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Dwivedi SL, Heslop-Harrison P, Spillane C, McKeown PC, Edwards D, Goldman I, Ortiz R. Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools. TRENDS IN PLANT SCIENCE 2023; 28:685-697. [PMID: 36764870 DOI: 10.1016/j.tplants.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 12/03/2022] [Accepted: 01/18/2023] [Indexed: 05/13/2023]
Abstract
Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.
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Affiliation(s)
| | - Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Irwin Goldman
- Department of Horticulture, College of Agricultural and Life Sciences, University of Wisconsin Madison, WI 53706, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SE 23053, Sweden.
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Agre PA, Edemodu A, Obidiegwu JE, Adebola P, Asiedu R, Asfaw A. Variability and genetic merits of white Guinea yam landraces in Nigeria. FRONTIERS IN PLANT SCIENCE 2023; 14:1051840. [PMID: 36814760 PMCID: PMC9940711 DOI: 10.3389/fpls.2023.1051840] [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: 09/23/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Landraces represent a significant gene pool of African cultivated white Guinea yam diversity. They could, therefore, serve as a potential donor of important traits such as resilience to stresses as well as food quality attributes that may be useful in modern yam breeding. This study assessed the pattern of genetic variability, quantitative trait loci (QTLs), alleles, and genetic merits of landraces, which could be exploited in breeding for more sustainable yam production in Africa. METHODS A total of 86 white Guinea yam landraces representing the popular landraces in Nigeria alongside 16 elite clones were used for this study. The yam landraces were genotyped using 4,819 DArTseq SNP markers and profiled using key productivity and food quality traits. RESULTS AND DISCUSSION Genetic population structure through admixture and hierarchical clustering methods revealed the presence of three major genetic groups. Genome-wide association scan identified thirteen SNP markers associated with five key traits, suggesting that landraces constitute a source of valuable genes for productivity and food quality traits. Further dissection of their genetic merits in yam breeding using the Genomic Prediction of Cross Performance (GPCP) allowed identifying several landraces with high crossing merit for multiple traits. Thirteen landraces were identified as potential genitors to develop segregating progenies to improve multiple traits simultaneously for desired gains in yam breeding. Results of this study provide valuable insights into the patterns and the merits of local genetic diversity which can be utilized for identifying desirable genes and alleles of interest in yam breeding for Africa.
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Affiliation(s)
- Paterne A. Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Alex Edemodu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Jude E. Obidiegwu
- National Root Crops Research Institute, Umudike, Abia State, Nigeria
| | - Patrick Adebola
- International Institute of Tropical Agriculture (IITA), Abuja, Nigeria
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Abuja, Nigeria
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Natsume S, Sugihara Y, Kudoh A, Oikawa K, Shimizu M, Ishikawa Y, Nishihara M, Abe A, Innan H, Terauchi R. Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea. PLANT & CELL PHYSIOLOGY 2022; 63:1667-1678. [PMID: 35876055 PMCID: PMC9680860 DOI: 10.1093/pcp/pcac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/17/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
A rhizomatous Dioscorea crop 'Edo-dokoro' was described in old records of Japan, but its botanical identity has not been characterized. We found that Edo-dokoro is still produced by four farmers in Tohoku-machi of the Aomori prefecture, Japan. The rhizomes of Edo-dokoro are a delicacy to the local people and are sold in the markets. Morphological characters of Edo-dokoro suggest its hybrid origin between the two species, Dioscorea tokoro and Dioscorea tenuipes. Genome analysis revealed that Edo-dokoro likely originated by hybridization of a male D. tokoro to a female D. tenuipes, followed by a backcross with a male plant of D. tokoro. Edo-dokoro is a typical minor crop possibly maintained for more than 300 years but now almost forgotten by the public. We hypothesize that there are many such uncharacterized genetic heritages passed over generations by small-scale farmers that await serious scientific investigation for future use and improvement by using modern genomics information.
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Affiliation(s)
- Satoshi Natsume
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Yu Sugihara
- Crop Evolution Laboratory, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | - Aoi Kudoh
- Crop Evolution Laboratory, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | - Kaori Oikawa
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Yuko Ishikawa
- Crop Evolution Laboratory, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | | | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Hideki Innan
- Laboratory of Population Genetics and Genome Evolution, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
- Crop Evolution Laboratory, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
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Kipkiror N, Muge EK, Ochieno DMW, Nyaboga EN. DNA barcoding markers provide insight into species discrimination, genetic diversity and phylogenetic relationships of yam (Dioscorea spp.). Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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Sugihara Y, Darkwa K, Yaegashi H, Natsume S, Shimizu M, Abe A, Hirabuchi A, Ito K, Oikawa K, Tamiru-Oli M, Ohta A, Matsumoto R, Agre P, De Koeyer D, Pachakkil B, Yamanaka S, Muranaka S, Takagi H, White B, Asiedu R, Innan H, Asfaw A, Adebola P, Terauchi R. Genome analyses reveal the hybrid origin of the staple crop white Guinea yam ( Dioscorea rotundata). Proc Natl Acad Sci U S A 2020; 117:31987-31992. [PMID: 33268496 PMCID: PMC7749330 DOI: 10.1073/pnas.2015830117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding.
