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Liu S, He G, Xie G, Gong Y, Zhu N, Xiao C. De novo assembly of Iron-Heart Cunninghamia lanceolata transcriptome and EST-SSR marker development for genetic diversity analysis. PLoS One 2023; 18:e0293245. [PMID: 37917740 PMCID: PMC10621985 DOI: 10.1371/journal.pone.0293245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/09/2023] [Indexed: 11/04/2023] Open
Abstract
Iron-Heart Cunninghamia lanceolata, a wild relative of Chinese fir with valuable genetic and breeding traits, has been limited in genetic studies due to a lack of genomic resources and markers. In this study, we conducted transcriptome sequencing of Iron-Heart C. lanceolata leaves using Illumina NovaSeq 6000 and performed assembly and analysis. We obtained 45,326,576 clean reads and 115,501 unigenes. Comparative analysis in five functional databases resulted in successful annotation of 26,278 unigenes, with 6,693 unigenes annotated in all databases (5.79% of the total). UniProt and Pfam databases provided annotations for 22,673 and 18,315 unigenes, respectively. Gene Ontology analysis categorized 23,962 unigenes into three categories. KEGG database alignment annotated 10,195 unigenes, classifying them into five categories: metabolism, genetic information, biological systems, cellular processes, and environmental information processing. From the unigenes, we identified 5,645 SSRs, with dinucleotides repeats being the most common (41.47%). We observed variations in repeat numbers and base compositions, with the majority of markers ranging from 12 to 29 bp in length. We randomly selected 200 primer pairs and successfully amplified 15 pairs of polymorphic SSR primers, which effectively distinguished Chinese fir plants of different origins. This study provides insights into the genetic characteristics of Iron-Heart C. lanceolata and offers a foundation for future molecular marker development, breeding programs, genetic diversity analysis, and conservation strategies.
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Affiliation(s)
- Sen Liu
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Gongxiu He
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Gongliang Xie
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yamei Gong
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Ninghua Zhu
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
- National Long-Term Scientific Research Base for Forestry in Mid-Subtropics China, Central South University of Forestry and Technology, Changsha, China
| | - Can Xiao
- Jiangxi Environmental Engineering Vocational College, Ganzhou, China
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Tripodi P, Beretta M, Peltier D, Kalfas I, Vasilikiotis C, Laidet A, Briand G, Aichholz C, Zollinger T, van Treuren R, Scaglione D, Goritschnig S. Development and application of Single Primer Enrichment Technology (SPET) SNP assay for population genomics analysis and candidate gene discovery in lettuce. FRONTIERS IN PLANT SCIENCE 2023; 14:1252777. [PMID: 37662148 PMCID: PMC10471991 DOI: 10.3389/fpls.2023.1252777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023]
Abstract
Single primer enrichment technology (SPET) is a novel high-throughput genotyping method based on short-read sequencing of specific genomic regions harboring polymorphisms. SPET provides an efficient and reproducible method for genotyping target loci, overcoming the limits associated with other reduced representation library sequencing methods that are based on a random sampling of genomic loci. The possibility to sequence regions surrounding a target SNP allows the discovery of thousands of closely linked, novel SNPs. In this work, we report the design and application of the first SPET panel in lettuce, consisting of 41,547 probes spanning the whole genome and designed to target both coding (~96%) and intergenic (~4%) regions. A total of 81,531 SNPs were surveyed in 160 lettuce accessions originating from a total of 10 countries in Europe, America, and Asia and representing 10 horticultural types. Model ancestry population structure clearly separated the cultivated accessions (Lactuca sativa) from accessions of its presumed wild progenitor (L. serriola), revealing a total of six genetic subgroups that reflected a differentiation based on cultivar typology. Phylogenetic relationships and principal component analysis revealed a clustering of butterhead types and a general differentiation between germplasm originating from Western and Eastern Europe. To determine the potentiality of SPET for gene discovery, we performed genome-wide association analysis for main agricultural traits in L. sativa using six models (GLM naive, MLM, MLMM, CMLM, FarmCPU, and BLINK) to compare their strength and power for association detection. Robust associations were detected for seed color on chromosome 7 at 50 Mbp. Colocalization of association signals was found for outer leaf color and leaf anthocyanin content on chromosome 9 at 152 Mbp and on chromosome 5 at 86 Mbp. The association for bolting time was detected with the GLM, BLINK, and FarmCPU models on chromosome 7 at 164 Mbp. Associations were detected in chromosomal regions previously reported to harbor candidate genes for these traits, thus confirming the effectiveness of SPET for GWAS. Our findings illustrated the strength of SPET for discovering thousands of variable sites toward the dissection of the genomic diversity of germplasm collections, thus allowing a better characterization of lettuce collections.
