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Higgins J, Osorio-Guarín JA, Olave-Achury C, Toloza-Moreno DL, Enriquez A, Di Palma F, Yockteng R, De Vega JJ. Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages. ANNALS OF BOTANY 2024; 133:349-364. [PMID: 38097270 PMCID: PMC11005773 DOI: 10.1093/aob/mcad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/12/2023] [Indexed: 04/11/2024]
Abstract
BACKGROUND Bananas and plantains (Musa spp.) are among the most important crops worldwide. The cultivated varieties are vegetatively propagated, so their genetic diversity is essentially fixed over time. Musa acuminata, M. balbisiana and M. schizocarpa have provided the named A, B and S subgenomes that predominantly constitute these varieties. Here we aimed to characterize intergenetic recombination and chromosomal imbalances between these A/B/S subgenomes, which often result in copy-number variants (CNVs) leading to changes in gene dosage and phenotype, in a diverse panel of bananas and plantains. This will allow us to characterize varietal lineages better and identify sources of genetic variation. METHODS We delimited population structure and clonal lineages in a diverse panel of 188 banana and plantain accessions from the most common cultivars using admixture, principal component and phylogenetic analyses. We used new scalable alignment-based methods, Relative Averaged Alignment (RAA) and Relative Coverage, to infer subgenome composition (AA, AAB, etc.) and interspecific recombination. RESULTS In our panel, we identified ten varietal lineages composed of somatic clones, plus three groups of tetraploid accessions. We identified chromosomal exchanges resulting in gains/losses in chromosomal segments (CNVs), particularly in AAB and ABB varieties. CONCLUSIONS We demonstrated alignment-based RAA and Relative Coverage can identify subgenome composition and introgressions with similar results to more complex approaches based on single nucleotide polymorphism (SNP) databases. These ab initio species-agnostic methods can be used without sequencing a panel of wild ancestors to find private SNPs, or in recently diverged pools where private SNPs are uncommon. The extensive A/B/S exchanges and the variation in the length of some introgressions between lineages further support multiple foundational events of hybridization and residual backcrossing. Imbalances between A/B/S may have resulted in CNVs and gene dosage variation. Since most edible banana genomes are fixed on time, these CNVs are stable genetic variations probably associated with phenotypic variation for future genetic studies.
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Affiliation(s)
- Janet Higgins
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Jaime Andrés Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, km 14 vía Mosquera, Bogotá, Colombia
| | | | - Deisy Lisseth Toloza-Moreno
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, km 14 vía Mosquera, Bogotá, Colombia
| | - Ayda Enriquez
- Centro de Investigación Palmira, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Palmira, Colombia
| | | | - Roxana Yockteng
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, km 14 vía Mosquera, Bogotá, Colombia
- Muséum National d’Histoire Naturelle, UMR-CNRS 7205, Paris, France
| | - Jose J De Vega
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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2
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Xie WZ, Zheng YY, He W, Bi F, Li Y, Dou T, Zhou R, Guo YX, Deng G, Zhang W, Yuan MH, Sanz-Jimenez P, Zhu XT, Xu XD, Zhou ZW, Zhou ZW, Feng JW, Liu S, Li C, Yang Q, Hu C, Gao H, Dong T, Dang J, Guo Q, Cai W, Zhang J, Yi G, Song JM, Sheng O, Chen LL. Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control. PLANT COMMUNICATIONS 2024; 5:100766. [PMID: 37974402 PMCID: PMC10873913 DOI: 10.1016/j.xplc.2023.100766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Bananas (Musa spp.) are one of the world's most important fruit crops and play a vital role in food security for many developing countries. Most banana cultivars are triploids derived from inter- and intraspecific hybridizations between the wild diploid ancestor species Musa acuminate (AA) and M. balbisiana (BB). We report two haplotype-resolved genome assemblies of the representative AAB-cultivated types, Plantain and Silk, and precisely characterize ancestral contributions by examining ancestry mosaics across the genome. Widespread asymmetric evolution is observed in their subgenomes, which can be linked to frequent homologous exchange events. We reveal the genetic makeup of triploid banana cultivars and verify that subgenome B is a rich source of disease resistance genes. Only 58.5% and 59.4% of Plantain and Silk genes, respectively, are present in all three haplotypes, with >50% of genes being differentially expressed alleles in different subgenomes. We observed that the number of upregulated genes in Plantain is significantly higher than that in Silk at one-week post-inoculation with Fusarium wilt tropical race 4 (Foc TR4), which confirms that Plantain can initiate defense responses faster than Silk. Additionally, we compared genomic and transcriptomic differences among the genes related to carotenoid synthesis and starch metabolism between Plantain and Silk. Our study provides resources for better understanding the genomic architecture of cultivated bananas and has important implications for Musa genetics and breeding.
