Biology subjects

Alabdullah, A. K.

Publications and source records attributed to Alabdullah, A. K..

7 recordsLinked to original sources

bioRxiv2026

Genetic architecture of soluble arabinoxylan fibre in elite genotypes of bread wheat revealed by genome-wide association analysis

Dietary fibre intake remains below recommended levels, and increasing fibre content of widely consumed white wheat flour (derived from the starchy endosperm) represents a scalable strategy to improve public health. In wheat starchy endosperm, arabinoxylan (AX) is the dominant fibre component, with the water-extractable (WE) fraction being particularly beneficial to health. We assembled an Elite Fibre Panel (EFP) of 384 elite modern wheat genotypes from UK commercial breeding programmes and quantified the content of WE-AX in wholemeal, as a proxy for soluble AX in white flour, across two UK field environments. Wholemeal WE-AX, showed substantial quantitative variation and moderate genotype-by-environment interaction, with a broad-sense heritability of 0.68. Genome-wide association analyses using 6,791 SNPs identified seven loci associated with WE-AX content. The strongest and most stable effects were mapped to major loci on chromosomes 1B and 6B, previously implicated in AX regulation, while additional loci of smaller and sometimes environment-dependent effect were detected on chromosomes 3A, 5B, and 7A. Favourable alleles increased WE-AX content by [~]5-15% and combined additively. LD-defined intervals contained several high-confidence candidate genes involved in cell-wall biosynthesis, remodelling and post-depositional modification, including PER1, a validated regulator of arabinoxylan cross-linking, together with genes encoding a UTP-glucose-1-phosphate uridylyltransferase, trichome birefringence-like proteins and xyloglucan endotransglucosylase/hydrolases. These findings demonstrate that substantial gains in soluble AX can be achieved by pyramiding favourable alleles already segregating within elite germplasm, providing a practical route for breeding wheat with enhanced dietary fibre content and improved nutritional quality. Key messageMultiple additive loci controlling soluble arabinoxylan content were identified in elite wheat germplasm, enabling marker-assisted breeding for increased dietary fibre in white flour.

genomics↗

bioRxiv2025

Spatial transcriptomics identifies distinct domains regulating yield-related traits of the wheat ear

Cereal inflorescences are complex, highly ordered structures composed of grain-producing florets that form within specialised branches called spikelets. The spikelets of wheat are arranged in two alternating rows along a central rachis, in a pattern determined during early reproductive development. While several genes that control spikelet development have been identified, the molecular processes that regulate their morphology and the formation of supporting structures, such as meristems and the rachis, remain poorly understood. Here, we used spatial transcriptomics to investigate the dynamic transcriptional landscape of a wheat inflorescence during spikelet development. We identified two spatially distinct regions that regulate spikelet architecture, including a primordium region characterised by RAMOSA2 activity, and a boundary region that expresses ALOG1 and known regulators of bract suppression. Developmental assays indicate that spikelets differentiate from meristematic regions, which is accompanied by formation of central vascular regions of the rachis and inflorescence base that express genes controlling spikelet number. The combined spatial transcriptome and genetic data reveal key regulators of spikelet development, including target genes for improving spikelet number and yield.

plant biology↗

bioRxiv2021

A separation-of-function ZIP4 wheat mutant allows crossover between related chromosomes and is meiotically stable

Many species, including most flowering plants, are polyploid, possessing multiple genomes. During polyploidisation, fertility is preserved via the evolution of mechanisms to control the behaviour of these multiple genomes during meiosis. On the polyploidisation of wheat, the major meiotic gene ZIP4 duplicated and diverged, with the resulting new gene TaZIP4-B2 being inserted into chromosome 5B. Previous studies showed that this TaZIP4-B2 promotes pairing and synapsis between wheat homologous chromosomes, whilst suppressing crossover between related (homoeologous) chromosomes. Moreover, in wheat, the presence of TaZIP4-B2 preserves up to 50% of grain number. The present study exploits a separation-of-function wheat Tazip4-B2 mutant named zip4-ph1d, in which the Tazip4-B2 copy still promotes correct pairing and synapsis between homologues (resulting in the same pollen profile and fertility normally found in wild type wheat), but which also allows crossover between the related chromosomes in wheat haploids of this mutant. This suggests an improved utility for the new zip4-ph1d mutant line during wheat breeding exploitation, compared to the previously described CRISPR Tazip4-B2 and ph1 mutant lines. The results also reveal that loss of suppression of homoeologous crossover between wheat chromosomes does not in itself reduce wheat fertility when promotion of homologous pairing and synapsis by TaZIP4-B2 is preserved.

genetics↗

bioRxiv2021

A duplicated copy of the meiotic gene ZIP4 preserves up to 50% pollen viability and grain number in polyploid wheat