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Affiliation(s)
- Yu Sugihara
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kwabena Darkwa
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria
| | - Hiroki Yaegashi
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Satoshi Natsume
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Akiko Hirabuchi
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Kazue Ito
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Kaori Oikawa
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Muluneh Tamiru-Oli
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
- Department of Animal, Plant, and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia
| | - Atsushi Ohta
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Ryo Matsumoto
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria
| | - Paterne Agre
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria
| | - David De Koeyer
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Babil Pachakkil
- Japan International Research Center for Agricultural Sciences, Tsukuba 305-8686, Japan
- Department of International Agricultural Development, Tokyo University of Agriculture, Tokyo 183-8538, Japan
| | - Shinsuke Yamanaka
- Japan International Research Center for Agricultural Sciences, Tsukuba 305-8686, Japan
| | - Satoru Muranaka
- Japan International Research Center for Agricultural Sciences, Tsukuba 305-8686, Japan
| | - Hiroko Takagi
- Japan International Research Center for Agricultural Sciences, Tsukuba 305-8686, Japan
| | - Ben White
- Earlham Institute, Norwich NR4 7UZ, United Kingdom
| | - Robert Asiedu
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria
| | - Hideki Innan
- Laboratory of Population Genetics and Genome Evolution, The Graduate University for Advanced Studies, Hayama 240-0193, Japan
| | - Asrat Asfaw
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria;
| | - Patrick Adebola
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria;
| | - Ryohei Terauchi
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan;
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
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Sousa EC, Raizada MN. Contributions of African Crops to American Culture and Beyond: The Slave Trade and Other Journeys of Resilient Peoples and Crops. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.586340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is a general unawareness of food crops indigenous to the African continent that have contributed to Western culture. This under-appreciation is particularly relevant in the current context of societal movements to end historic racism and value the contributions of peoples of African origin and African skin colors. Lack of awareness of the contributions of Africa's crops has negative practical consequences, including inadequate investments in preserving and maximizing the use of crop diversity to facilitate breeding. This paper provides an overview and analysis of African crops that have made significant contributions to the United States and globally, and/or hold potential in the twenty-first century. The paper specifically discusses watermelon, coffee, kola, rooibos, oil palm, shea, cowpea/black eyed pea, leafy greens, okra, yam, sorghum, pearl millet, finger millet, teff, and fonio. The review focuses on the intersection of these crops with racialized peoples, with a particular focus on African-Americans starting with slavery. The analysis includes the sites of domestication of African crops, their historical migration out of Africa, their sociocultural contributions to cuisines and products around the world, their uses today, and the indigenous knowledge associated with traditional cultivation and landrace selection. The untapped potential of local genetic resources and indigenous agronomic strategies are also described. The review demonstrates that African crops played an important role in the development of American cuisine, beverages and household products. Many of these crops are nutritious, high value and stress tolerant. The paper concludes that African crops hold significant promise in improving the resiliency of global food production systems, to mitigate climate change and alleviate food insecurity and rural poverty, especially in dry regions of the world. It is hoped that this review contributes to teaching the next generation of agriculturalists, food scientists and international development professionals about the valuable contributions of Africa's resilient crops and peoples.
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Sharif BM, Burgarella C, Cormier F, Mournet P, Causse S, Van KN, Kaoh J, Rajaonah MT, Lakshan SR, Waki J, Bhattacharjee R, Badara G, Pachakkil B, Arnau G, Chaïr H. Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata). ANNALS OF BOTANY 2020; 126:1029-1038. [PMID: 32592585 PMCID: PMC7596366 DOI: 10.1093/aob/mcaa122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/22/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample. METHODS We characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach. KEY RESULTS Diploid genotypes were more frequent than triploids and tetraploids worldwide. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. The genetic make-up of triploids and tetraploids suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced to the Caribbean region. CONCLUSIONS Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation.
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Affiliation(s)
- Bilal Muhammad Sharif
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- University of Vienna, Department of Evolutionary Anthropology, Vienna, Austria
| | - Concetta Burgarella
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- Uppsala University, Department of Organismal Biology, Uppsala, Sweden
| | - Fabien Cormier
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Petit Bourg, Guadeloupe, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Sandrine Causse
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Kien Nguyen Van
- Plant Resources Center (PRC), An Khanh, Hoai Duc, Hanoi, Vietnam
| | - Juliane Kaoh
- Vanuatu Agricultural Research and Technical Centre (VARTC), Espiritu Santo PB, Vanuatu
| | | | | | - Jeffrey Waki
- National Agricultural Research Institute (NARI), Lae, Morobe Province, Papua New Guinea
| | - Ranjana Bhattacharjee
- International Institute of Tropical Agriculture (IITA), PMB, Ibadan, Oyo State, Nigeria
| | - Gueye Badara
- International Institute of Tropical Agriculture (IITA), PMB, Ibadan, Oyo State, Nigeria
| | - Babil Pachakkil
- Tokyo University of Agriculture (TUA), Sakuragaoka, Setagaya-ku, Tokyo, Japan
| | - Gemma Arnau
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Petit Bourg, Guadeloupe, France
| | - Hana Chaïr
- CIRAD, UMR AGAP, F34398-Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers. Sci Rep 2020; 10:13191. [PMID: 32764649 PMCID: PMC7413250 DOI: 10.1038/s41598-020-69925-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 07/16/2020] [Indexed: 11/11/2022] Open
Abstract
Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = − 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops.
