Genome-Wide Association Studies for Sex Determination and Cross-Compatibility in Water Yam (Dioscorea alata L.)

Abstract

Yam (Dioscorea spp.) species are predominantly dioecious, with male and female flowers borne on separate individuals. Cross-pollination is, therefore, essential for gene flow among and within yam species to achieve breeding objectives. Understanding genetic mechanisms underlying sex determination and cross-compatibility is crucial for planning a successful hybridization program. This study used the genome-wide association study (GWAS) approach for identifying genomic regions linked to sex and cross-compatibility in water yam (Dioscorea alata L.). We identified 54 markers linked to flower sex determination, among which 53 markers were on chromosome 6 and one on chromosome 11. Our result ascertained that D. alata is characterized by the male heterogametic sex determination system (XX/XY). The cross-compatibility indices, average crossability rate (ACR) and percentage high crossability (PHC), were controlled by loci on chromosomes 1, 6 and 17. Of the significant loci, SNPs located on chromosomes 1 and 17 were the most promising for ACR and PHC, respectively, and should be validated for use in D. alata hybridization activities to predict cross-compatibility success. A total of 61 putative gene/protein families with direct or indirect influence on plant reproduction were annotated in chromosomic regions controlling the target traits. This study provides valuable insights into the genetic control of D. alata sexual reproduction. It opens an avenue for developing genomic tools for predicting hybridization success in water yam breeding programs.

Optimum time for hand pollination in yam (Dioscorea spp.)

“…In vitro pollen germination testing was performed regularly to ensure pollination results were not influenced by the pollen viability status. The previously optimized pollen germination testing protocol by Mondo et al (2021a) was used. This consisted of culturing anthers with pollen on Petri dishes containing a nutritive medium made of 10% sucrose, 100 ppm H 3 BO 3 , 300 ppm Ca(NO 3 ) 2 .4H 2 O, 200 ppm MgSO 4 .7H 2 O, and 100 ppm KNO 3 .…”

“…Most yam species, including D. alata and D. rotundata , are dioecious with male and female flowers on separate individuals (Agre et al, 2020; Mondo et al, 2020; 2021a; 2022). The gene flow between and among these species to meet breeding objectives depends, therefore, on crosspollination success.…”

Diversity of Water Yam (Dioscorea alata L.) Accessions from Côte d’Ivoire Based on SNP Markers and Agronomic Traits

“…In 2018, Côte d'Ivoire ranked as the third-largest yam producing country in the world after Nigeria and Ghana, with a cumulative yam production of 7.25 million tons [10]. The massive adoption of D. alata cultivation in the country stems from many factors, including ease of propagation, rapid growth allowing it to suppress weeds, stable yield under ranges of soil fertility and ecologies, long post-harvest tuber storage, and high nutritional values for human consumption and livestock feed [11][12][13][14].…”

“…Despite the importance of water yam as a staple food, youth employment, and income generation, many biotic and abiotic constraints threaten its production worldwide [14,15]. Yam production has mainly relied on the rapid increase in cultivated acreage rather than increased productivity per unit area, a farming system that encourages deforestation and degradation of natural resources [16].…”

“…Several Next-Generation Sequencing (NGS) techniques, including Genotyping-by-Sequencing (GBS) and Diversity Array Technology (DArT), have recently been developed. They have enabled the discovery and generation of genome-wide high-throughput markers, such as SNPs, for genetic mapping, quantitative trait loci (QTL) identification, and molecular plant breeding and genetic diversity studies in yam [2,14,18,[21][22][23][24]. However, little has been done to include molecular marker systems in the genetic diversity studies of D. alata accessions in Côte d'Ivoire, and existing information is still based on morphological data and marker systems with low reproducibility.…”