A consensus map for quality traits in durum wheat based on genome-wide association studies and detection of ortho-meta QTL across cereal species

The present work focused on the identification of durum wheat QTL hotspots from a collection of genome-wide association studies, for quality traits, such as grain protein content and composition, yellow color, fiber, grain microelement content (iron, magnesium, potassium, selenium, sulfur, calcium, cadmium), kernel vitreousness, semolina, and dough quality test. For the first time a total of 10 GWAS studies, comprising 395 marker-trait associations (MTA) on 57 quality traits, with more than 1,500 genotypes from 9 association panels, were used to investigate consensus QTL hotspots representative of a wide durum wheat genetic variation. MTA were found distributed on all the A and B genomes chromosomes with minimum number of MTA observed on chromosome 5B (15) and a maximum of 45 on chromosome 7A, with an average of 28 MTA per chromosome. The MTA were equally distributed on A (48%) and B (52%) genomes and allowed the identification of 94 QTL hotspots. Synteny maps for QTL were also performed in Zea mays, Brachypodium, and Oryza sativa, and candidate gene identification allowed the association of genes involved in biological processes playing a major role in the control of quality traits.info:eu-repo/semantics/publishedVersio

Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

The genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.info:eu-repo/semantics/publishedVersio

A durum wheat recombinant inbred line (RIL) population: Data on β-glucans, grain protein content, grain yield per spike, and heading time

Data presented are on genetic variation of quality trait and production in a recombinant inbred line (RIL) population derived from a cross between two elite durum wheat cultivars grown in two different locations (Valenzano, metropolitan city of Bari -Italy) and Policoro (metropolitan city of Matera – Italy). The data of the two environment include: 1. β-glucan content; 2. grain protein content; 3. grain yield per spike; 4. heading time. In addition data on high-density SNP-based genetic linkage map and linkage analysis are reported. The data in this article support and augment information presented in the research article “Development of a high-density SNP-based linkage map and detection of QTL for β-glucans, protein content, grain yield per spike and heading time in durum wheat” (Int J Mol Sci. 18(6):1329, 2017, https://doi.org/10.3390/ijms18061329)

From Genetic Maps to QTL Cloning: An Overview for Durum Wheat

Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.info:eu-repo/semantics/publishedVersio

Mapping QTLs for Fusarium head blight resistance in an interspecific wheat population

Fusarium head blight (scab) is one of the most widespread and damaging diseases of wheat, causing grain yield and quality losses and production of harmful mycotoxins. Development of resistant varieties is hampered by lack of effective resistance sources in the tetraploid wheat primary gene pool. Here we dissected the genetic basis of resistance in a new durum wheat (Triticum turgidum ssp. durum) Recombinant inbred lines (RILs) population obtained by crossing an hexaploid resistant line and a durum susceptible cultivar. A total of 135 RILs were used for constituting a genetic linkage map and mapping loci for head blight incidence, severity, and disease-related plant morphological traits (plant height, spike compactness, and awn length). The new genetic map accounted for 4,366 single nucleotide polymorphism markers assembled in 52 linkage groups covering a total length of 4,227.37 cM. Major quantitative trait loci (QTL) for scab incidence and severity were mapped on chromosomes 2AS, 3AL, and 2AS, 2BS, 4BL, respectively. Plant height loci were identified on 3A, 3B, and 4B, while major QTL for ear compactness were found on 4A, 5A, 5B, 6A, and 7A. In this work, resistance to Fusarium was transferred from hexaploid to durum wheat, and correlations between the disease and morphological traits were assessed

