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Meiotic chromosome pairing in F1 plants of LDN-Su1-Ph1 × Chinese Spring (2n = 35). (A–C) Pentaploid plants negative for Xpsr1205-3S. (D–F) Pentaploid plants positive for Xpsr1205-3S. Each PMC is from a different plant.
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Meiotic pairing between homoeologous chromosomes in polyploid wheat is inhibited by the Ph1 locus on the long arm of chromosome 5 in the B genome. Aegilops speltoides (genomes SS), the closest relative of the progenitor of the wheat B genome, is polymorphic for genetic suppression of Ph1. Using this polymorphism, two major suppressor loci, Su1-Ph1...
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Prompted by recent changes in climate trends, cropping areas, and management practices, Fusarium head blight (FHB), a threatening disease of cereals worldwide, is also spreading in unusual environments, where bread wheat (BW) and durum wheat (DW) are largely cultivated. The scarcity of efficient resistance sources within adapted germplasm is partic...
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... In addition, two unlinked genes that inhibit Ph function, designated PhI and Su1-Ph1, were identified from Ae. specltoides and transferred to wheat. These two genes inhibit the activity of the Ph1 gene in wheat, further promoting meiotic homoeologous recombination for alien introgressions [115][116][117][118]. ...
... Numerous genes for many favorable traits have been incorporated into the wheat genome from wild species, including wild species under the genera of Aegilops, Thinopyrum (Agropyron), Haynaldia (Dasypyrum), and Leymus, by inducing meiotic homoeologous recombination using the ph1b mutant and the Ae. speltoides-derived Ph1 suppressor gene Su1-Ph1 [3,6,7,10,11,32,41,42,63,118,[146][147][148][149][150][151]. The alien chromosome segments integrated into the wheat genome via homoeologous recombination generally inherit as a single, stable locus because they usually do not recombine with their homoeologous counterparts of wheat in the presence of the Ph1 gene [111][112][113][114]. ...
Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome’s polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era.
... Regulation of HeR is a key component to ensure the success of distant hybridization that influences the genetic structure of next generations. It may be restricted or promoted by either a single gene in wheat Copete-parada et al. 2021), Aegilops speltoides (Li et al. 2017), Aegilops geniculata (Koo et al. 2020), corn (Zhao et al. 2021) or major QTL in Brassica (Higgins 2021) and multilocus interactions in polyploid cotton (Jiang et al. 2000). However, induction of homoeologous recombinations between chromosomes of related subgenomes to transfer traits of interest into crop species should be followed by urgent reactivation of homoeologous recombinations repressing genes, such as Ph1 in wheat, to prevent rapid removal of target DNA segment(s) resulting in diploid-like behavior of chromosomes during meiosis. ...
... Mg 2+ along with the application of anti-COs mutant or suppressor genes such as phb1 (Rey et al. 2015), phKL (Hao et al. 2011), Su1-Ph1 and Su2-Ph1 (H. Li et al. 2017). Virus Induced Gene Silencing and newly developed genome editing techniques such as CRISPR/Cas9 gene inactivation, Zinc-Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and Targeting Induced Local Lesions IN Genomes (TILLING) approaches are promising approaches providing opportunities for efficient manipulation of meiotic recombination. ...
Gene introgression that involves the transfer of favorable allelic diversity for broadening the genetic base of breeding materials is a powerful 'toolkit' for creating novel allelic combinations during plant sexual reproduction. It is a key factor playing an important role in plant breeding schemes by reintroducing genetic variation at selective sweeps or introgression of desirable traits required for the development of new varieties. Meiosis is a specialized cell division not only enables sexually reproducing organisms to reduce their genomic constituent by half, also provides indefinitely novel combinations of allelic diversity by reshuffling the parental genetic makeup. Crossing over that takes place during prophase-I facilitates the meiotically exchange of genetic materials between homolog pairs as well as their accurate segregations. It is tightly modulated and many intrinsic factors and extrinsic agents are associated with regulation of the process, however, the modulation of meiosis is possible. Although, advanced approaches such as CRIPR/Cas and Virus-Induced gene Silencing (VIGS) have opened new horizons for manipulation of meiotic recombination, distant hybridization could effectively influence the frequency and distribution of homologous (HR) and particularly homoeologous recombination (HeR). In this review, we provide a brief overview of the recent advances in the plant mechanisms for manipulation of HR and HeR employing distant hybridization.
