Association Mapping of Agronomic traits in Bread Wheat using a high Density 90k SNP Array

A genome-wide association study (GWAS) was performed using a high-density infinium 90K SNP array. We identified a total markers traits associations (MTAs) (p ?0.000) for the following plant traits; days taken to 50% heading(DH), days to 50% maturity (DM), plant height (Ph) cm, flag leaf area cm2 (FLA), tillers number per plant, spike length (SL) cm and grain yield per plant (GP) g. Most of the SNPs were identified in the A and B genome as compared to the D genome. The significant associated SNPs were mainly distributed on the chromosome 2B, 3B, 5A, and 5B. Nine SNPs on chromosome 5A, 2B and 2D were identified having pleiotropic effects The correlation analysis showed a significant positive association among SL, NT, GP. Which depicted that these traits are promising for breeding high yielding wheat cultivars. This study provided useful information of the valuable genetic loci for marker-assisted breeding.

Karyotype and plasmotype characteristics in wheat-rye hybrids with the different structural organization of the nuclear genome

Aim. Genome structure analysis and plasmotype identification in wheat-rye hybrids of various types (triti- cale, secalotriticum) and ploidy level. Mcth0ds. Cytological and molecular-genetic analysis. Rcsults. The karyotype and plasmotype analysis was carried out in 11 stable lines of secondary recombinant hexaploid triticale with the introgression of D-genome chromosomes of the wheat (A/B/DRR, 2n = 6x = 42), 14 stable and highly productive secalotriticum lines of F6–16 generations (Secalotriticum, S/RRAABB, 2n = 6x = 42), 9 stable lines of tetraploid triticale (A/BRR, 2n = 4x = 28). By means of differential chromosome staining, the chromosomal composition of the experimental material was characterized and the intergenomic substitution and translocation of chromosomes were detected. The PCR-RFLP analysis of the 18S/5S mitochondrial (mt) repeat and the ndhH-region of chloroplast DNA showed that these organ- elle DNA regions are in the homoplasmic state and belong to rye-type cytoplasm in secalotriticum lines and wheat-type cytoplasm in tetraploid and secondary recombinant hexaploid triticale lines. C0nclusi0ns. Cytological and molecular genetic analysis revealed significant genetic diversity of the created gene pool of wheat-rye hybrids by nuclear-cytoplasmic structure. The synthesized linear material of wheat-rye hybrids may be used in cytogenetic research and practical breeding.

Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization

Array-based single nucleotide polymorphism (SNP) genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Illumina Infinium Wheat Barley 40K SNP array Version 1.0. We show that the approach delivers high quality and high resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimizing ascertainment bias. Comprising mostly biallelic markers that were designed to be species-specific and single-copy, the array permits highly accurate imputation in diverse germplasm to improve the statistical power of genome-wide association studies (GWAS) and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Aegilops tauschii Coss. (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheat, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley, as well as direct connections to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool, Pretzel (https://plantinformatics.io/) which enables the content of the array to be visualized and interrogated interactively in the context of numerous genetic and genomic resources to be connected more seamlessly to research and breeding. The array is available for use by the international wheat and barley community.

Genotyping-by-sequencing and genomic selection applications in hexaploid triticale

Triticale, a hybrid species between wheat and rye, is one of the newest additions to the plant kingdom with a very short history of improvement. It has very limited genomic resources because of its large and complex genome. Objectives of this study were to generate dense marker data, understand genetic diversity, population structure, linkage disequilibrium (LD), and estimate accuracies of commonly used genomic selection (GS) models on forage yield of triticale. Genotyping-by-sequencing (GBS), using PstI and MspI restriction enzymes for reducing genome complexity, was performed on a triticale diversity panel (n = 289). After filtering for biallelic loci with more than 70% genome coverage, and minor allele frequency (MAF) > 0.05, de novo variant calling identified 16,378 single nucleotide polymorphism (SNP) markers. Sequences of these variants were mapped to wheat and rye reference genomes to infer their homologous groups and chromosome positions. About 45% (7,430), and 58% (9,500) of the de novo identified SNPs were mapped to the wheat and rye reference genomes, respectively. Interestingly, 28.9% (2,151) of the 7,430 SNPs were mapped to the D genome of hexaploid wheat, indicating substantial substitution of the R genome with D genome in cultivated triticale. About 27% of marker pairs were in significant LD with an average r2 > 0.18 (P < 0.05). Genome-wide LD declined rapidly to r2 < 0.1 beyond 10 kb physical distance. The three sub-genomes (A, B, and R) showed comparable LD decay patterns. Genetic diversity and population structure analyses identified five distinct clusters. Genotype grouping did not follow prior winter vs. spring type classification. However, one of the clusters was largely dominated by winter triticale. Genomic selection accuracies were estimated for forage yield using three commonly used models with different training population sizes and marker densities. Genomic selection accuracy increased with increasing training population size while gain in accuracy tended to plateau with marker densities of 2,000 SNPs or more. Average GS accuracy was about 0.52, indicating the potential of using GS in triticale forage yield improvement.

