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Cho MS, Kim Y, Kim SH, Jeon JH, Yang J, Kim SC. Phylogenetic relationships and genetic diversity of the Korean endemic Phedimus latiovalifolius (Crassulaceae) and its close relatives. Sci Rep 2024; 14:16255. [PMID: 39009598 PMCID: PMC11251145 DOI: 10.1038/s41598-024-63272-9] [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: 01/31/2024] [Accepted: 05/27/2024] [Indexed: 07/17/2024] Open
Abstract
Phedimus latiovalifolius (Y.N.Lee) D.C.Son & H.J.Kim is exclusively distributed in the high mountains in the Korean Peninsula, mainly along the Baekdudaegan mountain range. Despite its morphological and distributional distinction from other Phedimus Raf. species, its taxonomic identity and phylogenetic relationship with congeneric species remain unclear. This study employs genotyping-by-sequencing-derived genome-wide single nucleotide polymorphisms to establish the monophyly of P. latiovalifolius and its relationship with closely related species. Genetic diversity and population differentiation of P. latiovalifolius are also assessed to provide baseline genetic information for future conservation and management strategies. Our phylogenetic analyses robustly demonstrate the monophyletic nature of P. latiovalifolius, with P. aizoon (L.) 't Hart identified as its closest sister lineage. There is no genetic evidence supporting a hybrid origin of P. latiovalifolius from P. aizoon involving either P. ellacombeanus (Praeger) 't Hart or P. kamtschaticus (Fisch.) 't Hart. Population genetic analyses reveal two major groups within P. latiovalifolius. A higher genetic variation is observed in P. ellacombeanus than in the congeneric species. Notably, most of the genetic variation exists within P. latiovalifolius populations. Given its distribution and the potential role of Baekdudaegan as an East Asian Pleistocene refugia, P. latiovalifolius could be considered rare and endemic, persisting in the refugium across glacial/interglacial cycles.
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Affiliation(s)
- Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yongsung Kim
- Honam National Institute of Biological Resources, Mokpo, 58762, Korea
| | - Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Ji-Hyeon Jeon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - JiYoung Yang
- Institute for Dok-Do and Ulleung-Do Island, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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Yadav IS, Singh N, Wu S, Raupp J, Wilson DL, Rawat N, Gill BS, Poland J, Tiwari VK. Exploring genetic diversity of wild and related tetraploid wheat species Triticum turgidum and Triticum timopheevii. J Adv Res 2023; 48:47-60. [PMID: 36084813 PMCID: PMC10248793 DOI: 10.1016/j.jare.2022.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION The domestication bottleneck has reduced genetic diversity inwheat, necessitating the use of wild relatives in breeding programs. Wild tetraploid wheat are widely used in the breeding programs but with morphological characters, it is difficult to distinguish these, resulting in misclassification/mislabeling or duplication of accessions in the Gene bank. OBJECTIVES The study aims to exploreGenotyping by sequencing (GBS) to characterize wild and domesticated tetraploid wheat accessions to generate a core set of accessions to be used in the breeding program. METHODS TASSEL-GBS pipeline was used for SNP discovery, fastStructure was used to determine the population structure and PowerCore was used to generate a core sets. Nucleotide diversity matrices of Nie's and F-statistics (FST) index were used to determine the center of genetic diversity. RESULTS We found 65 % and 47 % duplicated accessions in Triticum timopheevii and T. turgidum respectively. Genome-wide nucleotide diversity and FST scan uncovered a lower intra and higher inter-species differentiation. Distinct FST regions were identified in genomic regions belonging to domestication genes: non-brittle rachis (Btr1) and vernalization (VRN-1).Our results suggest that Israel, Jordan, Syria, and Lebanonas the hub of genetic diversity of wild emmer;Turkey, and Georgia for T. durum; and Iraq, Azerbaijan, and Armenia for theT. timopheevii. Identified core set accessions preserved more than 93 % of the available genetic diversity. Genome wide association study (GWAS) indicated the potential chromosomal segment for resistance to leaf rust in T. timopheevii. CONCLUSION The present study explored the potential of GBS technology in data reduction while maintaining the significant genetic diversity of the species. Wild germplasm showed more differentiation than domesticated accessions, indicating the availability of sufficient diversity for crop improvement. With reduced complexity, the core set preserves the genetic diversity of the gene bank collections and will aid in a more robust characterization of wild germplasm.