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Affiliation(s)
- Wen-Zhao Xie
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Yu Zheng
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Weidi He
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Fangcheng Bi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Yaoyao Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Tongxin Dou
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Run Zhou
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Xiong Guo
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Wenhui Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Min-Hui Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Pablo Sanz-Jimenez
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi-Tong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xin-Dong Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zu-Wen Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhi-Wei Zhou
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia-Wu Feng
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Siwen Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Qiaosong Yang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Chunhua Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Huijun Gao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Tao Dong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Jiangbo Dang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Wenguo Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jianwei Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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3
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Li X, Yu S, Cheng Z, Chang X, Yun Y, Jiang M, Chen X, Wen X, Li H, Zhu W, Xu S, Xu Y, Wang X, Zhang C, Wu Q, Hu J, Lin Z, Aury JM, Van de Peer Y, Wang Z, Zhou X, Wang J, Lü P, Zhang L. Origin and evolution of the triploid cultivated banana genome. Nat Genet 2024; 56:136-142. [PMID: 38082204 DOI: 10.1038/s41588-023-01589-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 10/23/2023] [Indexed: 01/14/2024]
Abstract
Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.
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Affiliation(s)
- Xiuxiu Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhihao Cheng
- Haikou Experimental Station, National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaojun Chang
- Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yingzi Yun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengwei Jiang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuequn Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohui Wen
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Hua Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjun Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shiyao Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanbing Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xianjun Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chen Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Qiong Wu
- Haikou Experimental Station, National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jin Hu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China.
| | - Xiaofan Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China.
| | | | - Peitao Lü
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Liangsheng Zhang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Sanya, China.
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4
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Capo-Chichi DBE, Tchokponhoué DA, Sogbohossou DEO, Achigan-Dako EG. Narrow genetic diversity in germplasm from the Guinean and Sudano-Guinean zones in Benin indicates the need to broaden the genetic base of sweet fig banana (Musa acuminata cv Sotoumon). PLoS One 2023; 18:e0294315. [PMID: 37972084 PMCID: PMC10653437 DOI: 10.1371/journal.pone.0294315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
Sweet fig (M. acuminata cv. Sotoumon) is an economically important dessert banana in Benin, with high nutritional, medicinal, and cultural values. Nevertheless, its productivity and yield are threatened by biotic and abiotic stresses. Relevant knowledge of the genetic diversity of this economically important crop is essential for germplasm conservation and the development of breeding programs. However, very little is known about the genetic makeup of this cultivar in Benin. To advance the understanding of genetic diversity in sweet fig banana germplasm, a Genotype-By-Sequencing (GBS) was performed on a panel of 273 accessions collected in different phytogeographical zones of Benin. GBS generated 8,457 quality SNPs, of which 1992 were used for analysis after filtering. The results revealed a low diversity in the studied germplasm (He = 0.0162). Genetic differentiation was overall very low in the collection as suggested by the negative differentiation index (Fstg = -0.003). The Analysis of Molecular Variance (AMOVA) indicated that the variation between accessions within populations accounted for 83.8% of the total variation observed (P < 0.001). The analysis of population structure and neighbor-joining tree partitioned the germplasm into three clusters out of which a predominant major one contained 98.1% of all accessions. These findings demonstrate that current sweet fig banana genotypes shared a common genetic background, which made them vulnerable to biotic and abiotic stress. Therefore, broadening the genetic base of the crop while maintaining its quality attributes and improving yield performance is of paramount importance. Moreover, the large genetic group constitutes an asset for future genomic selection studies in the crop and can guide the profiling of its conservation strategies.
