Biology subjects

Akhunova, A.

Publications and source records attributed to Akhunova, A..

15 recordsLinked to original sources

bioRxiv2026

Rye stem rust is a reservoir of diversity and virulence for wheat stem rust

Sexual populations of the stem rust pathogen (Puccinia graminis or Pg) are producing new race types globally. An analysis of 385 Pg genomes (204 from this study) illuminated international migration and admixture events. Within Kazakhstan, a novel and diverse sexual clade of P. graminis is described. An analysis of the highly divergent mating type homeodomain (HD) locus found that the 75 Kazakhstan isolates had 41 different HD haplotypes, out of a total of 99 P. graminis HD haplotypes found globally. Kazakh isolates share HD haplotypes with isolates in clade 1 (Ug99), 3-B (TTRTF), and 4 (TKTTF). There are 148 unique combinations of HD locus haplotypes within the 385 isolates. Rye (Pgs) and wheat (Pgt) stem rust share multiple HD locus haplotypes and have conserved pheromone receptors and precursors, while oat stem rust (Pga) does not. Virulent alleles for AvrSr13, AvrSr22, and AvrSr50 in Pgt are frequently derived from admixture with Pgs. Pgs also contains virulent effectors for AvrSr33, AvrSr62, and AvrSr27. Pgt isolates virulent on Sr31, such as Ug99 and isolates from Spain, have genetic links to North American Pgs isolates which are present in regions of the United States where barberry is common.

plant biology↗

bioRxiv2025

Genetic architecture and evolution of stripe rust resistance uncovered using diverse panels of wheat lines and North American Puccinia striiformis f. sp. tritici isolates

Newly emerging highly virulent races of Puccinia striiformis f. sp. tritici (Pst) often defeat deployed resistance genes (Yr), highlighting the need for novel sources of durable resistance. A global diversity panel of 377 spring wheat (Triticum aestivum L.) lines was screened for all-stage resistance (ASR) against 20 diverse Pst isolates at the seedling stage and adult plant resistance (APR) against natural mix of field races. Genome-wide association mapping identified 77 unique Yr loci. Of these, 33 overlapped with the previously reported ~1,100 loci, while 44 were likely novel. Nine mapped Yr loci were effective at the adult plant stage and showed no overlap with the known APR genes. Two wheat lines, though lacked the widely effective Yr5 and Yr15 genes, exhibited resistance to all 20 Pst races at the seedling stage and natural field races at the adult stage, suggesting that they may carry novel, broad-spectrum resistance alleles. APR genes Yr18, Yr29, and Yr36 were detected at low frequencies, indicating that much of the observed resistance may arise from less characterized or novel sources. Wheat improvement had no effect on the frequency of ASR alleles but resulted in a three-fold increase in the frequency of APR alleles, suggesting that the latter were subjected to more consistent breeding selection over time. Our findings underscore the value of combined screening of diverse germplasm with the diverse panels of pathogen races to identify novel sources of broad-spectrum resistance for breeding stripe rust resistant cultivars.

genetics↗

bioRxiv2025

Pathogenic and genetic diversity of Sclerotium rolfsii, the causal agent of Southern blight of common bean in Uganda

Sclerotium rolfsi Sacc. is a soil born fungus that causes southern blight to many crops in the tropical and subtropical regions. In 2018, Southern blight was reported to be the most prevalent bean root rot in Uganda. Earlier studies ascertained the morphological and pathogenic diversity of S. rolfsii, but limited understanding of its genetic diversity exists. Knowledge of S. rolfsii genetic diversity is a critical resource in the development of common bean varieties with durable resistance to the pathogen. A total of 188 S. rolfsii strains were collected from seven agro-ecological zones of Uganda in 2013, 2020 and 2021, and characterized for pathogenecity, growth rate, the number and colour of sclerotia produced and colony texture. The genetic diversity of the 188 strains was assessed using single nucleotide polymorphisms (SNPs) obtained from whole genome sequencing. The growth rate of the strains ranged between 1.1 to 3.6 cm/day while the number of sclerotia produced ranged between 0 to 543 per strain. The strains had fluffy, fibrous and compact colony texture. The sclerotia were either brown or dark brown. The analyzed strains were pathogenic on common bean and caused a disease severity indices between 10.1% and 93.3%. Average polymorphic information content across all chromosomes was 0.322 with a minimum of 0.145 and maximum of 0.525. Average observed heterozygosity across all the chromosomes was 0.782. Population structure analysis identified five genetically distinct groups. The results of analysis of molecular variance revealed that 0.39% of the variation was between population while 11.98% was between samples within population and 87.62% between samples across populations. The average genetic distances between the isolates from different agro-ecological zones was 0.038 while the average similarity coefficient was 0.968 There were significant differences in the morphological traits and pathogenicity across the different genetic clusters. This high levels of genetic diversity within strains needs to be taken into consideration while selecting strains for screening breeding lines. Key word: Pathogenicity, genetic diversity, Characterisation, Southern blight, common bean

microbiology↗

bioRxiv2024

Non-additive dosage-dependent effects of TaGS3 gene editing on grain size and weight in wheat

