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Zhu H, Song P, Koo DH, Guo L, Li Y, Sun S, Weng Y, Yang L. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis. BMC Genomics 2016; 17:557. [PMID: 27495254 PMCID: PMC4974753 DOI: 10.1186/s12864-016-2870-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/01/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. RESULTS A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis clustered in another group. Furthermore, structure analysis was consistent with the dendrogram indicating the 134 watermelon accessions were classified into two populations. CONCLUSION The large number of genome wide SSR markers developed herein from the watermelon genome provides a valuable resource for genetic map construction, QTL exploration, map-based gene cloning and marker-assisted selection in watermelon which has a very narrow genetic base and extremely low polymorphism among cultivated lines. Furthermore, the cross-species transferable SSR markers identified herein should also have practical uses in many applications in species of Cucurbitaceae family whose whole genome sequences are not yet available.
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Affiliation(s)
- Huayu Zhu
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Pengyao Song
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Dal-Hoe Koo
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
| | - Luqin Guo
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Yanman Li
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Shouru Sun
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- US Department of Agriculture/Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI 53706 USA
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
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Wang Y, VandenLangenberg K, Wehner TC, Kraan PAG, Suelmann J, Zheng X, Owens K, Weng Y. QTL mapping for downy mildew resistance in cucumber inbred line WI7120 (PI 330628). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1493-505. [PMID: 27147071 DOI: 10.1007/s00122-016-2719-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/20/2016] [Indexed: 05/02/2023]
Abstract
Host resistance in WI7120 cucumber to prevailing downy mildew pathogen field populations is conferred by two major-effect, one moderate-effect and two minor-effect QTL. Downy mildew (DM) caused by the obligate oomycete Pseudoperonospora cubensis is the most devastating fungal disease of cucumber worldwide. The molecular mechanism of DM resistance in cucumber is poorly understood, and use of marker-assisted breeding for DM resistance is not widely available. Here, we reported QTL mapping results for DM resistance with 243 F2:3 families from the cross between DM-resistant inbred line WI7120 (PI 330628) and susceptible '9930'. A linkage map was developed with 348 SSR and SNP markers. Phenotyping of DM inoculation responses were conducted in four field trails in 2 years at three locations. Four QTL, dm2.1, dm4.1, dm5.1, and dm6.1 were consistently and reliably detected across at least three of the four environments which together could explain 62-76 % phenotypic variations (R (2)). Among them, dm4.1 and dm5.1 were major-effect QTL (R (2) = 15-30 %) with only additive effects; dm2.1 (R (2) = 5-15 %) and dm6.1 (R (2) = 4-8 %) had moderate and minor effects, respectively. Epistatic effects were detected for dm2.1 and dm6.1 with both dm4.1 and dm5.1. One additional minor-effect QTL, dm6.2 (R (2) = 3-5 %) was only detectable with the chlorosis rating criterion. All alleles contributing to DM resistance were from WI7120. This study revealed two novel QTL for DM resistance and the unique genetic architecture of DM resistance in WI7120 conferring high level resistance to prevailing DM populations in multiple countries. The effects of disease rating scales, rating time and criteria, population size in phenotyping DM resistance on the power of QTL detection, and the use of DM resistance in WI7120 in cucumber breeding were discussed.
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Affiliation(s)
- Yuhui Wang
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Kyle VandenLangenberg
- Horticultural Science Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Todd C Wehner
- Horticultural Science Department, North Carolina State University, Raleigh, NC, 27695, USA
| | | | | | | | | | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, 53705, USA.
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Bastías A, Correa F, Rojas P, Almada R, Muñoz C, Sagredo B. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS). PLoS One 2016; 11:e0159825. [PMID: 27459734 PMCID: PMC4961369 DOI: 10.1371/journal.pone.0159825] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 07/09/2016] [Indexed: 12/18/2022] Open
Abstract
Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species.
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Affiliation(s)
- Adriana Bastías
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Av. Salamanca s/n, Sector Los Choapinos, Rengo, Chile
| | - Francisco Correa
- Facultad de Ingeniería, Universidad de Talca, Avenida Lircay s/n, Talca
| | - Pamela Rojas
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Av. Salamanca s/n, Sector Los Choapinos, Rengo, Chile
| | - Rubén Almada
- Centro de Estudios Avanzados en Fruticultura (CEAF), Av. Salamanca s/n, Sector Los Choapinos, Rengo, Chile
| | - Carlos Muñoz
- Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa N° 11315, La Pintana, Santiago de Chile, Chile
| | - Boris Sagredo
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Av. Salamanca s/n, Sector Los Choapinos, Rengo, Chile
- * E-mail:
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Zheng JS, Sun CZ, Zhang SN, Hou XL, Bonnema G. Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis. FRONTIERS IN PLANT SCIENCE 2016; 7:1049. [PMID: 27507974 PMCID: PMC4961004 DOI: 10.3389/fpls.2016.01049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 07/04/2016] [Indexed: 05/29/2023]
Abstract
A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis.
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Affiliation(s)
- Jin-shuang Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Horticulture, Nanjing Agricultural University, NanjingChina
- Hebei Normal University of Science and Technology, QinhuangdaoChina
| | - Cheng-zhen Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Horticulture, Nanjing Agricultural University, NanjingChina
- Hebei Normal University of Science and Technology, QinhuangdaoChina
| | - Shu-ning Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Horticulture, Nanjing Agricultural University, NanjingChina
| | - Xi-lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Horticulture, Nanjing Agricultural University, NanjingChina
| | - Guusje Bonnema
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, WageningenNetherlands
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105
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Zhou X, Dong Y, Zhao J, Huang L, Ren X, Chen Y, Huang S, Liao B, Lei Y, Yan L, Jiang H. Genomic survey sequencing for development and validation of single-locus SSR markers in peanut (Arachis hypogaea L.). BMC Genomics 2016; 17:420. [PMID: 27251557 PMCID: PMC4888616 DOI: 10.1186/s12864-016-2743-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/14/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single-locus markers have many advantages compared with multi-locus markers in genetic and breeding studies because their alleles can be assigned to particular genomic loci in diversity analyses. However, there is little research on single-locus SSR markers in peanut. Through the de novo assembly of DNA sequencing reads of A. hypogaea, we developed single-locus SSR markers in a genomic survey for better application in genetic and breeding studies of peanut. RESULTS In this study, DNA libraries with four different insert sizes were used for sequencing with 150 bp paired-end reads. Approximately 237 gigabases of clean data containing 1,675,631,984 reads were obtained after filtering. These reads were assembled into 2,102,446 contigs with an N50 length of 1,782 bp, and the contigs were further assembled into 1,176,527 scaffolds with an N50 of 3,920 bp. The total length of the assembled scaffold sequences was 2.0 Gbp, and 134,652 single-locus SSRs were identified from 375,180 SSRs. Among these developed single-locus SSRs, trinucleotide motifs were the most abundant, followed by tetra-, di-, mono-, penta- and hexanucleotide motifs. The most common motif repeats for the various types of single-locus SSRs have a tendency to be A/T rich. A total of 1,790 developed in silico single-locus SSR markers were chosen and used in PCR experiments to confirm amplification patterns. Of them, 1,637 markers that produced single amplicons in twelve inbred lines were considered putative single-locus markers, and 290 (17.7 %) showed polymorphisms. A further F2 population study showed that the segregation ratios of the 97 developed SSR markers, which showed polymorphisms between the parents, were consistent with the Mendelian inheritance law for single loci (1:2:1). Finally, 89 markers were assigned to an A. hypogaea linkage map. A subset of 100 single-locus SSR markers was shown to be highly stable and universal in a collection of 96 peanut accessions. A neighbor-joining tree of this natural population showed that genotypes have obviously correlation with botanical varieties. CONCLUSIONS We have shown that the detection of single-locus SSR markers from a de novo genomic assembly of a combination of different-insert-size libraries is highly efficient. This is the first report of the development of genome-wide single-locus markers for A. hypogaea, and the markers developed in this study will be useful for gene tagging, sequence scaffold assignment, linkage map construction, diversity analysis, variety identification and association mapping in peanut.
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Affiliation(s)
- Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yang Dong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Jiaojiao Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Shunmou Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.,Databridge Technologies Corporation, Wuhan, 430062, Hubei, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
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Li S, Pan Y, Wen C, Li Y, Liu X, Zhang X, Behera TK, Xing G, Weng Y. Integrated analysis in bi-parental and natural populations reveals CsCLAVATA3 (CsCLV3) underlying carpel number variations in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1007-22. [PMID: 26883041 DOI: 10.1007/s00122-016-2679-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 01/23/2016] [Indexed: 05/26/2023]
Abstract
Carpel number variation in cucumber was controlled by a single gene, Cn . Linkage and association analysis revealed CsCLV3 as the candidate gene of the Cn locus. Carpel number (CN) is an important fruit quality trait of cucumber, but the genetic basis of CN variations is largely unknown. In the present study, segregating analysis in multiple bi-parental mapping populations (F2, F3, and RILs) derived from WI2757 (CN = 3) × True Lemon (CN = 5) suggested that CN is controlled by a simply inherited gene, Cn, with CN = 3 being incompletely dominant to CN = 5. Initial linkage mapping located Cn in a 1.9-Mb region of cucumber chromosome 1. Exploration of DNA sequence variations in this region with in silico bulked segregant analysis among eight re-sequenced lines allowed delimiting the Cn locus to a 16-kb region with five predicted genes including CsCLV3, a homolog of the Arabidopsis gene CLAVATA3. Fine genetic mapping in F2 and RIL populations and association analysis in natural populations confirmed CsCLV3 as the candidate gene for Cn, which was further evidenced from gene expression analysis and microscopic examination of floral meristem size in the two parent lines. This study highlights the importance of integrated use of linkage and association analysis as well as next-gen high-throughput sequencing in mapping and cloning genes that are difficult in accurate genotyping. The results provide new insights into the genetic control of CN variations in cucumber, which were discussed in the context of the well-characterized CLAVATA pathway for stem cell homeostasis and regulation of meristem sizes in plants. The associations of carpel number with fruit shape, size, and weight in cucumber and melon are also discussed.
