Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross

Paternally imprinted LATE-FLOWERING2 transcription factor contributes to paternal-excess interploidy hybridization barriers in wheat

Interploidy hybridization between hexaploid and tetraploid genotypes occurred repeatedly during genomic introgression events throughout wheat evolution, and is commonly employed in wheat breeding programs. Hexaploid wheat usually serves as maternal parent because the reciprocal cross generates progeny with severe defects and poor seed germination, but the underlying mechanism is poorly understood. Here, we performed detailed analysis of phenotypic variation in endosperm between two interploidy reciprocal crosses arising from tetraploid (Triticum durum, AABB) and hexaploid wheat (Triticum aestivum, AABBDD). In the paternal- versus the maternal-excess cross, the timing of endosperm cellularization was delayed and starch granule accumulation in the endosperm was repressed, causing reduced germination percentage. The expression profiles of genes involved in nutrient metabolism differed strongly between these endosperm types. Furthermore, expression patterns of parental alleles were dramatically disturbed in interploidy versus intraploidy crosses, leading to increased number of imprinted genes. The endosperm-specific TaLFL2 showed a paternally imprinted expression pattern in interploidy crosses partially due to allele-specific DNA methylation. Paternal TaLFL2 binds to and represses a nutrient accumulation regulator TaNAC019, leading to reduced storage protein and starch accumulation during endosperm development in paternal-excess cross, as confirmed by interploidy crosses between tetraploid wild-type and clustered regularly interspaced palindromic repeats (CRISPR) - CRISPR-associated protein 9 generated hexaploid mutants. These findings reveal a contribution of genomic imprinting to paternal-excess interploidy hybridization barriers during wheat evolution history and explains why experienced breeders preferentially exploit maternal-excess interploidy crosses in wheat breeding programs.

Asymmetric gene expression in grain development of reciprocal crosses between tetraploid and hexaploid wheats

Production of viable progeny from interploid crosses requires precise regulation of gene expression from maternal and paternal chromosomes, yet the transcripts contributed to hybrid seeds from polyploid parent species have rarely been explored. To investigate the genome-wide maternal and paternal contributions to polyploid grain development, we analyzed the transcriptomes of developing embryos, from zygote to maturity, alongside endosperm in two stages of development, using reciprocal crosses between tetraploid and hexaploid wheats. Reciprocal crosses between species with varied levels of ploidy displayed broad impacts on gene expression, including shifts in alternative splicing events in select crosses, as illustrated by active splicing events, enhanced protein synthesis and chromatin remodeling. Homoeologous gene expression was repressed on the univalent D genome in pentaploids, but this suppression was attenuated in crosses with a higher ploidy maternal parent. Imprinted genes were identified in endosperm and early embryo tissues, supporting predominant maternal effects on early embryogenesis. By systematically investigating the complex transcriptional networks in reciprocal-cross hybrids, this study presents a framework for understanding the genomic incompatibility and transcriptome shock that results from interspecific hybridization and uncovers the transcriptional impacts on hybrid seeds created from agriculturally-relevant polyploid species.

Marker-assisted transfer of leaf and stripe rust resistance from Triticum turgidum var. durum cv. Trinakria to wheat variety HD2932

A marker-assisted backcrossing program initiated to transfer leaf rust resistance gene LrTrk from Triticum turgidum cv. Trinakria to hexaploid wheat variety HD2932 cotransferred a stripe rust resistance gene, YrTrk, along with LrTrk. The cross of hexaploid recurrent parent HD2932 with tetraploid donor parent Trinakria produced pentaploid F₁ plants. F₁s were backcrossed with recurrent parent HD2932 to produce BC₁F₁ generation. Foreground and background selection was conducted in each backcross generation to identify plants for backcrossing or selfing. While foreground selection for LrTrk was carried out with linked and validated molecular marker Xgwm234, for background selection, 86 polymorphic SSR markers from the A and B genomes were used. Single selected plants from BC₁F₁ and BC₂F₁ generations backcrossed and selfed to produce BC₂F₁and BC₂F₂ generations, respectively. Background selection resulted in 83.72%, 91.86%, and 98.25% of RPG recovery in BC₁F₁, BC₂F₁, and BC₂F₂ generations, respectively. A total of 27 plants with LrTrk in homozygous state were identified in BC₂F₂ generation and selfed to produce 27 BC₂F₃ NILs. All the NILs were tested for leaf and stripe rust resistance at the seedling stage using seven Puccinia triticina and one Puccinia striiformis f.sp. tritici rust pathotypes. All the 27 NILs were found to be resistant to both leaf and stripe rust pathotypes. So, these NILs are designated to carry leaf and stripe rust resistance genes LrTrk/YrTrk.

