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.

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.

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.