Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD.

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.

Quantitative trait loci and candidate genes for physico-chemical traits related to tuber quality in greater yam (Dioscorea alata L.).

BACKGROUND: Starch, dry matter content (DMC), proteins, and sugars are among the major influences on yam tuber quality. Genetic improvement programs need simple, rapid, and low-cost tools to screen large populations. The objectives of this work were, using a quantitative trait loci mapping approach (QTL) on two diploid full-sib segregating populations, (i) to acquire knowledge about the genetic control of these traits; (ii) to identify markers linked to the genomic regions controlling each trait, which are useful for marker-assisted selection (MAS); (iii) to validate the QTLs on a diversity panel; and (iv) to identify candidate genes from the validated QTLs. RESULTS: Heritability for all traits was moderately high to high. Significant correlations were observed between traits. A total of 25 QTLs were identified, including six for DMC, six for sugars, six for proteins, and seven for starch. The phenotypic variance explained by individual QTLs ranged from 14.3% to 28.6%. The majority of QTLs were validated on a diversity panel, showing that they are not specific to the genetic background of the progenitors. The approximate physical location of validated QTLs allowed the identification of candidate genes for all studied traits. Those detected for starch content were mainly enzymes involved in starch and sucrose metabolism, whereas those detected for sugars were mainly involved in respiration and glycolysis. CONCLUSION: The validated QTLs will be useful for breeding programs using MAS to improve the quality of yam tubers. The putative genes should be useful in providing a better understanding of the physiological and molecular basis of these important tuber quality traits. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genome-wide association studies reveal novel loci controlling tuber flesh color and oxidative browning in Dioscorea alata.

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 min 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 three 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. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Identification and validation of QTLs for tuber quality related traits in greater yam (Dioscorea alata L.).

Two Dioscorea alata populations were generated by hand pollination between contrasted diploid genitors. Population A (74F × Kabusa) was composed of 121 progenies while population B (74F × 14M) involved 193 progenies. These two populations were assessed over two consecutive years regarding important tuber quality traits. Analysis of variance showed that the genotype had the greatest influence on the phenotypic scores. Also for some traits, effect of the year_replicate was strong. The heritabilities of most traits were high. Based on these data and a reference high-density genetic map of greater yam, a total of 34 quantitative trait loci (QTLs) were detected on 8 of the 20 yam chromosomes. They corresponded to five of each of the following traits: tuber size, shape regularity, tubercular roots, skin texture, tuber flesh oxidation, six for oxidation ratio and three for flesh colour. The fraction of total phenotypic variance attributable to a single QTL ranged from 11.1 to 43.5%. We detected significant correlations between traits and QTL colocalizations that were consistent with these correlations. A majority of QTLs (62%) were found on linkage group LG16, indicating that this chromosome could play a major role in genetic control of the investigated traits. In addition, an inversion involving this chromosome was detected in the Kabusa male. Nine QTLs were validated on a diversity panel, including three for tuber size, three for shape regularity, two for skin texture and one for tubercular roots. The approximate physical localization of validated QTLs allowed the identification of various candidates genes. The validated QTLs should be useful for breeding programs using marker-assisted selection to improve yam tuber quality.

Genetic control of flowering in greater yam (Dioscorea alata L.).

BACKGROUND: Greater yam (Dioscorea alata L.) is a major tropical and subtropical staple crop cultivated for its starchy tubers. Breeding of this dioecious species is hampered by its erratic flowering, yet little is currently known on the genetic determinism of its sexual reproduction. RESULT: Here we used a genome-wide association approach and identified a major genetic barrier to reproduction in yam on chromosome 1, as represented by two candidate genes. A deleterious effect on male fitness could be hypothesized considering the involvement of these two genes in male reproduction and the low frequency of this non-flowering dominant allele within the male genepool. We also extended the hypothesis of a XX/XY sex-determination system located on chromosome 6 in D. alata to encompass most of the species diversity. Moreover, a kompetitive allele-specific PCR (KASPar) marker was designed and validated that enables accurate cultivar sex estimation. The reconstruction of chromosome 6 associated with the detection of highly putative structural variations confirmed the possible involvement of a major part of the chromosome. CONCLUSION: The findings of this study, combined with proper estimation of accession ploidy levels to avoid endosperm incompatibility issues, could facilitate the design of future promising parental combinations in D. alata breeding programs. Moreover, the discovery of this genetic barrier to reproduction opens new avenues for gaining insight into yam reproductive biology and diversification.

Development of a cost-effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections.

Using genome-wide single nucleotide polymorphism (SNP) discovery in greater yam (Discorea alata L.), 4,593 good quality SNPs were identified in 40 accessions. One hundred ninety six of these SNPs were selected to represent the overall dataset and used to design a competitive allele specific PCR array (KASPar). This array was validated on 141 accessions from the Tropical Plants Biological Resources Centre (CRB-PT) and CIRAD collections that encompass worldwide D. alata diversity. Overall, 129 SNPs were successfully converted as cost-effective genotyping tools. The results showed that the ploidy levels of accessions could be accurately estimated using this array. The rate of redundant accessions within the collections was high in agreement with the low genetic diversity of D. alata and its diversification by somatic clone selection. The overall diversity resulting from these 129 polymorphic SNPs was consistent with the findings of previously published studies. This KASPar array will be useful in collection management, ploidy level inference, while complementing accurate agro-morphological descriptions.

A reference high-density genetic map of greater yam (Dioscorea alata L.).

KEY MESSAGE: This study generated the first high-density genetic map for D. alata based on genotyping-by-sequencing and provides new insight on sex determination in yam. Greater yam (Dioscorea alata L.) is a major staple food in tropical and subtropical areas. This study aimed to produce the first reference genetic map of this dioecious species using genotyping-by-sequencing. In this high-density map combining information of two F1 outcrossed populations, 20 linkage groups were resolved as expected and 1579 polymorphic markers were ordered. The consensus map length was 2613.5 cM with an average SNP interval of 1.68 cM. An XX/XY sex determination system was identified on LG6 via the study of sex ratio, homology of parental linkage groups and the identification of a major QTL for sex determination. Homology with the sequenced D. rotundata is described, and the median physical distance between SNPs was estimated at 139.1 kb. The effects of segregation distortion and the presence of heteromorphic sex chromosomes are discussed. This D. alata linkage map associated with the available genomic resources will facilitate quantitative trait mapping, marker-assisted selection and evolutionary studies in the important yet scarcely studied yam species.