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Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. PANOMICS meets germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1507-1525. [PMID: 32163658 PMCID: PMC7292548 DOI: 10.1111/pbi.13372] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
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Affiliation(s)
- Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
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Tao R, Xu C, Wang Y, Sun X, Li C, Ma J, Hao J, Yang Q. Spatiotemporal Differentiation of Alpine Butterfly Parnassius glacialis (Papilionidae: Parnassiinae) in China: Evidence from Mitochondrial DNA and Nuclear Single Nucleotide Polymorphisms. Genes (Basel) 2020; 11:genes11020188. [PMID: 32053967 PMCID: PMC7073557 DOI: 10.3390/genes11020188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 11/24/2022] Open
Abstract
The Apollo butterfly, Parnassius glacialis, is one of the most charming members of its genus and includes two subspecies locally distributed in montane areas of south-central China and Japan. In this study, we investigated the genetic structure and demographic history of P. glacialis by analyzing partial sequences of four mitochondrial genes and nuclear single nucleotide polymorphisms (SNPs) via genotyping-by-sequencing (GBS) of samples from nearly the entire known distributional range in China. The mitochondrial DNA (mtDNA) data demonstrated that a total of 39 haplotypes were present, and the species was estimated to have diverged about 0.95 million years ago during the middle Pleistocene transition into two main clades that likely formed during the Kunlun-Huanghe tectonic movement. The two clades then dispersed independently in distinct geographic areas alongside the mountainous routes in central and southern China, most likely driven by the Pleistocene glacial-interglacial cycles. Nuclear SNP analysis was generally congruent with mtDNA results at the individual level. A minor incongruence of genetic structures that was detected between mtDNA and nuclear SNP data from the Laojunshan and Tiantangzhai populations was likely due to secondary contact and male-biased dispersal. Our work demonstrates that complicated dispersal-vicariance evolutionary processes likely led to the current geographic distribution of P. glacialis in China, particularly the uplift of the Qinghai-Tibet Plateau and related climatic oscillations during the Quaternary period.
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Affiliation(s)
- Ruisong Tao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.T.); (C.X.); (Y.W.)
- College of Life Sciences, Hefei Normal University, Hefei 230000, China
| | - Chang Xu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.T.); (C.X.); (Y.W.)
| | - Yunliang Wang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.T.); (C.X.); (Y.W.)
| | - Xiaoyan Sun
- SKLPS and Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; (X.S.); (C.L.); (J.M.)
| | - Chunxiang Li
- SKLPS and Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; (X.S.); (C.L.); (J.M.)
| | - Junye Ma
- SKLPS and Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; (X.S.); (C.L.); (J.M.)
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.T.); (C.X.); (Y.W.)
- Correspondence: (J.H.); (Q.Y.)
| | - Qun Yang
- SKLPS and Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; (X.S.); (C.L.); (J.M.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.H.); (Q.Y.)
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Girma G, Natsume S, Carluccio AV, Takagi H, Matsumura H, Uemura A, Muranaka S, Takagi H, Stavolone L, Gedil M, Spillane C, Terauchi R, Tamiru M. Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling. PLoS One 2019; 14:e0216912. [PMID: 31545796 PMCID: PMC6756524 DOI: 10.1371/journal.pone.0216912] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/05/2019] [Indexed: 01/03/2023] Open
Abstract
Dioecy (distinct male and female individuals) and scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata), generating 20,236 unique tags. Of these, 13,901 were represented by a minimum of 10 tags. A total 88 tags were significantly differentially expressed in male, female and monoecious plants, of which 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of three candidate genes. We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two consecutive years. Over 85% of accessions were either male or non-flowering, less than 15% were female, while monoecious plants were rare. Intensity of flowering varied between male and female plants, with the former flowering more abundantly than the latter. Candidate genes identified in this study can be targeted for further validation and to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve efficiency of yam breeding.
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Affiliation(s)
- Gezahegn Girma
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Satoshi Natsume
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Anna Vittoria Carluccio
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Hiroki Takagi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Hideo Matsumura
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Aiko Uemura
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Satoru Muranaka
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Japan
- * E-mail:
| | - Hiroko Takagi
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Japan
| | - Livia Stavolone
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Melaku Gedil
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Ryohei Terauchi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Muluneh Tamiru
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
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Soto Gomez M, Pokorny L, Kantar MB, Forest F, Leitch IJ, Gravendeel B, Wilkin P, Graham SW, Viruel J. A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae). APPLICATIONS IN PLANT SCIENCES 2019; 7:e11254. [PMID: 31236313 PMCID: PMC6580989 DOI: 10.1002/aps3.11254] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/01/2019] [Indexed: 05/14/2023]
Abstract
PREMISE We developed a target enrichment panel for phylogenomic studies of Dioscorea, an economically important genus with incompletely resolved relationships. METHODS Our bait panel comprises 260 low- to single-copy nuclear genes targeted to work in Dioscorea, assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent-based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species. RESULTS The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm-wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives. DISCUSSION Our customized panel reliably retrieves targeted loci from Dioscorea, is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.