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Affiliation(s)
- Sen Li
- Horticulture College, Shanxi Agricultural University, Taigu, 030801, China
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Yupeng Pan
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Changlong Wen
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Yuhong Li
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Xiaofeng Liu
- Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaolan Zhang
- Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Tusar K Behera
- Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi, 10012, India
| | - Guoming Xing
- Horticulture College, Shanxi Agricultural University, Taigu, 030801, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI, 53706, USA.
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107
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Li S, Zhang G, Li X, Wang L, Yuan J, Deng C, Gao W. Genome-wide identification and validation of simple sequence repeats (SSRs) from Asparagus officinalis. Mol Cell Probes 2016; 30:153-60. [PMID: 26987412 DOI: 10.1016/j.mcp.2016.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/26/2016] [Accepted: 03/08/2016] [Indexed: 11/29/2022]
Abstract
Garden asparagus (Asparagus officinalis), an important vegetable cultivated worldwide, can also serve as a model dioecious plant species in the study of sex determination and sex chromosome evolution. However, limited DNA marker resources have been developed and used for this species. To expand these resources, we examined the DNA sequences for simple sequence repeats (SSRs) in 163,406 scaffolds representing approximately 400 Mbp of the A. officinalis genome. A total of 87,576 SSRs were identified in 59,565 scaffolds. The most abundant SSR repeats were trinucleotide and tetranucleotide, accounting for 29.2 and 29.1% of the total SSRs, respectively, followed by di-, penta-, hexa-, hepta-, and octanucleotides. The AG motif was most common among dinucleotides and was also the most frequent motif in the entire A. officinalis genome, representing 14.7% of all SSRs. A total of 41,917 SSR primers pairs were designed to amplify SSRs. Twenty-two genomic SSR markers were tested in 39 asparagus accessions belonging to ten cultivars and one accession of Asparagus setaceus for determination of genetic diversity. The intra-species polymorphism information content (PIC) values of the 22 genomic SSR markers were intermediate, with an average of 0.41. The genetic diversity between the ten A. officinalis cultivars was low, and the UPGMA dendrogram was largely unrelated to cultivars. It is here suggested that the sex of individuals is an important factor influencing the clustering results. The information reported here provides new information about the organization of the microsatellites in A. officinalis genome and lays a foundation for further genetic studies and breeding applications of A. officinalis and related species.
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Affiliation(s)
- Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China
| | - Guojun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan, PR China
| | - Xu Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China
| | - Lianjun Wang
- Institute of Food Corps, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, PR China
| | - Jinhong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, PR China.
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108
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Wang YL, Nie JT, Chen HM, Guo CL, Pan J, He HL, Pan JS, Cai R. Identification and mapping of Tril, a homeodomain-leucine zipper gene involved in multicellular trichome initiation in Cucumis sativus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:305-16. [PMID: 26518574 DOI: 10.1007/s00122-015-2628-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/17/2015] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Using map-based cloning of Tril gene, we identified a homeodomain-leucine zipper gene involved in the initiation of multicellular trichomes (including the spines of fruit) in cucumber. ABSTRACT Fruit spines are a special type of trichome that impacts the quality and appearance of cucumber (Cucumis sativus L.) fruit. Scanning electron microscopy revealed that the trichome-less (tril) mutant originating from European greenhouse cucumber has a completely glabrous phenotype on cotyledons, hypocotyls, young leaves, fruits, and fruit stalks. Genetic analysis revealed that tril was inherited as a recessive allele at a single locus. Using 1058 F2 individuals derived from a cross between cucumber tril mutant CGN19839 and the micro-trichome (mict) mutant 06-2, tril was mapped to chromosome 6, and narrowed down to a 37.4 kb genomic region which carries seven predicted genes. Genetic and molecular analyses revealed that gene Cucsa.045360 is a possible candidate gene for the differentiation of epidermal cells to trichomes. It is a member of the class IV homeodomain-leucine zipper (HD-Zip IV) family and encodes homeodomain and START domain, sharing 66.7% predicted amino acid sequence identity to PROTODERMAL FACTOR2 (PDF2) and 35.0% to GLABRA2 (GL2) of Arabidopsis. The homeobox domain had changed amino acid sequence because of an insertion in tril mutant. The results of genetic analysis and transcriptome profiling indicated that the Tril gene had an epistatic effect on the Mict gene in trichome development. Phenotypes of the tril mutant such as glabrous fruits and female flowers at every node could be used in developing new cultivars.
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Affiliation(s)
- Yun-Li Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Jing-tao Nie
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Hui-Ming Chen
- Hunan Vegetable Research Institute, Hunan Academy of Agriculture Sciences, Changsha, 410125, China
| | - Chun-li Guo
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Jian Pan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Huan-Le He
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Jun-Song Pan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
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109
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Cheng J, Zhao Z, Li B, Qin C, Wu Z, Trejo-Saavedra DL, Luo X, Cui J, Rivera-Bustamante RF, Li S, Hu K. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Sci Rep 2016; 6:18919. [PMID: 26739748 PMCID: PMC4703971 DOI: 10.1038/srep18919] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/30/2015] [Indexed: 02/05/2023] Open
Abstract
The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zicheng Zhao
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Bo Li
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Qin
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Diana L. Trejo-Saavedra
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Xirong Luo
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Junjie Cui
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Rafael F. Rivera-Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Zhu WY, Huang L, Chen L, Yang JT, Wu JN, Qu ML, Yao DQ, Guo CL, Lian HL, He HL, Pan JS, Cai R. A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber. FRONTIERS IN PLANT SCIENCE 2016; 7:437. [PMID: 27148281 PMCID: PMC4835494 DOI: 10.3389/fpls.2016.00437] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/21/2016] [Indexed: 05/10/2023]
Abstract
High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected.
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Affiliation(s)
- Wen-Ying Zhu
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Long Huang
- Biomarker Technologies CorporationBeijing, China
| | - Long Chen
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Jian-Tao Yang
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Jia-Ni Wu
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Mei-Ling Qu
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | | | - Chun-Li Guo
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Hong-Li Lian
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Huan-Le He
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Jun-Song Pan
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
- *Correspondence: Jun-Song Pan, ; Run Cai,
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
- *Correspondence: Jun-Song Pan, ; Run Cai,
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Pawełkowicz M, Zieliński K, Zielińska D, Pląder W, Yagi K, Wojcieszek M, Siedlecka E, Bartoszewski G, Skarzyńska A, Przybecki Z. Next generation sequencing and omics in cucumber (Cucumis sativus L.) breeding directed research. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:77-88. [PMID: 26566826 DOI: 10.1016/j.plantsci.2015.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/29/2015] [Accepted: 07/28/2015] [Indexed: 05/10/2023]
Abstract
In the post-genomic era the availability of genomic tools and resources is leading us to novel generation methods in plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. In this study we have mainly concentrated on the Cucumis sativus and (but much less) Cucurbitaceae family several important vegetable crops. There are many reports on research conducted in Cucurbitaceae plant breeding programs on the ripening process, phloem transport, disease resistance, cold tolerance and fruit quality traits. This paper presents the role played by new omic technologies in the creation of knowledge on the mechanisms of the formation of the breeding features. The analysis of NGS (NGS-next generation sequencing) data allows the discovery of new genes and regulatory sequences, their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Firstly a high density map should be created for the reference genome, then each re-sequencing data could be mapped and new markers brought out into breeding populations. The paper also presents methods that could be used in the future for the creation of variability and genomic modification of the species in question. It has been shown also the state and usefulness in breeding the chloroplastomic and mitochondriomic study.