Allelic response of yield component traits to resource availability in spring wheat

Investigation of resource availability on allele effects for four yield component quantitative trait loci provides guidance for the improvement of grain yield in high and low yielding environments. A greater understanding of grain yield (GY) and yield component traits in spring wheat may increase selection efficiency for improved GY in high and low yielding environments. The objective of this study was to determine allelic response of four yield component quantitative trait loci (QTL) to variable resource levels which were manipulated by varying intraspecific plant competition and seeding density. The four QTL investigated in this study had been previously identified as impacting specific yield components. They included QTn.mst-6B for productive tiller number (PTN), WAPO-A1 for spikelet number per spike (SNS), and QGw.mst-3B and TaGW2-A1 for kernel weight (KWT). Near-isogenic lines for each of the four QTL were grown in multiple locations with three competition (border, no-border and space-planted) and two seeding densities (normal 216 seeds m^-2 and low 76 seeds m^-2). Allele response at QTn.mst-6B was driven by changes in resource availability, whereas allele response at WAPO-A1 and TaGW2-A1 was relatively unaffected by resource availability. The QTn.mst-6B.1 allele at QTn.mst-6B conferred PTN plasticity resulting in significant GY increases in high resource environments. The gw2-A1 allele at TaGW2-A1 significantly increased KWT, SNS and GPC offering a source of GY improvement without negatively impacting end-use quality. QGw.mst-3B allelic variation did not significantly impact KWT but did significantly impact SPS. Treatment effects in both experiments often resulted in significant positive impacts on GY and yield component traits when resource availability was increased. Results provide guidance for leveraging yield component QTL to improve GY performance in high- and low-yield environments.

Additive Genetic Behavior of Stem Solidness in Wheat (Triticum aestivum L.)

Stem solidness in wheat is an important architectural trait to support the erect behavior of the plant. The varieties with high yield potential due to increased sink strength tend to lodge either because of poor anchorage or weak stem. The solid stem can partially counter the tradeoff between biomass driven yield gain irrespective of the plant height. Stem solidness being a complex trait with highly variable expressivity, understanding its genetic behavior in different genetic backgrounds is highly essential to integrate this trait in the breeding program. In this study, the expressivity of a solid stem in different internodes was investigated in nine F₂ populations selected from 34 F₁s (solid stem × hollow stem and hollow stem × hollow stem). The progeny of solid stem type F₁ plants from hollow stem parents indicated the complementation of favorable alleles dispersed among the parents. Non-confirmation to digenic complementary (9:7) model of inheritance and polynomial distribution of the trait in all F₂ populations indicates multiple factors complementation in the additive fashion for stem solidness.

The Use of Pentaploid Crosses for the Introgression of Amblyopyrum muticum and D-Genome Chromosome Segments Into Durum Wheat