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Affiliation(s)
- Marybel Soto Gomez
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
- UBC Botanical Garden and Centre for Plant ResearchUniversity of British Columbia6804 Marine Drive SWVancouverBritish ColumbiaV6T 1Z4Canada
| | - Lisa Pokorny
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Michael B. Kantar
- Department of Tropical Plant and Soil SciencesUniversity of Hawai‘i at ManoaHonoluluHawai‘i96822USA
| | - Félix Forest
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Ilia J. Leitch
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Barbara Gravendeel
- Naturalis Biodiversity CenterEndless FormsSylviusweg 72Leiden2333 BEThe Netherlands
- Institute Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
- Faculty of Science and TechnologyUniversity of Applied Sciences LeidenZernikedreef 11Leiden2333 CKThe Netherlands
| | - Paul Wilkin
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Sean W. Graham
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
- UBC Botanical Garden and Centre for Plant ResearchUniversity of British Columbia6804 Marine Drive SWVancouverBritish ColumbiaV6T 1Z4Canada
| | - Juan Viruel
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
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14
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Hu P, Shao Y, Xu J, Wang T, Li Y, Liu H, Rong M, Su W, Chen B, Cui S, Cui X, Yang F, Tamate H, Xing X. Genome-wide study on genetic diversity and phylogeny of five species in the genus Cervus. BMC Genomics 2019; 20:384. [PMID: 31101010 PMCID: PMC6525406 DOI: 10.1186/s12864-019-5785-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 05/08/2019] [Indexed: 01/01/2023] Open
Abstract
Background Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. Methods In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using reduced-representation genome sequencing. Results A total of 197,543 SNPs were identified with an average sequencing depth of 16 x. A total of 21 SNP matrices for each subspecies/population and 1 matrix for individual analysis were constructed, respectively. Nucleotide diversity and heterozygosity analysis showed that all 21 subspecies/populations had different degrees of genetic diversity. C. eldii, C. unicolor and C. albirostris showed relatively high expected and observed heterozygosity, while observed heterozygosity in C. nippon was the lowest, indicating there was a certain degree of inbreeding rate in these subspecies/populations. Phylogenetic ML tree of all Cervus based on the 21 SNP matrices showed 5 robustly supported clades that clearly separate C. eldii, C. unicolor, C. albirostris, C. elaphus and C. nippon. Within C. elaphus clade, 4 subclades were well differentiated and statistically highly supported: C. elaphus (New Zealand), C. e. yarkandensis, C. c. canadensis and the other grouping the rest of C. canadensis from China. In the C. nippon clade, 2 well-distinct subclades corresponding to C. n. aplodontus and other C. nippon populations were separated. Phylogenetic reconstruction indicated that the first evolutionary event of the genus Cervus occurred approximately 7.4 millions of years ago. The split between C. elaphus and C. nippon could be estimated at around 3.6 millions of years ago. Phylogenetic ML tree of all samples based on individual SNP matrices, together with geographic distribution, have shown that there were 3 major subclades of C. elaphus and C. canadensis in China, namely C. e. yarkandensis (distributed in Tarim Basin), C. c. macneilli/C. c. kansuensis/C. c. alashanicus (distributed in middle west of China), and C. c. songaricus/C. c. sibiricus (distributed in northwest of China). Among them, C. e. yarkandensis was molecularly the most primitive subclade, with a differentiation dating back to 0.8–2.2 Myr ago. D statistical analysis showed that there was high probability of interspecific gene exchange between C. albirostris and C. eldii, C. albirostris and C. unicolor, C. nippon and C. unicolor, and there might be 2 migration events among 5 species in the genus Cervus. Conclusions Our results provided new insight to the genetic diversity and phylogeny of Cervus deer. In view of the current status of these populations, their conservation category will need to be reassessed. Electronic supplementary material The online version of this article (10.1186/s12864-019-5785-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengfei Hu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Yuanchen Shao
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Jiaping Xu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Tianjiao Wang
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Yiqing Li
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Huamiao Liu
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Min Rong
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Weilin Su
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Binxi Chen
- Animal Health Supervision Institute of Hainan Province, Haikou, China
| | - Songhuan Cui
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Xuezhe Cui
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | - Fuhe Yang
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China
| | | | - Xiumei Xing
- State key laboratory for molecular biology of special economic animals, Key laboratory of genetics, breeding and reproduction of special economic animals, Institute of special animal and plant sciences, Chinese academy of agricultural sciences, Changchun, China.