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Affiliation(s)
- Inderjit S. Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | | | - Shuangye Wu
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jon Raupp
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Duane L. Wilson
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Bikram S. Gill
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesse Poland
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Vijay K. Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
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De Luca D, Del Guacchio E, Cennamo P, Paino L, Caputo P. Genotyping-by-sequencing provides new genetic and taxonomic insights in the critical group of Centaurea tenorei. FRONTIERS IN PLANT SCIENCE 2023; 14:1130889. [PMID: 37260938 PMCID: PMC10228698 DOI: 10.3389/fpls.2023.1130889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/18/2023] [Indexed: 06/02/2023]
Abstract
Centaurea L. is one of the most widespread, differentiated, and critical genera of Asteraceae in the Euro-Mediterranean area, with more than 100 currently recognized species inhabiting the region. The controversial C. tenorei group, narrowly endemic to the Peninsula of Sorrento (Campania region, southern Italy), includes three weakly differentiated microspecies: C. tenorei Guss. ex Lacaita, C. montaltensis (Fiori) Peruzzi and C. lacaitae Peruzzi. However, their taxonomic distinctiveness and relationships with close or sympatric species are still unclear. In particular, the existence in several localities of individuals with intermediate morphology suggests inadequate taxonomic assessment within the group or hybridization and introgression with other species. In this study we aimed at defining population structure in this complex. With this objective, we sampled the three currently accepted species from their loci classici (i.e., the localities in which the taxa were originally described) and from other localities throughout the range, including populations of difficult identification occurring where the ranges of different taxa overlap. We employed a panel of SNPs obtained via genotyping-by-sequencing for investigations on genetic structure, admixture and ploidy inference, the latter also compared with chromosome counts. Our results showed that Centaurea tenorei s.l. is consistently tetraploid, contradicting the current taxonomy that was also based on ploidy level. Population structure analyses indicated the presence of four to seven clusters, most of which with clear evidence of admixture. Furthermore, contrarily to what previously supposed, we demonstrated a remarkable contribution of C. deusta, more that of C. cineraria in the genetic make-up of C. tenorei. However, we found a population of C. cineraria outside its ecological range, probably driven by climate change, which could be responsible in the future of further hybridization phenomena.
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Affiliation(s)
- Daniele De Luca
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Emanuele Del Guacchio
- Department of Biology, University of Naples Federico II, Naples, Italy
- Botanical Garden of Naples, University of Naples Federico II, Naples, Italy
| | - Paola Cennamo
- Department of Humanities, University Suor Orsola Benincasa, Naples, Italy
| | - Luca Paino
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Paolo Caputo
- Department of Biology, University of Naples Federico II, Naples, Italy
- Botanical Garden of Naples, University of Naples Federico II, Naples, Italy
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Abstract
Over the past decade, advances in plant genotyping have been critical in enabling the identification of genetic diversity, in understanding evolution, and in dissecting important traits in both crops and native plants. The widespread popularity of single-nucleotide polymorphisms (SNPs) has prompted significant improvements to SNP-based genotyping, including SNP arrays, genotyping by sequencing, and whole-genome resequencing. More recent approaches, including genotyping structural variants, utilizing pangenomes to capture species-wide genetic diversity and exploiting machine learning to analyze genotypic data sets, are pushing the boundaries of what plant genotyping can offer. In this chapter, we highlight these innovations and discuss how they will accelerate and advance future genotyping efforts.