... Filtered reads were mapped to RefSeq v1.0 using minimap2 (Li, 2018) with parameters -axe map-ont and --secondary = no. Mapped reads around the breakpoint (chr4D:51283000-51 595 000) were extracted using samtools (Li et al., 2009), including clipped portions of mapped reads, and assembled using wtdbg2 (Ruan and Li, 2020). The resulting contigs were mapped to RefSeq v1.0 using minimap2 (Li, 2018) with parameters -axe map-ont and visualized in IGV (Robinson et al., 2011) along with the mapped Illumina paired-end short reads from the parent lines and DH65. ...
Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat’s wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterise introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilisation of introgression pre‐breeding material in wheat breeding programmes.
... Ae. speltoides was considered to be the most suppressant because it can promote more meiotic pairing even in presence of the Ph1 gene (Dover and Riley 1977). Ae. speltoides (2n = 2x = 14, genome SS) are more likely the diploid donor of the B genome, therefore, expected to most suppressor of Ph1, due to the presence of the two major suppressor loci, Su1-Ph1 (long arm of chromosome 3S) and Su2-Ph1 (long arm of chromosome 7S) (Dvorak et al. 2006;Li et al. 2017). The hybrids are then backcrossed with wheat to obtain direct genetic transmission from Ae. speltoides to wheat. ...
Among the cereal crops, wheat is an important food crop and acts as the staple food for more than half of the world's population. The genetic bottleneck of domestication and modernization has narrowed down the genetic base for different economically important traits in wheat. The involvement of wild species in the wheat hybridization program faced the difficulties of pre- and post-fertilization barriers and the presence of Ph1 locus. The distant crosses provide useful variation which is beneficial for wheat improvement programs. The wild relative species of wheat harbor several important genes for nutritional traits such as gluten protein, micronutrients (grain Fe and Zn), vitamins, and other minerals and play a significant role in end-use quality. The gluten strength relies upon the glutenin protein. The glutenin consists of two types, i.e., high molecular weight glutenins (HMW-GS) and low molecular weight glutenins (LMW-GS) which help in improving wheat processing quality. In wheat, gene transfer occurs as a consequence of direct cross, breeding protocols, and genetic recombination assisted by special manipulation techniques. Alien introgression from wild relatives is an important source of new allelic variation for the genetic enhancement of nutritional quality. The wild relative species such as Aegilops spp., T. boeoticum, and T. dicoccoides have been used in hybridization, and genes related to protein, and micronutrients have been transferred in the cultivated varieties. Through this review, an attempt has been made to compile comprehensive information on the potential of wild species for the improvement of nutritional and end-use quality traits through alien introgression.
... On the contrary, if the level of pairing of the Aegilops accession is super-high, the Ph1 locus is strongly inactivated and even some hexavalents were observed in hybrid plants (Fernandez-Calvin and Orellana, 1992). The most studied loci are Su-Ph1, derived from Ae. speltoides (Dvorak et al., 2006;Li et al., 2017), and chromosome 5Mg of Ae. geniculata Roth (Koo et al., 2017(Koo et al., , 2020; neither of these have been cloned. There are two different loci for Su-Ph1, which map to Ae. speltoides chromosome arms 3SL (Su1-Ph1) and 7SL (Su2-Ph1) (Dvorak et al., 2006). ...
In the recent years, the agricultural world has been progressing towards integrated crop protection, in the context of sustainable and reasoned agriculture to improve food security and quality, and to preserve the environment through reduced uses of water, pesticides, fungicides or fertilizers. For this purpose, one possible issue is to cross elite varieties widely used in fields for crop productions with exotic or wild genetic resources in order to introduce new diversity for genes or alleles of agronomical interest to accelerate the development of new improved‐cultivars. However, crossing ability (or crossability) often depends on genetic background of the recipient varieties or of the donor, which hampers a larger use of wild resources in breeding programmes of many crops. In this review we tried to provide a comprehensive summary of genetic factors controlling crossing ability between Triticeae species with a special focus on the crossability between wheat (Triticum aestivum L.) and rye (Secale cereale), which lead to the creation of Triticale (xTriticosecale Wittm.). We also discussed potential applications of newly identified genes or markers associated with crossability for accelerating wheat and Triticale improvement by application of modern genomics technologies in breeding programmes.