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Affiliation(s)
- Dènoumi B. E. Capo-Chichi
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology and Plant Breeding (PAGEV), Faculty of Agricultural Sciences (FSA), University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
| | - Dèdéou A. Tchokponhoué
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology and Plant Breeding (PAGEV), Faculty of Agricultural Sciences (FSA), University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
| | - Dêêdi E. O. Sogbohossou
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology and Plant Breeding (PAGEV), Faculty of Agricultural Sciences (FSA), University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
| | - Enoch G. Achigan-Dako
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Crop Production, Physiology and Plant Breeding (PAGEV), Faculty of Agricultural Sciences (FSA), University of Abomey-Calavi, Abomey-Calavi, Republic of Benin
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5
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Wang T, van Dijk ADJ, Bucher J, Liang J, Wu J, Bonnema G, Wang X. Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus. Mol Biol Evol 2023; 40:msad199. [PMID: 37707440 PMCID: PMC10504873 DOI: 10.1093/molbev/msad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guusje Bonnema
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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6
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Huang HR, Liu X, Arshad R, Wang X, Li WM, Zhou Y, Ge XJ. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. HORTICULTURE RESEARCH 2023; 10:uhad153. [PMID: 37701454 PMCID: PMC10493638 DOI: 10.1093/hr/uhad153] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/27/2023] [Indexed: 09/14/2023]
Abstract
Banana is one of the most important crops of the world. Cavendish-type bananas, which have a monospecific Musa acuminata origin (AAA), account for around half of the global banana production, thereby are of great significance for human societies. However, until now, the high-quality haplotype-resolved reference genome was still undecoded for banana cultivars. Here, we reported the telomere-to-telomere (T2T) and haplotype-resolved reference genome of 'Baxijiao' (Cavendish) consisting of three haploid assemblies. The sizes of the three haploid assemblies were estimated to be 477.16 Mb, 477.18 Mb, and 469.57 Mb, respectively. Although with monospecific origins, the three haploid assemblies showed great differences with low levels of sequence collinearity. Several large reciprocal translocations were identified among chromosomes 1, 4, and 7. An expansion of gene families that might affect fruit quality and aroma was detected, such as those belonging to sucrose/disaccharide/oligosaccharide catabolic processes, sucrose metabolic process, starch metabolic process, and aromatic compound biosynthetic process. Besides, an expansion of gene families related to anther and pollen development was observed, which could be associated with parthenocarpy and sterility of the Cavendish cultivar. Finally, much fewer resistance genes were identified in 'Baxijiao' than in M. acuminata, particularly in the gene clusters in chromosomes 3 and 10, providing potential targets to explore for molecular analysis of disease resistance in banana. This T2T haplotype-resolved reference genome will thus be a valuable genetic resource for biological studies, molecular breeding, and genetic improvement of banana.
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Affiliation(s)
- Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Xin Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rida Arshad
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xu Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wei-Ming Li
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning 530008, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
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Martin G, Baurens FC, Labadie K, Hervouet C, Salmon F, Marius F, Paulo-de-la-Reberdiere N, Van den Houwe I, Aury JM, D’Hont A, Yahiaoui N. Shared pedigree relationships and transmission of unreduced gametes in cultivated banana. ANNALS OF BOTANY 2023; 131:1149-1161. [PMID: 37267450 PMCID: PMC10457027 DOI: 10.1093/aob/mcad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/02/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND AND AIMS Cultivated bananas resulted from inter(sub)specific hybridizations involving Musa species and subspecies (M. acuminata subspecies, M. schizocarpa, M. balbisiana) and the subsequent selection, centuries ago, of hybrids with parthenocarpic, seedless fruits. Cultivars have low fertility and are vegetatively propagated, forming groups of somaclones. Relatively few of them, mainly triploids, are grown on a large scale and characterization of their parental relationships may be useful for breeding strategies. Here we investigate parental relationships and gamete-type contributions among diploid and polyploid banana cultivars. METHODS We used SNP genotyping data from whole-genome sequencing of 178 banana individuals, including 111 cultivars, 55 wild bananas and 12 synthetic F1 hybrids. We analysed the proportion of SNP sites in accordance with direct parentage with a global statistic and along chromosomes for selected individuals. KEY RESULTS We characterized parentage relationships for 7 diploid cultivars, 11 triploid cultivars and 1 tetraploid cultivar. Results showed that both diploid and triploid cultivars could have contributed gametes to other banana cultivars. Diploids may have contributed 1x or 2x gametes and triploids 1x to 3x gametes. The Mchare diploid cultivar group, nowadays only found in East Africa, was found as parent of two diploid and eight triploid cultivars. In five of its identified triploid offspring, corresponding to main export or locally popular dessert bananas, Mchare contributed a 2x gamete with full genome restitution without recombination. Analyses of remaining haplotypes in these Mchare offspring suggested ancestral pedigree relationships between different interspecific banana cultivars. CONCLUSIONS The current cultivated banana resulted from different pathways of formation, with implication of recombined or un-recombined unreduced gametes produced by diploid or triploid cultivars. Identification of dessert banana's parents and the types of gametes they contributed should support the design of breeding strategies.
