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Jiang Y, Lu XY, Qin YL, Zhang YM, Shao ZQ. Genome-Wide Identification and Evolutionary Analysis of Receptor-like Kinase Family Genes Provides Insights into Anthracnose Resistance of Dioscorea alata. PLANTS (BASEL, SWITZERLAND) 2024; 13:1274. [PMID: 38732488 PMCID: PMC11085297 DOI: 10.3390/plants13091274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Dioscorea alata, commonly known as "greater yam", is a vital crop in tropical and subtropical regions of the world, yet it faces significant threats from anthracnose disease, mainly caused by Colletotrichum gloeosporioides. However, exploring disease resistance genes in this species has been challenging due to the difficulty of genetic mapping resulting from the loss of the flowering trait in many varieties. The receptor-like kinase (RLK) gene family represents essential immune receptors in plants. In this study, genomic analysis revealed 467 RLK genes in D. alata. The identified RLKs were distributed unevenly across chromosomes, likely due to tandem duplication events. However, a considerable number of ancient whole-genome or segmental duplications dating back over 100 million years contributed to the diversity of RLK genes. Phylogenetic analysis unveiled at least 356 ancient RLK lineages in the common ancestor of Dioscoreaceae, which differentially inherited and expanded to form the current RLK profiles of D. alata and its relatives. The analysis of cis-regulatory elements indicated the involvement of RLK genes in diverse stress responses. Transcriptome analysis identified RLKs that were up-regulated in response to C. gloeosporioides infection, suggesting their potential role in resisting anthracnose disease. These findings provide novel insights into the evolution of RLK genes in D. alata and their potential contribution to disease resistance.
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Affiliation(s)
- Yuqian Jiang
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.J.); (Y.-L.Q.)
| | - Xin-Yu Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China;
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Ya-Li Qin
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.J.); (Y.-L.Q.)
| | - Yan-Mei Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China;
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Zhu-Qing Shao
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (Y.J.); (Y.-L.Q.)
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Mota APZ, Dossa K, Lechaudel M, Cornet D, Mournet P, Santoni S, Lopez D, Chaïr H. Whole-genome sequencing and comparative genomics reveal candidate genes associated with quality traits in Dioscorea alata. BMC Genomics 2024; 25:248. [PMID: 38443859 PMCID: PMC10916269 DOI: 10.1186/s12864-024-10135-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Quality traits are essential determinants of consumer preferences. Dioscorea alata (Greater Yam), is a starchy tuber crop in tropical regions. However, a comprehensive understanding of the genetic basis underlying yam tuber quality remains elusive. To address this knowledge gap, we employed population genomics and candidate gene association approaches to unravel the genetic factors influencing the quality attributes of boiled yam. METHODS AND RESULTS Comparative genomics analysis of 45 plant species revealed numerous novel genes absent in the existing D. alata gene annotation. This approach, adding 48% more genes, significantly enhanced the functional annotation of three crucial metabolic pathways associated with boiled yam quality traits: pentose and glucuronate interconversions, starch and sucrose metabolism, and flavonoid biosynthesis. In addition, the whole-genome sequencing of 127 genotypes identified 27 genes under selection and 22 genes linked to texture, starch content, and color through a candidate gene association analysis. Notably, five genes involved in starch content and cell wall composition, including 1,3-beta Glucan synthase, β-amylase, and Pectin methyl esterase, were common to both approaches and their expression levels were assessed by transcriptomic data. CONCLUSIONS The analysis of the whole-genome of 127 genotypes of D. alata and the study of three specific pathways allowed the identification of important genes for tuber quality. Our findings provide insights into the genetic basis of yam quality traits and will help the enhancement of yam tuber quality through breeding programs.
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Affiliation(s)
- Ana Paula Zotta Mota
- UMR AGAP, CIRAD, 34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
- Université Côte d'Azur, Institut Sophia Agrobiotech, INRAE, CNRS, Sophia Antipolis, PACA, 06903, France
| | - Komivi Dossa
- UMR AGAP, CIRAD, 34398, Montpellier, France
- CIRAD, UMR AGAP Institut, 97170, Petit Bourg, Guadeloupe, France
| | - Mathieu Lechaudel
- UMR Qualisud, CIRAD, F97130, Capesterre-Belle-Eau, Guadeloupe, France
- QualiSud, Université Montpellier, Institut Agro, CIRAD, Avignon Université, Université de La Réunion, 34398, Montpellier, France
| | - Denis Cornet
- UMR AGAP, CIRAD, 34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
| | - Pierre Mournet
- UMR AGAP, CIRAD, 34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
| | - David Lopez
- UMR AGAP, CIRAD, 34398, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France.
| | - Hana Chaïr
- UMR AGAP, CIRAD, 34398, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France.