The grain size in cereals is one of the main component traits contributing to yield. Previous studies showed that loss-of-function (LOF) mutations in GS3, encoding G{gamma} subunit of the multimeric G protein complex, increase grain size and weight in rice. While association between allelic variation in GS3 homologs of wheat and grain weight/size was detected previusly, the effects of LOF alleles on these traits remain unknown. We used genome editing to create the TaGS3 mutant lines with the LOF homeo-allele dosage variation. Contrary to results obtained for rice, editing of all three TaGS3 copies result in significant decrease in grain length, width, grain area and weight, without affecting number of grains per spike. Compared to wild type, the highest increase in grain weight and area was observed in mutants with the intermediate dosage of the LOF alleles, indicating that suppressive effects of TaGS3 on grain size and weight in wheat are dosage-dependent and non-additive. Our results suggest that TaGS3 likely represents a functionally diverged homolog of GS3 evolved in the wheat lineage. The newly developed LOF alleles of TaGS3 expand the set of CRISPR-Cas9-induced variants of yield component genes that could be used for increasing grain weight in wheat.

genetics↗

bioRxiv2024

Ecogeographic signals of local adaptation in a wild relative help to identify variants associated with improved wheat performance under drought stress

Prioritizing wild relative diversity for improving crop adaptation to emerging drought-prone environments is challenging. Here, we combined the genome-wide environmental scans (GWES) in wheat diploid ancestor Aegilops tauschii with allele testing in the genetic backgrounds of adapted cultivars to identify new diversity for improving wheat adaptation to water-limiting conditions. Evaluation of adaptive allele effects was carried out in Ae. tauschii-wheat introgression lines (ILs) phenotyped for multiple agronomic traits under irrigated and water-limiting conditions using both UAS-based imaging and conventional approaches. The GWES showed that climatic gradients alone explain most (57.8%) of genomic variation in Ae. tauschii, with many alleles associated with climatic factors in Ae. tauschii being linked with improved performance of ILs under water-limiting conditions. The most significant GWES SNP located on chromosome 4D and associated with temperature annual range was linked with reduced canopy temperature in ILs. Our results suggest that (i) introgression of climate-adaptive alleles from Ae. tauschii have potential to improve wheat performance under water-limiting conditions, (ii) variants controlling physiological processes responsible for maintaining leaf temperature are likely among the targets of adaptive selection in a wild relative, and (iii) adaptive variation uncovered by GWES in wild relatives has potential to improve climate resilience of crop varieties.

genetics↗

bioRxiv2023

Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression

Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. New functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more non-synonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the new promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop. Significance StatementWe sequenced 4.3 million induced mutations in the promoters and 4.7 million in the coding regions of most wheat genes. We also show how this public resource can be used to understand gene function, modulate gene expression, and generate changes in valuable wheat agronomic traits.

genomics↗

bioRxiv2023

Allelic variation in the wheat homolog of topoisomerase II is associated with crossover rate

Meiotic recombination is a fundamental biological process that impacts genetic diversity and response of variants to selection. The increase in crossover (CO) frequency by modulating the activity of meiotic genes has been suggested as potential means to improve the efficiency of selection and mitigate the negative impact of linkage drag in crop improvement programs. In this study, we used the wheat nested association mapping (NAM) population to map QTL associated with CO rate and harboring TaTOPII-A1, a gene encoding topoisomerase II that is involved in the regulation of meiosis. An amino acid changing SNP (T/C) located in exon 19 of TaTOPII-A1 with a predicted functional effect showed an association with CO rate. The T-allele of TaTOPII-A1 was associated with a statistically significant 5.9 % increase in COs across several NAM families. The involvement of TaTOPII-A1 in processes affecting CO rate in wheat was confirmed using a TaTOPII-A1 mutant. A strong-effect missense mutation in the TaTOPII-A1 coding region resulted in 1.4-fold increase in the genetic map length and 53% increase in CO rate compared to the wild-type allele. These results demonstrate that functional mutations in TaTOPII-A1 can lead to increased CO frequency. The mutant and natural alleles of TaTOPII-A1 identified in our study could serve as new sources of recombination-promoting genes to manipulate CO rate in wheat and possibly other crops.