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Affiliation(s)
- Guillaume Martin
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Frédéric Salmon
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
| | - Franck Marius
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, Guadeloupe, FranceFrance
| | - Nilda Paulo-de-la-Reberdiere
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, CRB-PT, F-97170 Roujol Petit-Bourg, Guadeloupe, FranceFrance
| | - Ines Van den Houwe
- Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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8
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Eyland D, Gambart C, Swennen R, Carpentier S. Unravelling the diversity in water usage among wild banana species in response to vapour pressure deficit. FRONTIERS IN PLANT SCIENCE 2023; 14:1068191. [PMID: 37670859 PMCID: PMC10475999 DOI: 10.3389/fpls.2023.1068191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/03/2023] [Indexed: 09/07/2023]
Abstract
The rise in global temperature is not only affecting plant functioning directly, but is also increasing air vapour pressure deficit (VPD). The yield of banana is heavily affected by water deficit but so far breeding programs have never addressed the issue of water deficit caused by high VPD. A reduction in transpiration at high VPD has been suggested as a key drought tolerance breeding trait to avoid excessive water loss, hydraulic failure and to increase water use efficiency. In this study, stomatal and transpiration responses under increasing VPD at the leaf and whole-plant level of 8 wild banana (sub)species were evaluated, displaying significant differences in stomatal reactivity. Three different phenotypic groups were identified under increasing VPD. While (sub)species of group III maintained high transpiration rates under increasing VPD, M. acuminata ssp. errans (group I), M. acuminata ssp. zebrina (group II) and M. balbisiana (group II) showed the highest transpiration rate limitations to increasing VPD. In contrast to group I, group II only showed strong reductions at high VPD levels, limiting the cost of reduced photosynthesis and strongly increasing their water use efficiency. M. acuminata ssp. zebrina and M. balbisiana thus show the most favourable responses. This study provides a basis for the identification of potential parent material in gene banks for breeding future-proof bananas that cope better with lack of water.
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Affiliation(s)
- David Eyland
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
| | - Clara Gambart
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
- International Institute of Tropical Agriculture, Banana Breeding, Kampala, Uganda
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
- Bioversity International, Biodiversity for Food and Agriculture, Leuven, Belgium
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9
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Deb SK, Edger PP, Pires JC, McKain MR. Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective. THE NEW PHYTOLOGIST 2023; 238:2284-2304. [PMID: 37010081 DOI: 10.1111/nph.18927] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/16/2023] [Indexed: 05/19/2023]
Abstract
Allopolyploids result from hybridization between different evolutionary lineages coupled with genome doubling. Homoeologous chromosomes (chromosomes with common shared ancestry) may undergo recombination immediately after allopolyploid formation and continue over successive generations. The outcome of this meiotic pairing behavior is dynamic and complex. Homoeologous exchanges (HEs) may lead to the formation of unbalanced gametes, reduced fertility, and selective disadvantage. By contrast, HEs could act as sources of novel evolutionary substrates, shifting the relative dosage of parental gene copies, generating novel phenotypic diversity, and helping the establishment of neo-allopolyploids. However, HE patterns vary among lineages, across generations, and even within individual genomes and chromosomes. The causes and consequences of this variation are not fully understood, though interest in this evolutionary phenomenon has increased in the last decade. Recent technological advances show promise in uncovering the mechanistic basis of HEs. Here, we describe recent observations of the common patterns among allopolyploid angiosperm lineages, underlying genomic and epigenomic features, and consequences of HEs. We identify critical research gaps and discuss future directions with far-reaching implications in understanding allopolyploid evolution and applying them to the development of important phenotypic traits of polyploid crops.