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Siadjeu C, Mayland-Quellhorst E, Albach DC. Genetic diversity and population structure of trifoliate yam (Dioscorea dumetorum Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS). BMC PLANT BIOLOGY 2018; 18:359. [PMID: 30563456 PMCID: PMC6299658 DOI: 10.1186/s12870-018-1593-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/06/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND Yams (Dioscorea spp.) are economically important food for millions of people in the humid and sub-humid tropics. Dioscorea dumetorum (Kunth) is the most nutritious among the eight-yam species, commonly grown and consumed in West and Central Africa. Despite these qualities, the storage ability of D. dumetorum is restricted by severe postharvest hardening of the tubers that can be addressed through concerted breeding efforts. The first step of any breeding program is bound to the study of genetic diversity. In this study, we used the Genotyping-By-Sequencing of Single Nucleotide Polymorphism (GBS-SNP) to investigate the genetic diversity and population structure of 44 accessions of D. dumetorum in Cameroon. Ploidy was inferred using flow cytometry and gbs2ploidy. RESULTS We obtained on average 6371 loci having at least information for 75% accessions. Based on 6457 unlinked SNPs, our results demonstrate that D. dumetorum is structured into four populations. We clearly identified, a western/north-western, a western, and south-western populations, suggesting that altitude and farmers-consumers preference are the decisive factors for differential adaptation and separation of these populations. Bayesian and neighbor-joining clustering detected the highest genetic variability in D. dumetorum accessions from the south-western region. This variation is likely due to larger breeding efforts in the region as shown by gene flow between D. dumetorum accessions from the south-western region inferred by maximum likelihood. Ploidy analysis revealed diploid and triploid levels in D. dumetorum accessions with mostly diploid accessions (77%). Male and female accessions were mostly triploid (75%) and diploid (69%), respectively. The 1C genome size values of D. dumetorum accessions were on average 0.333 ± 0.009 pg and 0.519 ± 0.004 pg for diploids and triploids, respectively. CONCLUSIONS Germplasm characterization, population structure and ploidy are an essential basic information in a breeding program as well as for conservation of intraspecific diversity. Thus, results obtained in this study provide valuable information for the improvement and conservation of D. dumetorum. Moreover, GBS appears as an efficient powerful tool to detect intraspecific variation.
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Affiliation(s)
- Christian Siadjeu
- Institute for Biology and Environmental Sciences, Biodiversity and Evolution of Plants, Carl-von-Ossietzky University Oldenburg, Carl-von-Ossietzky Str. 9-11, 26111 Oldenburg, Germany
| | - Eike Mayland-Quellhorst
- Institute for Biology and Environmental Sciences, Biodiversity and Evolution of Plants, Carl-von-Ossietzky University Oldenburg, Carl-von-Ossietzky Str. 9-11, 26111 Oldenburg, Germany
| | - Dirk C. Albach
- Institute for Biology and Environmental Sciences, Biodiversity and Evolution of Plants, Carl-von-Ossietzky University Oldenburg, Carl-von-Ossietzky Str. 9-11, 26111 Oldenburg, Germany
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16
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Fatokun C, Girma G, Abberton M, Gedil M, Unachukwu N, Oyatomi O, Yusuf M, Rabbi I, Boukar O. Genetic diversity and population structure of a mini-core subset from the world cowpea (Vigna unguiculata (L.) Walp.) germplasm collection. Sci Rep 2018; 8:16035. [PMID: 30375510 PMCID: PMC6207765 DOI: 10.1038/s41598-018-34555-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/12/2018] [Indexed: 11/08/2022] Open
Abstract
The International Institute of Tropical Agriculture maintains the world's largest collection of cowpea germplasm of over 15,000 accessions. A sub-set of 298 lines from the loosely composed mini core collection of 370 landraces were genotyped based on genotyping by sequencing (GBS). Ward's minimum variance hierarchical cluster analysis, model-based ancestry analysis and discriminant analysis of principal component (DAPC) were carried out on this sub-set. Three clusters were identified by the different clustering methods. Principal component analysis further supported the three clusters especially when accessions are scattered along the axes of the first two principal components. The first two principal components explained a total of 22.30% of the variation. Cluster one comprises 115 accessions from the largest number of countries and has the highest gene diversity, heterozygosity and polymorphic information content (PIC) values. Cluster two is made up of 102 accessions, 90 percent of which are from West and Central Africa. Analysis of molecular variance shows that the most variation is among accessions and lowest among clusters. No cluster is made exclusively of accessions from a single country. Based on SNP markers, the sub set of cowpea mini core germplasm collection used in this study encompasses the diversity in the crop.
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Affiliation(s)
- Christian Fatokun
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.
| | - Gezahegn Girma
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN, 47907-2054, USA
| | - Michael Abberton
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Nnanna Unachukwu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Olaniyi Oyatomi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Muyideen Yusuf
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ousmane Boukar
- International Institute of Tropical Agriculture (IITA), Kano, Nigeria
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Price EJ, Bhattacharjee R, Lopez-Montes A, Fraser PD. Carotenoid profiling of yams: Clarity, comparisons and diversity. Food Chem 2018; 259:130-138. [DOI: 10.1016/j.foodchem.2018.03.066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
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Hallahan BF, Fernandez-Tendero E, Fort A, Ryder P, Dupouy G, Deletre M, Curley E, Brychkova G, Schulz B, Spillane C. Hybridity has a greater effect than paternal genome dosage on heterosis in sugar beet (Beta vulgaris). BMC PLANT BIOLOGY 2018; 18:120. [PMID: 29907096 PMCID: PMC6003118 DOI: 10.1186/s12870-018-1338-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/31/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND The phenomenon of heterosis is critical to plant breeding and agricultural productivity. Heterosis occurs when F1 hybrid offspring display quantitative improvements in traits to levels that do not occur in the parents. Increasing the genome dosage (i.e. ploidy level) of F1 offspring can contribute to heterosis effects. Sugar beet (Beta vulgaris) provides a model for investigating the relative effects of genetic hybridity and genome dosage on heterosis. Sugar beet lines of different ploidy levels were crossed to generate diploid and triploid F1 offspring to investigate the effect of; (1) paternal genome dosage increase on F1 heterosis, and; (2) homozygous versus heterozygous tetraploid male parents on F1 triploid heterosis. A range of traits of agronomic and commercial importance were analyzed for the extent of heterosis effects observed in the F1 offspring. RESULTS Comparisons of parental lines to diploid (EA, EB) and triploid (EAA, EBB) F1 hybrids for total yield, root yield, and sugar yield indicated that there was no effect of paternal genome dosage increases on heterosis levels, indicating that hybridity is the main contributor to the heterosis levels observed. For all traits measured (apart from seed viability), F1 triploid hybrids derived from heterozygous tetraploid male parents displayed equivalent levels of heterosis as F1 triploid hybrids generated with homozygous tetraploid male parents, suggesting that heterosis gains in F1 triploids do not arise by simply increasing the extent of multi-locus heterozygosity in sugar beet F1 offspring. CONCLUSIONS Overall, our study indicates that; (1) increasing the paternal genome dosage does not enhance heterosis in F1 hybrids, and; (2) increasing multi-locus heterozygosity using highly heterozygous paternal genomes to generate F1 triploid hybrids does not enhance heterosis. Our findings have implications for the design of future F1 hybrid improvement programs for sugar beet.