To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum

Nucleolar dominance (ND) is an epigenetic, developmentally regulated phenomenon that describes the selective inactivation of 35S rDNA loci derived from one progenitor of a hybrid or allopolyploid. The presence of ND was documented in an allotetraploid grass, Brachypodium hybridum (genome composition DDSS), which is a polyphyletic species that arose from crosses between two putative ancestors that resembled the modern B. distachyon (DD) and B. stacei (SS). In this work, we investigated the developmental stability of ND in B. hybridum genotype 3-7-2 and compared it with the reference genotype ABR113. We addressed the question of whether the ND is established in generative tissues such as pollen mother cells (PMC). We examined condensation of rDNA chromatin by fluorescence in situ hybridization employing state-of-art confocal microscopy. The transcription of rDNA homeologs was determined by reverse-transcription cleaved amplified polymorphic sequence analysis. In ABR113, the ND was stable in all tissues analyzed (primary and adventitious root, leaf, and spikes). In contrast, the 3-7-2 individuals showed a strong upregulation of the S-genome units in adventitious roots but not in other tissues. Microscopic analysis of the 3-7-2 PMCs revealed extensive decondensation of the D-genome loci and their association with the nucleolus in meiosis. As opposed, the S-genome loci were always highly condensed and localized outside the nucleolus. These results indicate that genotype-specific loss of ND in B. hybridum occurs probably after fertilization during developmental processes. This finding supports our view that B. hybridum is an attractive model to study ND in grasses.

Using the synthetic form RS5 to obtain new introgressive lines of common wheat

The use of the gene pool of wild relatives, which have a significant reserve of genetic diversity, is of immediate interest for breeding common wheat. The creation and use of synthetic forms as “bridges” is an effective method of transferring valuable genetic material from wild relatives to cultivated wheat. For this purpose, genome addition, genome substitution and recombinant “secondary” synthetic forms have been created in the P.P. Lukyanenko National Center of Grain. The synthetic recombination form RS5 (BBAASDt ), in which the third genome consists of chromosomes of Aegilops speltoides (S) and Aegilops tauschii (Dt ), was obtained from crossing the synthetic forms Avrodes (BBAASS) and M.it./Ae. tauschii (BBAADt Dt ), in which the D genome from Ae. tauschii was added to the BBAA genomes of the durum wheat cultivar Mutico italicum. Introgression lines resistant to leaf rust, yellow rust and powdery mildew have been obtained from backcrosses with the susceptible common wheat cultivars Krasnodarskaya 99, Rostislav and Zhirovka. Twelve resistant lines that additionally have high technological characteristics of grain and flour have been selected. The cytological study (С-banding) has revealed chromosomal modifications in 6 of 8 lines under study. The rearrangements mainly affected the chromosomes of the D genome, 1D, 3D, 4D, 6D and 7D. It was found that in most cases the genetic material from the synthetic form RS5 in the studied lines was represented by substituted chromosomes from Ae. tauschii. In line 5791p17, the substitution of chromosomes 6D from Ae. tauschii and 7D from Ae. speltoides was revealed. Substitutions 4D(4Dt ), 6D(6Dt ) from Ae. tauschii and 7D(7S) from Ae. speltoides were obtained for the first time. Molecular analysis of 12 lines did not reveal effective leaf rust resistance genes, presumably present in synthetic forms of M.it./Ae. tauschii and Avrodes. It is assumed that the lines may carry previously unidentified genes for fungal disease resistance, in particular for resistance to leaf rust, from Ae. tauschii and Ae. speltoides.