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Raj SRG, Nadarajah K. QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals. Int J Mol Sci 2022; 24:ijms24010006. [PMID: 36613450 PMCID: PMC9820233 DOI: 10.3390/ijms24010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.
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Nasiri A, Kazempour-Osaloo S, Hamzehee B, Bull RD, Saarela JM. A phylogenetic analysis of Bromus (Poaceae: Pooideae: Bromeae) based on nuclear ribosomal and plastid data, with a focus on Bromus sect. Bromus. PeerJ 2022; 10:e13884. [PMID: 36193423 PMCID: PMC9526414 DOI: 10.7717/peerj.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/21/2022] [Indexed: 01/18/2023] Open
Abstract
To investigate phylogenetic relationships among and within major lineages of Bromus, with focus on Bromus sect. Bromus, we analyzed DNA sequences from two nuclear ribosomal (ITS, ETS) and two plastid (rpl32-trnLUAG , matK) regions. We sampled 103 ingroup accessions representing 26 taxa of B. section Bromus and 15 species of other Bromus sections. Our analyses confirm the monophyly of Bromus s.l. and identify incongruence between nuclear ribosomal and plastid data partitions for relationships within and among major Bromus lineages. Results support classification of B. pumilio and B. gracillimus within B. sect. Boissiera and B. sect. Nevskiella, respectively. These species are sister groups and are closely related to B. densus (B. sect. Mexibromus) in nrDNA trees and Bromus sect. Ceratochloa in plastid trees. Bromus sect. Bromopsis is paraphyletic. In nrDNA trees, species of Bromus sects. Bromopsis, Ceratochloa, Neobromus, and Genea plus B. rechingeri of B. sect. Bromus form a clade, in which B. tomentellus is sister to a B. sect. Genea-B. rechingeri clade. In the plastid trees, by contrast, B. sect. Bromopsis species except B. tomentosus form a clade, and B. tomentosus is sister to a clade comprising B. sect. Bromus and B. sect. Genea species. Affinities of B. gedrosianus, B. pulchellus, and B. rechingeri (members of the B. pectinatus complex), as well as B. oxyodon and B. sewerzowii, are discordant between nrDNA and plastid trees. We infer these species may have obtained their plastomes via chloroplast capture from species of B. sect. Bromus and B. sect. Genea. Within B. sect. Bromus, B. alopecuros subsp. caroli-henrici, a clade comprising B. hordeaceus and B. interruptus, and B. scoparius are successive sister groups to the rest of the section in the nrDNA phylogeny. Most relationships among the remaining species of B. sect. Bromus are unresolved in the nrDNA and plastid trees. Given these results, we infer that most B. sect. Bromus species likely diversified relatively recently. None of the subdivisional taxa proposed for Bromus sect. Bromus over the last century correspond to natural groups identified in our phylogenetic analyses except for a group including B. hordeaceus and B. interruptus.
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Affiliation(s)
- Akram Nasiri
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran,Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Shahrokh Kazempour-Osaloo
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behnam Hamzehee
- Botany Research Division, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Roger D. Bull
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Jeffery M. Saarela
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, Ontario, Canada
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Omire A, Neondo J, Budambula NLM, Wangai L, Ogada S, Mweu C. Genetic Diversity and Population Structure of Doum Palm (Hyphaene compressa) Using Genotyping by Sequencing. Front Genet 2022; 13:762202. [PMID: 35186022 PMCID: PMC8854861 DOI: 10.3389/fgene.2022.762202] [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: 08/21/2021] [Accepted: 01/03/2022] [Indexed: 11/19/2022] Open
Abstract
Doum palm (Hyphaene compressa) is a perennial economic plant primarily growing in Kenya’s Arid and Semi-Arid Lands (ASALs). It is heavily relied upon for food, animal feed, construction materials and medicine, making it an ideal plant for resource sustainability. However, the limited information on its genetic resources has hindered its breeding and conservation studies. This study used the genotyping by sequencing approach to identify Single Nucleotide Polymorphisms. These SNPs were further used to assess the genetic diversity and population structure of 96 H. compressa accessions from Coastal, Northern and Eastern ASAL regions of Kenya using two approaches; reference-based and de novo-based assemblies. STRUCTURE analysis grouped the sampled accessions into two genetic clusters (Cluster 1 and Cluster 2). Cluster 1 included accessions from the Northern region, whereas Cluster 2 included all accessions from Eastern and Coastal regions. Accessions from Kwale (Coastal) had mixed ancestry from both Cluster 1 and Cluster 2. These STRUCTURE findings were further supported by principal components analysis, discriminant analysis of principal components and phylogenetic analysis. Analysis of molecular variance indicated greater genetic variation within populations (92.7%) than among populations (7.3%). An overall FST of 0.074 was observed, signifying moderate genetic differentiation among populations. The results of this study will provide information useful in breeding, marker-assisted selection and conservation management of H. compressa.