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Affiliation(s)
- Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Konrad Zieliński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Dorota Zielińska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Kouhei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Michał Wojcieszek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
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Qu J, Huang C, Zhang J. Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus. Gene 2016; 575:524-530. [DOI: 10.1016/j.gene.2015.09.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/03/2015] [Accepted: 09/14/2015] [Indexed: 11/16/2022]
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113
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Pan Y, Bo K, Cheng Z, Weng Y. The loss-of-function GLABROUS 3 mutation in cucumber is due to LTR-retrotransposon insertion in a class IV HD-ZIP transcription factor gene CsGL3 that is epistatic over CsGL1. BMC PLANT BIOLOGY 2015; 15:302. [PMID: 26714637 PMCID: PMC4696102 DOI: 10.1186/s12870-015-0693-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Trichomes, developed from the protodermal cells (the outermost cell layer of the embryo), are hair-like structures covering the aerial parts of plants. The genetic network regulating trichome development has been extensively studied and well understood in the model species Arabidopsis thaliana, which bears unicellular, non-glandular and branched trichomes. However, little is known about the genetic and molecular basis of organogenesis of multi-cellular trichomes in plant species like cucumber (Cucumis sativus L.), which are likely different from Arabidopsis. RESULTS We identified a new trichome mutant in cucumber which exhibited a completely glabrous phenotype on all aerial organs. Genetic analysis indicated that the glabrous phenotype was inherited as a single recessive gene, csgl3. Fine genetic mapping delimited the csgl3 locus into a 68.4 kb region with 12 predicted genes. Genetic analysis, sequence alignment and allelic variation survey in natural populations identified Csa6G514870 encoding a class IV homeodomain-associated leucine zipper (HD-ZIP) transcription factor as the only candidate for CsGL3, which was 5188 bp in length with 10 predicted exons. Gene expression analysis revealed the loss-of-function of CsGL3 in the mutant due to the insertion of a 5-kb long terminal repeat (LTR) retrotransposon in the 4th exon of CsGL3. Linkage analysis in a segregating population and gene expression analysis of the CsGL1 and CsGL3 genes in csgl1, csgl3, and csgl1 + 3 genetic backgrounds uncovered interactions between the two genes. Phylogenetic analysis among 28 class IV HD-ZIP protein sequences from five species placed cucumber CsGL3 into the same clade with 7 other members that play important roles in trichome initiation. CONCLUSIONS The new glabrous mutation in cucumber was controlled by a single recessive locus csgl3, which was phenotypically and genetically distinct from two previously reported glabrous mutants csgl1 and csgl2. The glabrous phenotype in csgl3 was due to insertion of an autonomous, active, class I transposable element in CsGL3, a class IV HD-ZIP transcription factor. CsGL3 was epistatic to CsGL1. CsGL3 seemed to play important roles in cucumber trichome initiation whereas CsGL1 may act downstream in the trichome development pathway(s). Findings from the present study provide new insights into genetic control of trichome development in cucumber.
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Affiliation(s)
- Yupeng Pan
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- Horticulture College, Northwest A&F University, Yangling, 712100, China.
| | - Kailiang Bo
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
| | - Zhihui Cheng
- Horticulture College, Northwest A&F University, Yangling, 712100, China.
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI, 53706, USA.
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114
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Liu H, Meng H, Pan Y, Liang X, Jiao J, Li Y, Chen S, Cheng Z. Fine genetic mapping of the white immature fruit color gene w to a 33.0-kb region in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2375-85. [PMID: 26239410 DOI: 10.1007/s00122-015-2592-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 07/23/2015] [Indexed: 05/25/2023]
Abstract
The white immature fruit color gene w was rapidly mapped to a 33.0-kb region to identify a valuable candidate gene that encodes peroxidase. The skin color of immature fruit is a crucial external trait of cucumbers, and white skin is shared by limited numbers of commercial cultivars. Herein, one BC1 population and two F2 segregating populations were constructed using four inbred parental lines (WD3 × B-2-2 and Q30 × Q24) to investigate the inheritance patterns and chromosomal locations of immature fruit color genes in cucumbers. Consequently, a single recessive gene, w, was identified that controls white immature fruit color. A total of 526 markers, which were derived from published genetic maps, two reference cucumber genomes ("9930" and GY14), and two parents (Q30 and Q24) for which whole-genome sequence information is available, were used to map the target gene w to a 33.0-kb region flanked by two SNP-based markers, ASPCR39262 and ASPCR39229, which are physically located at 39262450 and 39229482 of chromosome 3 ("9930" draft genome assembly), respectively. Gene prediction indicated that four potential genes were located in the target region. One gene that encodes peroxidase is likely to be a valuable candidate gene because quantitative real-time PCR revealed an eightfold difference in its transcriptional level, and several amino acid variations were found when the deduced amino acid sequence was aligned. A co-segregating marker was used synergistically to test its ability to predict the skin colors of 83 dark green/white germplasms, and the validity of its utility in marker-assisted selection was confirmed. Fine mapping of this locus will assist in cloning the gene and in marker-assisted breeding to develop dark green/white cucumber cultivars.
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Affiliation(s)
- Hanqiang Liu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huanwen Meng
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yupeng Pan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinjing Liang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jianqing Jiao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuxia Chen
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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115
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Tan J, Tao Q, Niu H, Zhang Z, Li D, Gong Z, Weng Y, Li Z. A novel allele of monoecious (m) locus is responsible for elongated fruit shape and perfect flowers in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2483-93. [PMID: 26350497 DOI: 10.1007/s00122-015-2603-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/28/2015] [Indexed: 05/20/2023]
Abstract
A 14 bp deletion in CsACS2 gene encoding a truncated loss-of-function protein is responsible for elongated fruit shape and perfect flowers in cucumber. In cucumber (Cucumis sativus L.), sex expression and fruit shape are important components of biological and marketable yield. The association of fruit shape and sex expression is a very interesting phenomenon. The sex determination is controlled primarily by the F (female) and M (monoecy) loci. Homozygous recessive mm plants bear bisexual (perfect) flowers, and the fruits are often round shaped. CsACS2 encoding the 1-aminocyclopropane-1-carboxylic acid synthase has been shown to be the candidate gene for the m locus. We recently identified an andromonoecious cucumber line H38 that has bisexual flowers but elongated fruits. To rapidly clone this monoecious gene in H38, we developed a tri-parent mapping strategy, which took advantage of the high-density Gy14 × 9930 cucumber genetic map and the powder of bulk segregant analysis. Microsatellite markers from the Gy14 × 9930 map were used to screen two pairs of unisexual and bisexual bulks constructed from H38 × Gy14 and H38 × 9930 F2 populations. Polymorphic markers were identified and used to quickly develop a framework map and place the monoecious locus of H38 in cucumber chromosome 1. Further fine mapping allowed identification of a novel allele, m-1, at the monoecious locus to control the bisexual flower in H38, which was due to a 14 bp deletion in the third exon of the CsACS2 gene encoding a truncated loss-of-function protein of the cucumber 1-aminocyclopropane-1-carboxylic acid synthase. This new allele provides a valuable tool in understanding the molecular mechanisms of CsACS2 in the relationships of sex determination, fruit shape, and CsACS activities in cucumber.
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Affiliation(s)
- Junyi Tan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qianyi Tao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huanhuan Niu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhen Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dandan Li
- Agricultural College, Heilongjiang Bayi Agriculture University, Daqing, 163319, Heilongjiang, China
| | - Zhenhui Gong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Zheng Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Wen C, Mao A, Dong C, Liu H, Yu S, Guo YD, Weng Y, Xu Y. Fine genetic mapping of target leaf spot resistance gene cca-3 in cucumber, Cucumis sativus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2495-506. [PMID: 26385372 DOI: 10.1007/s00122-015-2604-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/29/2015] [Indexed: 05/26/2023]
Abstract
The cucumber target leaf spot resistance gene cca - 3 was fine mapped in a 79-kb region harboring a CC-NB-ARC type R gene that may be responsible for the hypersensitive responses to infection of the target leaf spot pathogen in cucumber. The target leaf spot (TLS) is one of the most important foliar diseases in cucumber (Cucumis sativus L.). In this study, we conducted fine genetic mapping of a simply inherited recessive resistance gene, cca-3 against TLS with 193 F2:3 families and 890 F2 plants derived from the resistant cucumber inbred line D31 and the susceptible line D5. Initial mapping with microsatellite markers and bulked segregant analysis placed cca-3 in a 2.5-Mbp region of cucumber chromosome 6. The D5 and D31 lines were re-sequenced at 10× genome coverage to explore new markers in the target region. Genetic mapping in the large F2 population delimited the cca-3 locus in a 79-kb region with flanking markers Indel16874230 and Indel16953846. Additional fine mapping and gene annotation in this region revealed that a CC-NB-ARC type resistance gene analog, Csa6M375730, seems to be the candidate gene for cca-3. One single nucleotide polymorphism (SNP) was found in the NB-ARC domain of this candidate gene sequence between D31 and D5 that may lead to amino acid change, thus altering the function of the conserved NB-ARC motif. This SNP was validated in the segregating population as well as 24 independent cucumber lines. There was significantly higher level of cca-3 expression in the leaves of D5 (susceptible) than in D31 (resistant), and the expression level was positively correlated with the areas of necrotic spots on leaves after inoculation. It seems the cca-3 resistance gene was able to induce hypersensitive responses to the infection by TLS pathogen.