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Mondo JM, Agre PA, Chuma GB, Asiedu R, Akoroda MO, Asfaw A. Agronomic and hormonal approaches for enhancing flowering intensity in white Guinea yam ( Dioscorea rotundata Poir.). FRONTIERS IN PLANT SCIENCE 2023; 14:1250771. [PMID: 37877088 PMCID: PMC10593412 DOI: 10.3389/fpls.2023.1250771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023]
Abstract
Developing novel white Guinea yam (Dioscorea rotundata) varieties is constrained by the sparse, erratic, and irregular flowering behavior of most genotypes. We tested the effectiveness of nine agronomic and hormonal treatments to enhance flowering on D. rotundata under field conditions. Genotypes responded differently to flower-inducing treatments (p<0.001). Of the test treatments, pruning and silver thiosulfate (STS) were effective in increasing the number of spikes per plant and the flowering intensity on both sparse flowering and monoecious cultivars. STS and tuber removal treatments promoted female flowers on the monoecious variety while pruning and most treatments involving pruning favored male flowers. None of the treatments induced flowering on Danacha, a non-flowering yam landrace. Flower-enhancing treatments had no significant effect on flower fertility translated by the fruit set, since most treatments recorded fruit sets above the species' average crossability rate. Flower-enhancing techniques significantly influenced number of tubers per plant (p = 0.024) and tuber dry matter content (DMC, p = 0.0018) but did not significantly affect plant tuber yield. Nevertheless, treatments that could enhance substantially flowering intensity, such as pruning and STS, reduced tuber yield. DMC had negative associations with all flowering-related traits. This study provided insights into white yam flower induction and suggests promising treatments that can be optimized and used routinely to increase flowering in yam crop, without significantly affecting flower fertility and tuber yield.
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Affiliation(s)
- Jean M. Mondo
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Institute of Life and Earth Sciences, Pan African University, University of Ibadan, Ibadan, Nigeria
- Department of Crop Production, Université Evangélique en Afrique (UEA), Bukavu, Democratic Republic of Congo
| | - Paterne A. Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Géant B. Chuma
- Department of Crop Production, Université Evangélique en Afrique (UEA), Bukavu, Democratic Republic of Congo
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Asfaw A, Mondo JM, Agre PA, Asiedu R, Akoroda MO. Association mapping of plant sex and cross-compatibility related traits in white Guinea yam (Dioscorea rotundata Poir.) clones. BMC PLANT BIOLOGY 2022; 22:294. [PMID: 35705900 PMCID: PMC9199169 DOI: 10.1186/s12870-022-03673-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
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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Affiliation(s)
- Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan, 5320, Nigeria
| | - Jean M Mondo
- International Institute of Tropical Agriculture (IITA), Ibadan, 5320, Nigeria
- Institute of Life and Earth Sciences, Pan African University, University of Ibadan, Ibadan, 200284, Nigeria
- Department of Crop Production, Université Evangélique en Afrique (UEA), Bukavu, 3323, Democratic Republic of Congo
| | - Paterne A Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, 5320, Nigeria.
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, 5320, Nigeria
| | - Malachy O Akoroda
- Department of Agronomy, University of Ibadan, Ibadan, 200284, Nigeria
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Ehounou AE, Cormier F, Maledon E, Nudol E, Vignes H, Gravillon MC, N'guetta ASP, Mournet P, Chaïr H, Kouakou AM, Arnau G. Identification and validation of QTLs for tuber quality related traits in greater yam (Dioscorea alata L.). Sci Rep 2022; 12:8423. [PMID: 35589821 PMCID: PMC9120205 DOI: 10.1038/s41598-022-12135-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
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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Affiliation(s)
- Adou Emmanuel Ehounou
- CNRA, Station de Recherche sur les Cultures Vivrières (SRCV), 01 BP 633, Bouaké, Côte d'Ivoire
| | - Fabien Cormier
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France
| | - Erick Maledon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France
| | - Elie Nudol
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France
| | - Hélène Vignes
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Marie Claire Gravillon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France
| | | | - Pierre Mournet
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Hâna Chaïr
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France.,CIRAD, UMR AGAP Institut, 34398, Montpellier, France
| | - Amani Michel Kouakou
- CNRA, Station de Recherche sur les Cultures Vivrières (SRCV), 01 BP 633, Bouaké, Côte d'Ivoire
| | - Gemma Arnau
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398, Montpellier, France. .,CIRAD, UMR AGAP Institut, 97170, Petit-Bourg, Guadeloupe, France.
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Mondo JM, Agre PA, Asiedu R, Akoroda MO, Asfaw A. Genome-Wide Association Studies for Sex Determination and Cross-Compatibility in Water Yam ( Dioscorea alata L.). PLANTS (BASEL, SWITZERLAND) 2021; 10:1412. [PMID: 34371615 PMCID: PMC8309230 DOI: 10.3390/plants10071412] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022]
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.
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Affiliation(s)
- Jean M. Mondo
- International Institute of Tropical Agriculture (IITA), Ibadan 5320, Nigeria; (J.M.M.); (R.A.); (A.A.)
- Institute of Life and Earth Sciences, Pan African University, University of Ibadan, Ibadan 200284, Nigeria
- Department of Crop Production, Université Evangélique en Afrique (UEA), Bukavu 3323, Democratic Republic of the Congo
| | - Paterne A. Agre
- International Institute of Tropical Agriculture (IITA), Ibadan 5320, Nigeria; (J.M.M.); (R.A.); (A.A.)
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan 5320, Nigeria; (J.M.M.); (R.A.); (A.A.)
| | | | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan 5320, Nigeria; (J.M.M.); (R.A.); (A.A.)
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