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Affiliation(s)
- Pasquale Tripodi
- Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Pontecagnano Faiano, SA, Italy
| | | | | | | | | | - Anthony Laidet
- Gautier Semences Route d’Avignon 13630, Eyragues, France
| | - Gael Briand
- Gautier Semences Route d’Avignon 13630, Eyragues, France
| | | | | | - Rob van Treuren
- Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research, Wageningen, Netherlands
| | | | - Sandra Goritschnig
- European Cooperative Programme for Plant Genetic Resources (ECPGR) Secretariat c/o Alliance of Bioversity International and CIAT, Rome, Italy
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Özkan G, Haliloğlu K, Türkoğlu A, Özturk HI, Elkoca E, Poczai P. Determining Genetic Diversity and Population Structure of Common Bean ( Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers. Genes (Basel) 2022; 13:1410. [PMID: 36011321 PMCID: PMC9407889 DOI: 10.3390/genes13081410] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Assessment of genetic diversity among different varieties helps to improve desired characteristics of crops, including disease resistance, early maturity, high yield, and resistance to drought. Molecular markers are one of the most effective tools for discovering genetic diversity that can increase reproductive efficiency. Simple sequence repeats (SSRs), which are codominant markers, are preferred for the determination of genetic diversity because they are highly polymorphic, multi-allelic, highly reproducible, and have good genome coverage. This study aimed to determine the genetic diversity of 40 common bean (Phaseolus vulgaris L.) landraces collected from the Ispir district located in the Northeast Anatolia region of Türkiye and five commercial varieties using SSR markers. The Twenty-seven SSR markers produced a total of 142 polymorphic bands, ranging from 2 (GATS91 and PVTT001) to 12 (BM153) alleles per marker, with an average number of 5.26 alleles. The gene diversity per marker varied between 0.37 and 0.87 for BM053 and BM153 markers, respectively. When heterozygous individuals are calculated proportional to the population, the heterozygosity ranged from 0.00 to 1.00, with an average of 0.30. The expected heterozygosity of the SSR locus ranged from 0.37 (BM053) to 0.88 (BM153), with an average of 0.69. Nei's gene diversity scored an average of 0.69. The polymorphic information content (PIC) values of SSR markers varied from 0.33 (BM053) to 0.86 (BM153), with an average of 0.63 per locus. The greatest genetic distance (0.83) was between lines 49, 50, 53, and cultivar Karacaşehir-90, while the shortest (0.08) was between lines 6 and 26. In cluster analysis using Nei's genetic distance, 45 common bean genotypes were divided into three groups and very little relationship was found between the genotypes and the geographical distances. In genetic structure analysis, three subgroups were formed, including local landraces and commercial varieties. The result confirmed that the rich diversity existing in Ispir bean landraces could be used as a genetic resource in designing breeding programs and may also contribute to Türkiye bean breeding programs.