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Affiliation(s)
- Changlong Wen
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
| | - Aijun Mao
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Congjuan Dong
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Huyu Liu
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Shuancang Yu
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Yang-Dong Guo
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Yiqun Weng
- USDA-ARS, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
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117
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Transcriptome profiling of differentially expressed genes in floral buds and flowers of male sterile and fertile lines in watermelon. BMC Genomics 2015; 16:914. [PMID: 26552448 PMCID: PMC4640349 DOI: 10.1186/s12864-015-2186-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 11/02/2015] [Indexed: 12/03/2022] Open
Abstract
Background Male sterility is an important mechanism for the production of hybrid seeds in watermelon. Although fruit development has been studied extensively in watermelon, there are no reports on gene expression in floral organs. In this study, RNA-sequencing (RNA-seq) was performed in two near-isogenic watermelon lines (genic male sterile [GMS] line, DAH3615-MS and male fertile line, DAH3615) to identify the differentially expressed genes (DEGs) related to male sterility. Results DEG analysis showed that 1259 genes were significantly associated with male sterility at a FDR P-value of < 0.01. Most of these genes were only expressed in the male fertile line. In addition, 11 functional clusters were identified using DAVID functional classification analysis. Of detected genes in RNA-seq analysis, 19 were successfully validated by qRT-PCR. Conclusions In this study, we carried out a comprehensive floral transcriptome sequence comparison of a male fertile line and its near-isogenic male sterile line in watermelon. This analysis revealed essential genes responsible for stamen development, including pollen development and pollen tube elongation, and allowed their functional classification. These results provided new information on global mechanisms related to male sterility in watermelon. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2186-9) contains supplementary material, which is available to authorized users.
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118
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Han B, Wang C, Tang Z, Ren Y, Li Y, Zhang D, Dong Y, Zhao X. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0141540. [PMID: 26536014 PMCID: PMC4633229 DOI: 10.1371/journal.pone.0141540] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/10/2015] [Indexed: 12/12/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.
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Affiliation(s)
- Bin Han
- College of Bio-engineering, Shanxi University, Taiyuan, China
| | - Changbiao Wang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- * E-mail: (ZHT); (DYZ); (CBW)
| | - Zhaohui Tang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- * E-mail: (ZHT); (DYZ); (CBW)
| | - Yongkang Ren
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yali Li
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Dayong Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail: (ZHT); (DYZ); (CBW)
| | - Yanhui Dong
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xinghua Zhao
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
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RNA-Seq SSRs of Moth Orchid and Screening for Molecular Markers across Genus Phalaenopsis (Orchidaceae). PLoS One 2015; 10:e0141761. [PMID: 26523377 PMCID: PMC4629892 DOI: 10.1371/journal.pone.0141761] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/13/2015] [Indexed: 11/25/2022] Open
Abstract
Background The moth orchid (Phalaenopsis species) is an ornamental crop that is highly commercialized worldwide. Over 30,000 cultivars of moth orchids have been registered at the Royal Horticultural Society (RHS). These cultivars were obtained by artificial pollination of interspecific hybridization. Therefore, the identification of different cultivars is highly important in the worldwide market. Methods/Results We used Illumina sequencing technology to analyze an important species for breeding, Phalaenopsis aphrodite subsp. formosana and develop the expressed sequence tag (EST)-simple sequence repeat (SSR) markers. After de novo assembly, the obtained sequence covered 29.1 Mb, approximately 2.2% of the P. aphrodite subsp. formosana genome (1,300 Mb), and a total of 1,439 EST-SSR loci were detected. SSR occurs in the exon region, including the 5’ untranslated region (UTR), coding region (CDS), and 3’UTR, on average every 20.22 kb. The di- and tri-nucleotide motifs (51.49% and 35.23%, respectively) were the two most frequent motifs in the P. aphrodite subsp. formosana. To validate the developed EST-SSR loci and to evaluate the transferability to the genus Phalaenopsis, thirty tri-nucleotide motifs of the EST-SSR loci were randomly selected to design EST-SSR primers and to evaluate the polymorphism and transferability across 22 native Phalaenopsis species that are usually used as parents for moth orchid breeding. Of the 30 EST-SSR loci, ten polymorphic and transferable SSR loci across the 22 native taxa can be obtained. The validated EST-SSR markers were further proven to discriminate 12 closely related Phalaenopsis cultivars. The results show that it is not difficult to obtain universal SSR markers by transcriptome deep sequencing in Phalaenopsis species. Conclusions This study supported that transcriptome analysis based on deep sequencing is a powerful tool to develop SSR loci in non-model species. A large number of EST-SSR loci can be isolated, and about 33.33% EST-SSR loci are universal markers across the Phalaenopsis breeding germplasm after preliminary validation. The potential universal EST-SSR markers are highly valuable for identifying all of Phalaenopsis cultivars.
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Xu X, Lu L, Zhu B, Xu Q, Qi X, Chen X. QTL mapping of cucumber fruit flesh thickness by SLAF-seq. Sci Rep 2015; 5:15829. [PMID: 26508560 PMCID: PMC4623748 DOI: 10.1038/srep15829] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/21/2015] [Indexed: 11/24/2022] Open
Abstract
Cucumber is an agriculturally and economically important vegetable crop worldwide. Fruit flesh thickness is an important trait for cucumber and also a central determinant of yield, yet little is known about the underlying mechanism of this trait. In this study, bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) was applied to finely map the gene that underlies fruit flesh thickness in cucumber. A 0.19-Mb-long quantitative trait locus on chromosome 2 controlling fruit flesh thickness (QTL fft2.1) was identified and further confirmed by simple sequence repeat (SSR) marker-based classical QTL mapping in 138 F2 individuals. Gene prediction of this 0.19-Mb region identified 20 genes. Quantitative RT-PCR revealed higher expression levels of Csa2 M058670.1 (SET domain protein-lysine methyltransferase) in D8 (thick fruit flesh parent) compared with that in XUE1 (thin fruit flesh parent) during fruit development. Sequence alignment analysis of Csa2M058670.1 from thick and thin fruit flesh cucumber lines revealed a 4-bp deletion mutation in the promoter region of this candidate gene, which may result in the loss of Csa2M058670.1 activation in thin fruit flesh lines. The data presented herein suggest that Csa2M058670.1 is a possible candidate gene for controlling flesh thickness in cucumber.
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Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lu Lu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Biyun Zhu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
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Sethi K, Siwach P, Verma SK. Assessing genetic diversity among six populations of Gossypium arboreum L. using microsatellites markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2015; 21:531-9. [PMID: 26600679 PMCID: PMC4646864 DOI: 10.1007/s12298-015-0326-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/20/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
Among the four cultivated cotton species, G. hirsutum (allotetraploid) presently holds a primary place in cultivation. Efforts to further improve this primary cotton face the constraints of its narrow genetic base due to repeated selective breeding and hence demands enrichment of diversity in the gene pool. G. arboreum (diploid species) is an invaluable genetic resource with great potential in this direction. Based on the dispersal and domestication in different directions from Indus valley, different races of G. arboreum have evolved, each having certain traits like drought and disease resistance, which the tetraploid cotton lack. Due to lack of systematic, race wise characterization of G. arboreum germplasm, it has not been explored fully. During the present study, 100 polymorphic SSR loci were used to genotype 95 accessions belonging to 6 races of G. arboreum producing 246 polymorphic alleles; mean number of effective alleles was 1.505. AMOVA showed 14 % of molecular variance among population groups, 34 % among individuals and remaining 52 % within individuals. UPGMA dendrogram, based on Nei's genetic distance, distributed the six populations in two major clusters of 3 populations each; race 'bengalense' was found more close to 'cernuum' than the others. The clustering of 95 genotypes by UPGMA tree generation as well as PCoA analysis clustered 'bengalense' genotypes into one group along with some genotypes of 'cernuum', while rest of the genotypes made separate clusters. Outcomes of this research should be helpful in identifying the genotypes for their further utilization in hybridization program to obtain high level of germplasm diversity.
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Affiliation(s)
- Khushboo Sethi
- />Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - Priyanka Siwach
- />Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
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Weng Y, Colle M, Wang Y, Yang L, Rubinstein M, Sherman A, Ophir R, Grumet R. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1747-63. [PMID: 26048092 DOI: 10.1007/s00122-015-2544-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/18/2015] [Indexed: 05/06/2023]
Abstract
QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.
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Affiliation(s)
- Yiqun Weng
- Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA,
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Olango TM, Tesfaye B, Pagnotta MA, Pè ME, Catellani M. Development of SSR markers and genetic diversity analysis in enset (Ensete ventricosum (Welw.) Cheesman), an orphan food security crop from Southern Ethiopia. BMC Genet 2015. [PMID: 26243662 DOI: 10.1186/s12863-12015-10250-12868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Enset (Ensete ventricosum (Welw.) Cheesman; Musaceae) is a multipurpose drought-tolerant food security crop with high conservation and improvement concern in Ethiopia, where it supplements the human calorie requirements of around 20 million people. The crop also has an enormous potential in other regions of Sub-Saharan Africa, where it is known only as a wild plant. Despite its potential, genetic and genomic studies supporting breeding programs and conservation efforts are very limited. Molecular methods would substantially improve current conventional approaches. Here we report the development of the first set of SSR markers from enset, their cross-transferability to Musa spp., and their application in genetic diversity, relationship and structure assessments in wild and cultivated enset germplasm. RESULTS SSR markers specific to E. ventricosum were developed through pyrosequencing of an enriched genomic library. Primer pairs were designed for 217 microsatellites with a repeat size > 20 bp from 900 candidates. Primers were validated in parallel by in silico and in vitro PCR approaches. A total of 67 primer pairs successfully amplified specific loci and 59 showed polymorphism. A subset of 34 polymorphic SSR markers were used to study 70 both wild and cultivated enset accessions. A large number of alleles were detected along with a moderate to high level of genetic diversity. AMOVA revealed that intra-population allelic variations contributed more to genetic diversity than inter-population variations. UPGMA based phylogenetic analysis and Discriminant Analysis of Principal Components show that wild enset is clearly separated from cultivated enset and is more closely related to the out-group Musa spp. No cluster pattern associated with the geographical regions, where this crop is grown, was observed for enset landraces. Our results reaffirm the long tradition of extensive seed-sucker exchange between enset cultivating communities in Southern Ethiopia. CONCLUSION The first set of genomic SSR markers were developed in enset. A large proportion of these markers were polymorphic and some were also transferable to related species of the genus Musa. This study demonstrated the usefulness of the markers in assessing genetic diversity and structure in enset germplasm, and provides potentially useful information for developing conservation and breeding strategies in enset.
