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Huang LS, Sun YQ, Jin Y, Gao Q, Hu XG, Gao FL, Yang XL, Zhu JJ, El-Kassaby YA, Mao JF. Development of high transferability cpSSR markers for individual identification and genetic investigation in Cupressaceae species. Ecol Evol 2018; 8:4967-4977. [PMID: 29876074 PMCID: PMC5980425 DOI: 10.1002/ece3.4053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/24/2018] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSRs (cpSSRs) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cpSSRs are mostly paternally inherited, thus, they are useful in mating systems and pollen flow studies. Using e-PCR, 92 SSR loci were identified across six Cupressaceae plastomes, and primers were designed for 26 loci with potential interspecific transferability. The 26 developed cpSSRs were polymorphic in four genera, Platycladus, Sabina, Juniperus, and Cupressus and are suitable for Cupressaceae molecular genetic studies and utilization. We genotyped 192 Platycladus orientalis samples from a core breeding population using 10 of the developed cpSSRs and 10 nuclear SSRs, and these individuals were identified with high confidence. The developed cpSSRs can be used in (1) a marker-assisted breeding scheme, specifically when paternity identification is required, (2) population genetics investigations, and (3) biogeography of Cupressaceae and unraveling the genetic relationships between related species.
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Affiliation(s)
- Li-Sha Huang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Yan-Qiang Sun
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Yuqing Jin
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Qiong Gao
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Xian-Ge Hu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Fu-Ling Gao
- Economic Forest and Seeding Management Station in Henan Province Zhengzhou China
| | - Xiao-Lei Yang
- National Tree Breeding Station for Platycladus orientalis in Jiaxian Forest Farm of Jiaxian County Henan China
| | - Ji-Jun Zhu
- National Tree Breeding Station for Platycladus orientalis in Jiaxian Forest Farm of Jiaxian County Henan China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences Faculty of Forestry The University of British Columbia Vancouver BC Canada
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
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102
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Liu L, Wang Y, He P, Li P, Lee J, Soltis DE, Fu C. Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data. BMC Genomics 2018; 19:235. [PMID: 29618324 PMCID: PMC5885378 DOI: 10.1186/s12864-018-4633-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
Background Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. Results The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. Conclusions In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4633-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luxian Liu
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Yuewen Wang
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Peizi He
- Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, Daejeon, 34134, South Korea
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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103
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Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
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Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication. Sci Rep 2017; 7:17902. [PMID: 29263331 PMCID: PMC5738346 DOI: 10.1038/s41598-017-17203-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/22/2017] [Indexed: 12/15/2022] Open
Abstract
Molecular markers are efficient tools for breeding and genetic studies. However, despite their ecological and economic importance, their development and application have long been hampered. In this study, we identified 524,170 simple sequence repeat (SSR), 267,636 intron length polymorphism (ILP), and 11,872 potential intron polymorphism (PIP) markers from 16 tree species based on recently available genome sequences. Larger motifs, including hexamers and heptamers, accounted for most of the seven different types of SSR loci. Within these loci, A/T bases comprised a significantly larger proportion of sequence than G/C. SSR and ILP markers exhibited an alternative distribution pattern. Most SSRs were monomorphic markers, and the proportions of polymorphic markers were positively correlated with genome size. By verifying with all 16 tree species, 54 SSR, 418 ILP, and four PIP universal markers were obtained, and their efficiency was examined by PCR. A combination of five SSR and six ILP markers were used for the phylogenetic analysis of 30 willow samples, revealing a positive correlation between genetic diversity and geographic distance. We also found that SSRs can be used as tools for duplication analysis. Our findings provide important foundations for the development of breeding and genetic studies in tree species.
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105
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Qin H, Yang G, Provan J, Liu J, Gao L. Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species. PLANT DIVERSITY 2017; 39:294-299. [PMID: 30159522 PMCID: PMC6112293 DOI: 10.1016/j.pld.2017.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/26/2017] [Accepted: 05/27/2017] [Indexed: 05/31/2023]
Abstract
Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies. In recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used. In this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851 (∼1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526 (∼18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Affiliation(s)
- Hantao Qin
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoqian Yang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jim Provan
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, UK
| | - Jie Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lianming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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Dossa K, Yu J, Liao B, Cisse N, Zhang X. Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase. FRONTIERS IN PLANT SCIENCE 2017; 8:1470. [PMID: 28878802 PMCID: PMC5572293 DOI: 10.3389/fpls.2017.01470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/08/2017] [Indexed: 05/21/2023]
Abstract
The sequencing of the full nuclear genome of sesame (Sesamum indicum L.) provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR) in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78%) were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/), which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.
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Affiliation(s)
- Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la SécheresseThiès, Senegal
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Ndiaga Cisse
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la SécheresseThiès, Senegal
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
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