Waxy genes from spelt wheat: new alleles for modern wheat breeding and new phylogenetic inferences about the origin of this species

Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement

Starch and seed storage protein (SSP) composition profoundly impact wheat grain yield and quality. To unveil regulatory mechanisms governing their biosynthesis, transcriptome, and epigenome profiling is conducted across key endosperm developmental stages, revealing that chromatin accessibility, H3K27ac, and H3K27me3 collectively regulate SSP and starch genes with varying impact. Population transcriptome and phenotype analyses highlight accessible promoter regions' crucial role as a genetic variation resource, influencing grain yield and quality in a core collection of wheat accessions. Integration of time-serial RNA-seq and ATAC-seq enables the construction of a hierarchical transcriptional regulatory network governing starch and SSP biosynthesis, identifying 42 high-confidence novel candidates. These candidates exhibit overlap with genetic regions associated with grain size and quality traits, and their functional significance is validated through expression-phenotype association analysis among wheat accessions and loss-of-function mutants. Functional analysis of wheat abscisic acid insensitive 3-A1 (TaABI3-A1) with genome editing knock-out lines demonstrates its role in promoting SSP accumulation while repressing starch biosynthesis through transcriptional regulation. Excellent TaABI3-A1Hap1 with enhanced grain weight is selected during the breeding process in China, linked to altered expression levels. This study unveils key regulators, advancing understanding of SSP and starch biosynthesis regulation and contributing to breeding enhancement.

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.

Wheat end-use quality: State of art, genetics, genomics-assisted improvement, future challenges, and opportunities

Wheat is the most important source of food, feed, and nutrition for humans and livestock around the world. The expanding population has increasing demands for various wheat products with different quality attributes requiring the development of wheat cultivars that fulfills specific demands of end-users including millers and bakers in the international market. Therefore, wheat breeding programs continually strive to meet these quality standards by screening their improved breeding lines every year. However, the direct measurement of various end-use quality traits such as milling and baking qualities requires a large quantity of grain, traits-specific expensive instruments, time, and an expert workforce which limits the screening process. With the advancement of sequencing technologies, the study of the entire plant genome is possible, and genetic mapping techniques such as quantitative trait locus mapping and genome-wide association studies have enabled researchers to identify loci/genes associated with various end-use quality traits in wheat. Modern breeding techniques such as marker-assisted selection and genomic selection allow the utilization of these genomic resources for the prediction of quality attributes with high accuracy and efficiency which speeds up crop improvement and cultivar development endeavors. In addition, the candidate gene approach through functional as well as comparative genomics has facilitated the translation of the genomic information from several crop species including wild relatives to wheat. This review discusses the various end-use quality traits of wheat, their genetic control mechanisms, the use of genetics and genomics approaches for their improvement, and future challenges and opportunities for wheat breeding.

Spanish Spelt Wheat: From an Endangered Genetic Resource to a Trendy Crop

Spelt wheat (Triticum aestivum L. ssp. spelta Thell.) is an ancient wheat that was widely cultivated in the past. This species derived from a cross between emmer wheat (T. turgidum spp. dicoccum Schrank em. Thell.) and Aegilops tauschii Coss. Its main origin was in the Fertile Crescent (Near East), with a secondary center of origin in Europe due to a second hybridization event between emmer and hexaploid wheat. This species has been neglected in most of Europe; however, the desire for more natural foods has driven a revival in interest. Iberian spelt is classified as a geographical group differing to the rest of European spelt. In this review, the particularities, genetic diversity and current situation of Spanish spelt, mainly for quality traits, are discussed.

Starch biosynthesis in cereal endosperms: An updated review over the last decade

Starch is a vital energy source for living organisms and is a key raw material and additive in the food and non-food industries. Starch has received continuous attention in multiple research fields. The endosperm of cereals (e.g., rice, corn, wheat, and barley) is the most important site for the synthesis of storage starch. Around 2010, several excellent reviews summarized key progress in various fields of starch research, serving as important references for subsequent research. In the past 10 years, many achievements have been made in the study of starch synthesis and regulation in cereals. The present review provides an update on research progress in starch synthesis of cereal endosperms over the past decade, focusing on new enzymes and non-enzymatic proteins involved in starch synthesis, regulatory networks of starch synthesis, and the use of elite alleles of starch synthesis-related genes in cereal breeding programs. We also provide perspectives on future research directions that will further our understanding of cereal starch biosynthesis and regulation to support the rational design of ideal quality grain.

