours with different maturities

Leaf angle is a key trait for maize plant architecture that plays a significant role in its morphological development, and ultimately impacting maize grain yield. Although many studies have been conducted on the association and localization of genes regulating leaf angle in maize, most of the candidate genes identified are associated with the regulation of ligule-ear development and phytohormone pathways, and only a few candidate genes have been reported to enhance the mechanical strength of leaf midrib and vascular tissues.To address this gap, we conducted a genome-wide association study (GWAS) using the leaf angle phenotype and genotyping-by-sequencing data generated from three recombinant inbred line (RIL) populations of maize. Through GWAS analysis, we identified 156 SNPs significantly associated with the leaf angle trait and detected a total of 68 candidate genes located within 10 kb upstream and downstream of these individual SNPs. Among these candidate genes, Zm00001d045408, located on chromosome 9 emerged as a key gene controlling the angles of both the ear leaf and the second leaf above the ear leaf. Notably, this new gene's homolog in Arabidopsis promotes cell division and vascular tissue development. Further analysis revealed that a SNP transversion (G/T) at 7.536 kb downstream of the candidate gene Zm00001d045408 may have caused a reduction in leaf angles of the ear and the second leaf above the ear leaf. Our analysis of the 10 kb region downstream of this candidate gene revealed a 4.337 kb solo long-terminal reverse transcription transposon (solo LTR), located 3.112 kb downstream of Zm00001d045408, with the SNP located 87 bp upstream of the solo LTR.In summary, we have identified a novel candidate gene, Zm00001d045408 and a solo LTR that are associated with the angles of both the ear leaf and the second leaf above the ear leaf. The future research holds great potential in exploring the precise role of newly identified candidate gene in leaf angle regulation. Functional characterization of this gene can help in gaining deeper insights into the complex genetic pathways underlying maize plant architecture. 

A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize

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