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Affiliation(s)
- Sontosh K Deb
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48823, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
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10
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Mbo Nkoulou LF, Tchinda Ninla LA, Cros D, Martin G, Ndiang Z, Houegban J, Ngalle HB, Bell JM, Achigan-Dako EG. Analysis of genetic diversity and agronomic variation in banana sub-populations for genomic selection under drought stress in southern Benin. Gene 2023; 859:147210. [PMID: 36681099 DOI: 10.1016/j.gene.2023.147210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
In the perspective of investigating genomic selection (GS) among Musa genotypes in West and Central Africa, banana accessions were phenotyped under natural drought stress in Benin and genotyped using genotyping by sequencing. Sixty-one (61) accessions grouped into three major genomic groups AAA, AAB and ABB and those without genomic affiliation information were used. Variation within the population was determined by phenotypic variables while population structure and clustering analysis were carried out to understand the genetic diversity at the molecular level. Among the genomic groups evaluated, the group AAB showed the best performance for fruit weight at maturity, (3.41 ± 1.99 kg) and for plant height (198.46 ± 12.66 cm). At the accession level, HD 117 S1 and NIA 27 showed the best plant height (263.16 ± 20.98 cm) and the best fruit weight at maturity (9.43 ± 0.0 kg) respectively. Phenotypic data did not reveal clear genetic diversity among accessions; however, the genetic diversity was conspicuous at the molecular level using 5000 markers. The affiliations of local accessions in genomic groups were determined for the first time based on the phenotypic and molecular data obtained in this study. The knowledge generated allows the possibility to apply GS in banana.
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Affiliation(s)
- Luther Fort Mbo Nkoulou
- Unit of Genetics, Biotechnology, and Seed Science (GBioS), Laboratory of Phytotechnics, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin; Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Po. Box 812, Yaoundé, Cameroon; Institute of Agricultural Research for Development, Mbalmayo Agricultural Research Centre (CRAM) Mbalmayo, Cameroon.
| | | | - David Cros
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, F-34398 Montpellier, France; Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Univ. Montpellier, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, F-34398 Montpellier, France
| | - Guillaume Martin
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, F-34398 Montpellier, France; Unité Mixte de Recherche (UMR), Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Univ. Montpellier, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut Agro, F-34398 Montpellier, France
| | - Zenabou Ndiang
- Department of Plant Biology and Physiology, Faculty of Science, University of Douala, Po. Box 24157, Douala, Cameroon
| | - Jordan Houegban
- Unit of Genetics, Biotechnology, and Seed Science (GBioS), Laboratory of Phytotechnics, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin
| | - Hermine Bille Ngalle
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Po. Box 812, Yaoundé, Cameroon
| | - Joseph Martin Bell
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Science, University of Yaoundé 1, Po. Box 812, Yaoundé, Cameroon
| | - Enoch G Achigan-Dako
- Unit of Genetics, Biotechnology, and Seed Science (GBioS), Laboratory of Phytotechnics, Physiology, Genetics and Plant Breeding (PAGEV), University of Abomey-Calavi, Abomey-Calavi, School of Plant Sciences, Cotonou, Republic of Benin.
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11
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Martin G, Cottin A, Baurens FC, Labadie K, Hervouet C, Salmon F, Paulo-de-la-Reberdiere N, Van den Houwe I, Sardos J, Aury JM, D'Hont A, Yahiaoui N. Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:802-818. [PMID: 36575919 DOI: 10.1111/tpj.16086] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Hybridizations between Musa species and subspecies, enabled by their transport via human migration, were proposed to have played an important role in banana domestication. We exploited sequencing data of 226 Musaceae accessions, including wild and cultivated accessions, to characterize the inter(sub)specific hybridization pattern that gave rise to cultivated bananas. We identified 11 genetic pools that contributed to cultivars, including two contributors of unknown origin. Informative alleles for each of these genetic pools were pinpointed and used to obtain genome ancestry mosaics of accessions. Diploid and triploid cultivars had genome mosaics involving three up to possibly seven contributors. The simplest mosaics were found for some diploid cultivars from New Guinea, combining three contributors, i.e., banksii and zebrina representing Musa acuminata subspecies and, more unexpectedly, the New Guinean species Musa schizocarpa. Breakpoints of M. schizocarpa introgressions were found to be conserved between New Guinea cultivars and the other analyzed diploid and triploid cultivars. This suggests that plants bearing these M. schizocarpa introgressions were transported from New Guinea and gave rise to currently cultivated bananas. Many cultivars showed contrasted mosaics with predominant ancestry from their geographical origin across Southeast Asia to New Guinea. This revealed that further diversification occurred in different Southeast Asian regions through hybridization with other Musa (sub)species, including two unknown ancestors that we propose to be M. acuminata ssp. halabanensis and a yet to be characterized M. acuminata subspecies. These results highlighted a dynamic crop formation process that was initiated in New Guinea, with subsequent diversification throughout Southeast Asia.