Molecular characterization of five novel Wx-A1 alleles in common wheat including one silent allele by transposon insertion

Wheat starch is composed of two glucose polymers, amylose and amylopectin. Although several starch synthases are responsible for its synthesis, only the waxy protein is associated with the amylose synthesis. The waxy protein composition of 45 Spanish common wheat landraces from Andalusia (southern Spain) was evaluated. Within these materials, five novel alleles for the Wx-A1 gene were detected. Four of them showed functional proteins (Wx-A1p, Wx-A1q, Wx-A1r and Wx-A1s), although some amino acid changes were found in the mature protein sequence. However, one of them (Wx-A1t) exhibited loss of the Wx-A1 protein, and its base sequence contained one large insert (1,073 bp) in the tenth exon, that interrupted the ORF of the Wx-A1 gene. This insert exhibited the characteristics of a Class II transposon of the Mutator superfamily, which had not been described previously, and has been named Baetica. The conservation of such inserts could be related to their low effect on vital properties of the plants, as occurs with most of the genes associated with technological quality. In conclusion, the evaluation of old wheat landraces showed that, in addition to their use as alternative crops, these materials could be a useful source of interesting genes in wheat quality improvement.

An Evaluation of Spelt Crosses for Breeding New Varieties of Spring Spelt

This study evaluated F5 breeding lines, which were obtained by crossing five parents of spring spelt from different geographical regions characterized by various morphological and performance traits. A total of 11 quantitative traits were analyzed, including six traits relating to yield components, four traits relating to grain quality, and one trait relating to plant height and sensitivity to lodging. The applied clustering method supported the identification of four groups of breeding lines which were presented graphically in a heatmap with dendrogram. Group I contained 33.0% of the breeding lines, and it was most distant from the remaining groups. It was composed of tall plants characterized by high values of yield components, high fat content, and high sensitivity to lodging. Groups III (30.4%) and IV (17.0%) were most similar and were characterized by lower values of yield components, a high content of protein, ash and fiber, and lower sensitivity to lodging. Group II contained 19.6% of the breeding lines, and it was more similar to groups III and IV than group I. Breeding lines with satisfactory performance traits can be selected from each group and used to breed new varieties with the desired traits.

Sequence divergence between spelt and common wheat

Sequence comparison between spelt and common wheat reveals that the former has huge potential in enriching the genetic variation of the latter. Genetic variation is the foundation of crop improvement. By comparing genome sequences of a Triticum spelta accession and one of its derived hexaploid lines with the sequences of the international reference genotype Chinese Spring, we detected variants more than tenfold higher than those present among common wheat (T. aestivum L) genotypes. Furthermore, different from the typical 'V-shaped' pattern of variant distribution often observed along wheat chromosomes, the sequence variation detected in this study was more evenly distributed along the 3B chromosome. This was also the case between T. spelta and the wild emmer genome. Genetic analysis showed that T. spelta and common wheat formed discrete groups. These results showed that, although it is believed that the spelt and common wheat are evolutionarily closely related and belong to the same species, a significant sequence divergence exists between them. Thus, the values of T. spelta in enriching the genetic variation of common wheat can be huge.

Current Trends in Ancient Grains-Based Foodstuffs: Insights into Nutritional Aspects and Technological Applications

For centuries, ancient grains fed populations, but due to their low yield, they were abandoned and replaced by high-yielding species. However, currently, there is a renewed interest in ancient wheat and pseudocereal grains from consumers, farmers, and manufacturers. Ancient wheat such as einkorn, emmer, spelt, and Kamut®, are being reintegrated because of their low fertilizer input, high adaptability and important genetic diversity. New trends in pseudocereal products are also emerging, and they are mostly appreciated for their nutritional outcomes, particularly by the gluten-free market. Toward healthier lifestyle, ancient grains-based foodstuffs are a growing business and their industrialization is taking 2 pathways, either as a raw ingredient or a functional ingredient. This paper deals with these grain characteristics by focusing on the compositional profile and the technological potential.