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Affiliation(s)
- Temesgen Magule Olango
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
- Hawassa University, School of Plant and Horticulture Science, P.O.Box 5, Awassa, Ethiopia.
| | - Bizuayehu Tesfaye
- Hawassa University, School of Plant and Horticulture Science, P.O.Box 5, Awassa, Ethiopia.
| | - Mario Augusto Pagnotta
- Department of Science and Technologies for Agriculture, Forestry, Nature and Energy (DAFNE), Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100, Viterbo, Italy.
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Marcello Catellani
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
- ENEA, UT BIORAD, Laboratory of Biotechnology, Research Center Casaccia, Via Anguillarese 301, 00123, Rome, Italy.
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Olango TM, Tesfaye B, Pagnotta MA, Pè ME, Catellani M. Development of SSR markers and genetic diversity analysis in enset (Ensete ventricosum (Welw.) Cheesman), an orphan food security crop from Southern Ethiopia. BMC Genet 2015; 16:98. [PMID: 26243662 PMCID: PMC4524394 DOI: 10.1186/s12863-015-0250-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/09/2015] [Indexed: 11/13/2022] Open
Abstract
Background Enset (Ensete ventricosum (Welw.) Cheesman; Musaceae) is a multipurpose drought-tolerant food security crop with high conservation and improvement concern in Ethiopia, where it supplements the human calorie requirements of around 20 million people. The crop also has an enormous potential in other regions of Sub-Saharan Africa, where it is known only as a wild plant. Despite its potential, genetic and genomic studies supporting breeding programs and conservation efforts are very limited. Molecular methods would substantially improve current conventional approaches. Here we report the development of the first set of SSR markers from enset, their cross-transferability to Musa spp., and their application in genetic diversity, relationship and structure assessments in wild and cultivated enset germplasm. Results SSR markers specific to E. ventricosum were developed through pyrosequencing of an enriched genomic library. Primer pairs were designed for 217 microsatellites with a repeat size > 20 bp from 900 candidates. Primers were validated in parallel by in silico and in vitro PCR approaches. A total of 67 primer pairs successfully amplified specific loci and 59 showed polymorphism. A subset of 34 polymorphic SSR markers were used to study 70 both wild and cultivated enset accessions. A large number of alleles were detected along with a moderate to high level of genetic diversity. AMOVA revealed that intra-population allelic variations contributed more to genetic diversity than inter-population variations. UPGMA based phylogenetic analysis and Discriminant Analysis of Principal Components show that wild enset is clearly separated from cultivated enset and is more closely related to the out-group Musa spp. No cluster pattern associated with the geographical regions, where this crop is grown, was observed for enset landraces. Our results reaffirm the long tradition of extensive seed-sucker exchange between enset cultivating communities in Southern Ethiopia. Conclusion The first set of genomic SSR markers were developed in enset. A large proportion of these markers were polymorphic and some were also transferable to related species of the genus Musa. This study demonstrated the usefulness of the markers in assessing genetic diversity and structure in enset germplasm, and provides potentially useful information for developing conservation and breeding strategies in enset. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0250-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Temesgen Magule Olango
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. .,Hawassa University, School of Plant and Horticulture Science, P.O.Box 5, Awassa, Ethiopia.
| | - Bizuayehu Tesfaye
- Hawassa University, School of Plant and Horticulture Science, P.O.Box 5, Awassa, Ethiopia.
| | - Mario Augusto Pagnotta
- Department of Science and Technologies for Agriculture, Forestry, Nature and Energy (DAFNE), Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100, Viterbo, Italy.
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.
| | - Marcello Catellani
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy. .,ENEA, UT BIORAD, Laboratory of Biotechnology, Research Center Casaccia, Via Anguillarese 301, 00123, Rome, Italy.
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Biswas MK, Liu Y, Li C, Sheng O, Mayer C, Yi G. Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential. PLoS One 2015; 10:e0131312. [PMID: 26121637 PMCID: PMC4488140 DOI: 10.1371/journal.pone.0131312] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/01/2015] [Indexed: 01/14/2023] Open
Abstract
The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species.
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Affiliation(s)
- Manosh Kumar Biswas
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- The College of Life Science, South China Agricultural University, Guangzhou, China
| | - Yuxuan Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chunyu Li
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
| | - Ou Sheng
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
| | - Christoph Mayer
- Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany
| | - Ganjun Yi
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- * E-mail:
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Wang Q, Fang L, Chen J, Hu Y, Si Z, Wang S, Chang L, Guo W, Zhang T. Genome-wide mining, characterization, and development of microsatellite markers in gossypium species. Sci Rep 2015; 5:10638. [PMID: 26030481 PMCID: PMC4650602 DOI: 10.1038/srep10638] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/01/2015] [Indexed: 12/02/2022] Open
Abstract
Although much research has been conducted to characterize microsatellites and develop markers, the distribution of microsatellites remains ambiguous and the use of microsatellite markers in genomic studies and marker-assisted selection is limited. To identify microsatellites for cotton research, we mined 100,290, 83,160, and 56,937 microsatellites with frequencies of 41.2, 49.1, and 74.8 microsatellites per Mb in the recently sequenced Gossypium species: G. hirsutum, G. arboreum, and G. raimondii, respectively. The distributions of microsatellites in their genomes were non-random and were positively and negatively correlated with genes and transposable elements, respectively. Of the 77,996 developed microsatellite markers, 65,498 were physically anchored to the 26 chromosomes of G. hirsutum with an average marker density of 34 markers per Mb. We confirmed 67,880 (87%) universal and 7,705 (9.9%) new genic microsatellite markers. The polymorphism was estimated in above three species by in silico PCR and validated with 505 markers in G. hirsutum. We further predicted 8,825 polymorphic microsatellite markers within G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. In our study, genome-wide mining and characterization of microsatellites, and marker development were very useful for the saturation of the allotetraploid genetic linkage map, genome evolution studies and comparative genome mapping.
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Affiliation(s)
- Qiong Wang
- 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China [2]
| | - Lei Fang
- 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China [2]
| | - Jiedan Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Zhanfeng Si
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Sen Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Lijing Chang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
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Genome-wide identification of SSR and SNP markers from the non-heading Chinese cabbage for comparative genomic analyses. BMC Genomics 2015; 16:328. [PMID: 25908429 PMCID: PMC4408590 DOI: 10.1186/s12864-015-1534-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 04/13/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Non-heading Chinese cabbage (NHCC), belonging to Brassica, is an important leaf vegetable in Asia. Although genetic analyses have been performed through conventional selection and breeding efforts, the domestication history of NHCC and the genetics underlying its morphological diversity remain unclear. Thus, the reliable molecular markers representative of the whole genome are required for molecular-assisted selection in NHCC. RESULTS A total of 20,836 simple sequence repeats (SSRs) were detected in NHCC, containing repeat types from mononucleotide to nonanucleotide. The average density was 62.93 SSRs/Mb. In gene regions, 5,435 SSRs were identified in 4,569 genes. A total of 5,008 primer pairs were designed, and 74 were randomly selected for validation. Among these, 60 (81.08%) were polymorphic in 18 Cruciferae. The number of polymorphic bands ranged from two to five, with an average of 2.70 for each primer. The average values of the polymorphism information content, observed heterozygosity, Hardy-Weinberg equilibrium, and Shannon's information index were 0.2970, 0.4136, 0.5706, and 0.5885, respectively. Four clusters were classified according to the unweighted pair-group method with arithmetic average cluster analysis of 18 genotypes. In addition, a total of 1,228,979 single nucleotide polymorphisms (SNPs) were identified in the NHCC through a comparison with the genome of Chinese cabbage, and the average SNP density in the whole genome was 4.33/Kb. The number of SNPs ranged from 341,939 to 591,586 in the 10 accessions, and the average heterozygous SNPs ratio was ~42.53%. All analyses showed these markers were high quality and reliable. Therefore, they could be used in the construction of a linkage map and for genetic diversity studies for NHCC in future. CONCLUSIONS This is the first systematic and comprehensive analysis and identification of SSRs in NHCC and 17 species. The development of a large number of SNP and SSR markers was successfully achieved for NHCC. These novel markers are valuable for constructing genetic linkage maps, comparative genome analysis, quantitative trait locus (QTL) mapping, genome-wide association studies, and marker-assisted selection in NHCC breeding system research.