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Affiliation(s)
- Agnes Omire
- Department of Botany, School of Biological Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Johnstone Neondo
- Institute for Biotechnology Research (IBR), Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Nancy L. M. Budambula
- Department of Biological Sciences, School of Pure and Applied Sciences, University of Embu, Embu, Kenya
| | - Laura Wangai
- Department of Biomedical Sciences, School of Health Sciences, Kirinyaga University, Kerugoya, Kenya
| | - Stephen Ogada
- Institute for Biotechnology Research (IBR), Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Cecilia Mweu
- Institute for Biotechnology Research (IBR), Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- *Correspondence: Cecilia Mweu,
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Keilwagen J, Lehnert H, Berner T, Badaeva E, Himmelbach A, Börner A, Kilian B. Detecting major introgressions in wheat and their putative origins using coverage analysis. Sci Rep 2022; 12:1908. [PMID: 35115645 PMCID: PMC8813953 DOI: 10.1038/s41598-022-05865-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.
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Affiliation(s)
| | | | | | - Ekaterina Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Keilwagen J, Lehnert H, Berner T, Badaeva E, Himmelbach A, Börner A, Kilian B. Detecting major introgressions in wheat and their putative origins using coverage analysis. Sci Rep 2022; 12:1908. [PMID: 35115645 DOI: 10.21203/rs.3.rs-910879/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/12/2022] [Indexed: 05/26/2023] Open
Abstract
Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.
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Affiliation(s)
| | | | | | - Ekaterina Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Volante A, Barabaschi D, Marino R, Brandolini A. Genome-wide association study for morphological, phenological, quality, and yield traits in einkorn (Triticum monococcum L. subsp. monococcum). G3 (BETHESDA, MD.) 2021; 11:jkab281. [PMID: 34849796 PMCID: PMC8527505 DOI: 10.1093/g3journal/jkab281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/27/2021] [Indexed: 11/12/2022]
Abstract
Einkorn (Triticum monococcum L. subsp. monococcum, 2n = 2× = 14, AmAm) is a diploid wheat whose cultivation was widespread in the Mediterranean and European area till the Bronze Age, before it was replaced by the more productive durum and bread wheats. Although scarcely cultivated nowadays, it has gained renewed interest due to its relevant nutritional properties and as source of genetic diversity for crop breeding. However, the molecular basis of many traits of interest in einkorn remain still unknown. A panel of 160 einkorn landraces, from different parts of the distribution area, was characterized for several phenotypic traits related to morphology, phenology, quality, and yield for 4 years in two locations. An approach based on co-linearity with the A genome of bread wheat, supported also by that with Triticum urartu genome, was exploited to perform association mapping, even without an einkorn anchored genome. The association mapping approach uncovered numerous marker-trait associations; for 37 of these, a physical position was inferred by homology with the bread wheat genome. Moreover, numerous associated regions were also assigned to the available T. monococcum contigs. Among the intervals detected in this work, three overlapped with regions previously described as involved in the same trait, while four other regions were localized in proximity of loci previously described and presumably refer to the same gene/QTL. The remaining associated regions identified in this work could represent a novel and useful starting point for breeding approaches to improve the investigated traits in this neglected species.