genetics↗

bioRxiv2023

CRISPR-based editing of the ω- and γ-gliadin gene clusters reduces wheat immunoreactivity without affecting grain protein quality

Wheat immunotoxicity is associated with abnormal reaction to gluten-derived peptides. Attempts to reduce immunotoxicity using breeding and biotechnology often affect dough quality. Here, the multiplexed CRISPR-Cas9 editing of cultivar Fielder was used to modify the {omega} -and {gamma}-gliadin gene clusters abundant in immunoreactive peptides identified in the genomes assembled using the long-read sequencing technologies. The whole genome sequencing of an edited line showed editing or deletion of nearly all {omega}-gliadin and half of the {gamma}-gliadin gene copies and lack of editing in the /{beta}-gliadin genes. The detected 62% and 52% reduction in {omega}- and {gamma}-gliadin content, respectively, had no negative impact on grain protein quality. A 47-fold immunoreactivity reduction compared to wild-type was detected using antibodies against immunotoxic peptides. Our results indicate that genome profiling to identify gliadin gene copies abundant in immunoreactive peptides and their targeted editing could be an effective mean for reducing immunotoxicity of wheat cultivars while minimizing the impact of editing on protein quality.

genetics↗

bioRxiv2022

Multiplexed promoter and gene editing in wheat using the virus-based guide RNA delivery system

The low efficiency of genetic transformation and gene editing across diverse cultivars hinders the broad application of CRISPR technology for crop improvement. The development of virus-based methods of CRISPR-Cas system delivery into the plant cells holds great promise to overcome these limitations. Here, we applied the barley stripe mosaic virus (BSMV) for delivering guide RNAs (sgRNA) into the Cas9-expressing wheat lines to create targeted deletions in the promoter of a transcription factor and to perform multiplexed editing of agronomic genes. We demonstrate that pooled BSMV-sgRNAs could be used to generate heritable targeted deletions and multiple mutations in the genome. We transferred the high-expressing allele of Cas9 into adapted spring and winter cultivars and successfully performed the BSMV-sgRNA-based editing of two agronomic genes. The strategies presented in our study could be applied to any cultivar for creating new cis-regulatory diversity or targeting multiple genes in biological pathways or QTL regions, opening possibilities for the effective engineering of crop genomes and accelerating gene discovery and trait improvement efforts.

genetics↗

bioRxiv2021

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 93% imputation accuracy with 0.01x sequence coverage, which was only slightly lower than the accuracy obtained using the 0.5x sequence coverage (96.9%). Compared to Beagle, on average, PHG imputation was ~4% (p-value = 0.00027) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. The reduced accuracy of imputation with GBS data (90.4%) 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 our reference panel. 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.

genomics↗

bioRxiv2020

Expanding the range of editable targets in the wheat genome using the variants of the Cas12a and Cas9 nucleases

The development of CRISPR-based editors having different protospacer adjacent motif (PAM) recognition specificities, or guide RNA length/structure requirements broadens the range of possible genome editing applications. Here, we evaluated the natural and engineered variants of Cas12a (FnCas12a from Francisella novicida and LbCas12a from Lachnospiraceae bacterium) and Cas9 for wheat genome editing efficiency and ability to induce heritable mutations in endogenous genes controlling important agronomic traits in wheat. Unlike FnCas12a, LbCas12a was able to induce mutations in the wheat genome in the current study, even though with a lower rate than that reported for SpCas9. The eight-fold improvement in the gene editing efficiency was achieved for LbCas12a by using the guide RNAs flanked by ribozymes and driven by the RNA polymerase II promoter from switchgrass. The efficiency of multiplexed genome editing (MGE) using LbCas12a was mostly similar to that obtained using the simplex RNA guides. A LbCas12a-MGE construct was successfully applied for generating heritable mutations in a gene controlling grain size and weight in wheat. We show that the range of editable loci in the wheat genome could be expanded by using the engineered variants of Cas12a (LbCas12a-RVR) and Cas9 (Cas9-NG and xCas9) that recognize the TATV and NG PAMs, respectively, with the Cas9-NG showing higher editing efficiency on the targets with atypical PAMs compared to xCas9. In conclusion, our study reports the set of validated natural and engineered variants of Cas12a and Cas9 editors for targeting loci in the wheat genome not amenable to Cas9-based modification.

genetics↗

bioRxiv2020

Differential chromatin accessibility landscape reveals the structural and functional features of the allopolyploid wheat chromosomes

