Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.10.18.562915

Identification and analysis of genomic regions influencing leaf morpho-physiological traits related to stress responses in Dioscorea alata

Dossa, K.·Houngbo, M. E.·Irep, J. L.·Chair, H.·Cornet, D.
View original source ↗Export metadata ↓

Abstract

BackgroundYams (Dioscorea spp.) are significant food security crops especially in West Africa. With the increasing tuber demand and climate change challenges, it is pertinent to strengthen breeding programs for developing high-yielding cultivars with climate resilience. The current study aimed at deciphering the genetic basis of leaf traits related to stress responses in a diverse panel of Dioscorea alata genotypes. ResultsPhenotypic characterization of 12 traits, including leaf dry matter content, leaf area, net photosynthesis, transpiration rate, transpiration use efficiency, stomatal density, stomatal index, node number, leaf thickness, competitor, stress-tolerator, ruderal (CSR) ecological strategy spectrum emphasized significant variations among the genotypes and across two planting locations. Weak correlations were observed among most of traits, suggesting that breeding simultaneously for some of these stress response-related traits would be possible. Heritability was highest for transpiration rate, leaf area and stomatal density, while it was lowest for stress-tolerator, ruderal ecological strategies. Genome-wide association study (GWAS) using high-quality single nucleotide polymorphism (SNPs) identified 24 significant associations on 11 chromosomes, where the association signals were consistent across two locations for traits with high heritability, viz., stomatal density (Chr18) and transpiration rate (Chr3). Further characterization of the significant signals and their related alleles identified advantageous alleles contributing positively to the studied traits. Moreover, 44 putative candidate genes were identified. Dioal.18G049300 (3 keto acyl-coenzyme A synthase) was identified as a strong candidate gene for stomatal density, while Dioal.12G033600 (Phosphatidyl inositol monophosphate 5 kinase 4) was identified for net photosynthesis. ConclusionTaken together, GWAS and allele segregation analysis for key SNPs provided significant insights into the marker-trait associations, which can be further utilized in breeding programs to improve climate resilience in greater yam.

Explore related subjects

plant biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Dossa, K., Houngbo, M. E., Irep, J. L., Chair, H., Cornet, D.. 2023-10-20. Identification and analysis of genomic regions influencing leaf morpho-physiological traits related to stress responses in Dioscorea alata. https://doi.org/10.1101/2023.10.18.562915

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Molecular and phytochemical investigation of medicinal Rhododendron spp. in the Qinghai-Xizang Plateau: the botanical sources of the traditional Tibetan medicine "Tale"

The Qinghai-Xizang Plateau in China is a hotspot for Rhododendron species, with approximately 400 species distributed across the region. Various Rhododendron species in this area have been used medicinally in traditional Tibetan medicine for a long time and are collectively referred to as "Tale." Furthermore, "Tale" is classified as "Talegabao" or "Talenabao," depending on the species. These two types of medicine have similar but distinct properties, and "Talenabao" is usually used as an alternative to "Talegabao." However, differences in their phytochemical compositions and methods for discriminating between them have not been examined. To solve these problems limited the use of "Tale" medicines, 46 plant specimens belonging to nine Rhododendron species were collected from the Qinghai-Xizang Plateau. Molecular methods based on the internal transcribed spacer 2 (ITS2) region of nuclear DNA and psbA-trnH regions of chloroplast DNA were applied to these samples. In addition, 10 flavonoid compounds were quantitatively determined by HPLC. The results indicated psbA-trnH region successfully distinguished the species used as "Talegabao" or "Talenabao," whereas ITS2 failed to distinguish them because of its high degree of conservation. All 10 compounds were detected in all samples. However, the species used as "Talegabao" had more than twice the total content of the 10 flavonoid compounds observed in the species used as "Talenabao." Moreover, differences in the contents of certain compounds among species were detected, indicating potential chemical markers for the quality evaluation of "Tale" medicines. "Talegabao" is the first choice among "Tale" medicines. "Talenabao" can be used as an alternative to "Talegabao"; however, the appropriate dose requires further discussion in practical use. The psbA-trnH region is recommended as a DNA barcode for distinguishing between these two types of medicines.

plant biology↗
bioRxiv2026

Accessory B Chromosomes Alter Chromatin Accessibility and Gene Expression in Maize Pollen Nuclei

B chromosomes in maize (Zea mays L.) are supernumerary, nonessential chromosomes that exhibit non-Mendelian inheritance through chromosome drive. During the second pollen mitosis, they undergo nondisjunction, resulting in their preferential transmission via B-containing sperm cells. Although their transmission mechanisms have been extensively characterized, the effects on chromatin organization and transcriptional regulation in gametophytic cells remain poorly understood. Here, we combined flow cytometric sorting of pollen nuclei with an assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to investigate the impact of B chromosomes on chromatin accessibility and gene expression in mature maize pollen. Using pollen nuclei isolated from a maize inbred line B73 carrying zero and two B chromosomes, we generated high-purity datasets suitable for integrated chromatin and transcriptomic analyses. We identified extensive chromatin accessibility and transcriptional activity at B-chromosome loci. Importantly, the presence of B chromosomes was also associated with altered chromatin accessibility and gene expression on the standard A chromosomes, revealing regulatory effects extending beyond the B chromosome itself. Together, these findings contribute to a broader understanding of effects of selfish genetic elements in plants.

plant biology↗
bioRxiv2026

Melanoidins Suppress Cucumber and Tomato Diseases Incited by Pathogens that are Oomycetes, Bacteria and a Virus

We recently reported that solutions of the nitrogenous compounds melanoidins (M), that are formed during the final stages of the Maillard Reaction, are inducers of plant resistance (Elad et al. 2026). M promoted immunity and induced disease resistance through an effect on the transcriptome, primarily through the salicylic acid pathway. Here we tested the effect of M on plant diseases that are caused by Oomycetes, bacteria and a tobamovirus. Drench and spray of M suppressed Pythium aphanidermatum damping off in cucumber, cucumber downy mildew (Pseudoperonospera cubensis), tomato late blight (Phytophthora infestans), bacterial speck (Pseudomonas syringae pv. tomato), bacterial canker (Clavibacter michiganensis subsp. michiganensis) and the Tobamovirus Tomato brown rugose fruit virus (ToBRFV) in tomato. In various experiments control was achieved by concentrations of 0.03 and 0.1% and on older and younger leaves and even in long term experiments where the M was applied for ca 11 weeks. It can be concluded that the disease resistance inducer M can suppress soilborne and foliar diseases that are caused by Oomycetes, bacteria and a virus of the genus Tobamovirus, in addition to the fungal pathogen Botrytis cinerea reported earlier.

plant biology↗