The wild relatives of wheat provide an important source of genetic variation for wheat improvement. Much of the work in the past aimed at transferring genetic variation from wild relatives into wheat has relied on the exploitation of the ph1b mutant, located on the long arm of chromosome 5B. This mutation allows homologous recombination to occur between chromosomes from related but different genomes, e.g. between the chromosomes of wheat and related chromosomes from a wild relative resulting in the generation of interspecific recombinant chromosomes. However, the ph1b mutant also enables recombination to occur between the homologous genomes of wheat, e.g. A/B, A/D, B/D, resulting in the generation of wheat intergenomic recombinant chromosomes. In this work we report on the presence of wheat intergenomic recombinants in the genomic background of hexaploid wheat/Amblyopyrum muticum introgression lines. The transfer of genomic rearrangements involving the D-genome through pentaploid crosses provides a strategy by which the D-genome of wheat can be introgressed into durum wheat. Hence, a pentaploid crossing strategy was used to transfer D-genome segments, introgressed with either the A- and/or the B-genome, into the tetraploid background of two durum wheat genotypes Karim and Om Rabi 5 in either the presence or absence of different Am. muticum (2n = 2x = 14, TT) introgressions. Introgressions were monitored in backcross generations to the durum wheat parents via multi-color genomic in situ hybridization (mc-GISH). Tetraploid lines carrying homozygous D-genome introgressions, as well as simultaneous homozygous D- and T-genome introgressions, were developed. Introgression lines were characterized via Kompetitive Allele-Specific PCR (KASP) markers and multi-color fluorescence in situ hybridization (FISH). Results showed that new wheat sub-genomic translocations were generated at each generation in progeny that carried any Am. muticum chromosome introgression irrespective of the linkage group that the segment was derived from. The highest frequencies of homologous recombination were observed between the A- and the D-genomes. Results indicated that the genotype Karim had a higher tolerance to genomic rearrangements and T-genome introgressions compared to Om Rabi 5. This indicates the importance of the selection of the parental genotype when attempting to transfer/develop introgressions into durum wheat from pentaploid crosses.

Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping

A high-resolution genetic map combined with haplotype analyses identified a wheat ortholog of rice gene APO1 as the best candidate gene for a 7AL locus affecting spikelet number per spike. A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. In this study, we identified a promising candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large heterogeneous inbred families ( > 10,000 plants) from two crosses to map the 7AL QTL to an 87-kb region (674,019,191-674,106,327 bp, RefSeq v1.0) containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high-SNS allele in both H1 × H2 and H2 × H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~ 1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A02G481600 showed a non-synonymous polymorphism that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 (WAPO1), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region.

A Novel QTL in Durum Wheat for Resistance to the Wheat Stem Sawfly Associated with Early Expression of Stem Solidness

The wheat stem sawfly (WSS) (Cephus cinctus Norton) is a major yield-reducing pest of wheat (Triticum aestivum L.). Varieties with pith-filled, or solid, stems provide a measure of resistance by inhibiting larval survival inside the stem. Durum wheat (Triticum turgidum L.) has resistance to the wheat stem sawfly even in the absence of known genes for stem solidness. To determine the genetic basis of resistance in durum wheat, a susceptible durum wheat, PI 41353, was identified from among 1,211 landrace accessions from around the world screened in WSS-infested sites. A recombinant inbred line (RIL) population of 105 individuals was developed from a cross of PI 41353 with a typically resistant variety, Pierce. The RIL were screened in a total of three WSS-infested locations in Montana over a two year period. A genetic map was constructed with 2,867 SNP-based markers. A quantitative trait locus (QTL) analysis identified six QTL associated with resistance. An allele from resistant cultivar Pierce at a QTL on chromosome 3A, Qss.msub-3AL, caused a 25% reduction in stem cutting. Assessment of near-isogenic lines that varied for alleles at Qss.msub-3AL showed that the Pierce allele was also associated with higher stem solidness as measured early in stem development, which is a critical stage for WSS oviposition and larval development. Stem solidness of Pierce and other resistant durum wheat lines largely disappeared later in plant development. Results suggest a genetic mechanism for WSS resistance observed in durum wheat, and provide an additional source of WSS resistance for hexaploid bread wheat.

Genotype Imputation in Winter Wheat Using First-Generation Haplotype Map SNPs Improves Genome-Wide Association Mapping and Genomic Prediction of Traits

Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. With the vast amount of SNP variation data accumulated for wheat in recent years, the presented imputation framework will greatly improve prediction accuracy in breeding populations and increase resolution of trait mapping hence, facilitate cross-referencing of genotype datasets available across different wheat populations.

