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Background: Consumers' preferences for food crops are guided by quality attributes. This study aimed at deciphering the genetic basis of quality traits, especially tuber flesh color (FC) and oxidative browning (OB) in Dioscorea alata, based on the genome-wide association studies (GWAS) approach. The D. alata panel was planted at two locations in Guadeloupe. At harvest, the FC was scored visually as white, cream, or purple on longitudinally sliced mature tubers. The OB was scored visually as the presence or absence of browning after 15 minutes of exposure of the sliced samples to ambient air. Results: Phenotypic characterization for FC and OB of a diverse panel of D. alata genotypes highlighted significant variation within the panel and across two locations. The genotypes within the panel displayed a weak structure and could be classified into 3 subpopulations. GWAS identified 14 and 4 significant associations for tuber FC and OB, respectively, with phenotypic variance, explained values ranging from 7.18 to 18.04%. Allele segregation analysis at the significantly associated loci highlighted the favorable alleles for the desired traits, i.e., white FC and no OB. A total of 24 putative candidate genes were identified around the significant signals. A comparative analysis with previously reported quantitative trait loci indicated that numerous genomic regions control these traits in D. alata. Conclusion: Our study provides important insights into the genetic control of tuber FC and OB in D. alata. The major and stable loci can be further utilized to improve selection in breeding programs for developing new cultivars with enhanced tuber quality.

Societal Impact Statement Yam plays an important role in ensuring food security in Côte d'Ivoire, serving as a staple crop for 60% of the population and a significant source of income. It holds deep cultural significance for the Akan and Gour ethnic groups. Preserving yam production is essential for both food security and the preservation of cultural heritage. However, productivity is decreasing while demand is expected to double in the next 30 years. Soil degradation and climate change are major threats to yam production. This article contextualizes the main factors threatening yam production (i.e., soil degradation and climate change) and discusses the consequences and ways to mitigate them. Summary The anticipated twofold increase in Côte d'Ivoire's population within the next three decades poses a significant challenge for agricultural research to sustain food security. Despite being an under-researched and often neglected crop, yam remains the primary staple food and a crucial source of income in the country. With an annual estimated market value of over 2000 billion CFA francs, yam ranks among the top five most economically valuable crops in Côte d'Ivoire. For the past 15 years, yam production has experienced a decline in productivity, which has been compensated for by expanding the cropped area. Unfortunately, this approach exacerbates the risk of deforestation and soil degradation. Additionally, the impact of climate change on yam production, coupled with a lack of financial resources to address it, has rendered this unsustainable mode of production even more precarious. The purpose of this study is to provide an overview of the effects of climate change on yam production in Côte d'Ivoire. We investigated the reasons for the productivity decline and described the risks on food security. Furthermore, we explained how varietal innovation of Dioscorea alata could play a critical role in mitigating these effects and outlined related research avenues that need to

Societal Impact Statement : Yam is a major tropical root crop and a staple food for millions of people in West Africa. The model used in this study shows that promoting the use of improved seed tubers would help increase yields and profitability for farmers. This could lead to improved food security, increased income and higher standards of living. Additionally, the model serves as a useful decision-support tool for farmers and technicians to choose, depending on the species, the optimum seed-tuber weight and planting date. This study provides agronomic arguments to justify investments in the improvement of yam planting materials in West Africa. Summary: Yam (Dioscorea spp.) is a major tropical root crop, grown mainly in West Africa using traditional extensive techniques. Farmers typically reuse seed tubers by setting aside up to 30% of their production for the next season, leading to high planting material variability that affects yields. Several initiatives aim to promote the use of improved seed tubers. However, to help their adoption, it is necessary to quantify the agronomic and economic advantages. To address this, a model for individual plant growth and development was developed based on six experiments in Benin from 2007 to 2009. This model simulates the combined effect of emergence (through photoperiod and temperature) and seed-tuber weight on yam plant growth and development. Its predictions were highly correlated with observed plant tuber yield (R2 > 0.83). Results highlight the crucial role of key processes such as seed-tuber physiological age and photoperiod sensitivity. The study shows that for the traditional planting dates, the use of improved planting material could lead to a yield increase of 22%–27% and a gain in profitability of 30% and 40% for Dioscorea alata and Dioscorea rotundata, respectively. The model proved to be a useful decision-support tool for choosing an optimum seed-tuber weight, depending on the species and the planting date. This

Various biological constraints including erratic and asynchronous flowering between male and female plants hinder successful hybrid development and genetic gains in greater yam breeding programs. Therefore, pollen storage has gained much attention to facilitate artificial pollinations and increase the genetic gains. This 4-year study aimed at developing a practical long-term pollen storage technique for the successful development of yam hybrids. Fresh pollens were collected from two Dioscorea alata males, then lyophilized (two lyophilization treatments were applied), followed by storage at room temperature (24°C–25°C) for 12 months. Moreover, the lyophilized and stored pollens were tested for viability by crossing with four female varieties. Our results showed that lyophilization is effective for achieving viable pollens after 12 months of storage. Treatment 1 (48 h drying) showed higher pollen germination and fertility rates than Treatment 2 (72 h drying). Although we observed a reduction in viability of lyophilized pollens after 12 months of storage, we generated hybrid seedlings with success rates from 12% to 21% compared to 21%–31% when using fresh pollens. Paternity testing based on molecular genotyping confirmed the hybrid status of the obtained seedlings, which grew well in a greenhouse. Lyophilization is a practical approach for a long-term storage of greater yam pollen samples. This protocol will positively impact yam breeding programs particularly in developing countries.