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Affiliation(s)
- Brendan F. Hallahan
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Eva Fernandez-Tendero
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Peter Ryder
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Gilles Dupouy
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Marc Deletre
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Edna Curley
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
| | | | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4 Ireland
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Akakpo R, Scarcelli N, Chaïr H, Dansi A, Djedatin G, Thuillet AC, Rhoné B, François O, Alix K, Vigouroux Y. Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes. BMC Genomics 2017; 18:782. [PMID: 29025393 PMCID: PMC5639766 DOI: 10.1186/s12864-017-4143-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 10/02/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. RESULTS We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. CONCLUSIONS Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication.
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Affiliation(s)
- Roland Akakpo
- Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), 911, avenue Agropolis, 34394 Montpellier, France
- Unité Mixte de Recherche Génétique Quantitative et Evolutive – Le Moulon, INRA – Univ. Paris-Sud – CNRS – AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- Faculté des Sciences et Techniques de Dassa, Laboratoire de Biotechnologie, Ressources Génétiques et Amélioration des Espèces Animales et Végétales (BIORAVE), Université d’Abomey, Dassa-Zoumè, Benin
| | - Nora Scarcelli
- Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), 911, avenue Agropolis, 34394 Montpellier, France
| | - Hana Chaïr
- Centre International de la Recherche Agronomique pour le Développement, UMR AGAP, F-34398 Montpellier, France
| | - Alexandre Dansi
- Faculté des Sciences et Techniques de Dassa, Laboratoire de Biotechnologie, Ressources Génétiques et Amélioration des Espèces Animales et Végétales (BIORAVE), Université d’Abomey, Dassa-Zoumè, Benin
| | - Gustave Djedatin
- Faculté des Sciences et Techniques de Dassa, Laboratoire de Biotechnologie, Ressources Génétiques et Amélioration des Espèces Animales et Végétales (BIORAVE), Université d’Abomey, Dassa-Zoumè, Benin
| | - Anne-Céline Thuillet
- Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), 911, avenue Agropolis, 34394 Montpellier, France
| | - Bénédicte Rhoné
- Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), 911, avenue Agropolis, 34394 Montpellier, France
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Lyon, France
| | | | - Karine Alix
- Unité Mixte de Recherche Génétique Quantitative et Evolutive – Le Moulon, INRA – Univ. Paris-Sud – CNRS – AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Yves Vigouroux
- Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), 911, avenue Agropolis, 34394 Montpellier, France
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Tamiru M, Natsume S, Takagi H, White B, Yaegashi H, Shimizu M, Yoshida K, Uemura A, Oikawa K, Abe A, Urasaki N, Matsumura H, Babil P, Yamanaka S, Matsumoto R, Muranaka S, Girma G, Lopez-Montes A, Gedil M, Bhattacharjee R, Abberton M, Kumar PL, Rabbi I, Tsujimura M, Terachi T, Haerty W, Corpas M, Kamoun S, Kahl G, Takagi H, Asiedu R, Terauchi R. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biol 2017; 15:86. [PMID: 28927400 PMCID: PMC5604175 DOI: 10.1186/s12915-017-0419-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. Results To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. Conclusions Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0419-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | | | | | | | - Aiko Uemura
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Kaori Oikawa
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | | | | | - Shinsuke Yamanaka
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Ryo Matsumoto
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Satoru Muranaka
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Gezahegn Girma
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Melaku Gedil
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Michael Abberton
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - P Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | | | | | | | | | | | - Hiroko Takagi
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan.
| | - Robert Asiedu
- International Institute of Tropical Agriculture, Ibadan, Nigeria.
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Japan. .,Kyoto University, Kyoto, Japan.