The Capacity to Buffer and Sustain Imbalanced D-Subgenome Chromosomes by the BBAA Component of Hexaploid Wheat Is an Evolved Dominant Trait

Successful generation of pentaploid wheat (genome, BBAAD) via interspecific hybridization between tetraploid wheat (BBAA) and hexaploid wheat (BBAADD) holds great promise to mutually exchange desirable traits between the two cultivated wheat species, as well as providing a novel facet for evolutionary studies of polyploid wheat. Taking advantage of the viable and fertile nature of an extracted tetraploid wheat (ETW) with a BBAA genome that is virtually identical with the BBAA component of a hexaploid common wheat, and a synthetic hexaploid wheat, we constructed four pentaploid wheats with several distinct yet complementary features, of which harboring homozygous BBAA subgenomes is a common feature. By using a combined FISH/GISH method that enables diagnosing all individual wheat chromosomes, we precisely karyotyped a larger number of cohorts from the immediate progenies of each of the four pentaploid wheats. We found that the BBAA component of hexaploid common wheat possesses a significantly stronger capacity to buffer and sustain imbalanced D genome chromosomes and appears to harbor more structural chromosome variations than the BBAA genome of tetraploid wheat. We also document that this stronger capacity of the hexaploid BBAA subgenomes behaves as a genetically controlled dominant trait. Our findings bear implications to the known greater than expected level of genetic diversity in, and the remarkable adaptability of, hexaploid common wheat as a staple crop of global significance, as well as in using pentaploidy as intermediates for reciprocal introgression of useful traits between tetraploid and hexaploid wheat cultivars.

Discovery of a Novel Stem Rust Resistance Allele in Durum Wheat that Exhibits Differential Reactions to Ug99 Isolates

Wheat stem rust, caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn, can incur yield losses in susceptible cultivars of durum wheat, Triticum turgidum ssp. durum (Desf.) Husnot. Although several durum cultivars possess the stem rust resistance gene Sr13, additional genes in durum wheat effective against emerging virulent races have not been described. Durum line 8155-B1 confers resistance against the P. graminis f. sp. tritici race TTKST, the variant race of the Ug99 race group with additional virulence to wheat stem rust resistance gene Sr24 However, 8155-B1 does not confer resistance to the first-described race in the Ug99 race group: TTKSK. We mapped a single gene conferring resistance in 8155-B1 against race TTKST, Sr8155B1, to chromosome arm 6AS by utilizing Rusty/8155-B1 and Rusty*2/8155-B1 populations and the 90K Infinium iSelect Custom bead chip supplemented by KASP assays. One marker, KASP_6AS_IWB10558, cosegregated with Sr8155B1 in both populations and correctly predicted Sr8155B1 presence or absence in 11 durum cultivars tested. We confirmed the presence of Sr8155B1 in cultivar Mountrail by mapping in the population Choteau/Mountrail. The marker developed in this study could be used to predict the presence of resistance to race TTKST in uncharacterized durum breeding lines, and also to combine Sr8155B1 with resistance genes effective to Ug99 such as Sr13 The map location of Sr8155B1 cannot rule out the possibility that this gene is an allele at the Sr8 locus. However, race specificity indicates that Sr8155B1 is different from the known alleles Sr8a and Sr8b.

Pentaploid Wheat Hybrids: Applications, Characterisation, and Challenges

Interspecific hybridisation between hexaploid and tetraploid wheat species leads to the development of F1 pentaploid hybrids with unique chromosomal constitutions. Pentaploid hybrids derived from bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum spp. durum Desf.) crosses can improve the genetic background of either parent by transferring traits of interest. The genetic variability derived from bread and durum wheat and transferred into pentaploid hybrids has the potential to improve disease resistance, abiotic tolerance, and grain quality, and to enhance agronomic characters. Nonetheless, pentaploid wheat hybrids have not been fully exploited in breeding programs aimed at improving crops. There are several potential barriers for efficient pentaploid wheat production, such as low pollen compatibility, poor seed set, failed seedling establishment, and frequent sterility in F1 hybrids. However, most of the barriers can be overcome by careful selection of the parental genotypes and by employing the higher ploidy level genotype as the maternal parent. In this review, we summarize the current research on pentaploid wheat hybrids and analyze the advantages and pitfalls of current methods used to assess pentaploid-derived lines. Furthermore, we discuss current and potential applications in commercial breeding programs and future directions for research into pentaploid wheat.