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CmMDb: a versatile database for Cucumis melo microsatellite markers and other horticulture crop research. PLoS One 2015; 10:e0118630. [PMID: 25885062 PMCID: PMC4401682 DOI: 10.1371/journal.pone.0118630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 01/21/2015] [Indexed: 12/02/2022] Open
Abstract
Cucumis melo L. that belongs to Cucurbitaceae family ranks among one of the highest valued horticulture crops being cultivated across the globe. Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family. However, very limited numbers of molecular markers were reported for Cucumis melo L. so far that limits the pace of functional genomic research in melon and other similar horticulture crops. We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family. The Cucumis melo L. microsatellite database (CmMDb: http://65.181.125.102/cmmdb2/index.html) encompasses 39,072 SSR markers along with its motif repeat, motif length, motif sequence, marker ID, motif type and chromosomal locations. The database is featured with novel automated primer designing facility to meet the needs of wet lab researchers. CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.
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Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array. PLoS One 2015; 10:e0124101. [PMID: 25874931 PMCID: PMC4395401 DOI: 10.1371/journal.pone.0124101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/26/2015] [Indexed: 01/30/2023] Open
Abstract
Genotyping arrays are tools for high-throughput genotyping, which is beneficial in constructing saturated genetic maps and therefore high-resolution mapping of complex traits. Since the report of the first cucumber genome draft, genetic maps have been constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and sequence-related amplified polymorphism (SRAP). In this study, we developed the first cucumber genotyping array consisting of 32,864 single-nucleotide polymorphisms (SNPs). These markers cover the cucumber genome with a median interval of ~2 Kb and have expected genotype calls in parents/F1 hybridizations as a training set. The training set was validated with Fluidigm technology and showed 96% concordance with the genotype calls in the parents/F1 hybridizations. Application of the genotyping array was illustrated by constructing a 598.7 cM genetic map based on a ‘9930’ × ‘Gy14’ recombinant inbred line (RIL) population comprised of 11,156 SNPs. Marker collinearity between the genetic map and reference genomes of the two parents was estimated at R2 = 0.97. We also used the array-derived genetic map to investigate chromosomal rearrangements, regional recombination rate, and specific regions with segregation distortions. Finally, 82% of the linkage-map bins were polymorphic in other cucumber variants, suggesting that the array can be applied for genotyping in other lines. The genotyping array presented here, together with the genotype calls of the parents/F1 hybridizations as a training set, should be a powerful tool in future studies with high-throughput cucumber genotyping. An ultrahigh-density linkage map constructed by this genotyping array on RIL population may be invaluable for assembly improvement, and for mapping important cucumber QTLs.
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Vartia S, Collins PC, Cross TF, Fitzgerald RD, Gauthier DT, McGinnity P, Mirimin L, Carlsson J. Multiplexing with three-primer PCR for rapid and economical microsatellite validation. Hereditas 2015; 151:43-54. [PMID: 25041267 DOI: 10.1111/hrd2.00044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/20/2014] [Indexed: 02/01/2023] Open
Abstract
The next generation sequencing revolution has enabled rapid discovery of genetic markers, however, development of fully functioning new markers still requires a long and costly process of marker validation. This study reports a rapid and economical approach for the validation and deployment of polymorphic microsatellite markers obtained from a 454 pyrosequencing library of Atlantic cod, Gadus morhua, Linnaeus 1758. Primers were designed from raw reads to amplify specific amplicon size ranges, allowing effective PCR multiplexing. Multiplexing was combined with a three-primer PCR approach using four universal tails to label amplicons with separate fluorochromes. A total of 192 primer pairs were tested, resulting in 73 polymorphic markers. Of these, 55 loci were combined in six multiplex panels each containing between six and eleven markers. Variability of the loci was assessed on G. morhua from the Celtic Sea (n = 46) and the Scotian Shelf (n = 46), two locations that have shown genetic differentiation in previous studies. Multilocus F(ST) between the two samples was estimated at 0.067 (P = 0.001). After three loci potentially under selection were excluded, the global F(ST) was estimated at 0.043 (P = 0.001). Our technique combines three-primer and multiplex PCR techniques, allowing simultaneous screening and validation of relatively large numbers of microsatellite loci.
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Affiliation(s)
- Salla Vartia
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Carna, Connemara, Co. Galway, Ireland; Area 52 Research Group, School of Biology & Environment Science, University College Dublin, Belfield, Dublin, Ireland.
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131
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Restrepo A, Páez VP, Vásquez A, Daza JM. Rapid microsatellite marker development in the endangered neotropical freshwater turtle Podocnemis lewyana (Testudines: Podocnemididae) using 454 sequencing. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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132
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Development of chromosome-specific markers with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple sequence repeats in diploid cottons (Gossypium arboreum L. and Gossypium raimondii Ulbrich). BMC Genomics 2015; 16:55. [PMID: 25652321 PMCID: PMC4325953 DOI: 10.1186/s12864-015-1265-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/22/2015] [Indexed: 02/04/2023] Open
Abstract
Background Tetraploid cotton contains two sets of homologous chromosomes, the At- and Dt-subgenomes. Consequently, many markers in cotton were mapped to multiple positions during linkage genetic map construction, posing a challenge to anchoring linkage groups and mapping economically-important genes to particular chromosomes. Chromosome-specific markers could solve this problem. Recently, the genomes of two diploid species were sequenced whose progenitors were putative contributors of the At- and Dt-subgenomes to tetraploid cotton. These sequences provide a powerful tool for developing chromosome-specific markers given the high level of synteny among tetraploid and diploid cotton genomes. In this study, simple sequence repeats (SSRs) on each chromosome in the two diploid genomes were characterized. Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes. Results A total of 200,744 and 142,409 SSRs were detected on the 13 chromosomes of Gossypium arboreum L. and Gossypium raimondii Ulbrich, respectively. Chromosome-specific SSRs were obtained by comparing SSR flanking sequences from each chromosome with those from the other 25 chromosomes. The average was 7,996 per chromosome. To confirm their chromosome specificity, these SSRs were used to distinguish two homologous chromosomes in tetraploid cotton through linkage group construction. The chromosome-specific SSRs and previously-reported chromosome markers were grouped together, and no marker mapped to another homologous chromosome, proving that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton. Because longer dinucleotide AT-rich repeats were the most polymorphic in previous reports, the SSRs on each chromosome were sorted by motif type and repeat length for convenient selection. The primer sequences of all chromosome-specific SSRs were also made publicly available. Conclusion Chromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers. The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses among Gossypium species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1265-2) contains supplementary material, which is available to authorized users.
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Transcriptome characterization and SSR discovery in large-scale loach Paramisgurnus dabryanus (Cobitidae, Cypriniformes). Gene 2015; 557:201-8. [DOI: 10.1016/j.gene.2014.12.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/02/2014] [Accepted: 12/15/2014] [Indexed: 12/26/2022]
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Ruperao P, Edwards D. Bioinformatics: identification of markers from next-generation sequence data. Methods Mol Biol 2015; 1245:29-47. [PMID: 25373747 DOI: 10.1007/978-1-4939-1966-6_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
With the advent of sequencing technology, next-generation sequencing (NGS) technology has dramatically revolutionized plant genomics. NGS technology combined with new software tools enables the discovery, validation, and assessment of genetic markers on a large scale. Among different markers systems, simple sequence repeats (SSRs) and Single nucleotide polymorphisms (SNPs) are the markers of choice for genetics and plant breeding. SSR markers have been a choice for large-scale characterization of germplasm collections, construction of genetic maps, and QTL identification. Similarly, SNPs are the most abundant genetic variations with higher frequencies throughout the genome of plant species. This chapter discusses various tools available for genome assembly and widely focuses on SSR and SNP marker discovery.
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Affiliation(s)
- Pradeep Ruperao
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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135
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Bo K, Ma Z, Chen J, Weng Y. Molecular mapping reveals structural rearrangements and quantitative trait loci underlying traits with local adaptation in semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis Qi et Yuan). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:25-39. [PMID: 25358412 DOI: 10.1007/s00122-014-2410-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 10/01/2014] [Indexed: 05/02/2023]
Abstract
Comparative genetic mapping revealed the origin of Xishuangbanna cucumber through diversification selection after domestication. QTL mapping provided insights into the genetic basis of traits under diversification selection during crop evolution. The Xishuangbanna cucumber, Cucumis sativus L. var. xishuangbannanesis Qi et Yuan (XIS), is a semi-wild landrace from the tropical southwest China with some unique traits that are very useful for cucumber breeding, such as tolerance to low light, large fruit size, heavy fruit weight, and orange flesh color in mature fruits. In this study, using 124 recombinant inbred lines (RILs) derived from the cross of the XIS cucumber with a cultivated cucumber inbred line, we developed a linkage map with 269 microsatellite (or simple sequence repeat) markers which covered 705.9 cM in seven linkage groups. Comparative analysis of orders of common marker loci or marker-anchored draft genome scaffolds among the wild (C. sativus var. hardwickii), semi-wild, and cultivated cucumber genetic maps revealed that the XIS cucumber shares major chromosomal rearrangements in chromosomes 4, 5, and 7 between the wild and cultivated cucumbers suggesting that the XIS cucumber originated through diversifying selection after cucumber domestication. Several XIS-specific minor structural changes were identified in chromosomes 1 and 6. QTL mapping with the 124 RILs in four environments identified 13 QTLs for domestication and diversifying selection-related traits including 2 for first female flowering time (fft1.1, fft6.1), 5 for mature fruit length (fl1.1, fl3.1, fl4.1, fl6.1, and fl7.1), 3 for fruit diameter (fd1.1, fd4.1, and fd6.1), and 3 for fruit weight (fw2.1, fw4.1, and fw6.1). Six of the 12 QTLs were consistently detected in all four environments. Among the 13 QTLs, fft1.1, fl1.1, fl3.1, fl7.1, fd4.1, and fw6.1 were major-effect QTLs for respective traits with each explaining at least 10 % of the observed phenotypic variations. Results from this study provide insights into the cytological and genetic basis of crop evolution leading to the XIS cucumber. The molecular markers associated with the QTLs should be useful in exploring the XIS cucumber genetic resources for cucumber breeding.