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21
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Li R, Erpelding JE. Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing. Genetica 2016; 144:535-545. [PMID: 27604991 DOI: 10.1007/s10709-016-9921-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
Abstract
The diploid cotton species Gossypium arboreum possesses many favorable agronomic traits such as drought tolerance and disease resistance, which can be utilized in the development of improved upland cotton cultivars. The USDA National Plant Germplasm System maintains more than 1600 G. arboreum accessions. Little information is available on the genetic diversity of the collection thereby limiting the utilization of this cotton species. The genetic diversity and population structure of the G. arboreum germplasm collection were assessed by genotyping-by-sequencing of 375 accessions. Using genome-wide single nucleotide polymorphism sequence data, two major clusters were inferred with 302 accessions in Cluster 1, 64 accessions in Cluster 2, and nine accessions unassigned due to their nearly equal membership to each cluster. These two clusters were further evaluated independently resulting in the identification of two sub-clusters for the 302 Cluster 1 accessions and three sub-clusters for the 64 Cluster 2 accessions. Low to moderate genetic diversity between clusters and sub-clusters were observed indicating a narrow genetic base. Cluster 2 accessions were more genetically diverse and the majority of the accessions in this cluster were landraces. In contrast, Cluster 1 is composed of varieties or breeding lines more recently added to the collection. The majority of the accessions had kinship values ranging from 0.6 to 0.8. Eight pairs of accessions were identified as potential redundancies due to their high kinship relatedness. The genetic diversity and genotype data from this study are essential to enhance germplasm utilization to identify genetically diverse accessions for the detection of quantitative trait loci associated with important traits that would benefit upland cotton improvement.
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Affiliation(s)
- Ruijuan Li
- Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, PO Box 345, Stoneville, MS, 38776, USA
| | - John E Erpelding
- Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, PO Box 345, Stoneville, MS, 38776, USA.
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22
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Price EJ, Wilkin P, Sarasan V, Fraser PD. Metabolite profiling of Dioscorea (yam) species reveals underutilised biodiversity and renewable sources for high-value compounds. Sci Rep 2016; 6:29136. [PMID: 27385275 PMCID: PMC4935876 DOI: 10.1038/srep29136] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/15/2016] [Indexed: 11/24/2022] Open
Abstract
Yams (Dioscorea spp.) are a multispecies crop with production in over 50 countries generating ~50 MT of edible tubers annually. The long-term storage potential of these tubers is vital for food security in developing countries. Furthermore, many species are important sources of pharmaceutical precursors. Despite these attributes as staple food crops and sources of high-value chemicals, Dioscorea spp. remain largely neglected in comparison to other staple tuber crops of tropical agricultural systems such as cassava (Manihot esculenta) and sweet potato (Ipomoea batatas). To date, studies have focussed on the tubers or rhizomes of Dioscorea, neglecting the foliage as waste. In the present study metabolite profiling procedures, using GC-MS approaches, have been established to assess biochemical diversity across species. The robustness of the procedures was shown using material from the phylogenetic clades. The resultant data allowed separation of the genotypes into clades, species and morphological traits with a putative geographical origin. Additionally, we show the potential of foliage material as a renewable source of high-value compounds.
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Affiliation(s)
- Elliott J. Price
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW20 3AB, UK
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW20 3AB, UK
| | | | - Paul D. Fraser
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
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23
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Wu Y, San Vicente F, Huang K, Dhliwayo T, Costich DE, Semagn K, Sudha N, Olsen M, Prasanna BM, Zhang X, Babu R. Molecular characterization of CIMMYT maize inbred lines with genotyping-by-sequencing SNPs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:753-765. [PMID: 26849239 PMCID: PMC4799255 DOI: 10.1007/s00122-016-2664-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 01/09/2016] [Indexed: 05/08/2023]
Abstract
Molecular characterization information on genetic diversity, population structure and genetic relationships provided by this research will help maize breeders to better understand how to utilize the current CML collection. CIMMYT maize inbred lines (CMLs) have been widely used all over the world and have contributed greatly to both tropical and temperate maize improvement. Genetic diversity and population structure of the current CML collection and of six temperate inbred lines were assessed and relationships among all lines were determined with genotyping-by-sequencing SNPs. Results indicated that: (1) wider genetic distance and low kinship coefficients among most pairs of lines reflected the uniqueness of most lines in the current CML collection; (2) the population structure and genetic divergence between the Temperate subgroup and Tropical subgroups were clear; three major environmental adaptation groups (Lowland Tropical, Subtropical/Mid-altitude and Highland Tropical subgroups) were clearly present in the current CML collection; (3) the genetic diversity of the three Tropical subgroups was similar and greater than that of the Temperate subgroup; the average genetic distance between the Temperate and Tropical subgroups was greater than among Tropical subgroups; and (4) heterotic patterns in each environmental adaptation group estimated using GBS SNPs were only partially consistent with patterns estimated based on combining ability tests and pedigree information. Combining current heterotic information based on combining ability tests and the genetic relationships inferred from molecular marker analyses may be the best strategy to define heterotic groups for future tropical maize improvement. Information resulting from this research will help breeders to better understand how to utilize all the CMLs to select parental lines, replace testers, assign heterotic groups and create a core set of breeding germplasm.
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Affiliation(s)
- Yongsheng Wu
- Maize Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, 530007, Guangxi, China
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Felix San Vicente
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Kaijian Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, 530007, Guangxi, China
| | - Thanda Dhliwayo
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Kassa Semagn
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621, Kenya
| | - Nair Sudha
- CIMMYT-India, C/O ICRISAT, Patancheru, 502324, Andhra Pradesh, India
| | - Michael Olsen
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621, Kenya
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621, Kenya
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| | - Raman Babu
- CIMMYT-India, C/O ICRISAT, Patancheru, 502324, Andhra Pradesh, India.