Genome of the bi-annual Rio Pearlfish (Nematolebias whitei), a killifish model species for Eco-Evo-Devo

The Rio Pearlfish Nematolebias whitei is a bi-annual killifish species inhabiting seasonal pools of the Rio de Janeiro region that dry twice per year. Embryos enter dormant diapause stages in the soil, waiting for the inundation of the habitat which triggers hatching and commencement of a new life cycle. This species represents a convergent, independent origin of annualism from other emerging killifish model species. While some transcriptomic datasets are available for Rio Pearlfish, thus far a sequenced genome has been unavailable. Here we present a high quality, 1.2Gb chromosome-level genome assembly, genome annotations and a comparative genomic investigation of the Rio Pearlfish as representative of a vertebrate clade that evolved environmentally-cued hatching. We show conservation of 3-D genome structure across teleost fish evolution, developmental stages, tissues and cell types. Our analysis of mobile DNA shows that Rio Pearlfish, like other annual killifishes, possesses an expanded transposable element profile with implications for rapid aging and adaptation to harsh conditions. We use the Rio Pearlfish genome to identify its hatching enzyme gene repertoire and the location of the hatching gland, a key first step in understanding the developmental genetic control of hatching. The Rio Pearlfish genome expands the comparative genomic toolkit available to study convergent origins of seasonal life histories, diapause, and rapid aging phenotypes. We present the first set of genomic resources for this emerging model organism, critical for future functional genetic and multi-omic explorations of Eco-Evo-Devo phenotypes in resilience and adaptation to extreme environments.

Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation

To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 92% imputation accuracy with 0.01x sequence coverage, which was slightly lower than the accuracy obtained using the 0.5x sequence coverage (96.6%). Compared to Beagle, on average, PHG imputation was ∼3.5% (p-value < 2 x 10−14) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. We found reduced accuracy of imputation with independent 2x GBS data (88.6%), which increases to 89.2% with the inclusion of parental haplotypes in the database. The accuracy reduction with GBS is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequlibrium and proportion of identity-by-descent regions among accessions in the PHG database. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.

High molecular weight glutenin gene diversity in Aegilops tauschii demonstrates unique origin of superior wheat quality

Central to the diversity of wheat products was the origin of hexaploid bread wheat, which added the D-genome of Aegilops tauschii to tetraploid wheat giving rise to superior dough properties in leavened breads. The polyploidization, however, imposed a genetic bottleneck, with only limited diversity introduced in the wheat D-subgenome. To understand genetic variants for quality, we sequenced 273 accessions spanning the known diversity of Ae. tauschii. We discovered 45 haplotypes in Glu-D1, a major determinant of quality, relative to the two predominant haplotypes in wheat. The wheat allele 2 + 12 was found in Ae. tauschii Lineage 2, the donor of the wheat D-subgenome. Conversely, the superior quality wheat allele 5 + 10 allele originated in Lineage 3, a recently characterized lineage of Ae. tauschii, showing a unique origin of this important allele. These two wheat alleles were also quite similar relative to the total observed molecular diversity in Ae. tauschii at Glu-D1. Ae. tauschii is thus a reservoir for unique Glu-D1 alleles and provides the genomic resource to begin utilizing new alleles for end-use quality improvement in wheat breeding programs.

The interphase period “germination–heading” of 8x and 6x triticale with different dominant Vrn genes

The existing spring forms of wheat-rye amphiploids are characterized by late maturity due to the long duration of the interphase period “germination–heading”. The manifestation of this trait is influenced by Vrn-1 genes. Their dominant alleles also determine the spring type of development. The results of studying the interphase period “germination–heading” of spring octaploid and hexaploid forms of triticale created for use in research and breeding programs under the conditions of forest-steppe of Western Siberia are given in this article. The interphase period of the primary forms 8xVrnA1, 8xVrnB1 and 8xVrnD1 obtained by artificial doubling of the chromosome number of the wheat-rye hybrids made by pollination of three lines of the soft wheat ‘Triple Dirk’ – donors of different dominant Vrn-1 genes – by a winter rye variety ‘Korotkostebel’naya 69’ was determined under the field conditions in the nursery of octaploid (8x) triticale. In the nursery of hexaploid triticale, this trait was studied in the populations of hybrids obtained by hybridization of these three primary forms of octaploid triticale with the hexaploid winter triticale variety ‘Sears 57’. In the offspring of crossing 8хVrnD1× ‘Sears 57’, spring genotypes of 6x triticale bearing Vrn-D1 were selected. This fact was determined by PСR. It means that the genetic material from the chromosome of the fifth homeologous group of the D genome of the bread wheat is included in the plant genotypes. This genome is absent in the winter 6x triticale ‘Sears 57’. The grain content of spikes of the created hexaploid forms of triticale is superiour to that of the maternal octaploid triticale forms. It was shown that plants of the hybrid populations 8xVrnA1× ‘Sears 57’ and 8xVrnD1× ‘Sears 57’ carrying the dominant alleles Vrn-A1a and Vrn-D1a, respectively, have a shorter duration of the “germination–heading” interphase period than the initial parental forms of primary 8x triticale. The short interphase period of “germination–heading” of the 6x triticale is a valuable breading trait for the creation of early maturing and productive genotypes of triticale.