... Recently, for some crops, new introgression lines have been created between commercial varieties and wild relatives. For improving resistance to abiotic stress, genes from Elytrigia elongata and Aegilops speltoides were introgressed into wheat (Li et al., 2017). ...
... U, M, C genomes compared to the A, B, and D genomes present in modern day wheat). Once an alien segment is introgressed into hexaploid wheat, it does not recombine due to the presence of the Ph1 locus [6][7][8]. ...
Stripe rust and leaf rust are among the most devastating diseases of wheat, limiting its production globally. Wheat wild relatives harbour genetic diversity for new genes and alleles for all major wheat diseases. However, the use of this genetic variation from wild progenitor and non-progenitor species has been limited in the breeding programs. Reasons include limited recombination of donor and recipient genomes and the lack of tertiary gene pool markers. Here, we describe the development of a SNP based marker from the flow-sorted and sequenced Aegilops umbellulata chromosome 5U which can be used for marker assisted selection of four pair of alien leaf rust and stripe rust resistance genes. Lr57-Yr40_CAPS16 marker was reported earlier to be linked with alien leaf and stripe rust resistance genes introgressed on wheat chromosome 5DS. Due to its dominant nature and laborious to work with, a new SNP-based KASP marker, XTa5DS-2754099_kasp23, was developed from the same CAPS marker contig. XTa5DS-2754099_kasp23 was tested in Aegilops umbellulata, Ae. geniculata, Ae. peregrina and Ae. caudata derived alien introgression lines, which harbour four pairs of linked leaf and stripe rust genes; Lr76-Yr70, Lr57-Yr40, LrP- YrP, LrAc-YrAc, respectively. This KASP marker was found to be effective for the selection of the aforesaid four pairs of leaf rust and stripe rust resistance genes. Further, we tested and validated XTa5DS-2754099_kasp23 on commercial varieties and advanced breeding lines from four countries (India, Egypt, Australia and UK) including hexaploid and durum wheat. Our results provide evidence that KASP marker, XTa5DS-2754099_kasp23 can be used in marker-assisted selection of the four pairs of rust resistance alien genes in wheat breeding programmes.
... For the wheat × Ae. speltoides hybrid, Dvorak et al. (2006b) identified two suppressors on chromosomes 3S (Su1-Ph1) and 7S (Su2-Ph1) that affected homoeologous chromosome associations, varying from 7.0 to 16.4 chiasmata per cell. The Su1-Ph1 was introgressed into both hexaploid and tetraploid wheat, opening new possibilities in inducing homoeologous chromosome recombinations for introgression into wheat (Li et al., 2017). This phenomenon can also be observed in lines where only a single chromosome was introgressed into the wheat background. ...
Polyploids are species in which three or more sets of chromosomes coexist. Polyploidy frequently occurs in plants and plays a major role in their evolution. Based on their origin, polyploid species can be divided into two groups: autopolyploids and allopolyploids. The autopolyploids arise by multiplication of the chromosome sets from a single species, whereas allopolyploids emerge from the hybridization between distinct species followed or preceded by whole genome duplication, leading to the combination of divergent genomes. Having a polyploid constitution offers some fitness advantages, which could become evolutionarily successful. Nevertheless, polyploid species must develop mechanism(s) that control proper segregation of genetic material during meiosis, and hence, genome stability. Otherwise, the coexistence of more than two copies of the same or similar chromosome sets may lead to multivalent formation during the first meiotic division and subsequent production of aneuploid gametes. In this review, we aim to discuss the pathways leading to the formation of polyploids, the occurrence of polyploidy in the grass family (Poaceae), and mechanisms controlling chromosome associations during meiosis, with special emphasis on wheat.