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Ngo Ngwe MFS, Omokolo DN, Joly S. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices. PLoS One 2015; 10:e0145364. [PMID: 26691919 PMCID: PMC4686806 DOI: 10.1371/journal.pone.0145364] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/01/2015] [Indexed: 11/25/2022] Open
Abstract
Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.
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Affiliation(s)
- Marie Florence Sandrine Ngo Ngwe
- Laboratory of Plant Physiology, Higher Teacher’s Training College, University of Yaoundé 1, P. O. Box 47, Yaounde, Cameroon
- Institute of Agricultural Research for Development-CEREFEN, BP 167, Meyomessala, Cameroon
- * E-mail:
| | - Denis Ndoumou Omokolo
- Laboratory of Plant Physiology, Higher Teacher’s Training College, University of Yaoundé 1, P. O. Box 47, Yaounde, Cameroon
| | - Simon Joly
- Institut de recherche en biologie végétale, Montreal Botanical Garden and Université de Montréal, 4101 Sherbrooke East, Montréal, QC, H1X 2B2, Canada
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Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries. PLoS One 2015. [PMID: 26222616 PMCID: PMC4519108 DOI: 10.1371/journal.pone.0134031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The reducing cost and rapid progress in next-generation sequencing techniques coupled with high performance computational approaches have resulted in large-scale discovery of advanced genomic resources in several model and non-model plant species. Yam (Dioscorea spp.) is a major food and cash crop in many countries but research efforts have been limited to understand the genetics and generate genomic information for the crop. The availability of a large number of genomic resources including genome-wide molecular markers will accelerate the breeding efforts and application of genomic selection in yams. In the present study, several methods including expressed sequence tags (EST)-sequencing, de novo sequencing, and genotyping-by-sequencing (GBS) profiles on two yam (Dioscorea alata L.) genotypes (TDa 95/00328 and TDa 95-310) was performed to generate genomic resources for use in its improvement programs. This includes a comprehensive set of EST-SSRs, genomic SSRs, whole genome SNPs, and reduced representation SNPs. A total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from the two genotypes. A set of 388 EST-SSRs were validated as polymorphic showing a polymorphism rate of 34% when tested on two diverse parents targeted for anthracnose disease. In addition, approximately 40X de novo whole genome sequence coverage was generated for each of the two genotypes, and a total of 18,584 and 15,952 genomic SSRs were identified for TDa 95/00328 and TDa 95-310, respectively. A custom made pipeline resulted in the selection of 573 genomic SSRs common across the two genotypes, of which only eight failed, 478 being polymorphic and 62 monomorphic indicating a polymorphic rate of 83.5%. Additionally, 288,505 high quality SNPs were also identified between these two genotypes. Genotyping by sequencing reads on these two genotypes also revealed 36,790 overlapping SNP positions that are distributed throughout the genome. Our efforts in using different approaches in generating genomic resources provides a non-biased glimpse into the publicly available EST-sequences, yam genome, and GBS profiles with affirmation that the genomic complexity can be methodically unraveled and constitute a critical foundation for future studies in linkage mapping, germplasm analysis, and predictive breeding.
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Wong MML, Gujaria-Verma N, Ramsay L, Yuan HY, Caron C, Diapari M, Vandenberg A, Bett KE. Classification and characterization of species within the genus lens using genotyping-by-sequencing (GBS). PLoS One 2015; 10:e0122025. [PMID: 25815480 PMCID: PMC4376907 DOI: 10.1371/journal.pone.0122025] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/08/2015] [Indexed: 11/18/2022] Open
Abstract
Lentil (Lens culinaris ssp. culinaris) is a nutritious and affordable pulse with an ancient crop domestication history. The genus Lens consists of seven taxa, however, there are many discrepancies in the taxon and gene pool classification of lentil and its wild relatives. Due to the narrow genetic basis of cultivated lentil, there is a need towards better understanding of the relationships amongst wild germplasm to assist introgression of favourable genes into lentil breeding programs. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows multiplexing of up to 384 samples or more per library to generate genome-wide single nucleotide Polymorphism (SNP) markers. In this study, we aimed to characterize our lentil germplasm collection using a two-enzyme GBS approach. We constructed two 96-plex GBS libraries with a total of 60 accessions where some accessions had several samples and each sample was sequenced in two technical replicates. We developed an automated GBS pipeline and detected a total of 266,356 genome-wide SNPs. After filtering low quality and redundant SNPs based on haplotype information, we constructed a maximum-likelihood tree using 5,389 SNPs. The phylogenetic tree grouped the germplasm collection into their respective taxa with strong support. Based on phylogenetic tree and STRUCTURE analysis, we identified four gene pools, namely L. culinaris/L. orientalis/L. tomentosus, L. lamottei/L. odemensis, L. ervoides and L. nigricans which form primary, secondary, tertiary and quaternary gene pools, respectively. We discovered sequencing bias problems likely due to DNA quality and observed severe run-to-run variation in the wild lentils. We examined the authenticity of the germplasm collection and identified 17% misclassified samples. Our study demonstrated that GBS is a promising and affordable tool for screening by plant breeders interested in crop wild relatives.
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Affiliation(s)
- Melissa M. L. Wong
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Neha Gujaria-Verma
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Hai Ying Yuan
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Carolyn Caron
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Marwan Diapari
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Kirstin E. Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
- * E-mail:
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