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Affiliation(s)
- Kailiang Bo
- Horticulture College, Nanjing Agricultural University, Nanjing, 210095, China
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136
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Han B, Wang C, Tang Z, Ren Y, Li Y, Zhang D, Dong Y, Zhao X. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0141540. [PMID: 26536014 DOI: 10.1371/journal.pone.0141540.t006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/10/2015] [Indexed: 05/21/2023] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.
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Affiliation(s)
- Bin Han
- College of Bio-engineering, Shanxi University, Taiyuan, China
| | - Changbiao Wang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Zhaohui Tang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yongkang Ren
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yali Li
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Dayong Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yanhui Dong
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xinghua Zhao
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
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137
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Wei Q, Wang Y, Qin X, Zhang Y, Zhang Z, Wang J, Li J, Lou Q, Chen J. An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing. BMC Genomics 2014; 15:1158. [PMID: 25534138 PMCID: PMC4367881 DOI: 10.1186/1471-2164-15-1158] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 12/11/2014] [Indexed: 11/29/2022] Open
Abstract
Background Cucumber, Cucumis sativus L., is an economically important vegetable crop which is processed or consumed fresh worldwide. However, the narrow genetic base in cucumber makes it difficult for constructing high-density genetic maps. The development of massively parallel genotyping methods and next-generation sequencing (NGS) technologies provides an excellent opportunity for developing single nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of horticultural traits. Specific-length amplified fragment sequencing (SLAF-seq) is a recent marker development technology that allows large-scale SNP discovery and genotyping at a reasonable cost. In this study, we constructed a high-density SNP map for cucumber using SLAF-seq and detected fruit-related QTLs. Results An F2 population of 148 individuals was developed from an intra-varietal cross between CC3 and NC76. Genomic DNAs extracted from two parents and 148 F2 individuals were subjected to high-throughput sequencing and SLAF library construction. A total of 10.76 Gb raw data and 75,024,043 pair-end reads were generated to develop 52,684 high-quality SLAFs, out of which 5,044 were polymorphic. 4,817 SLAFs were encoded and grouped into different segregation patterns. A high-resolution genetic map containing 1,800 SNPs was constructed for cucumber spanning 890.79 cM. The average distance between adjacent markers was 0.50 cM. 183 scaffolds were anchored to the SNP-based genetic map covering 46% (168.9 Mb) of the cucumber genome (367 Mb). Nine QTLs for fruit length and weight were detected, a QTL designated fl3.2 explained 44.60% of the phenotypic variance. Alignment of the SNP markers to draft genome scaffolds revealed two mis-assembled scaffolds that were validated by fluorescence in situ hybridization (FISH). Conclusions We report herein the development of evenly dispersed SNPs across cucumber genome, and for the first time an SNP-based saturated linkage map. This 1,800-locus map would likely facilitate genetic mapping of complex QTL loci controlling fruit yield, and the orientation of draft genome scaffolds. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1158) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No,1, Nanjing 210095, China.
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138
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Reddy UK, Abburi L, Abburi VL, Saminathan T, Cantrell R, Vajja VG, Reddy R, Tomason YR, Levi A, Wehner TC, Nimmakayala P. A genome-wide scan of selective sweeps and association mapping of fruit traits using microsatellite markers in watermelon. J Hered 2014; 106:166-76. [PMID: 25425675 DOI: 10.1093/jhered/esu077] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our genetic diversity study uses microsatellites of known map position to estimate genome level population structure and linkage disequilibrium, and to identify genomic regions that have undergone selection during watermelon domestication and improvement. Thirty regions that showed evidence of selective sweep were scanned for the presence of candidate genes using the watermelon genome browser (www.icugi.org). We localized selective sweeps in intergenic regions, close to the promoters, and within the exons and introns of various genes. This study provided an evidence of convergent evolution for the presence of diverse ecotypes with special reference to American and European ecotypes. Our search for location of linked markers in the whole-genome draft sequence revealed that BVWS00358, a GA repeat microsatellite, is the GAGA type transcription factor located in the 5' untranslated regions of a structure and insertion element that expresses a Cys2His2 Zinc finger motif, with presumed biological processes related to chitin response and transcriptional regulation. In addition, BVWS01708, an ATT repeat microsatellite, located in the promoter of a DTW domain-containing protein (Cla002761); and 2 other simple sequence repeats that association mapping link to fruit length and rind thickness.
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Affiliation(s)
- Umesh K Reddy
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Lavanya Abburi
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Venkata Lakshmi Abburi
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Thangasamy Saminathan
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Robert Cantrell
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Venkata Gopinath Vajja
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Rishi Reddy
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Yan R Tomason
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Amnon Levi
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Todd C Wehner
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
| | - Padma Nimmakayala
- From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner)
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139
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Jia X, Deng Y, Sun X, Liang L, Ye X. Characterization of the global transcriptome using Illumina sequencing and novel microsatellite marker information in seashore paspalum. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0231-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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140
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Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil.) by NGS and de novo transcriptome assembly. PLoS One 2014; 9:e109835. [PMID: 25330175 PMCID: PMC4199719 DOI: 10.1371/journal.pone.0109835] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/31/2014] [Indexed: 12/28/2022] Open
Abstract
Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes, and is presented as the first genomic resource of this important crop.
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141
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Saxena S, Singh A, Archak S, Behera TK, John JK, Meshram SU, Gaikwad AB. Development of novel simple sequence repeat markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries and their utilization in analysis of genetic diversity and cross-species transferability. Appl Biochem Biotechnol 2014; 175:93-118. [PMID: 25240849 DOI: 10.1007/s12010-014-1249-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/10/2014] [Indexed: 11/24/2022]
Abstract
Microsatellite or simple sequence repeat (SSR) markers are the preferred markers for genetic analyses of crop plants. The availability of a limited number of such markers in bitter gourd (Momordica charantia L.) necessitates the development and characterization of more SSR markers. These were developed from genomic libraries enriched for three dinucleotide, five trinucleotide, and two tetranucleotide core repeat motifs. Employing the strategy of polymerase chain reaction-based screening, the number of clones to be sequenced was reduced by 81 % and 93.7 % of the sequenced clones contained in microsatellite repeats. Unique primer-pairs were designed for 160 microsatellite loci, and amplicons of expected length were obtained for 151 loci (94.4 %). Evaluation of diversity in 54 bitter gourd accessions at 51 loci indicated that 20 % of the loci were polymorphic with the polymorphic information content values ranging from 0.13 to 0.77. Fifteen Indian varieties were clearly distinguished indicative of the usefulness of the developed markers. Markers at 40 loci (78.4 %) were transferable to six species, viz. Momordica cymbalaria, Momordica subangulata subsp. renigera, Momordica balsamina, Momordica dioca, Momordica cochinchinesis, and Momordica sahyadrica. The microsatellite markers reported will be useful in various genetic and molecular genetic studies in bitter gourd, a cucurbit of immense nutritive, medicinal, and economic importance.
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Affiliation(s)
- Swati Saxena
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
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142
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De novo sequencing and transcriptome analysis of Ustilaginoidea virens by using Illumina paired-end sequencing and development of simple sequence repeat markers. Gene 2014; 547:202-10. [DOI: 10.1016/j.gene.2014.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 02/06/2023]
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143
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Biswas MK, Xu Q, Mayer C, Deng X. Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis). PLoS One 2014; 9:e104182. [PMID: 25148383 PMCID: PMC4141690 DOI: 10.1371/journal.pone.0104182] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/09/2014] [Indexed: 11/18/2022] Open
Abstract
Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.
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Affiliation(s)
- Manosh Kumar Biswas
- Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | | | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China
- * E-mail:
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Yang X, Zhang W, He H, Nie J, Bie B, Zhao J, Ren G, Li Y, Zhang D, Pan J, Cai R. Tuberculate fruit gene Tu encodes a C2 H2 zinc finger protein that is required for the warty fruit phenotype in cucumber (Cucumis sativus L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:1034-46. [PMID: 24708549 DOI: 10.1111/tpj.12531] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 03/18/2014] [Accepted: 04/01/2014] [Indexed: 05/06/2023]
Abstract
Cucumber fruits that have tubercules and spines (trichomes) are known to possess a warty (Wty) phenotype. In this study, the tuberculate fruit gene Tu was identified by map-based cloning, and was found to encode a transcription factor (TF) with a single C2 H2 zinc finger domain. Tu was identified in all 38 Wty lines examined, and was completely absent from all 56 non-warty (nWty) lines. Cucumber plants transgenic for Tu (TCP) revealed that Tu was required for the Wty fruit phenotype. Subcellular localization showed that the fusion protein GFP-Tu was localized mainly to the nucleus. Based on analyses of semi-quantitative and quantitative reverse transcription polymerase chain reaction (RT-PCR), and mRNA in situ hybridization, we found that Tu was expressed specifically in fruit spine cells during development of fruit tubercules. Moreover, cytokinin (CTK) content measurements and cytological observations in Wty and nWty fruits revealed that the Wty fruit phenotype correlated with high endogenous CTK concentrations. As a result of further analyses on the transcriptomic profile of the nWty fruit epidermis and TCP fruit warts, expression of CTK-associated genes, and hormone content in nWty fruit epidermis, Wty fruit warts and epidermis, and TCP fruit warts and epidermis, we found that Tu probably promoted CTK biosynthesis in fruit warts. Here we show that Tu could not be expressed in the glabrous and tubercule-free mutant line gl that contained Tu, this result that futher confirmed the epistatic effect of the trichome (spine) gene Gl over Tu. Taken together, these data led us to propose a genetic pathway for the Wty fruit trait that could guide future mechanistic studies.