BackgroundWe have a limited understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes. Using a differential nuclease sensitivity (DNS) assay, we investigated the chromatin states in the coding and transposon element (TE) -rich repetitive regions of the allopolyploid wheat genome. ResultsWe observed a negative chromatin accessibility gradient along the telomere-centromere axis with mostly open and closed chromatin located in the distal and pericentromeric regions of chromosomes, respectively. This trend was mirrored by the TE-rich intergenic regions, but not by the genic regions, which showed similar averages of chromatin accessibility levels along the chromosomes. The genes proximity to TEs was negatively associated with chromatin accessibility. The chromatin states of TEs was dependent on their type, proximity to genes, and chromosomal position. Both the distance between genes and TE composition appear to play a more important role in the chromatin accessibility along the chromosomes than chromosomal position. The majority of MNase hypersensitive regions were located within the TEs. The DNS assay accurately predicted previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within closed chromatin. ConclusionsThe chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.

genomics↗

bioRxiv2019

Sequence based mapping identifies AWNS1, a candidate transcription repressor underlying awn suppression at the B1 locus in wheat

Awns are stiff, hair-like structures that grow from the spikelets of wheat (Triticum aestivum L.) and other grasses. In wild wheat relatives, awns play a role in seed dispersal. Awn suppression in domesticated wheat, where awns are shortened or even eliminated entirely, is variably adaptive with both awned and awnless types under widespread cultivation. Although the B1 locus on the long arm of chromosome 5A is a major determinant of awn suppression, no underlying gene or mechanism of action has been identified. Using association mapping, we identified a SNP marker located on the distal end of 5AL (5A28417) predictive of awn status in a panel of 640 U.S. winter wheat breeding lines, indicating that B1 was the determinant of awn suppression in this germplasm. Analysis of historical data available for the panel determined 5A28417 was also significantly associated with grain test weight. Evaluation of spike morphology and kernel traits was undertaken in a 341 RIL population developed from a cross between awned soft winter wheat cultivar LA95135 and awnless cultivar SS-MPV57. Awn suppression in the population co-segregated with 5A28417 and was co-located with QTL for number of spikelets per spike, kernel weight and kernel length. Fine-mapping located B1 to a region containing only two predicted genes, including a C2H2 zinc finger transcription factor 219 bp from 5A28417 that we named AWNS-A1. Deletions encompassing both genes were present in awned mutants of the awnless cultivar Brundage. Polymorphisms in the AWNS-A1 coding region were not observed in diverse wheat germplasm. However, sequencing of wheat lines representing different marker haplotypes in the surrounding region identified a deletion 3 kb downstream of AWNS-A1. A marker for this deletion was highly predictive of awn suppression in a collection of diverse wheat accessions, and indicates that AWNS-A1 is likely the major determinant of awn suppression in global wheat germplasm. AWNS-A1 is more highly expressed in developing spikes of awnless individuals, suggesting a mechanism for awn suppression.

genetics↗

bioRxiv2018

Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat

BackgroundWhole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits.\n\nResultsWe present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and promoter capture.\n\nConclusionsWe show that a capture design employing an island strategy can enable analysis of the large gene/promoter space of wheat with only 2x160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.

genomics↗

bioRxiv2018

Gene editing and mutagenesis reveal inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat

The TaGW2 gene homoeologues have been reported to be negative regulators of grain size (GS) and thousand grain weight (TGW) in wheat. However, the contribution of each homoeologue to trait variation among different wheat cultivars is not well documented. We used the CRISPR-Cas9 system and TILLING to mutagenize each homoeologous gene copy in cultivars Bobwhite and Paragon, respectively. Plants carrying single-copy nonsense mutations in different genomes showed different levels of GS/TGW increase, with TGW increasing by an average of 5.5% (edited lines) and 5.3% (TILLING mutants). In any combination, the double homoeologue mutants showed higher phenotypic effects than the respective single-genome mutants. The double mutants had on average 12.1% (edited) and 10.5% (TILLING) higher TGW with respect to wild-type lines. The highest increase in GS and TGW was shown for triple mutants of both cultivars, with increases of 16.3% (edited) and 20.7% (TILLING) in TGW. The additive effects of the TaGW2 homoeologues were also demonstrated by the negative correlation between the functional gene copy number and GS/TGW in Bobwhite mutants and an F2 population. The highest single-genome increases in GS and TGW in Paragon and Bobwhite were obtained by mutations in the B and D genomes, respectively. These inter-cultivar differences in the phenotypic effects between the TaGW2 gene homoeologues coincide with inter-cultivar differences in the homoeologue expression levels. These results indicate that GS/TGW variation in wheat can be modulated by the dosage of homoeologous genes with inter-cultivar differences in the magnitude of the individual homoeologue effects.

genetics↗