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Affiliation(s)
- Guillaume Martin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurélien Cottin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Frédéric Salmon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
| | - Nilda Paulo-de-la-Reberdiere
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, CRB-PT, F-97170 Roujol Petit-Bourg, Guadeloupe, France
| | - Ines Van den Houwe
- Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium
| | - Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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12
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Sardos J, Breton C, Perrier X, Van den Houwe I, Carpentier S, Paofa J, Rouard M, Roux N. Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas. FRONTIERS IN PLANT SCIENCE 2022; 13:969220. [PMID: 36275535 PMCID: PMC9586208 DOI: 10.3389/fpls.2022.969220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 06/08/2023]
Abstract
Hybridization and introgressions are important evolutionary forces in plants. They contribute to the domestication of many species, including understudied clonal crops. Here, we examine their role in the domestication of a clonal crop of outmost importance, banana (Musa ssp.). We used genome-wide SNPs generated for 154 diploid banana cultivars and 68 samples of the wild M. acuminata to estimate and geo-localize the contribution of the different subspecies of M. acuminata to cultivated banana. We further investigated the wild to domesticate transition in New Guinea, an important domestication center. We found high levels of admixture in many cultivars and confirmed the existence of unknown wild ancestors with unequal contributions to cultivated diploid. In New Guinea, cultivated accessions exhibited higher diversity than their direct wild ancestor, the latter recovering from a bottleneck. Introgressions, balancing selection and positive selection were identified as important mechanisms for banana domestication. Our results shed new lights on the radiation of M. acuminata subspecies and on how they shaped banana domestication. They point candidate regions of origin for two unknown ancestors and suggest another contributor in New Guinea. This work feed research on the evolution of clonal crops and has direct implications for conservation, collection, and breeding.
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Affiliation(s)
- Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Catherine Breton
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Xavier Perrier
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Janet Paofa
- Papua New Guinea (PNG) National Agricultural Research Institute, Southern Regional Centre, Laloki, Port Moresby, Papua New Guinea
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
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13
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Droc G, Martin G, Guignon V, Summo M, Sempéré G, Durant E, Soriano A, Baurens FC, Cenci A, Breton C, Shah T, Aury JM, Ge XJ, Harrison PH, Yahiaoui N, D’Hont A, Rouard M. The banana genome hub: a community database for genomics in the Musaceae. HORTICULTURE RESEARCH 2022; 9:uhac221. [PMID: 36479579 PMCID: PMC9720444 DOI: 10.1093/hr/uhac221] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.
