Yam belongs to the Dioscorea species and plays a crucial role in ensuring food security in East and West Africa (Kilimo Trust, 2013). It is well-suited for market-driven production intensification because of its high market value and strong consumer demand (Haneishi et al., 2013). Dioscorea rotundata, often known as white yam or Guinea yam is a vital tuber crop with significant economic and dietary importance in several regions worldwide. The crop often known as the “old man” crop is cultivated by older individuals in Uganda (Adjei et al., 2022a). It is sometimes confused with the Colocasia species due to their similar tuber-producing nature (Kagoda et al., 2005). Over the past two decades, there has been limited progress in enhancing the production and quality of yams compared to other roots and tuber crops. This is particularly evident in East Africa, despite the significant socio-economic importance of yams. Nevertheless, in Uganda, yam breeding endeavors have not adequately explored the genetic foundation of valuable characteristics such as tuber quality and yield. This has hindered the rapid development of improved cultivars (Adjei et al., 2022a).. The improvement of several characteristics of yam such as resistance to pests and diseases, tuber production and quality is a challenging task due to their quantitative inheritance (Mignouna et al., 2001; Nemorin et al., 2012). While conventional breeding methods (Mass selection, phenotypic classification and hybridization) have been successful in improving many crop traits, there are certain traits that are not easily manipulated using these techniques. These traits often involve complex genetic traits influenced by multiple genes and environmental interactions (Acquaah, 2012).

The behavior of yams specifically in relation to their dry matter content (DMC), yield (TWY), and susceptibility to yam mosaic virus (YMV) has captured the attention of scholars, farmers, and breeders alike. To achieve sustainable yam production, provide food security and effectively manage diseases, it is critical to have a thorough understanding of these traits. The agricultural relevance and socio-economic effect of D. rotundata are greatly influenced by its dry matter content, yield, and sensitivity to yam mosaic virus (Mignouna et al., 2001). Continued research and innovative approaches in yam production are crucial for fully utilizing the potential of this important commodity. This is especially important as global concerns in food security and sustainable agriculture persist and evolve over time (Adeniji et al., 2012).

Dry matter content is a determinant of yam quality representing the remaining portion of the yam tuber after the removal of water content. The trait has a direct influence on the taste, consistency and nutritional composition of the yam. Due to its indication of a greater abundance of essential nutrients such as carbohydrates, a larger dry matter content is sometimes favored (Gatarira et al., 2020). To improve tuber quality and increase consumer satisfaction, researchers have been investigating the traits that influence dry matter content in Dioscorea rotundata. These traits include environmental conditions, cultivation methods, and genetic factors (Adjei et al., 2022b).. Yield, a significant trait of Dioscorea rotundata which constitutes the quantity of tubers generated within a given area (Wu et al., 2015). Optimizing yam output is important for meeting the food needs of growing populations and ensuring the economic prosperity of farmers (Adeniji et al., 2012). Yam productivity is influenced by crucial elements such as soil quality, planting density, pest and disease control, and proper watering. Scientists and agricultural experts are still exploring efficient methods to enhance yam production while maintaining environmental sustainability.

The cultivation of Dioscorea rotundata is significantly threatened by Yam mosaic virus (Mignouna et al., 2001). It is a viral disease that results in the formation of unique mosaic patterns on the leaves of yam plants. This leads to a decrease in the plant’s ability to carry out photosynthesis, resulting in stunted growth and reduced output of yam tubers (Sorho Fatogoma Brahima Kone YKA& GOEDJB and Ettien Djecthi Jean Baptiste SFBKYKA& GO, 2014). Effectively managing YMV requires implementing a range of preventative strategies. These include using virus-free planting materials, adhering to proper sanitation practices, and employing cultivars that are resistant to the virus (Sorho Fatogoma Brahima Kone YKA& GOEDJB and Ettien Djecthi Jean Baptiste SFBKYKA& GO, 2014). Gaining insight into the interplay between Dioscorea rotundata and YMV is essential for devising efficient approaches to alleviate the adverse effects of this disease on yam cultivation (Adjei et al., 2022b).