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Affiliation(s)
- Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, Ankara 06100, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye
- Department of Biology, Faculty of Science, Cankiri Karatekin University, Çankırı 18200, Türkiye
| | - Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
| | - Halil Ibrahim Özturk
- Health Services Vocational School, Binali Yıldırım University, Erzincan 24100, Türkiye
| | - Erdal Elkoca
- Vocational High School, Department of Plant and Animal Production, İbrahim Çeçen University, Ağrı 04100, Türkiye
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, FI-00014 Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), H-9731 Kőszeg, Hungary
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Park JS, Kang MY, Shim EJ, Oh J, Seo KI, Kim KS, Sim SC, Chung SM, Park Y, Lee GP, Lee WS, Kim M, Jung JK. Genome-wide core sets of SNP markers and Fluidigm assays for rapid and effective genotypic identification of Korean cultivars of lettuce ( Lactuca sativa L.). HORTICULTURE RESEARCH 2022; 9:uhac119. [PMID: 35928401 PMCID: PMC9343917 DOI: 10.1093/hr/uhac119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/04/2022] [Indexed: 05/08/2023]
Abstract
Lettuce is one of the economically important leaf vegetables and is cultivated mainly in temperate climate areas. Cultivar identification based on the distinctness, uniformity, and stability (DUS) test is a prerequisite for new cultivar registration. However, DUS testing based on morphological features is time-consuming, labor-intensive, and costly, and can also be influenced by environmental factors. Thus, molecular markers have also been used for the identification of genetic diversity as an effective, accurate, and stable method. Currently, genome-wide single nucleotide polymorphisms (SNPs) using next-generation sequencing technology are commonly applied in genetic research on diverse plant species. This study aimed to establish an effective and high-throughput cultivar identification system for lettuce using core sets of SNP markers developed by genotyping by sequencing (GBS). GBS identified 17 877 high-quality SNPs for 90 commercial lettuce cultivars. Genetic differentiation analyses based on the selected SNPs classified the lettuce cultivars into three main groups. Core sets of 192, 96, 48, and 24 markers were further selected and validated using the Fluidigm platform. Phylogenetic analyses based on all core sets of SNPs successfully discriminated individual cultivars that have been currently recognized. These core sets of SNP markers will support the construction of a DNA database of lettuce that can be useful for cultivar identification and purity testing, as well as DUS testing in the plant variety protection system. Additionally, this work will facilitate genetic research to improve breeding in lettuce.
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Affiliation(s)
- Jee-Soo Park
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Min-Young Kang
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Eun-Jo Shim
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - JongHee Oh
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyoung-In Seo
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames IA 50011, USA
| | - Sung-Chur Sim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Sang-Min Chung
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, South Korea
| | - Gung Pyo Lee
- Department of Plant Science and Technology, Chung-Ang University, Ansung 17546, South Korea
| | - Won-Sik Lee
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Minkyung Kim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
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Shen Y, Wang J, Shaw RK, Yu H, Sheng X, Zhao Z, Li S, Gu H. Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli ( Brassica oleracea L. var. italica) in China. FRONTIERS IN PLANT SCIENCE 2021; 12:655254. [PMID: 34149754 PMCID: PMC8213352 DOI: 10.3389/fpls.2021.655254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Broccoli (Brassica oleracea var. italica) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.
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Affiliation(s)
- Yusen Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiansheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ranjan K. Shaw
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huifang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoguang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenqing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sujuan Li
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Kandel R, Lu H, Sandoya GV. Identification and mapping of quantitative trait loci for resistance to Liriomyza trifolii in romaine lettuce cultivar 'Valmaine'. Sci Rep 2021; 11:998. [PMID: 33441768 PMCID: PMC7807064 DOI: 10.1038/s41598-020-80050-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 12/15/2020] [Indexed: 01/29/2023] Open
Abstract
Liriomyza trifolii (Diptera: Agromyzidae) is a leafminer that causes ruinous damage to many leafy vegetables including lettuce (Lactuca sativa L.) by stippling and tunneling the leaves. In this study, a population of 125 F3 families was developed from the intraspecific cross of 'Valmaine' (resistant) and 'Okeechobee' (susceptible) romaine cultivars for inheritance analysis and molecular mapping of the resistance loci controlling stippling damage. The experiments were conducted in an insectarium (controlled environment). Stippling damage proved to be heritable because the broad-sense heritability (H2) was 0.58. A segregation analysis suggested that a single dominant allele, Sd1 locus, controls resistance against L. trifolii. Furthermore, a quantitative trait loci (QTL) analysis identified one novel QTL, named Stippling on LG5 (qSTP5), flanked by two SNPs that were mapped to a 5.2 cM (8.5 Mb region) interval, explaining over 13% of the total phenotypic variance. Desirable allele for resistance to L. trifolii was derived from resistant cultivar Valmaine. Identification of SNPs closely linked to the QTL responsible for L. trifolii resistance should facilitate plant breeders to develop resistant romaine lettuce cultivars.