Breeding Innovations in Underutilized Temperate Fruit Trees

The recent growing interest in minor species (i.e., fig, pomegranate, feijoa, etc.) has recently driven new research on breeding and genetics to address producer and consumer traits. Since these species have received little attention from the scientific community, they were less improved via conventional breeding, and lacked detailed genomic information on important traits. This lack of data, together with a general poor genetic knowledge of these species, has limited a wider cultivation of varieties with improved characteristics. For these reasons, and with the objective to increase the interest of scientists, farmers, and consumers for these fruits, this Research Topic “Breeding Innovations in Underutilized Temperate Fruit Trees” comprises biochemical, morphological, and genetic studies on some minor species regarding fruit trait variation, resistance, evolution, or sex determination. In this context, Marcotuli et al. examined the mechanisms behind the bud evolution toward breba or main crop in fig (Ficus carica L.), since this aspect remains unclear. The X-ray images of buds showed a great structural similarity between breba and the main crop during the initial stages of development, but breba inflorescence differentiation was completed in two seasons whereas that of main crop started at the end of winter and was completed within 2–3 months in the same season. The higher expression of floral homeotic protein AGAMOUS in breba compared to the main crop may indicate a role of these fruits on staminate flowers’ production for pollination of the main crop, as profichi act in the caprifig. Within the same species (Ficus carica L.) and for sexual determination, Ikegami et al. analyzed the FcRAN1 gene (during a breeding program for the selection of female plants) strongly associated with the sex phenotype. A male-biased segregation ratio distortion was obtained in 12 F1 populations, suggesting some genetic factor(s) affecting it. A comparison between the annotated genes and the genes required for normal embryo or gametophyte development and function identified several candidate genes responsible for the segregation distortion in fig. Following the same topic, Wang et al. hypothesized an early sex-identification method to improve breeding efficiency. The use of a deletion as a forward primer, a newly established AG-Marker, was as accurate as the RAN1-Marker, and provided the identification of male plants, giving new clues to understanding Ficus sex determination. Moving toward another attracting species, i.e., pomegranate (Punica granatum L.), Trainin et al. investigated the black peel color of some pomegranate varieties. Biochemical analysis revealed that delphinidin is highly abundant in the peel of black varieties and the pattern of anthocyanin accumulation is different from that of other pomegranates with red or pink colors of the peel. Genetic analysis of an F2 population segregating for the black phenotype revealed that it is determined by a single recessive gene. Pomegranate was also studied by Goudappa Patil et al. with regards to the SSR of “Tunisia” pomegranate variety. There was a positive trend in chromosome length and the SSR abundance, as marker density, enhanced with a shorter chromosome length. Examination of the distribution of SSR motif types within a chromosome suggested the abundance of hexanucleotide repeats in each chromosome followed by dinucleotides. A comprehensive set of highly polymorphic genome-wide SSRs was successively developed and tested. These chromosome-specific SSRs could serve as a powerful genomic tool to leverage future genetic studies, germplasm management, and genomics-assisted breeding in pomegranate varieties. Some evolutionary aspects of pear were investigated by Kumar et al. who put a light on runs of homozygosity (ROH) in self-incompatible plants, in particular Asian pears, European pears, and interspecific hybrids using genotyping-by-sequencing. The observed ROH patterns suggested that systematic breeding of European pears would have started earlier than Asian pears. Fruit trait variation in Persian walnut (Juglans regia L.) was addressed by Bernard et al. who conducted a genome-wide association study (GWAS) using multi-locus models in a panel of 170 accessions of J. regia to elucidate the genetic determinants of fruit quality traits in walnut toward the breeding of new varieties. The authors proposed several candidate genes involved in nut characteristics, such as a gene coding for a beta-galactosidase linked to several size-related traits and known to also be involved in fruit development in other species. With regards of fruit traits, Kyratzis et al. investigated the germplasm of an ancient species, the carob (Ceratonia siliqua L.), on the island of Cyprus. The domestic germplasm varies both in terms of pod morphology and composition, reflecting the genetic and physiological characteristics of both grafted and non-grafted accessions, and possibly the impact of agro-environmental conditions. Morphological traits, such as seeds-to-pod weight ratio, pod width, and thickness, were principally under genetic control. Contrarily, chemical compounds, particularly total phenolic content, including condensed tannins, in vitro antioxidant capacity, and to a lesser extent gallic acid, organic acids, sugars (glucose and fructose), and minerals were more under agro-environmental control. In the Southern Hemisphere, Quezada et al. worked on feijoa (Acca sellowiana Berg.), a fruit tree species native to Uruguay and Brazil. A high-density composite genetic linkage map of feijoa was constructed using two genetically populations. Genotyping by sequencing (GBS) approach was successfully applied for developing single nucleotide polymorphism (SNP) markers. They used both the reference genome of the closely related species Eucalyptus grandis and a de novo pipeline to construct a composite map. A novel approach for the construction of composite maps where the meiosis information of individuals of two connected populations is captured in a single estimator is described. The topic of resistance was carried out by Alves et al. in order to find sources of genetic resistance to Huanglongbing (HLB)-associated “Candidatus Liberibacter asiaticus” (Las), one of the most destructive diseases of citrus. Some genotypes from subtribe Citrinae, sexually incompatible but graft-compatible with Citrus, may provide new rootstocks able to restrict bacterial titer in the canopy. Authors tested for Las resistance a wide collection of graft-compatible Citrinae species using an aggressive and consistent challenge-inoculation and evaluation procedure. Eremocitrus glauca and Papua/New Guinea Microcitrus species as well as their hybrids resulted in full resistance, opening the way for using these underutilized genotypes as Las resistance sources in breeding programs