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Affiliation(s)
| | - Guillaume Martin
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Valentin Guignon
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Marilyne Summo
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Guilhem Sempéré
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France
- INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | - Eloi Durant
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Syngenta Seeds SAS, Saint-Sauveur, 31790, France
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, 34830, France
| | - Alexandre Soriano
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Alberto Cenci
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Catherine Breton
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510520, China
| | - Pat Heslop Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
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14
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Summo M, Comte A, Martin G, Perelle P, Weitz EM, Droc G, Rouard M. GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics. Database (Oxford) 2022; 2022:6645005. [PMID: 35849014 PMCID: PMC9290862 DOI: 10.1093/database/baac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 11/12/2022]
Abstract
In silico chromosome painting is a technique by which contributions of distinct genetic groups are represented along chromosomes of hybrid individuals. This type of analysis is used to study the mechanisms by which these individuals were formed. Such techniques are well adapted to identify genetic groups contributing to these individuals as well as hybridization events. It can also be used to follow chromosomal recombinations that occurred naturally or were generated by selective breeding. Here, we present GeMo, a novel interactive web-based and user-oriented interface to visualize in a linear-based fashion results of in silico chromosome painting. To facilitate data input generation, a script to execute analytical commands is provided and an interactive data curation mode is supported to ensure consistency of the automated procedure. GeMo contains preloaded datasets from published studies on crop domestication but can be applied to other purposes, such as breeding programs Although only applied so far on plants, GeMo can handle data from animals as well. Database URL: https://gemo.southgreen.fr/
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Affiliation(s)
- Marilyne Summo
- CIRAD, UMR AGAP Institut , Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier, 34398, France
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
| | - Aurore Comte
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
- IRD, CIRAD, INRAE, Institut Agro, PHIM Plant Health Institute, Montpellier University , Montpellier 34398, France
| | - Guillaume Martin
- CIRAD, UMR AGAP Institut , Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier, 34398, France
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
| | - Pierrick Perelle
- CIRAD, UMR AGAP Institut , Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier, 34398, France
| | - Eric M Weitz
- Data Sciences Platform, Broad Institute of MIT and Harvard , 105 Broadway, Cambridge, MA 02142, USA
| | - Gaëtan Droc
- CIRAD, UMR AGAP Institut , Montpellier 34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier, 34398, France
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
| | - Mathieu Rouard
- French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD , Montpellier 34398, France
- Bioversity International, Parc Scientifique Agropolis II , 34397, Montpellier, France
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15
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He JC, Li SY, He WZ, Xian JJ, Ma XY, Wang YC, Zhang MC, Ye GX, Liang B, Xia Q, Li Q. Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human. Cytogenet Genome Res 2021; 161:406-413. [PMID: 34657031 DOI: 10.1159/000518930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022] Open
Abstract
At present, low-pass whole-genome sequencing (WGS) is frequently used in clinical research and in the screening of copy number variations (CNVs). However, there are still some challenges in the detection of triploids. Restriction site-associated DNA sequencing (RAD-Seq) technology is a reduced-representation genome sequencing technology developed based on next-generation sequencing. Here, we verified whether RAD-Seq could be employed to detect CNVs and triploids. In this study, genomic DNA of 11 samples was extracted employing a routine method and used to build libraries. Five cell lines of known karyotypes and 6 triploid abortion tissue samples were included for RAD-Seq testing. The triploid samples were confirmed by STR analysis and also tested by low-pass WGS. The accuracy and efficiency of detecting CNVs and triploids by RAD-Seq were then assessed, compared with low-pass WGS. In our results, RAD-Seq detected 11 out of 11 (100%) chromosomal abnormalities, including 4 deletions and 1 aneuploidy in the purchased cell lines and all triploid samples. By contrast, these triploids were missed by low-pass WGS. Furthermore, RAD-Seq showed a higher resolution and more accurate allele frequency in the detection of triploids than low-pass WGS. Our study shows that, compared with low-pass WGS, RAD-Seq has relatively higher accuracy in CNV detection at a similar cost and is capable of identifying triploids. Therefore, the application of this technique in medical genetics has a significant potential value.