The use of advanced breeding methods, such as genomic selection into yam improvement initiatives is anticipated to address complex challenges by enhancing the pace and effectiveness of breeding (Sugihara et al., 2020). The development of next-generation sequencing (NGS) technology has allowed for the discovery and utilization of single nucleotide polymorphism (SNP) markers that are associated with certain traits. These markers may be used to aid in breeding programs for important crops (Bhattacharjee et al., 2013). A genome sequence assembly for Dioscorea rotundata has been recently published (Siadjeu et al., 2020). This development enables the utilization of high-density markers for Genome-Wide Association Studies (GWAS) to identify genomic regions associated with specific traits (Tamiru et al., 2017). Additionally, it allows for the accurate placement of SNPs at these specific locations. GWAS has been extensively employed to identify the intricate genes responsible for economic traits in crops. These qualities encompass disease resistance and quality improvement which are crucial for efficient breeding and genetic analysis (Cuevas et al., 2018; Ahn et al., 2019).

SNP Markers have been utilized in yams for a range of research, encompassing genetic analysis of tuber yield and yam mosaic tolerance (Agre et al., 2021), analysis of sex determination and cross-compatibility (Mondo et al., 2021), determination of paternity in yams (Norman et al., 2020), development of molecular markers (Girma et al., 2019), examination of yam hybrid origin at the genome level (Sugihara et al., 2020), and exploration of yam diversity (Loko et al., 2016; Agre et al., 2019; Bhattacharjee et al., 2020; Sugihara et al., 2020; Amponsah Adjei et al., 2023). The identification of favorable SNP alleles through QTL discovery is relevant for enhancing key traits via marker-assisted selection (MAS). Incorporating genomic-assisted breeding tools into yam breeding programs is anticipated to expedite genetic improvements for prioritized traits. This objective can be realized by elucidating the genetic mechanisms governing these traits, thereby enabling the systematic application of MAS for forward breeding.

Thus, this study aimed at identifying genomic regions associated with yield, YMV and dry matter content in Dioscorea rotundata species. The yam breeding program will benefit from the identified genomic areas in the marker-assisted selection process for the important traits under investigation. Furthermore, this study will establish a basis for genetic improvement and variety breeding for yams in Uganda by offering information for the investigation of high yielding, disease resistance-related, and high dry matter genes.

The study revealed an extensive genome-wide association analysis to pinpoint quantitative trait nucleotides associated with key agronomic traits in yam, such as Yam Mosaic Virus resistance, yield, and dry matter content. The analysis uncovered significant and informative variances among these traits. Employing multi-random mixed linear model approaches in mrMLM, five different gene action models were utilized. Across two seasons, a total of 16 SNP markers were identified. Similar chromosomal regions linked to yield and dry matter content were reported in previous studies (Agre et al., 2021).

This study identified four gene/protein families linked to yam mosaic virus disease: Glucan endo-1,3-beta-glucosidase 8 (Henrissat and Davies, 2000; Mouyna et al., 2000; Barral et al., 2004), Nuclear pore complex protein NUP62 (Bailer et al., 2001), Cold-responsive protein kinase 1; Probable LRR receptor-like (Manning et al., 2002; Li et al., 2004; Stout et al., 2004) and G-type lectin S-receptor-like serine/threonine-protein (Hanks and Quinn, 1991). These genes are located on chromosomes 9, 15 and 19, respectively.