Allelic variation of gliadin-encoding genes in a collection of tetraploid wheat genotypes

Wheat is one of the main crops bred worldwide. Durum wheat, specifcally, is a key element of the Mediterranean diet, representing an élite crop grown in Italy. Durum wheat nutritional and technological values are largely due to the grain protein content (GPC), a complex genetic trait strongly afected by environmental factors and management practices. In the last decades, several breeding programs have been focused on improving GPC by both traditional and innovative approaches. Among seed storage proteins, prolamins, including both gliadins and glutenins, represent the major component. These two classes of proteins are indeed responsible of gluten formation and confer the extensibility and elasticity to the dough. Besides being of crucial importance for both technological properties and rheological characteristics, prolamins, and especially gliadins, have been found to be major triggers for human health, as involved in a number of wheat consumption-related conditions, such as the celiac disease, non-celiac gluten sensitivity, defned as the onset of a variety of manifestations related to wheat, rye and barley ingestion, and wheat allergies, both due to wheat ingestion or inhalation (of four or pollen). The identifcation of loci responsible for the gliadin expression, and particularly of polymorphism in the aforementioned genes, which could result in a lower immunogenic/toxic potential, could be of great importance in breeding programs. For this purpose, we screened a collection of tetraploid wheat genotypes for allelic variants of annotated gliadin genes in the durum wheat genome, in order to identify genetic resources available to breeders to improve wheat nutritional and technological properties. Phylogenetic analysis among diferent species of Triticum genus and an in silico expression data analysis may also be useful in the exploitation of the complex scenario of gliadin–glutenin interaction and gluten role in the adverse reactions due to wheat consumption

Genetic diversity and genome wide association study of β-glucan content in tetraploid wheat grains

Non-starch polysaccharides (NSPs) have many health benefits, including immunomodulatory activity, lowering serum cholesterol, a faecal bulking effect, enhanced absorption of certain minerals, prebiotic effects and the amelioration of type II diabetes. The principal components of the NSP in cereal grains are (1,3;1,4)-β-glucans and arabinoxylans. Although (1,3;1,4)-β-glucan (hereafter called β-glucan) is not the most representative component of wheat cell walls, it is one of the most important types of soluble fibre in terms of its proven beneficial effects on human health. In the present work we explored the genetic variability of β-glucan content in grains from a tetraploid wheat collection that had been genotyped with a 90k-iSelect array, and combined this data to carry out an association analysis. The β-glucan content, expressed as a percentage w/w of grain dry weight, ranged from 0.18% to 0.89% across the collection. Our analysis identified seven genomic regions associated with β-glucan, located on chromosomes 1A, 2A (two), 2B, 5B and 7A (two), confirming the quantitative nature of this trait. Analysis of marker trait associations (MTAs) in syntenic regions of several grass species revealed putative candidate genes that might influence β-glucan levels in the endosperm, possibly via their participation in carbon partitioning. These include the glycosyl hydrolases endo-β-(1,4)-glucanase (cellulase), β-amylase, (1,4)-β-xylan endohydrolase, xylanase inhibitor protein I, isoamylase and the glycosyl transferase starch synthase II

Identification and characterization of the sucrose synthase 2 gene (Sus2) in durum wheat

Sucrose transport is the central system for the allocation of carbon resources in vascular plants. Sucrose synthase (SUS), which reversibly catalyzes sucrose synthesis and cleavage, represents a key enzyme in the control of the flow of carbon into starch biosynthesis. In the present study the genomic identification and characterization of the Sus2-2A and Sus2-2B genes coding for SUS in durum wheat (cultivars Ciccio and Svevo) is reported. The genes were analyzed for their expression in different tissues and at different seed maturation stages, in four tetraploid wheat genotypes (Svevo, Ciccio, Primadur, and 5-BIL42). The activity of the encoded proteins was evaluated by specific activity assays on endosperm extracts and their structure established by modeling approaches. The combined results of sucrose synthase 2 expression and activity levels were then considered in the light of their possible involvement in starch yield