Biology subjects

Mitchell, R. A. C.

Publications and source records attributed to Mitchell, R. A. C..

4 recordsLinked to original sources

bioRxiv2023

A high soluble-fibre allele in wheat encodes a defective cell wall peroxidase responsible for dimerization of ferulate moieties on arabinoxylan

Increasing dietary fibre (DF) intake is an important target to improve health and an attractive strategy for this is to increase the fibre content of staple foods, particularly white bread which is the staple food in many countries. DF in wheat white flour is derived principally from the endosperm cell wall polysaccharide arabinoxylan (AX) and the water-extractable form of this (WE-AX) accounts for the majority of soluble dietary fibre (SDF), which is believed to confer particular health benefits. We previously identified QTLs for soluble dietary fibre (SDF) on 1B and 6B chromosomes in wheat in biparental populations. Here we show that the 6B high SDF allele encodes a peroxidase protein (PER1-v) with a single missense compared to the more common low SDF form (PER1). Wheat lines with the natural PER1-v allele and with an induced knock-out mutation in PER1 showed similar characteristics of reduced dimerization of ferulate associated with water-extractable WE-AX. Decreased ferulate dimerization is associated with decreased cross-linking of the WE-AX chains and increased solubility of AX. Transiently expressed PER1_RFP fusion driven by native promoter in wheat endosperm was shown to localise to cell walls whereas PER1-v_RFP did not; we therefore propose that PER1-v lacks capacity to dimerise AX ferulate in vivo due to mis-localisation. PER1 is the first peroxidase reported to be responsible for oxidative coupling of ferulate on AX, a key process in all grass cell walls. Understanding its role and the effect of variants on AX properties offers a route to control the properties of wheat DF in the human diet.

plant biology↗

bioRxiv2021

Flow cytometry-based determination of ploidy from dried leaf specimens in genomically complex collections of the tropical forage grass Urochloa s. l.

We aimed to develop an optimized approach to determine ploidy for dried leaf material in a germplasm collection of a tropical forage grass group, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. The methods enable robust identification of ploidy levels (coefficient of variation, CV, typically <5%). Ploidy of some 353 forage grass accessions (ploidy range from 2 to 9), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes used in the current breeding programs at CIAT and EMBRAPA: the brizantha and humidicola agamic complexes are variable, with multiple ploidy levels and DNA content. U. brizantha has odd level of ploidy (x=5), and the relative differences in nuclear DNA content between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed some aneuploidy.

genomics↗

bioRxiv2021

Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

Background and AimsDiploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa and now planted worldwide are important for food security and the environment, often being planted in marginal lands. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. MethodsSome 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis with in situ hybridization to chromosomes were used to identify chromosomes and genomes in Urochloa accessions belonging to the different agamic complexes. Key ResultsGenome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. ConclusionsWe suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.

genomics↗

bioRxiv2020

Allele Mining in Diverse Accessions of Urochloa and Megathyrsus spp. Tropical Grasses to Improve Forage Quality and Reduce Environmental Impact

The C4 Urochloa spp (syn. Brachiaria) and Megathyrsus maximus (syn. Panicum maximum) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease amount of land required per unit production and enhanced lipid content could decrease methane emissions from cattle. For these traits, loss-of-function (LOF) alleles in known gene targets are predicted to improve them, making a reverse genetics approach of allele mining feasible. We studied allelic diversity of 20 target genes (11 for digestibility, 9 for lipid content) in 104 accessions selected to represent genetic diversity and ploidy levels of U. brizantha, U. decumbens, U. humidicola, U. ruziziensis and M. maximum. We used RNAseq and then bait-capture DNA-seq to improve gene models in a U. ruziziensis reference genome to assign polymorphisms with high confidence. We found 953 non-synonymous polymorphisms across all genes and accessions; within these, we identified 7 putative LOF alleles with high confidence, including ones in the non-redundant SDP1 and BAHD01 genes present in diploid and tetraploid accessions. These LOF alleles could respectively confer increased lipid content and digestibility if incorporated into a breeding programme. HighlightWe found gene variants in a collection of tropical grasses that could help reduce environmental impact of cattle production.

plant biology↗