Biology subjects

Paofa, J.

Publications and source records attributed to Paofa, J..

4 recordsLinked to original sources

bioRxiv2025

Shotgun sequencing data and SSR mining data of aibika (Abelmoschus manihot, Malvaceae)

Aibika (Abelmoschus manihot) is a tropical leafy vegetable with great potential in the prevention of malnutrition. Its high fibre and micronutrient content makes it a valuable complement to staple foods such as rice and starchy crops consumed in South Asia and the Pacific. The present study is the first to report the development of a set of 21 nuclear single sequence repeat (SSR) markers of A. manihot from genomic sequence data obtained using NGS technology. The DNA library was prepared from a pool of four aibika accessions and sequenced using an Illumina MiSeq system. A total of 1,295,217 pair-end reads were generated. Raw data are available in the European Nucleotide Archive (accession number PRJEB88210; https://www.ebi.ac.uk/ena/browser/view/PRJEB88210). The sequences were assembled using the ABySS software. In total 651,320 contigs were generated. Using MISA Perl script and Primer3 software, we identified 8014 SSR motifs, of which 4637 had a suitable primer design. The contigs were blasted with NCBI-BLAST on okra reference genome. After selection based on motif type, repeat length, amplicon size and occurrence blast, we retained 91 candidate SSR loci, which were tested on 23 aibika accessions. Finally, we validated 21 high quality SSR loci by genotyping 45 accessions from three Pacific countries. The number of alleles per locus ranged from 3 to 21 with an average of 7.81 alleles/locus. The 21 selected SSRs were found to be useful in discriminating between accessions and revealing the diversity structure of A. manihot. They will help to optimize genebanks management and breeding programmes, and guide future collection activities.

molecular biology↗

bioRxiv2024

Painting the diversity of a world's favourite fruit: A next generation catalogue of cultivated bananas

Societal impact statementBananas are nutritious fruits of major importance in the tropics and subtropics. Characterizing their diversity is essential to ensure their conservation and use. A catalogue showcasing cultivated bananas genomic diversity was compiled and is to be used as a tool to support the classification of banana cultivars. This research revealed that cultivated banana groups are not all made of identical clones. Materials from recent collecting missions indicated that more banana diversity is expected to be found as the exploration of the banana gene pool continues. These discoveries will drive dynamic conservation strategies for banana genetic resources and will increase their use. SummaryO_LIBanana is an important food crop cultivated in many tropical and subtropical regions around the world. Due to their low fertility, banana landraces are clonally propagated. However, different factors, such as synonymy and the effects of environment, make their assignment to described sets of clones, or cultivar groups, difficult. Consequently, passport data of accessions in genebanks is often uncomplete and sometimes inaccurate. C_LIO_LIWith the recent advances in genomics, a new powerful tool was developed enabling the fine-scale characterization of bananas ancestry along chromosomes, i.e. in silico chromosome painting. We applied this method to a high-throughput genotyping data set obtained from 317 banana accessions spanning most of the known cultivar groups. This set included both genebank and new uncharacterized materials. C_LIO_LIBy comparing curated morphological assignation to the genomic patterns resulting from in silico chromosome painting, we were able to compile a catalogue referencing the chromosome painting patterns of most of the described cultivar groups. C_LIO_LIExamining the genomic patterns obtained, we discovered intra-cultivar group variability. In some cultivar groups, mitotic recombination or deletions were clonally accumulated in cultivars. In addition, we identified at least 4 cultivar groups in which cultivars likely resulting from distinct sexual events co-existed, notably Pisang Awak in which 5 distinct genomic patterns of two ploidy levels were identified. New patterns were also discovered in the newest materials of the set, showing that a wider diversity of clones still exist on farm. C_LI

genomics↗

bioRxiv2021

Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives

BackgroundConservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were Musa acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16-20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples and 16 seed samples from one infructescence ( bunch) for each population. ResultsAllelic richness of seeds compared to populations was 51%, 81% and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (>15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch. ConclusionsWe demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.

genetics↗

bioRxiv2021

Wild to domesticates: genomes of edible diploid bananas hold traces of several undefined genepools

This study is an unprecedent exploration of the diversity of 226 diploid bananas genotyped with restriction-site-associated DNA sequencing data (RADseq) to clarify the processes that led to the creation of edible diploid AA bananas. This wide set included 72 seedy bananas, mostly M. acuminata from different genepools, and 154 edible, i.e. parthenocarpic and sterile, AA accessions obtained from genebanks and recent collecting missions. We highlighted the geographic organisation of the diversity of edible AAs and confirmed the admixed nature of many and further conducted introgressions tests within AAs from South East Asia and New Guinea. Lastly, taking advantage of the presence of an important number of M. acuminata ssp. banksii (22) and of AA from Papua New Guinea (76) in the set, we investigated the patterns of differentiation between wild and cultivated bananas seemingly belonging to the same genepool. We discovered a few cultivated AAs that may be of pure origins both in South-East Asia and in New Guinea. We also detected two undefined parental genepools in South East Asia for which regions of origin could be Thailand and a region between north Borneo and the Philippines, respectively. Finally, we suggest the existence of a third genepool in New Guinea island that might be a source population for both edible AAs and the local M. acuminata ssp. banksii.

plant biology↗