Polyphenol oxidase genes as integral part of the evolutionary history of domesticated tetraploid wheat

Potential of tetraploid wheats in plant breeding: A review

Domestication syndrome, selection pressure, and modern plant breeding programs have reduced the genetic diversity of the wheat germplasm. For the genetic gains of breeding programs to be sustainable, plant breeders require a diverse gene pool to select genes for resistance to biotic stress factors, tolerance to abiotic stress factors, and improved quality and yield components. Thus, old landraces, subspecies and wild ancestors are rich sources of genetic diversity that have not yet been fully exploited, and it is possible to utilize this diversity. Compared with durum wheat, tetraploid wheat subspecies have retained much greater genetic diversity despite genetic drift and various environmental influences, and the identification and utilization of this diversity can make a greater contribution to the genetic enrichment of wheat. In addition, using the pre-breeding method, the valuable left-behind alleles in the wheat gene pool can be re-introduced through hybridization and introgressive gene flow to create a sustainable opportunity for the genetic gain of wheat. This review provides some insights about the potential of tetraploid wheats in plant breeding and the genetic gains made by them in plant breeding across past decades, and gathers the known functional information on genes/QTLs, metabolites, traits and their direct involvement in wheat resistance/tolerance to biotic/abiotic stresses.

Breeding effects on durum wheat traits detected using GWAS and haplotype block analysis

Introduction

The recent boosting of genomic data in durum wheat (Triticum turgidum subsp. durum) offers the opportunity to better understand the effects of breeding on the genetic structures that regulate the expression of traits of agronomic interest. Furthermore, the identification of DNA markers useful for marker-assisted selection could also improve the reliability of technical protocols used for variety protection and registration.

Methods

Within this motivation context, 123 durum wheat accessions, classified into three groups: landraces (LR), ancient (OC) and modern cultivars (MC), were evaluated in two locations, for 34 agronomic traits, including UPOV descriptors, to assess the impact of changes that occurred during modern breeding.

Results

The association mapping analysis, performed with 4,241 SNP markers and six multi-locus-GWAS models, revealed 28 reliable Quantitative Trait Nucleotides (QTNs) related to plant morphology and kernel-related traits. Some important genes controlling flowering time and plant height were in linkage disequilibrium (LD) decay with QTNs identified in this study. A strong association for yellow berry was found on chromosome 6A (Q.Yb-6A) in a region containing the nadh-ubiquinone oxidoreductase subunit, a gene involved in starch metabolism. The Q.Kcp-2A harbored the PPO locus, with the associated marker (Ku_c13700_1196) in LD decay with Ppo-A1 and Ppo-A2. Interestingly, the Q.FGSGls-2B.1, identified by RAC875_c34512_685 for flag leaf glaucosity, mapped less than 1 Mb from the Epistatic inhibitors of glaucousness (Iw1), thus representing a good candidate for supporting the morphological DUS traits also with molecular markers. LD haplotype block approach revealed a higher diversity, richness and length of haploblocks in MC than OC and LR (580 in LR, 585 in OC and 612 in MC), suggesting a possible effect exerted by breeding programs on genomic regions associated with the agronomic traits.

Discussion

Our findings pave new ways to support the phenotypic characterization necessary for variety registration by using a panel of cost-effectiveness SNP markers associated also to the UPOV descriptors. Moreover, the panel of associated SNPs might represent a reservoir of favourable alleles to use in durum wheat breeding and genetics.

Phenotypic evolution in durum wheat (Triticum durum Desf.) based on SNPs, morphological traits, UPOV descriptors and kernel-related traits

Durum wheat is a worldwide staple crop cultivated mainly in the Mediterranean basin. Progress in durum wheat breeding requires the exploitation of genetic variation among the gene pool enclosed in landraces, old cultivars and modern cultivars. The aim of this study was to provide a more comprehensive view of the genetic architecture evolution among 123 durum wheat accessions (41 landraces, 41 old cultivars and 41 modern cultivars), grown in replicated randomized complete block in two areas, Metaponto (Basilicata) and Foggia (Apulia), using the Illumina iSelect 15K wheat SNP array and 33 plant and kernel traits including the International Union for the Protection of new Varieties of Plants (UPOV) descriptors. Through DAPC and Bayesian population structure five groups were identified according to type of material data and reflecting the genetic basis and breeding strategies involved in their development. Phenotypic and genotypic coefficient of variation were low for kernel width (6.43%) and for grain protein content (1.03%). Highly significant differences between environments, genotypes and GEI (Genotype x Environment Interaction) were detected by mixed ANOVAs for agro-morphological-quality traits. Number of kernels per spike (h2 = 0.02) and grain protein content (h2 = 0.03) were not a heritability character and highly influenced by the environment. Nested ANOVAs revealed highly significant differences between DAPC clusters within environments for all traits except kernel roundness. Ten UPOV traits showed significant diversity for their frequencies in the two environments. By PCAmix multivariate analysis, plant height, heading time, spike length, weight of kernels per spike, thousand kernel weight, and the seed related traits had heavy weight on the differentiation of the groups, while UPOV traits discriminated moderately or to a little extent. The data collected in this study provide useful resources to facilitate management and use of wheat genetic diversity that has been lost due to selection in the last decades.

An Overview of Factors Affecting the Functional Quality of Common Wheat (Triticum aestivum L.)