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Affiliation(s)
- Ramkrishna Kandel
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Huangjun Lu
- Everglades Research and Education Center, Institute of Food and Agricultural Sciences/University of Florida, Belle Glade, FL, 33430, USA
| | - Germán V Sandoya
- Everglades Research and Education Center, Institute of Food and Agricultural Sciences/University of Florida, Belle Glade, FL, 33430, USA.
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Ke YZ, Wu YW, Zhou HJ, Chen P, Wang MM, Liu MM, Li PF, Yang J, Li JN, Du H. Genome-wide survey of the bHLH super gene family in Brassica napus. BMC PLANT BIOLOGY 2020; 20:115. [PMID: 32171243 PMCID: PMC7071649 DOI: 10.1186/s12870-020-2315-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/27/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. RESULTS We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. CONCLUSION The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.
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Affiliation(s)
- Yun-Zhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Yun-Wen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Hong-Jun Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Ping Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Mang-Mang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Ming-Ming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Peng-Feng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Jia-Na Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
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Patella A, Palumbo F, Galla G, Barcaccia G. The Molecular Determination of Hybridity and Homozygosity Estimates in Breeding Populations of Lettuce ( Lactuca sativa L.). Genes (Basel) 2019; 10:E916. [PMID: 31717592 PMCID: PMC6895879 DOI: 10.3390/genes10110916] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/26/2022] Open
Abstract
The development of new varieties of horticultural crops benefits from the integration of conventional and molecular marker-assisted breeding schemes in order to combine phenotyping and genotyping information. In this study, a selected panel of 16 microsatellite markers were used in different steps of a breeding programme of lettuce (Lactuca sativa L., 2 n = 18). Molecular markers were first used to genotype 71 putative parental lines and to plan 89 controlled crosses designed to maximise recombination potentials. The resulting 871 progeny plants were then molecularly screened, and their marker allele profiles were compared with the profiles expected based on the parental lines. The average cross-pollination success rate was 68 ± 33%, so 602 F1 hybrids were completely identified. Unexpected genotypes were detected in 5% of cases, consistent with this species' spontaneous out-pollination rate. Finally, in a later step of the breeding programme, 47 different F3 progenies, selected by phenotyping for a number of morphological descriptors, were characterised in terms of their observed homozygosity and within-population genetic uniformity and stability. Ten of these populations had a median homozygosity above 90% and a median genetic similarity above 95% and are, therefore, particularly suitable for pre-commercial trials. In conclusion, this study shows the synergistic effects and advantages of conventional and molecular methods of selection applied in different steps of a breeding programme aimed at developing new varieties of lettuce.
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Affiliation(s)
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro PD, Italy; (A.P.); (G.G.); (G.B.)
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Purwoko D, Cartealy IC, Tajuddin T, Dinarti D, Sudarsono S. SSR identification and marker development for sago palm based on NGS genome data. BREEDING SCIENCE 2019; 69:1-10. [PMID: 31086478 PMCID: PMC6507712 DOI: 10.1270/jsbbs.18061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/26/2018] [Indexed: 06/09/2023]
Abstract
Sago palm (Metroxylon sagu Rottb.) is one of the most productive carbohydrate-producing crops. Unfortunately, only limited information regarding sago palm genetics is available. This study aimed to develop simple sequence repeat (SSR) markers using sago palm NGS genomic data and use these markers to evaluate the genetic diversity of sago palm from Indonesia. De novo assembly of partial sago palm genomic data and subsequent SSR mining identified 29,953 contigs containing 31,659 perfect SSR loci and 31,578 contigs with 33,576 imperfect SSR loci. The perfect SSR loci density was 132.57/Mb, and AG, AAG and AAAT were the most frequent SSR motifs. Five hundred perfect SSR loci were randomly selected and used for designing SSR primers; 93 SSR primer pairs were identified. After synteny analysis using rice genome sequences, 20 primer pairs were validated using 11 sago palm accessions, and seven primers generated polymorphic alleles. Genetic diversity analysis of 41 sago palm accessions from across Indonesia using polymorphic SSR loci indicated the presence of three clusters. These results demonstrated the success of SSR identification and marker development for sago palm based on NGS genome data, which can be further used for assisting sago palm breeding in the future.