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Affiliation(s)
- Andrea Volante
- CREA—Research Centre for Cereal and Industrial Crops, 13100 Vercelli, Italy
| | - Delfina Barabaschi
- CREA—Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy and
| | - Rosanna Marino
- CREA—Research Centre for Animal Production and Aquaculture, 26900 Lodi, Italy
| | - Andrea Brandolini
- CREA—Research Centre for Animal Production and Aquaculture, 26900 Lodi, Italy
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Hyun DY, Sebastin R, Lee GA, Lee KJ, Kim SH, Yoo E, Lee S, Kang MJ, Lee SB, Jang I, Ro NY, Cho GT. Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon ( Cucumis melo L.) Varieties Using Genotyping-by-Sequencing. Int J Mol Sci 2021; 22:ijms22136722. [PMID: 34201603 PMCID: PMC8268568 DOI: 10.3390/ijms22136722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/29/2022] Open
Abstract
Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.
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Affiliation(s)
- Do Yoon Hyun
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
- Correspondence:
| | - Raveendar Sebastin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Kyung Jun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
- Honam National Institute of Biological Resources, Mokpo-si 58762, Korea
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Eunae Yoo
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Sookyeong Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Man-Jung Kang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Seung Bum Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Ik Jang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Na-Young Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Jeonju 54874, Korea; (R.S.); (G.-A.L.); (K.J.L.); (S.-H.K.); (E.Y.); (S.L.); (M.-J.K.); (S.B.L.); (I.J.); (N.-Y.R.); (G.-T.C.)
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12
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Liber M, Duarte I, Maia AT, Oliveira HR. The History of Lentil ( Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions. FRONTIERS IN PLANT SCIENCE 2021; 12:628439. [PMID: 33841458 PMCID: PMC8030269 DOI: 10.3389/fpls.2021.628439] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/15/2021] [Indexed: 05/06/2023]
Abstract
Protein-rich legumes accompanied carbohydrate-rich cereals since the beginning of agriculture and yet their domestication history is not as well understood. Lentil (Lens culinaris Medik. subsp. culinaris) was first cultivated in Southwest Asia (SWA) 8000-10,000 years ago but archeological evidence is unclear as to how many times it may have been independently domesticated, in which SWA region(s) this may have happened, and whether wild species within the Lens genus have contributed to the cultivated gene pool. In this study, we combined genotyping-by-sequencing (GBS) of 190 accessions from wild (67) and domesticated (123) lentils from the Old World with archeological information to explore the evolutionary history, domestication, and diffusion of lentils to different environments. GBS led to the discovery of 87,647 single-nucleotide polymorphisms (SNPs), which allowed us to infer the phylogeny of genus Lens. We confirmed previous studies proposing four groups within it. The only gene flow detected was between cultivated varieties and their progenitor (L. culinaris subsp. orientalis) albeit at very low levels. Nevertheless, a few putative hybrids or naturalized cultivars were identified. Within cultivated lentil, we found three geographic groups. Phylogenetics, population structure, and archeological data coincide in a scenario of protracted domestication of lentils, with two domesticated gene pools emerging in SWA. Admixed varieties are found throughout their range, suggesting a relaxed selection process. A small number of alleles involved in domestication and adaptation to climatic variables were identified. Both novel mutation and selection on standing variation are presumed to have played a role in adaptation of lentils to different environments. The results presented have implications for understanding the process of plant domestication (past), the distribution of genetic diversity in germplasm collections (present), and targeting genes in breeding programs (future).
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Affiliation(s)
- Marta Liber
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
| | - Isabel Duarte
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
- Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, Portugal
| | - Ana Teresa Maia
- Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
- Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, Portugal
| | - Hugo R. Oliveira
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
- *Correspondence: Hugo R. Oliveira,
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