... At present, the genome databases of wheat, barley, and other cereal crops are gradually improving with the rapid development and cost reduction of sequencing technology [38][39][40][41][42], which provides great convenience for the study of wild wheat species without genomic information. The ph1b gene can induce pairing and exchange between alien chromosomes and their homoeologous chromosomes in wheat backgrounds [43,44]. The paired homoeologous chromosomes need to have high collinearity, and structural variation of chromosomes including the inversion of fragments may influence the chromosomes pairing and exchanging. ...
Normal pairing and exchanging is an important basis to evaluate the genetic relationship between homologous chromosomes in a wheat background. The pairing behavior between 6V#2 and 6V#4, two chromosomes from different Dasypyrum villosum accessions, is still not clear. In this study, two wheat alien substitution lines, 6V#2 (6A) and 6V#4 (6D), were crossed to obtain the F1 hybrids and F2 segregating populations, and the testcross populations were obtained by using the F1 as a parent crossed with wheat variety Wan7107. The chromosomal behavior at meiosis in pollen mother cells (PMCs) of the F1 hybrids was observed using a genomic in situ hybridization (GISH) technique. Exchange events of two alien chromosomes were investigated in the F2 populations using nine polymerase chain reaction (PCR) markers located on the 6V short arm. The results showed that the two alien chromosomes could pair with each other to form ring- or rod-shaped bivalent chromosomes in 79.76% of the total PMCs, and most were pulled to two poles evenly at anaphase I. Investigation of the F2 populations showed that the segregation ratios of seven markers were consistent with the theoretical values 3:1 or 1:2:1, and recombinants among markers were detected. A genetic linkage map of nine PCR markers for 6VS was accordingly constructed based on the exchange frequencies and compared with the physical maps of wheat and barley based on homologous sequences of the markers, which showed that conservation of sequence order compared to 6V was 6H and 6B > 6A > 6D. In the testcross populations with 482 plants, seven showed susceptibility to powdery mildew (PM) and lacked amplification of alien chromosomal bands. Six other plants had amplification of specific bands of both the alien chromosomes at multiple sites, which suggested that the alien chromosomes had abnormal separation behavior in about 1.5% of the PMCs in F1, which resulted in some gametes containing two alien chromosomes. In addition, three new types of chromosome substitution were developed. This study lays a foundation for alien allelism tests and further assessment of the genetic relationship among 6V#2, 6V#4, and their wheat homoeologous chromosomes.
... The resulting nullisomic gametes produce monosomic progeny. We did not observe monosomic plants either here or previously (Dvorak and Gorham 1992;Li et al. 2017), which indicates that nullisomic gametes function poorly in durum wheat. A chiasma, a cytological equivalent of a crossover, between homoeologous chromosomes leads to their regular disjunction and the production of euploid gametes. ...
Key message
Su1-Ph1, which we previously introgressed into wheat from Aegilops speltoides, is a potent suppressor of Ph1 and a valuable tool for gene introgression in tetraploid wheat.
Abstract
We previously introgressed Su1-Ph1, a suppressor of the wheat Ph1 gene, from Aegilops speltoides into durum wheat cv Langdon (LDN). Here, we evaluated the utility of the introgressed suppressor for inducing introgression of alien germplasm into durum wheat. We built LDN plants heterozygous for Su1-Ph1 that simultaneously contained a single LDN chromosome 5B and a single Ae. searsii chromosome 5Sse, which targeted them for recombination. We genotyped 28 BC1F1 and 84 F2 progeny with the wheat 90-K Illumina single-nucleotide polymorphism assay and detected extensive recombination between the two chromosomes, which we confirmed by non-denaturing fluorescence in situ hybridization (ND-FISH). We constructed BC1F1 and F2 genetic maps that were 65.31 and 63.71 cM long, respectively. Recombination rates between the 5B and 5Sse chromosomes were double the expected rate computed from their meiotic pairing, which we attributed to selection against aneuploid gametes. Recombination rate between 5B and 5Sse was depressed compared to that between 5B chromosomes in the proximal region of the long arm. We integrated ND-FISH signals into the genetic map and constructed a physical map, which we used to map a 172,188,453-bp Ph1 region. Despite the location of the region in a low-recombination region of the 5B chromosome, we detected three crossovers in it. Our data show that Su1-Ph1 is a valuable tool for gene introgression and gene mapping based on recombination between homoeologous chromosomes in wheat.