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Affiliation(s)
- Devit Purwoko
- Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology,
Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten,
Indonesia
| | - Imam Civi Cartealy
- Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology,
Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten,
Indonesia
| | - Teuku Tajuddin
- Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology,
Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten,
Indonesia
| | - Diny Dinarti
- Plant Molecular Biology Laboratory, Department of Agronomy and Horticulture, Bogor Agricultural University,
Darmaga, Bogor 16680, West Java,
Indonesia
| | - Sudarsono Sudarsono
- Plant Molecular Biology Laboratory, Department of Agronomy and Horticulture, Bogor Agricultural University,
Darmaga, Bogor 16680, West Java,
Indonesia
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10
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Wang S, Wang B, Liu J, Ren J, Huang X, Zhou G, Wang A. Novel polymorphic EST-based microsatellite markers characterized in lettuce (Lactuca sativa). Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Göl Ş, Doğanlar S, Frary A. Relationship between geographical origin, seed size and genetic diversity in faba bean (Vicia faba L.) as revealed by SSR markers. Mol Genet Genomics 2017; 292:991-999. [PMID: 28497168 DOI: 10.1007/s00438-017-1326-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 05/07/2017] [Indexed: 01/20/2023]
Abstract
Faba bean (Vicia faba L.) is an important legume species because of its high protein and starch content. Broad bean can be grown in different climatic conditions and is an ideal rotation crop because of the nitrogen fixing bacteria in its roots. In this work, 255 faba bean germplasm accessions were characterized using 32 SSR primers which yielded 302 polymorphic fragments. According to the results, faba bean individuals were divided into two main groups based on the neighbor-joining algorithm (r = 0.91) with some clustering based on geographical origin as well as seed size. Population structure was also determined and agreed with the dendrogram analysis in splitting the accessions into two subpopulations. Analysis of molecular variance (AMOVA) revealed high levels of within population genetic variation. Genetic similarity and geographical proximity were related with separation of European accessions from African and Asian ones. Interestingly, there was no significant difference between landrace (38%) and cultivar (40%) diversity indicating that genetic variability has not yet been lost due to breeding. A total of 44 genetically well-characterized faba bean individuals were selected for a core collection to be further examined for yield and nutritional traits.
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Affiliation(s)
- Şurhan Göl
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, 35430, Turkey
| | - Sami Doğanlar
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, 35430, Turkey
| | - Anne Frary
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, 35430, Turkey.
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Rebaa F, Abid G, Aouida M, Abdelkarim S, Aroua I, Muhovski Y, Baudoin JP, M’hamdi M, Sassi K, Jebara M. Genetic variability in Tunisian populations of faba bean ( Vicia faba L. var. major) assessed by morphological and SSR markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:397-409. [PMID: 28461727 PMCID: PMC5391353 DOI: 10.1007/s12298-017-0419-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 06/07/2023]
Abstract
The genetic diversity of 21 faba bean populations was examined using morphological and molecular markers. DNA was extracted from 189 individuals and 8 microsatellite markers were genotyped individually in these 21 populations. A total of 53 alleles were obtained in all populations, with an average of 6.62 alleles per locus. The expected and observed heterozygosity was 0.38 and 0.62 respectively. The average polymorphism index content of SSR markers was 0.61, ranging from 0.31 to 0.81. The unweighted pair group method with arithmetic mean dendrogram clustered all the populations into two groups, each for them subdivided into 3 sub-groups according to geographical origin. Morphological variation showed that the populations were not grouped according to their geographical origin. Therefore, patterns of differentiation of morphological traits did not coincide with molecular differentiation, indicating that morphological variation does not reflect genetic subdivision in studied faba bean populations. Analysis of molecular variance revealed high levels of genetic variation (83%) within population and provides a good base for designing genetic improvement programs. The result of Principal Component Analysis (PCA) revealed that three dimensional principal components (PC1, PC2 and PC3) contributed 40.56% of the total variability and accounted with values of 20.64, 11.22 and 8.70%, respectively. Cluster analysis based on PCA indicated three separate groups of populations. The genetic relationships found between the 21 populations samples were the same in both the PCA and STRUCTURE analysis which support the results observed. These data may serve as a foundation for the development of faba bean breeding programs.