Harnessing Diversity in Wheat to Enhance Grain Yield, Climate Resilience, Disease and Insect Pest Resistance and Nutrition Through Conventional and Modern Breeding Approaches

Current trends in population growth and consumption patterns continue to increase the demand for wheat, a key cereal for global food security. Further, multiple abiotic challenges due to climate change and evolving pathogen and pests pose a major concern for increasing wheat production globally. Triticeae species comprising of primary, secondary, and tertiary gene pools represent a rich source of genetic diversity in wheat. The conventional breeding strategies of direct hybridization, backcrossing and selection have successfully introgressed a number of desirable traits associated with grain yield, adaptation to abiotic stresses, disease resistance, and bio-fortification of wheat varieties. However, it is time consuming to incorporate genes conferring tolerance/resistance to multiple stresses in a single wheat variety by conventional approaches due to limitations in screening methods and the lower probabilities of combining desirable alleles. Efforts on developing innovative breeding strategies, novel tools and utilizing genetic diversity for new genes/alleles are essential to improve productivity, reduce vulnerability to diseases and pests and enhance nutritional quality. New technologies of high-throughput phenotyping, genome sequencing and genomic selection are promising approaches to maximize progeny screening and selection to accelerate the genetic gains in breeding more productive varieties. Use of cisgenic techniques to transfer beneficial alleles and their combinations within related species also offer great promise especially to achieve durable rust resistance.

Phylogenetic Analysis of Different Ploidy Saccharum spontaneum Based on rDNA-ITS Sequences

Saccharum spontaneum L. is a crucial wild parent of modern sugarcane cultivars whose ploidy clones have been utilized successfully in improving the stress resistance and yield related traits of sugarcane cultivars. To establish knowledge regarding the genetic variances and evolutional relationships of ploidy clones of Saccharum spontaneum collected in China, the rDNA-ITS sequences of 62 ploidy clones including octaploid clones (2n = 64), nonaploid clones (2n = 72), decaploid clones (2n = 80), and dodecaploid clones (2n = 96), were obtained and analyzed. The rDNA-ITS sequences of four species from Saccharum and Sorghum bicolor selected as controls. The results showed that decaploid clones (2n = 80) possess the most abundant variances with 58 variable sites and 20 parsim-informative sites in ITS sequences, which were then followed by octaploid clones with 43 variable sites and 17 parsim-informative sites. In haplotype diversity, all four population exhibited high diversity, especially nonaploid and decaploid populations. By comparing the genetic distances among four ploidy populations, the dodecaploid population exhibited the closest relationship with the nonaploid population, and then the relationship strength decreased successively for the decaploid population and then for the octaploid population. Population differentiation analysis showed that the phenomena of population differentiation were not found among different ploidy populations, and low coefficient of gene differentiation(Gst) and high gene flow(Nm) occur among these populations possessing close genetic relationship. These results mentioned above will contribute to the understanding of the evolution of different ploidy populations of Saccharum spontaneum and provide vital knowledge for their utilization in sugarcane breeding and innovation.

Wheat waxy proteins: polymorphism, molecular characterization and effects on starch properties

The starch fraction, comprising about 70% of the total dry matter in the wheat grain, can greatly affect the end-use quality of products made from wheat kernels, especially Asian noodles. Starch is associated with the shelf life and nutritional value (glycaemic index) of different wheat products. Starch quality is closely associated with the ratio of amylose to amylopectin, the two main macromolecules forming starch. In this review, we briefly summarise the discovery of waxy proteins-shown to be the sole enzymes responsible for amylose synthesis in wheat. The review particularly focuses on the different variants of these proteins, together with their molecular characterisation and evaluation of their effects on starch composition. There have been 19 different waxy protein variants described using protein electrophoresis; and at a molecular level 19, 15 and seven alleles described for Wx-A1, Wx-B1 and Wx-D1, respectively. This large variability, found in modern wheat and genetic resources such as wheat ancestors and wild relatives, is in some cases not properly ordered. The proper ordering of all the data generated is the key to enhancing use in breeding programmes of the current variability described, and thus generating wheat with novel starch properties to satisfy the demand of industry and consumers for novel high-quality processed food.

Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene

BACKGROUND

Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes.

FINDINGS

The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (F(ST) = 0.005), moderate differentiation between sali and jum (F(ST) = 0.108) and high differentiation between jum and boro (F(ST) = 0.230) ecotypes.

CONCLUSION

The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.

Origins and domestication of cultivated banana inferred from chloroplast and nuclear genes

BACKGROUND

Cultivated bananas are large, vegetatively-propagated members of the genus Musa. More than 1,000 cultivars are grown worldwide and they are major economic and food resources in numerous developing countries. It has been suggested that cultivated bananas originated from the islands of Southeast Asia (ISEA) and have been developed through complex geodomestication pathways. However, the maternal and parental donors of most cultivars are unknown, and the pattern of nucleotide diversity in domesticated banana has not been fully resolved.

METHODOLOGY/PRINCIPAL FINDINGS

We studied the genetics of 16 cultivated and 18 wild Musa accessions using two single-copy nuclear (granule-bound starch synthase I, GBSS I, also known as Waxy, and alcohol dehydrogenase 1, Adh1) and two chloroplast (maturase K, matK, and the trnL-F gene cluster) genes. The results of phylogenetic analyses showed that all A-genome haplotypes of cultivated bananas were grouped together with those of ISEA subspecies of M. acuminata (A-genome). Similarly, the B- and S-genome haplotypes of cultivated bananas clustered with the wild species M. balbisiana (B-genome) and M. schizocarpa (S-genome), respectively. Notably, it has been shown that distinct haplotypes of each cultivar (A-genome group) were nested together to different ISEA subspecies M. acuminata. Analyses of nucleotide polymorphism in the Waxy and Adh1 genes revealed that, in comparison to the wild relatives, cultivated banana exhibited slightly lower nucleotide diversity both across all sites and specifically at silent sites. However, dramatically reduced nucleotide diversity was found at nonsynonymous sites for cultivated bananas.

CONCLUSIONS/SIGNIFICANCE

Our study not only confirmed the origin of cultivated banana as arising from multiple intra- and inter-specific hybridization events, but also showed that cultivated banana may have not suffered a severe genetic bottleneck during the domestication process. Importantly, our findings suggested that multiple maternal origins and a reduction in nucleotide diversity at nonsynonymous sites are general attributes of cultivated bananas.

Human coronaviruses: Clinical features and phylogenetic analysis

Strains of human coronavirus (HCoV), namely HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1, primarily infect the upper respiratory and gastrointestinal tracts and are the most common cause of non-rhinovirus-induced common cold in humans. Although the manifestations of coronavirus infection (i.e., rhinorrhea, sneezing, cough, nasal obstruction, and bronchitis) are generally self-limiting in healthy adults, certain strains such as HCoV-NL63 and HCoV-HKU1 can cause severe lower respiratory tract infection and febrile seizure, especially in infants, people of advanced age, and immunocompromised hosts. In 2003, a novel HCoV strain was identified as the causative agent of the severe acute respiratory syndrome (SARS) epidemic that began in Asia in 2002. The strain has hence been referred to as SARS-CoV. In addition, as recently as September 2012, another novel HCoV, human betacoronavirus 2c EMC2012, was identified as being the cause of fever, renal failure, pneumonia, and severe respiratory distress in two patients in the Middle East. Phylogenetic analysis has revealed highly conserved sequences of ORF1ab, spike, nucleocapsid, and envelope protein genes, but not membrane protein genes, between human betacoronavirus 2c EMC2012 and SARS-CoV. This review focuses on the differences in the genomes of certain HCoV strains, the pathogenesis of said strains, and recent developments in the establishment of therapeutic agents that might aid in the treatment of patients with such infections.