Wheat (Triticum aestivum L.) is one of the most important crops worldwide, and, as a resilient cereal, it grows in various climatic zones. Due to changing climatic conditions and naturally occurring environmental fluctuations, the priority problem in the cultivation of wheat is to improve the quality of the crop. Biotic and abiotic stressors are known factors leading to the deterioration of wheat grain quality and to crop yield reduction. The current state of knowledge on wheat genetics shows significant progress in the analysis of gluten, starch, and lipid genes responsible for the synthesis of the main nutrients in the endosperm of common wheat grain. By identifying these genes through transcriptomics, proteomics, and metabolomics studies, we influence the creation of high-quality wheat. In this review, previous works were assessed to investigate the significance of genes, puroindolines, starches, lipids, and the impact of environmental factors, as well as their effects on the wheat grain quality.

Chitosan oligosaccharide as a plant immune inducer on the Passiflora spp. (passion fruit) CMV disease

Cucumber mosaic virus (CMV), one of the main viruses, is responsible for Passiflora spp. (passion fruit) virus diseases, which negatively affect its planting, cultivation, and commercial quality. In this study, a laboratory anti-CMV activity screening model for Passiflora spp. CMV disease was first established. Then, the effects of different antiviral agents of chitosan oligosaccharide (COS), dufulin (DFL), and ningnanmycin (Ning) on CMV virulence rate in Passiflora spp. were determined. The virulence rate and anti-CMV activity in Passiflora spp. treated with COS were 50% and 45.48%, respectively, which were even better than those of DFL (66.67% and 27.30%, respectively) and Ning (83.30% and 9.17%, respectively). Field trials test results showed COS revealed better average control efficiency (47.35%) against Passiflora spp. CMV disease than those of DFL (40.93%) and Ning (33.82%), indicating that COS is effective in the control of the Passiflora spp. CMV disease. Meanwhile, the nutritional quality test results showed that COS could increase the contents of soluble solids, titratable acids, vitamin C, and soluble proteins in Passiflora spp. fruits as well as enhance the polyphenol oxidase (PPO), superoxide dismutase (SOD), and peroxidase (POD) activity in the leaves of Passiflora spp. seedlings. In addition, the combined transcriptome and proteome analysis results showed that COS mainly acted on the Brassinosteroids (BRs) cell signaling pathway, one of plant hormone signal transduction pathway, in Passiflora spp., thus activating the up-regulated expression of TCH4 and CYCD3 genes to improve the resistance to CMV disease. Therefore, our study results demonstrated that COS could be used as a potential plant immune inducer to control the Passiflora spp. CMV disease in the future.

Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS

BACKGROUND

Rapid reductions in emissions from fossil fuel burning are needed to curb global climate change. Biofuel production from crop residues can contribute to reducing the energy crisis and environmental deterioration. Wheat is a renewable source for biofuels owing to the low cost and high availability of its residues. Thus, identifying candidate genes controlling these traits is pivotal for efficient biofuel production. Here, six multi-locus genome-wide association (ML-GWAS) models were applied using 185 tetraploid wheat accessions to detect quantitative trait nucleotides (QTNs) for fifteen traits associated with biomass composition.

RESULTS

Among the 470 QTNs, only 72 identified by at least two models were considered as reliable. Among these latter, 16 also showed a significant effect on the corresponding trait (p.value < 0.05). Candidate genes survey carried out within 4 Mb flanking the QTNs, revealed putative biological functions associated with lipid transfer and metabolism, cell wall modifications, cell cycle, and photosynthesis. Four genes encoded as Cellulose Synthase (CeSa), Anaphase promoting complex (APC/C), Glucoronoxylan 4-O Methyltransferase (GXM) and HYPONASTIC LEAVES1 (HYL1) might be responsible for an increase in cellulose, and natural and acid detergent fiber (NDF and ADF) content in tetraploid wheat. In addition, the SNP marker RFL_Contig3228_2154 associated with the variation in stem solidness (Q.Scsb-3B) was validated through two molecular methods (High resolution melting; HRM and RNase H²-dependent PCR; rhAMP).

CONCLUSIONS

The study provides new insights into the genetic basis of biomass composition traits on tetraploid wheat. The application of six ML-GWAS models on a panel of diverse wheat genotypes represents an efficient approach to dissect complex traits with low heritability such as wheat straw composition. The discovery of genes/genomic regions associated with biomass production and straw quality parameters is expected to accelerate the development of high-yielding wheat varieties useful for biofuel production.

Comparative Genetic Analysis of Durum Wheat Landraces and Cultivars Widespread in Tunisia

The durum wheat (Triticum turgidum L. ssp. durum Desf.) landraces constitute a useful natural germplasm to increase the genetic diversity in the modern durum cultivars. The Tunisian durum germplasm constitutes 28 accessions conserved in Genebank of Tunisia, which are still unexplored. In this study, a comparative genetic analysis was performed to investigate the relationships between the Tunisian durum lines and the modern cultivars and detect divergent loci involved in breeding history. The genetic diversity analyses carried out using nine morphological descriptors and the 25K single-nucleotide polymorphism (SNP) array allowed us to distinguish two groups of Tunisian landraces and one of durum cultivars. The analysis of molecular variance and diversity indices confirmed the genetic variability among the groups. A total of 529 SNP loci were divergent between Tunisian durum landraces and modern cultivars. Candidate genes related to plant and spike architecture, including FLOWERING LOCUS T (FT-B1), zinc finger CONSTANS, and AP2/EREBPs transcription factors, were identified. In addition, divergent genes involved in grain composition and biotic stress nucleotide-binding site and leucine-reach repeats proteins and disease resistance proteins (NBS-LRR and RPM) were found, suggesting that the Tunisian durum germplasm may represent an important source of favorable alleles to be used in future durum breeding programs for developing well-adapted and resilient cultivars.