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Affiliation(s)
- Feten Rebaa
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Ghassen Abid
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Marwa Aouida
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Souhir Abdelkarim
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Ibtissem Aroua
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
| | - Yordan Muhovski
- Department of Life Sciences, Unit of Biological Engineering, Walloon Agricultural Research Centre, Chaussée de Charleroi, 234, 5030 Gembloux, Belgium
| | - Jean-Pierre Baudoin
- Laboratory of Tropical Agroecology, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Mahmoud M’hamdi
- Laboratory of Vegetable Crops, Higher Agronomic Institute of Chott Mariem (ISA-CM), 47, 4042 Chott-Mariem, Tunisia
| | - Khaled Sassi
- Department of Agronomy and Plant Biotechnology, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, 43, 1082 Tunis-Mahrajène, Tunisia
| | - Moez Jebara
- Laboratory of Legumes, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, 901, 2050 Hammam-Lif, Tunisia
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13
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Vining KJ, Johnson SR, Ahkami A, Lange I, Parrish AN, Trapp SC, Croteau RB, Straub SCK, Pandelova I, Lange BM. Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement. MOLECULAR PLANT 2017; 10:323-339. [PMID: 27867107 DOI: 10.1016/j.molp.2016.10.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/28/2016] [Accepted: 10/29/2016] [Indexed: 05/08/2023]
Abstract
The genus Mentha encompasses mint species cultivated for their essential oils, which are formulated into a vast array of consumer products. Desirable oil characteristics and resistance to the fungal disease Verticillium wilt are top priorities for the mint industry. However, cultivated mints have complex polyploid genomes and are sterile. Breeding efforts, therefore, require the development of genomic resources for fertile mint species. Here, we present draft de novo genome and plastome assemblies for a wilt-resistant South African accession of Mentha longifolia (L.) Huds., a diploid species ancestral to cultivated peppermint and spearmint. The 353 Mb genome contains 35 597 predicted protein-coding genes, including 292 disease resistance gene homologs, and nine genes determining essential oil characteristics. A genetic linkage map ordered 1397 genome scaffolds on 12 pseudochromosomes. More than two million simple sequence repeats were identified, which will facilitate molecular marker development. The M. longifolia genome is a valuable resource for both metabolic engineering and molecular breeding. This is exemplified by employing the genome sequence to clone and functionally characterize the promoters in a peppermint cultivar, and demonstrating the utility of a glandular trichome-specific promoter to increase expression of a biosynthetic gene, thereby modulating essential oil composition.
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Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA.
| | - Sean R Johnson
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Amirhossein Ahkami
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Iris Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Amber N Parrish
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Susan C Trapp
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Rodney B Croteau
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456, USA
| | - Iovanna Pandelova
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - B Markus Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA.
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Wang Y, Lu H, Hu J. Molecular Mapping of High Resistance to Bacterial Leaf Spot in Lettuce PI 358001-1. PHYTOPATHOLOGY 2016; 106:1319-1325. [PMID: 27454703 DOI: 10.1094/phyto-09-15-0238-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Lettuce (Lactuca sativa L.) is a diploid (2n = 18) with a genome size of 2,600 Mbp, and belongs to the family Compositae. Bacterial leaf spot (BLS), caused by Xanthomonas campestris pv. vitians, is a major disease of lettuce worldwide. Leaf lettuce PI 358001-1 has been characterized as an accession highly resistant to BLS and has white seed. In order to understand inheritance of the high resistance in this germplasm line, an F3 population consisting of 163 families was developed from the cross PI 358001-1 × 'Tall Guzmaine' (a susceptible Romaine lettuce variety with black seed). The segregation ratio of reaction to disease by seedling inoculation with X. campestris pv. vitians L7 strain in the F3 families was shown to be 32:82:48 homozygous resistant/heterozygous/homozygous susceptible, fitting to 1:2:1 (n = 162, χ2 = 3.19, P = 0.20). The segregation ratio of seed color by checking F2 plants was 122:41 black/white, fitting to 3:1 (n = 163, χ2 = 0.002, P = 0.96). The results indicated that both BLS resistance and seed color were inherited as a dominant gene mode. A genetic linkage map based on 124 randomly selected F2 plants was developed to enable molecular mapping of the BLS resistance and the seed color trait. In total, 199 markers, comprising 176 amplified fragment length polymorphisms, 16 simple-sequence repeats, 5 resistant gene candidate markers, and 2 cleaved amplified polymorphic sequences (CAPS) markers were assigned to six linkage groups. The dominant resistance gene to BLS (Xcvr) was mapped on linkage group 2 and the gene locus y for seed color was identified on linkage group 5. Due to the nature of a single gene inheritance, the high-resistance gene should be readily transferred to adapted lettuce cultivars to battle against the devastating disease of lettuce.