Background: Cadmium (Cd) pollution of soils is a global concern because its accumulation in plants generates severe growth retardation and health problems. Hibiscus syriacus is an ornamental plant that can tolerate various abiotic stresses, including Cd stress. Therefore, it is proposed as a plant material in Cd-polluted areas. However, the molecular mechanisms of H. syriacus tolerance to Cd are not yet understood. Results: This study investigated the physiological and transcriptional response of “Hongxing”, a Cd2+-tolerant H. syriacus variety, grown on a substrate containing higher concentration of Cd (400 mg/kg). The Cd treatment induced only 28% of plant mortality, but a significant decrease in the chlorophyll content was observed. Malondialdehyde content and activity of the antioxidant enzymes catalase, peroxidase, and superoxide dismutase were significantly increased under Cd stress. Transcriptome analysis identified 29,921 differentially expressed genes (DEGs), including 16,729 down-regulated and 13,192 up-regulated genes, under Cd stress. Functional enrichment analyses assigned the DEGs mainly to plant hormone signal transduction, transport, nucleosome and DNA processes, mitogen-activated protein kinase signaling pathway, antioxidant process, fatty acid metabolism, and biosynthesis of secondary metabolites. Many MYB, EP2/ERF, NAC, WRKY family genes, and genes containing metal binding domains were up-regulated, implying that they are essential for the Cd-stress response in H. syriacus. The most induced genes were filtered out, providing valuable resources for future studies. Conclusions: Our findings provide insights into the molecular responses to Cd stress in H. syriacus. Moreover, this study offers comprehensive and important resources for future studies toward improving the plant Cd tolerance and its valorization in phytoremediation.

Sesame (Sesamum indicum L.) is a significantly lucrative cash crop for millions of small-holder farmers. Its seeds are an important source of a highly appreciated vegetable oil globally and two clinically essential antioxidant lignans, sesamin and sesamolin. Accordingly, many countries import millions of tons of sesame seed every year. The demand for lignan-rich sesame seeds has been increasing in recent years due to the continuous discovery of several pharmacological attributes of sesamin and sesamolin. To meet this demand, the sesame breeder's primary objective is to release sesame cultivars that are enriched in oil and lignans. Thus, it is necessary to summarize the information related to the sesamin and sesamolin contents in sesame in order to promote the joint efforts of specialized research teams on this important oilseed crop. In this article, we present the current knowledge on the sesamin and sesamolin contents in S. indicum L. with respect to the updated biosynthesis pathway, associated markers, governing loci, available variability in sesame germplasm, the in planta potential roles of these compounds in sesame, and the newly discovered pharmacological attributes. In addition, we propose and discuss some required studies that might facilitate genomics-assisted breeding of high lignan content sesame varieties.

Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.

Peroxidases and laccases are oxidative enzymes involved in physiological processes in plants, covering responses to biotic and abiotic stress as well as biosynthesis of health-promoting specialized metabolites. Although they are thought to be involved in the biosynthesis of (+)-pinoresinol, a comprehensive investigation of this class of enzymes has not yet been conducted in the emerging oil crop sesame and no information is available regarding the potential (+)-pinoresinol synthase genes in this crop. In the present study, we conducted a pan-genome-wide identification of peroxidase and laccase genes coupled with transcriptome profiling of diverse sesame varieties. A total of 83 and 48 genes have been identified as coding for sesame peroxidase and laccase genes, respectively. Based on their protein domain and Arabidopsis thaliana genes used as baits, the genes were classified into nine and seven groups of peroxidase and laccase genes, respectively. The expression of the genes was evaluated using dynamic transcriptome sequencing data from six sesame varieties, including one elite cultivar, white vs black seed varieties, and high vs low oil content varieties. Two peroxidase genes (SiPOD52 and SiPOD63) and two laccase genes (SiLAC1 and SiLAC39), well conserved within the sesame pan-genome and exhibiting consistent expression patterns within sesame varieties matching the kinetic of (+)-pinoresinol accumulation in seeds, were identified as potential (+)-pinoresinol synthase genes. Cis-acting elements of the candidate genes revealed their potential involvement in development, hormonal signaling, and response to light and other abiotic triggers. Transcription factor enrichment analysis of promoter regions showed the predominance of MYB binding sequences. The findings from this study pave the way for lignans-oriented engineering of sesame with wide potential applications in food, health and medicinal domains.

Developing crops with improved root system is crucial in current global warming scenario. Underexploited crops are valuable reservoirs of unique genes that can be harnessed for the improvement of major crops. In this study, we performed genome-wide association studies on seven root traits in sesame (Sesamum indicum L.) and uncovered 409 significant signals, 19 quantitative trait loci containing 32 candidate genes. A peak SNP significantly associated with root number and root dry weight traits was located in the promoter of the gene named 'Big Root Biomass' (BRB), which was subsequently validated in a bi-parental population. BRB has no functional annotation and is restricted to the Lamiales order. We detected the presence of a novel motif 'AACACACAC' located in the 5'-UTR of BRB in single and duplicated copy in accessions with high and small root biomass, respectively. A strong expression level of BRB was negatively correlated with high root biomass, and this was attributed to the gene SiMYB181 which represses the activity of BRB by binding specifically to the single motif but not to the duplicated one. Curiously, the allele that enhanced BRB expression has been intensively selected by modern breeding. Overexpression of BRB in Arabidopsis modulates auxin pathway leading to reduced root biomass, improved yield parameters under normal growth conditions and increased drought stress sensitivity. Overall, BRB represents a solid gene model for improving the performance of sesame and other crops.