O_LIAlthough most flowering plants are polyploid, little is known of how the meiotic process evolved to stabilise and preserve polyploid fertility. On wheat polyploidisation, the major meiotic gene ZIP4 on chromosome 3B duplicated onto 5B and subsequently diverged. This 5B meiotic gene copy (TaZIP4-B2) was recently shown to promote homologous pairing, synapsis and crossover, and suppress homoeologous crossover. We therefore suspected that these stabilising effects on meiosis could be important for the preservation of wheat polyploid fertility. C_LIO_LIA CRISPR Tazip4-B2 mutant was exploited to assess the contribution of the 5B duplicated ZIP4 copy in maintaining pollen viability and grain setting. C_LIO_LIAnalysis demonstrated abnormalities in 56% of meiocytes in the Tazip4-B2 mutant, with micronuclei in 50% of tetrads, reduced size in 48% of pollen grains and a near 50% reduction in grain number. Further studies showed that most of the reduced grain number resulted from pollination with less viable pollen, suggesting that the stabilising effect of TaZIP4-B2 on meiosis has a greater consequence in subsequent male, rather than female gametogenesis. C_LIO_LIThese studies reveal the extraordinary value of the wheat chromosome 5B TaZIP4-B2 duplication to agriculture and human nutrition. Future studies should assess whether different TaZIP4-B2 alleles exhibit variable effects on meiotic stabilisation and/or resistance to temperature change. C_LI

plant biology↗

bioRxiv2019

Dmc1 is a candidate for temperature tolerance during wheat meiosis

We have assessed the effects of high and low temperatures on meiotic chromosome synapsis and crossover formation in the hexaploid wheat (Triticum aestivum L.) variety Chinese Spring. At low temperatures, asynapsis and chromosome univalence have been observed before in Chinese Spring lines lacking the long arm of chromosome 5D (5DL), which led to the proposal that 5DL carries a gene (Ltp1) that stabilises wheat chromosome pairing at low temperatures. In the current study, Chinese Spring wild type and 5DL interstitial deletion mutant plants were exposed to low (13{degrees}C) or high (30{degrees}C) temperatures in controlled environment rooms during a period from premeiotic interphase to early meiosis I. A 5DL deletion mutant was identified whose meiotic chromosomes exhibit extremely high levels of asynapsis and chromosome univalence at metaphase I after seven days at 13{degrees}C. This suggests that the mutant, which we name ttmei1 (temperature tolerance in meiosis 1) has a deletion of a gene that, like Ltp1, normally stabilises chromosome pairing at low temperatures. Immunolocalisation of the meiotic proteins ASY1 and ZYP1 on ttmei1 mutants showed that low temperature results in a failure to complete synapsis at pachytene. After 24 hours at 30{degrees}C, ttmei1 mutants exhibited a reduced number of crossovers and increased univalence, but to a lesser extent than at 13{degrees}C. KASP genotyping revealed that ttmei1 has a 4 Mb deletion in 5DL. Of 41 genes within this deletion region, the strongest candidate for the stabilisation of chromosome pairing at low (and possibly high) temperatures is the meiotic recombination gene Dmc1.\n\nKey messageThe meiotic recombination gene Dmc1 on wheat chromosome 5D has been identified as a candidate for the maintenance of normal chromosome synapsis and crossover at low and possibly high temperatures.

plant biology↗

bioRxiv2019

A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization

Polyploidization has played an important role in plant evolution. However, upon polyploidization the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to stabilise the polyploid genome. Therefore, upon the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the stabilization process may have involved rapid changes in content and expression of MGs on homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were identified in wheat using co-expression network analysis and orthology informed approaches. In total, 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue samples but not with other tissue types. These modules were enriched for GO terms related to cell cycle, DNA replication and chromatin modification, and contained orthologs of known MGs. Overall 74.4 % of genes within these meiosis-related modules had three homeologous copies which was similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-expression, the majority (93.7 %) were either retained in hexaploid wheat at the same number of copies (78.4 %) or increased in copy number (15.3%) compared to ancestral wheat species. Furthermore, genes within meiosis-related modules showed more balanced expression levels between homeologs than genes in non-meiosis-related modules. Taken together our results do not support extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The construction of the MG co-expression network allowed identification of hub genes and provided key targets for future studies.\n\nAuthor summaryAll flowering plants have undergone a polyploidization event(s) during their evolutionary history. One of the biggest challenges faced by a newly-formed polyploid is meiosis, an essential event for sexual reproduction and fertility. This process must adapt to discriminate between multiple related chromosomes and to ensure their proper segregation to produce fertile gametes. The meiotic mechanisms responsible for the stabilisation of the extant polyploids remain poorly understood except in wheat, where there is now a better understanding of these processes. It has been proposed that meiotic adaptation in established polyploids could involve meiotic gene loss following the event of polyploidization. To test this hypothesis in hexaploid wheat, we have computationally predicted sets of hexaploid wheat meiotic genes based on expression data from different tissue types, including meiotic anther tissue, and orthology informed approaches. We have calculated homeolog expression patterns and number of gene copies for the predicted meiotic genes and compared them with proper control gene sets. Our findings did not support any significant meiotic gene loss upon wheat polyploidization. Furthermore, wheat meiotic genes showed more balanced expression levels between homeologs than non-meiotic genes.

bioinformatics↗

bioRxiv2018

Genome-wide transcription during early wheat meiosis is independent of synapsis, ploidy level and the Ph1 locus

Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologues and homoeologues at the onset of meiosis. In turn, these chromatin changes, can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-Seq data derived from six different genotypes: wheat, wheat-rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the Ph1 locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the telomere bouquet is forming and synapsis between homologues is beginning. The six genotypes exhibit different levels of synapsis and chromatin structure at this stage; therefore, recombination and consequently segregation, are also different. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the Ph1 locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. This suggests that post-transcriptional and post-translational processes are likely to be more important. Thus, further studies will be required to reveal whether these observations are specific to wheat meiosis, and whether there are significant changes in post-transcriptional and post-translational modifications in wheat and other polyploid species associated with their polyploidisation.

genomics↗