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Affiliation(s)
- Yunwen Wang
- First and second authors: Everglades Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences, Belle Glade 33430; and third author: United States Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman 99164
| | - Huangjun Lu
- First and second authors: Everglades Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences, Belle Glade 33430; and third author: United States Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman 99164
| | - Jinguo Hu
- First and second authors: Everglades Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences, Belle Glade 33430; and third author: United States Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman 99164
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Jia HM, Shen YT, Jiao Y, Wang GY, Dong X, Jia HJ, Du F, Liang SM, Zhou CC, Mao WH, Gao ZS. Development of 107 SSR markers from whole genome shotgun sequences of Chinese bayberry (Myrica rubra) and their application in seedling identification. J Zhejiang Univ Sci B 2015; 15:997-1005. [PMID: 25367792 DOI: 10.1631/jzus.b1400051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Chinese bayberry (Myrica rubra Sieb. et Zucc.) is one of the important subtropical fruit crops native to the South of China and Asian countries. In this study, 107 novel simple sequence repeat (SSR) molecular markers, a powerful tool for genetic diversity studies, cultivar identification, and linkage map construction, were developed and characterized from whole genome shotgun sequences. M13 tailing for forward primers was applied as a simple method in different situations. In total, 828 alleles across 45 accessions were detected, with an average of 8 alleles per locus. The number of effective alleles ranged from 1.22 to 10.41 with an average of 4.08. The polymorphic information content (PIC) varied from 0.13 to 0.89, with an average of 0.63. Moreover, these markers could also be amplified in their related species Myrica cerifera (syn. Morella cerifera) and Myrica adenophora. Seventy-eight SSR markers can be used to produce a genetic map of a cross between 'Biqi' and 'Dongkui'. A neighbor-joining (NJ) tree was constructed to assess the genetic relationships among accessions, and the elite accessions 'Y2010-70', 'Y2012-140', and 'Y2012-145', were characterized as potential new genotypes for cultivation.
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Affiliation(s)
- Hui-min Jia
- Department of Horticulture, Zhejiang University, Hangzhou 310058, China; Fruit Research Institute, Yuyao 315400, China; Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Yuyao Agricultural and Forestry Bureau, Yuyao 315400, China; Bio-Macromolecules Analysis Lab, Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
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Santos JCS, Barreto MA, Oliveira FA, Vigna BBZ, Souza AP. Microsatellite markers for Urochloa humidicola (Poaceae) and their transferability to other Urochloa species. BMC Res Notes 2015; 8:83. [PMID: 25889143 PMCID: PMC4365966 DOI: 10.1186/s13104-015-1044-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 03/03/2015] [Indexed: 11/29/2022] Open
Abstract
Background Urochloa humidicola is a warm-season grass commonly used as forage in the tropics and is recognized for its tolerance to seasonal flooding. This grass is an important forage species for the Cerrado and Amazon regions of Brazil. U. humidicola is a polyploid species with variable ploidy (6X–9X) and facultative apomixis with high phenotypic plasticity. However, this apomixis and ploidy, as well as the limited knowledge of the genetic basis of the germplasm collection, have constrained genetic breeding activities, yet microsatellite markers may enable a better understanding of the species’ genetic composition. This study aimed to develop and characterize new polymorphic microsatellite molecular markers in U. humidicola and to evaluate their transferability to other Urochloa species. Findings A set of microsatellite markers for U. humidicola was identified from two new enriched genomic DNA libraries: the first library was constructed from a single sexual genotype and the second from a pool of eight apomictic genotypes selected on the basis of previous results. Of the 114 loci developed, 72 primer pairs presented a good amplification product, and 64 were polymorphic among the 34 genotypes tested. The number of bands per simple sequence repeat (SSR) locus ranged from 1 to 29, with a mean of 9.6 bands per locus. The mean polymorphism information content (PIC) of all loci was 0.77, and the mean discrimination power (DP) was 0.87. STRUCTURE analysis revealed differences among U. humidicola accessions, hybrids, and other Urochloa accessions. The transferability of these microsatellites was evaluated in four species of the genus, U. brizantha, U. decumbens, U. ruziziensis, and U. dictyoneura, and the percentage of transferability ranged from 58.33% to 69.44% depending on the species. Conclusions This work reports new polymorphic microsatellite markers for U. humidicola that can be used for breeding programs of this and other Urochloa species, including genetic linkage mapping, quantitative trait loci identification, and marker-assisted selection.
