Biology subjects

Heslop-Harrison, J. S.

Publications and source records attributed to Heslop-Harrison, J. S..

3 recordsLinked to original sources

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↗

bioRxiv2020

Ten complete mitochondrial genomes of Gymnocharacini (Stethaprioninae, Characiformes): evolutionary relationships and a repetitive element in the Control Region (D-loop)

We are presenting the complete mitogenomes of eight fish species/cytotypes from Neotropical region belonging to the Astyanax and Psalidodon genus: A. aeneus, A. altiparanae, P. fasciatus (from two locations - Upper Parana and Sao Francisco river basins), A. lacustris, P. rivularis (two cytotypes) and P. rioparanaibano. We perform the whole-genome sequencing for six of these species in a Novaseq 6000 - by Illumina, meanwhile two genomes were assembled from raw data available in databases. Plus, we reassembled and annotated the mitochondrial genomes for A. mexicanus and P. paranae, both already described and with raw data available online. All the genomes presented the same organization, with 13 protein-coding genes, 22 tRNA genes and two rRNA genes. Aiming to contribute to the understanding of the several cryptic species complexes and phylogeny of the genus, we perform Bayesian analysis using the 13 protein-coding genes from these species, plus Deuterodon giton and using a Brycon species as outgroup.

genomics↗

bioRxiv2020

The genotypic and genetic diversity of enset (Ensete ventricosum) landraces used in traditional medicine is similar to the diversity found in starchy landraces

BackgroundEnset (Ensete ventricosum) is a multipurpose crop extensively cultivated in southern and southwestern Ethiopia for human food, animal feed and fiber. It contributes to the food security and rural livelihoods of 20 million people. Several distinct enset landraces are cultivated for their uses in traditional medicine. Socio-economic changes and the loss of indigenous knowledge might lead to the decline of important medicinal landraces and their associated genetic diversity. However, it is currently unknown whether medicinal landraces are genetically differentiated from other landraces. Here, we characterize the genetic diversity of medicinal enset landraces to support effective conservation and utilization of their diversity ResultsWe evaluated the genetic diversity of 51 enset landraces of which 38 have reported medicinal value. A total of 38 alleles were detected across the 15 SSR loci. AMOVA revealed that 97.6% of the total genetic variation is among individual with an FST of 0.024 between medicinal and non-medicinal landraces. A neighbor-joining tree showed four separate clusters with no correlation to the use values of the landraces. Principal coordinate analysis also confirmed the absence of distinct clustering between the groups, showing low differentiation among landraces used in traditional medicine and those having other use values. ConclusionWe found that enset landraces were clustered irrespective of their use value, showing no evidence for genetic differentiation between enset grown for medicinal uses and non-medicinal landraces. This suggests that enset medicinal properties may be restricted to a more limited number of genotypes, a product of interaction with the environment or management practice, or partly misreported. The study provide baseline information that promotes further investigations in exploiting the medicinal value of these specific landraces

genetics↗