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Affiliation(s)
- Jian-Chun He
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shao-Ying Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wen-Zhi He
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jia-Jia Xian
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Yan Ma
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yan-Chao Wang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min-Cong Zhang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guo-Xin Ye
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bo Liang
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Qin Xia
- Basecare Medical Device Co., Ltd, Suzhou, China,
| | - Qing Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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16
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Wu CS, Sudianto E, Chiu HL, Chao CP, Chaw SM. Reassessing Banana Phylogeny and Organelle Inheritance Modes Using Genome Skimming Data. FRONTIERS IN PLANT SCIENCE 2021; 12:713216. [PMID: 34456952 PMCID: PMC8385209 DOI: 10.3389/fpls.2021.713216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/16/2021] [Indexed: 05/10/2023]
Abstract
Bananas (Musa spp.) are some of the most important fruit crops in the world, contributing up to US$10 billion in export values annually. In this study, we use high-throughput sequencing to obtain genomic resources of high-copy DNA molecules in bananas. We sampled 13 wild species and eight cultivars that represent the three genera (Ensete, Musa, and Musella) of the banana family (Musaceae). Their plastomic, 45S rDNA, and mitochondrial scaffolds were recovered from genome skimming data. Two major clades (Clades I & II) within Musa are strongly supported by the three genomic compartment data. We document, for the first time, that the plastomes of Musaceae have expanded inverted repeats (IR) after they diverged from their two close relatives, Heliconiaceae (the lobster-claws) and Strelitziaceae (the traveler's bananas). The presence/absence of rps19 within IR regions reinforces the two intra-generic clades within Musa. Our comparisons of the bananas' plastomic and mitochondrial DNA sequence trees aid in identifying hybrid bananas' parentage. As the mitochondrial genes of Musa have elevated substitution rates, paternal inheritance likely plays an influential role on the Musa mitogenome evolution. We propose genome skimming as a useful method for reliable genealogy tracing and phylogenetics in bananas.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Edi Sudianto
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hui-Lung Chiu
- Plant Germplasm Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | | | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- *Correspondence: Shu-Miaw Chaw
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17
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Tomaszewska P. Understanding polyploid banana origins. A commentary on: 'Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas'. ANNALS OF BOTANY 2021; 127:iv-v. [PMID: 33289497 PMCID: PMC7750713 DOI: 10.1093/aob/mcaa183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 06/09/2023]
Abstract
This article comments on: Alberto Cenci, Julie Sardos, Yann Hueber, Guillaume Martin, Catherine Breton, Nicolas Roux, Rony Swennen, Sebastien Christian Carpentier and Mathieu Rouard, Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas, Annals of Botany, Volume 127, Issue 1, 01 January 2021, Pages 7–20, https://doi.org/10.1093/aob/mcaa032
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Affiliation(s)
- Paulina Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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18
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Martin G, Baurens F, Hervouet C, Salmon F, Delos J, Labadie K, Perdereau A, Mournet P, Blois L, Dupouy M, Carreel F, Ricci S, Lemainque A, Yahiaoui N, D’Hont A. Chromosome reciprocal translocations have accompanied subspecies evolution in bananas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1698-1711. [PMID: 33067829 PMCID: PMC7839431 DOI: 10.1111/tpj.15031] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/02/2020] [Indexed: 05/09/2023]
Abstract
Chromosome rearrangements and the way that they impact genetic differentiation and speciation have long raised questions from evolutionary biologists. They are also a major concern for breeders because of their bearing on chromosome recombination. Banana is a major crop that derives from inter(sub)specific hybridizations between various once geographically isolated Musa species and subspecies. We sequenced 155 accessions, including banana cultivars and representatives of Musa diversity, and genotyped-by-sequencing 1059 individuals from 11 progenies. We precisely characterized six large reciprocal translocations and showed that they emerged in different (sub)species of Musa acuminata, the main contributor to currently cultivated bananas. Most diploid and triploid cultivars analyzed were structurally heterozygous for 1 to 4 M. acuminata translocations, highlighting their complex origin. We showed that all translocations induced a recombination reduction of variable intensity and extent depending on the translocations, involving only the breakpoint regions, a chromosome arm, or an entire chromosome. The translocated chromosomes were found preferentially transmitted in many cases. We explore and discuss the possible mechanisms involved in this preferential transmission and its impact on translocation colonization.
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Affiliation(s)
- Guillaume Martin
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Franc‐Christophe Baurens
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Catherine Hervouet
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Frédéric Salmon
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
- CIRADUMR AGAPCapesterre‐Belle‐EauGuadeloupeF‐97130France
| | - Jean‐Marie Delos
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
- CIRADUMR AGAPCapesterre‐Belle‐EauGuadeloupeF‐97130France
| | - Karine Labadie
- GenoscopeInstitut de biologie François JacobCommissariat à l'Energie Atomique (CEA)Université Paris‐SaclayEvryFrance
| | - Aude Perdereau
- GenoscopeInstitut de biologie François JacobCommissariat à l'Energie Atomique (CEA)Université Paris‐SaclayEvryFrance
| | - Pierre Mournet
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Louis Blois
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Marion Dupouy
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Françoise Carreel
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Sébastien Ricci
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
- CIRADUMR AGAPCapesterre‐Belle‐EauGuadeloupeF‐97130France
| | - Arnaud Lemainque
- GenoscopeInstitut de biologie François JacobCommissariat à l'Energie Atomique (CEA)Université Paris‐SaclayEvryFrance
| | - Nabila Yahiaoui
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Angélique D’Hont
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
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