According to Barral (Barral et al., 2004), the X8 domain contains at least 6 conserved cysteine residues that presumably form three disulphide bridges. The domain is found in an Olive pollen allergen as well as at the C-terminus of several families of glycosyl hydrolases and observed to be involved in carbohydrate binding. It is characteristic of GPI-anchored domains. Moreover, some of the identified genes such as protein phosphorylation play a key role in most cellular activities. Additionally they serve as a reversible process mediated by protein kinases and phosphoprotein phosphatases (Hanks and Quinn, 1991). Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function (Hanks and Quinn, 1991). In contrast to the findings of Agre et al (Agre et al., 2021), they identified single nucleotide polymorphisms (SNPs) on chromosome 3 that are linked to yam mosaic virus. These SNPs are located close proximity to genes encoding the AP2/ERF domain, AUX/IAA protein, major facilitator, and sugar transporter-like proteins. The findings of these studies might expedite the use of SNP variations to assist selection decisions in breeding white Guinea yam for genotype selection with resistance to mosaic virus in Uganda.

For the yam tuber yield we identified several important genes related to total tuber weight, including Phoenix dactylifera coatomer subunit delta-2-like, COMPASS-like H3K4 histone methylase component WDR5AARATH, Vicilin-like seed storage protein At2g28490ARATH, Ananas comosus IAA-amino acid hydrolase ILR1-like 3 and Late exocytosis, associated with Golgi transport. According to Li and Roberts (2001), the Vicilin-like seed storage protein At2g28490 protein family is a representation of the conserved barrel domain of the ‘cupin’ superfamily. This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant (Dunwell, 1998). Also, Ananas comosus IAA-amino acid hydrolase gene consisted of 4 beta strands and two alpha helices which make up the dimerization surface of members of the M20 family of peptidases. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases (Rowsell et al., 1997).

The identification of protein function led to the discovery of two putative genes related to dry matter content. The potential genes identified on chromosome 18 including Transcription initiation factor TFIID subunit 12b and Growth-regulating factor 1 at 24.1 Mb and 21.6 Mb respectively. The TFIID is one of several General Transcription Factors (GTFs), which also include TFIIA, TFIIB, TFIIE, TFIIF and TFIIH, that are involved in the accurate initiation of transcription by RNA polymerase II in eukaryotes (Gazit et al., 2009). TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex (Gazit et al., 2009). In addition, Kim (Kim et al., 2003) indicated that the WRC domain, named after the conserved Trp-Arg-Cys motif, contains two distinctive features: a putative nuclear localization signal and a zinc-finger motif (C3H). It is suggested that the WRC domain functions in DNA binding. In their study on water yams, (Gatarira et al., 2020) presented findings that found QTLs correlated with tuber dry matter at different sites. (Kayondo et al., 2018) discovered similar results and revealed that traits such as panel size, harvest time, and environment influence the discovery of quantitative trait loci (QTLs) related to virus disease. To address this issue, the most effective approach for enhancing the connections between traits and (QTLs) is to combine phenotypic scores from numerous locations with genotypic data utilizing diverse panels of individuals (Jing et al., 2018).

The study revealed that loci with varying effects can influence the variability of the traits examined in Dioscorea rotundata. This study identified distinct genomic regions harboring genes related to flowering development and disease resistance in yam germplasm. These findings should be further confirmed and evaluated. To do this, the QTLs may be converted into cost-effective Kompetitive Allele-Specific PCR (KASPs) markers, which can then be efficiently utilized to transfer alleles into high-quality yam genotypes. The results of this work might potentially aid in the development of novel breeding strategies for preserving advantageous genetic traits related to disease resistance and tuber production in certain yam genotypes, with the aim of enhancing future marker-based breeding efforts. The chromosomal regions responsible for these analyzed traits might be utilized for the purpose of selecting and efficiently combining advantageous alleles in order to enhance the population of Dioscorea rotundata. Certain roles and characteristics of the identified genes remain unexplored. Future studies on investigating the action mode of these genes in yam will help to elucidate the expression/regulation of these

Using five models, we identified 12 SNP markers associated with the three important traits. Through the allele’s analysis, we identified as well promising alleles to be used for markers-assisted selection. Several genes linked to plant defense mechanism, plant growth, to tuber accumulation were reported. Future investigation such as gene expression may be required for gene profiling to understand the genetic basis in Uganda’s D. rotundata gene pool. Moreover, the discoveries might prove valuable for the verification and integration of markers in the process of yam breeding.