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Affiliation(s)
- Jean C S Santos
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas, SP, Brazil.
| | - Mariana A Barreto
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas, SP, Brazil.
| | - Fernanda A Oliveira
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas, SP, Brazil.
| | - Bianca B Z Vigna
- EMBRAPA Southeast Livestock, Brazilian Agricultural Research Corporation, CP 339, São Carlos, SP, CEP 13560-970, Brazil.
| | - Anete P Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas, SP, Brazil. .,Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6109, CEP 13083-862, Campinas, SP, Brazil.
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Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity. PLoS One 2014; 9:e88998. [PMID: 24558460 PMCID: PMC3928336 DOI: 10.1371/journal.pone.0088998] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 01/10/2014] [Indexed: 12/31/2022] Open
Abstract
Pomegranate is a valuable crop that is grown commercially in many parts of the world. Wild species have been reported from India, Turkmenistan and Socotra. Pomegranate fruit has a variety of health-beneficial qualities. However, despite this crop's importance, only moderate effort has been invested in studying its biochemical or physiological properties or in establishing genomic and genetic infrastructures. In this study, we reconstructed a transcriptome from two phenotypically different accessions using 454-GS-FLX Titanium technology. These data were used to explore the functional annotation of 45,187 fully annotated contigs. We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). A subset of 480 SNPs was sampled to investigate the genetic structure of the broad pomegranate germplasm collection at the Agricultural Research Organization (ARO), which includes accessions from different geographical areas worldwide. This subset of SNPs was found to be polymorphic, with 10.7% loci with minor allele frequencies of (MAF<0.05). These SNPs were successfully used to classify the ARO pomegranate collection into two major groups of accessions: one from India, China and Iran, composed of mainly unknown country origin and which was more of an admixture than the other major group, composed of accessions mainly from the Mediterranean basin, Central Asia and California. This study establishes a high-throughput transcriptome and genetic-marker infrastructure. Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature.
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Fu N, Wang PY, Liu XD, Shen HL. Use of EST-SSR markers for evaluating genetic diversity and fingerprinting celery (Apium graveolens L.) cultivars. Molecules 2014; 19:1939-55. [PMID: 24518809 PMCID: PMC6270925 DOI: 10.3390/molecules19021939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 11/26/2022] Open
Abstract
Celery (Apium graveolens L.) is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting celery molecular breeding are quite limited, thus few studies on celery have been conducted so far. In this study we made use of simple sequence repeat (SSR) markers generated from previous celery transcriptome sequencing and attempted to detect the genetic diversity and relationships of commonly used celery accessions and explore the efficiency of the primers used for cultivars identification. Analysis of molecular variance (AMOVA) of Apium graveolens L. var. dulce showed that approximately 43% of genetic diversity was within accessions, 45% among accessions, and 22% among horticultural types. The neighbor-joining tree generated by unweighted pair group method with arithmetic mean (UPGMA), and population structure analysis, as well as principal components analysis (PCA), separated the cultivars into clusters corresponding to the geographical areas where they originated. Genetic distance analysis suggested that genetic variation within Apium graveolens was quite limited. Genotypic diversity showed any combinations of 55 genic SSRs were able to distinguish the genotypes of all 30 accessions.
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Affiliation(s)
- Nan Fu
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
| | - Ping-Yong Wang
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
| | - Xiao-Dan Liu
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
| | - Huo-Lin Shen
- College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China.
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