Influence de quelques caractères agronomiques sur le rendement de l’igname sucrée (Dioscorea dumetorum Kunth Pax) au Cameroun

L’influence des caractères agronomiques sur le rendement de l’igname sucrée D. dumetorum a été étudiée en travaillant sur 43 accessions de D. dumetorum et 2 accessions de D. cayenensis utilisés comme espèce hors groupe. Les essais ont été réalisés dans deux zones agro-écologiques différentes Baham (05°20.040' N/010°22.572’ E et 1634 m asl, zone  agro-écologique III) et Ekona (04°12.773'N/009°19.425'E et 445 m asl, zone agro-écologique IV). Pour chacun des essais et chaque cultivars 20 semenceaux ont été semés suivant un dispositif en bloc complet   rendomisé (BCR) avec 10 plantes par répétitions et deux répétitions par site. L’analyse de variance (ANOVA) a permis de mettre en evidence  l’influence de quelques caractères agronomiques sur le rendement. Pour les caractères significatifs, les moyenne ont été regroupées par la methode de DUNCAN au seuil de 5%. Il ressort de cette étude que le poids optimum de semences permettant d’obtenir le maximum de rendement est de 300 g. Le rendement est influencé par les paramètres édaphoclimatiques et géographiques des zones de culture, du jour d’émergence, de la longueur et du diamètre de la tige et la longueur et largeur des feuilles. La diversité variétale met en évidence l’existence d’un potentiel génétique pouvant servir de base pour un programme d’amélioration portant sur  l’augmentation de rendement.Mots clés : Dioscorea dumetorum, caractères agronomiques, poids du semenceau, index de rendement, amélioration, Cameroun

High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing

Siadjeu C, Pucker B, Viehöver P, Albach DC, Weisshaar B. High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing. Genes. 2020;11(3): 274.Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. A total of 35,269 protein-encoding gene models as well as 9941 non-coding RNA genes were predicted, and functional annotations were assigned

Genetic diversity of sweet yam “Dioscorea dumetorum “(Kunth) Pax revealed by morphological traits in two agro-ecological zones of Cameroon

Genetic diversity of 43 Dioscorea dumetorum accessions and two of Dioscorea cayenensis Lam as out-group species was evaluated for qualitative and quantitative traits in two different agro-climatic zones Baham (05°20.040' N/010°22.572’ E and 1634±3 masl, agro-ecological zone III with rainfall of 1500 to 2000 mm, and mean annual temperature of 19°C) and Ekona (04°12.773'N/009°19.425'E and 445±3 masl, agro-ecological zone IV with rainfall of 2500 to 4000 mm and mean annual temperature of 26°C). Forty one (41) morphological characters according to International Plant Genetic Resources Institute (IPGRI) descriptor, including nine quantitative and 32 qualitative characters were analyzed for multivariate analysis using cluster analysis, principal component analysis (PCA), and analysis of variance. For quantitative characters, cluster analysis revealed three major clusters. The first three components with eigen values > 1 contributed 83% of the variability. The PCA results indicate that traits which largely contributed to the variability within and between the accessions were stem length, leaf length, internode number, leaf width, harvest index, leaf number and internode length. Traits such as harvest index, internode number and stem length showed high heritability and high genetic advance. For qualitative traits, cluster and principal component analysis revealed two major clusters in Baham as well as in Ekona. The traits such as spines on stem base, spines on stem above base, spines length contributed to the variability within and between the accessions. However, the limits of morphological characters in the study of diversity have been detected. Key words: Dioscorea dumetorum, morphological traits, characterization, agro-climatic zone, Cameroon

Genetic diversity and population structure of trifoliate yam (Dioscorea dumetorum Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS)

Abstract Background Yams (Dioscorea spp.) are economically important food for millions of people in the humid and sub-humid tropics. Dioscorea dumetorum (Kunth) is the most nutritious among the eight-yam species, commonly grown and consumed in West and Central Africa. Despite these qualities, the storage ability of D. dumetorum is restricted by severe postharvest hardening of the tubers that can be addressed through concerted breeding efforts. The first step of any breeding program is bound to the study of genetic diversity. In this study, we used the Genotyping-By-Sequencing of Single Nucleotide Polymorphism (GBS-SNP) to investigate the genetic diversity and population structure of 44 accessions of D. dumetorum in Cameroon. Ploidy was inferred using flow cytometry and gbs2ploidy. Results We obtained on average 6371 loci having at least information for 75% accessions. Based on 6457 unlinked SNPs, our results demonstrate that D. dumetorum is structured into four populations. We clearly identified, a western/north-western, a western, and south-western populations, suggesting that altitude and farmers-consumers preference are the decisive factors for differential adaptation and separation of these populations. Bayesian and neighbor-joining clustering detected the highest genetic variability in D. dumetorum accessions from the south-western region. This variation is likely due to larger breeding efforts in the region as shown by gene flow between D. dumetorum accessions from the south-western region inferred by maximum likelihood. Ploidy analysis revealed diploid and triploid levels in D. dumetorum accessions with mostly diploid accessions (77%). Male and female accessions were mostly triploid (75%) and diploid (69%), respectively. The 1C genome size values of D. dumetorum accessions were on average 0.333 ± 0.009 pg and 0.519 ± 0.004 pg for diploids and triploids, respectively. Conclusions Germplasm characterization, population structure and ploidy are an essential basic information in a breeding program as well as for conservation of intraspecific diversity. Thus, results obtained in this study provide valuable information for the improvement and conservation of D. dumetorum. Moreover, GBS appears as an efficient powerful tool to detect intraspecific variation

Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum

Storage ability of trifoliate yam (Dioscorea dumetorum) is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in D. dumetorum. To the best of our knowledge, the candidate genes responsible for the hardening of D. dumetorum have not been identified. Here, transcriptome analyses of D. dumetorum tubers were performed in yam tubers of four developmental stages: 4 months after emergence (4MAE), immediately after harvest (AH), 3 days after harvest (3DAH) and 14 days after harvest (14DAH) of four accessions (Bangou 1, Bayangam 2, Fonkouankem 1, and Ibo sweet 3) using RNA-Seq. In total, between AH and 3DAH, 165, 199, 128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3, respectively. Functional analysis of DEGs revealed that genes encoding for CELLULOSE SYNTHASE A (CESA), XYLAN O-ACETYLTRANSFERASE (XOAT), CHLOROPHYLL A/B BINDING PROTEIN1, 2, 3, 4 (LHCB1, LHCB2, LHCB3, and LCH4) and an MYB transcription factor were predominantly and significantly up-regulated 3DAH, implying that these genes were potentially involved in the PHH as confirmed by qRT-PCR. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into gene expression in yam tubers after harvest and valuable information for molecular breeding against the PHH

High Contiguity de novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing

Trifoliate yam (Dioscorea dumetorum) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. A total of 35,269 protein-encoding gene models as well as 9941 non-coding RNA genes were predicted, and functional annotations were assigned