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

Cormier, Fabien; Martin, Guillaume; Vignes, Hélène; Lachman, Laurie; Cornet, Denis; Faure, Yoana; Maledon, Erick; Mournet, Pierre; Arnau, Gemma; Chaïr, Hâna

doi:10.1186/s12870-021-02941-7

Cited by 19 publications

(29 citation statements)

References 47 publications

(46 reference statements)

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“…Moreover, the Kabusa male could also present inversions on other chromosomes and we intend to verify this through an exhaustive comparative analysis of the parental maps of all the chromosomes. Recently, we detected highly putative structural variations on chromosome 6, which is involved in the sex determinism (male = XY and female = XX) 19,62 . The latter study revealed significant differences in a region of about 3 Mb between chromosomes Y and X (probably related to structural variations).…”

Section: Qtl Colocalization and Yam Improvement Implicationsmentioning

confidence: 99%

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

Ehounou

Cormier²,

Maledon³

et al. 2022

Sci Rep

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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.

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Section: Qtl Colocalization and Yam Improvement Implicationsmentioning

confidence: 99%

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

Ehounou

Cormier²,

Maledon³

et al. 2022

Sci Rep

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“…Also, based on previous reports, there is a shift of sex determining locus across yam species. For example, recent studies on D. alata (using the GWAS) mapped significant sex-linked QTNs on chromosome 6 with a XX/XY sex-determination system [ 2 , 18 ]. These findings agreed with the conclusions from the quantitative trait loci (QTL) approach in two biparental populations [ 19 ].…”

Section: Discussionmentioning

confidence: 99%

“…Cormier et al [ 2 ] hypothesized that sex chromosome in yam is heteromorphic as putative highly male specific structural variants were detected between the sequenced male pools and the reconstructed male chromosome 6 of D. alata . No cytological evidence exists for D. rotundata on whether the sex chromosome 11 is acrocentric or metacentric, heteromorphic or homomorphic, due partly to the small size of Dioscorea chromosomes.…”

Section: Discussionmentioning

confidence: 99%

“…Creating variability for selection in plant breeding is achieved mainly through the hybridization of selected parents. However, in root and tuber crops, the ability for sexual reproduction (flowering, fertility, synchronization, and compatibility) was substantially affected as a consequence of the domestication process, which favored vegetative propagation at the expense of botanical seeds [ 1 , 2 ]. During the domestication process, traits related to sexual reproduction were neglected (not maintained), or in some contexts, directly counter-selected due to the associated costs [ 1 – 3 ].…”

Section: Introductionmentioning

confidence: 99%

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Association mapping of plant sex and cross-compatibility related traits in white Guinea yam (Dioscorea rotundata Poir.) clones

et al. 2022

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Background White Guinea yam (Dioscorea rotundata) is primarily a dioecious species with distinct male and female plants. Its breeding is constrained by sexual reproduction abnormalities, resulting in low success rates in cross-pollination. An accurate method for early detection of this plant’s sex and compatible fertile parents at the seedling stage would improve levels of cross-pollination success in breeding. We used the genome-wide association studies (GWAS) to dissect the molecular basis of plant sex and cross-compatibility-related traits in a panel of 112 parental clones used in D. rotundata crossing blocks from 2010 to 2020. Results Population structure and phylogeny analyses using 8326 single nucleotide polymorphism (SNP) markers grouped the 112 white yam clones into three subpopulations. Using Multi-locus random-SNP-effect Mixed Linear Model, we identified three, one, and three SNP markers that were significantly associated with the average crossability rate (ACR), the percentage of high crossability (PHC), and the plant sex, respectively. In addition, five genes considered to be directly linked to sexual reproduction or regulating the balance of sex hormones were annotated from chromosomal regions controlling the assessed traits. This study confirmed the female heterogametic sex determination (ZZ/ZW) system proposed for D. rotundata. Conclusions This study provides valuable insights on the genomic control of sex identity and cross-pollination success in D. rotundata. It, therefore, opens an avenue for developing molecular markers for predicting plant sex and cross-pollination success at the early growth stage before field sex expression in this crop.

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“…From the whole set used in this study, a total of 45 D. alata accessions harbouring a high genetic diversity were planted from 2018 to 2020 in May each year and harvested at full maturity in the following year between January and March at three different locations in Guadeloupe (Godet, Roujol and Duclos). The three locations have contrasting pedo-climatic conditions (Cormier et al, 2021). The phenotyping was performed on freshly harvested tubers.…”

Section: Plant Materialsmentioning

confidence: 99%

Genomic insights into greater yam tuber quality traits

Mota

Dossa

Léchaudel

et al. 2023

Preprint

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Yams are important tubers widely consumed in developing countries in various forms, mainly boiled, pounded and fried. Tuber quality is a key criterion for acceptance by the various actors in the value chain. However, the genetics of yam tuber quality has not yet been comprehensively investigated. Given this lack of knowledge, we used population genomics and candidate gene association approaches to unravel the genetic basis of the three main quality attributes of boiled yam, namely texture, starch content and colour indices. We re-sequenced the whole genome of 127 yam genotypes with different quality attributes and performed an enrichment of the already available functional genome annotation using comparative genomics. Population genomics analysis highlighted three main genetic groups and 1,053 genes under selection. We focused this work on three known quality trait-related pathways: pectin, starch content and flavonoid biosynthesis, and inventoried in the genome all the structural genes related to those pathways by comparative genomics. We improved the functional annotation of the three pathways with 48% more genes. A total of 18 candidate genes containing genetic variants significantly associated with the target traits were detected, including eight genes that were also found under selection. The texture-related candidate genes were distributed between the pectin and starch pathways. Overall, the use of comparative genomics has allowed the generation of an unprecedented genomic resource. The improved functional annotation of the yam genome is a promising predictive tool for identifying other core genes associated with any trait of interest to meet the growing need and diversified demands for yams.

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

Cited by 19 publications

References 47 publications

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

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

Association mapping of plant sex and cross-compatibility related traits in white Guinea yam (Dioscorea rotundata Poir.) clones

Genomic insights into greater yam tuber quality traits

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