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Affiliation(s)
- Xuqin Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, de Jong PJ, Mockaitis K, Main D, Langley CH, Neale DB. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 2014; 196:891-909. [PMID: 24653211 PMCID: PMC3948814 DOI: 10.1534/genetics.113.159996] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 12/13/2013] [Indexed: 01/08/2023] Open
Abstract
The largest genus in the conifer family Pinaceae is Pinus, with over 100 species. The size and complexity of their genomes (∼20-40 Gb, 2n = 24) have delayed the arrival of a well-annotated reference sequence. In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine (Pinus taeda L.), which comprises 20.1 Gb of sequence. The MAKER-P annotation pipeline combined evidence-based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 are classified as high confidence. Clustering these gene models with 13 other plant species resulted in 20,646 gene families, of which 1554 are predicted to be unique to conifers. Among the conifer gene families, 159 are composed exclusively of loblolly pine members. The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes. Conifer genomes are full of repetitive DNA, with the most significant contributions from long-terminal-repeat retrotransposons. In depth analysis of the tandem and interspersed repetitive content yielded a combined estimate of 82%.
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Affiliation(s)
- Jill L. Wegrzyn
- Department of Plant Sciences, University of California, Davis, California 95616
| | - John D. Liechty
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Kristian A. Stevens
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Le-Shin Wu
- National Center for Genome Analysis Support, Indiana University, Bloomington, Indiana 47405
| | - Carol A. Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas 77843
| | | | - William M. Dougherty
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Brian Y. Lin
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Jacob J. Zieve
- Department of Plant Sciences, University of California, Davis, California 95616
| | | | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112
| | - Aleksey V. Zimin
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742
| | - James A. Yorke
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742
- Departments of Mathematics and Physics, University of Maryland, College Park, Maryland 20742
| | - Marc W. Crepeau
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Steven L. Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Pieter J. de Jong
- Children’s Hospital Oakland Research Institute, Oakland, California 94609
| | | | - Doreen Main
- Department of Horticulture, Washington State University, Pullman, Washington 99163
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - David B. Neale
- Department of Plant Sciences, University of California, Davis, California 95616
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146
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Cha TS, Anne-Marie K, Chuah TS. Identification and characterization of RAPD-SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn. Mol Biol Rep 2014; 41:823-31. [PMID: 24374894 DOI: 10.1007/s11033-013-2922-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
Abstract
Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R6976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R6976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD-SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species.
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Affiliation(s)
- Thye San Cha
- School of Fundamental Science, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia,
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Low ETL, Rosli R, Jayanthi N, Mohd-Amin AH, Azizi N, Chan KL, Maqbool NJ, Maclean P, Brauning R, McCulloch A, Moraga R, Ong-Abdullah M, Singh R. Analyses of hypomethylated oil palm gene space. PLoS One 2014; 9:e86728. [PMID: 24497974 PMCID: PMC3907425 DOI: 10.1371/journal.pone.0086728] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 12/15/2013] [Indexed: 12/21/2022] Open
Abstract
Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.
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Affiliation(s)
- Eng-Ti L. Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Ab Halim Mohd-Amin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | | | - Paul Maclean
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Rudi Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Alan McCulloch
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Roger Moraga
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
- * E-mail:
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148
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Grover A, Kumari M, Singh S, Rathode SS, Gupta SM, Pandey P, Gilotra S, Kumar D, Arif M, Ahmed Z. Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2014; 20:139-42. [PMID: 24554848 PMCID: PMC3925477 DOI: 10.1007/s12298-013-0204-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 05/09/2023]
Abstract
Oil-rich seeds of Jatropha curcas are being focussed as a source of bio-diesel. However, prior to its industrial use, a lot of crop improvement efforts are required in Jatropha. Availability of a large number of EST sequences of Jatropha in public domain allow identification of candidate genes for several agronomic characters including oil content in seeds. Here, we have analysed 42,477 ESTs of Jatropha spanning 22.9 Mbp for microsatellites and fatty acid metabolism related sequences. Unigene sequences were built using CAP 3 programme resulted in 12,358 contigs and 5,730 singlets. Nearly, 8 % unigenes showed presence of microsatellites, slightly over-represented compared to their occurrence in ESTs. Most of the microsatellites were either di- or tri-nucleotide repeats, while other categories of tetra-, penta- and hexa-nucleotide repeats together constituted ~4 % of total microsatellites. Assessment of functional relevance of unigenes was carried out using Blast2GO using its default settings. The overall sequence similarity level against sequences in 'nr' database was >80 %. A total of 931 sequences that participated in any of the pathways related to fatty acid or lipid metabolism were found at GO level 6. Among these, GO terms "Fatty acid metabolic process" and "Fatty acid biosynthetic process" were most over-represented. Overall, our work has due relevance in identifying molecular markers for the candidate genes for oil content in Jatropha seeds, and will prove to be an important reference for further studies for identification of trait specific markers in Jatropha.
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Affiliation(s)
- Atul Grover
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Maya Kumari
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Sadhana Singh
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Shivender Singh Rathode
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Sanjay Mohan Gupta
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Pankaj Pandey
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Sween Gilotra
- />Department of Biotechnology, Indian Institute of Technology, Guwahati, India
| | - Devender Kumar
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Mohommad Arif
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
| | - Zakwan Ahmed
- />Biotechnology Division, Defence Institute of Bio-Energy Research, Goraparao, P.O. Arjunpur, Haldwani, 263 139 India
- />Directorate of Management Services, Defence Research and Development Organization, DRDO Bhawan, New Delhi, 110011 India
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Yang L, Koo DH, Li D, Zhang T, Jiang J, Luan F, Renner SS, Hénaff E, Sanseverino W, Garcia-Mas J, Casacuberta J, Senalik DA, Simon PW, Chen J, Weng Y. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:16-30. [PMID: 24127692 DOI: 10.1111/tpj.12355] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 10/07/2013] [Accepted: 10/10/2013] [Indexed: 05/22/2023]
Abstract
In the large Cucurbitaceae genus Cucumis, cucumber (C. sativus) is the only species with 2n = 2x = 14 chromosomes. The majority of the remaining species, including melon (C. melo) and the sister species of cucumber, C. hystrix, have 2n = 2x = 24 chromosomes, implying a reduction from n = 12 to n = 7. To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. We identified 14 inversions and a C. hystrix lineage-specific reciprocal inversion between C. hystrix and melon. The results reveal the location and orientation of 53 C. hystrix syntenic blocks on the seven cucumber chromosomes, and allow us to infer at least 59 chromosome rearrangement events that led to the seven cucumber chromosomes, including five fusions, four translocations, and 50 inversions. The 12 inferred chromosomes (AK1-AK12) of an ancestor similar to melon and C. hystrix had strikingly different evolutionary fates, with cucumber chromosome C1 apparently resulting from insertion of chromosome AK12 into the centromeric region of translocated AK2/AK8, cucumber chromosome C3 originating from a Robertsonian-like translocation between AK4 and AK6, and cucumber chromosome C5 originating from fusion of AK9 and AK10. Chromosomes C2, C4 and C6 were the result of complex reshuffling of syntenic blocks from three (AK3, AK5 and AK11), three (AK5, AK7 and AK8) and five (AK2, AK3, AK5, AK8 and AK11) ancestral chromosomes, respectively, through 33 fusion, translocation and inversion events. Previous results (Huang, S., Li, R., Zhang, Z. et al., , Nat. Genet. 41, 1275-1281; Li, D., Cuevas, H.E., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z., Weng, Y. 2011a, BMC Genomics, 12, 396) showing that cucumber C7 stayed largely intact during the entire evolution of Cucumis are supported. Results from this study allow a fine-scale understanding of the mechanisms of dysploid chromosome reduction that has not been achieved previously.
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Affiliation(s)
- Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
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150
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Ahn YK, Tripathi S, Cho YI, Kim JH, Lee HE, Kim DS, Woo JG, Cho MC. De novo transcriptome assembly and novel microsatellite marker information in Capsicum annuum varieties Saengryeg 211 and Saengryeg 213. BOTANICAL STUDIES 2013; 54:58. [PMID: 28510893 PMCID: PMC5430321 DOI: 10.1186/1999-3110-54-58] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 11/02/2013] [Indexed: 05/31/2023]
Abstract
BACKGROUND Pepper, Capsicum annuum L., Solanaceae, is a major staple economically important vegetable crop worldwide. Limited functional genomics resources and whole genome association studies could be substantially improved through the application of molecular approach for the characterization of gene content and identification of molecular markers. The massive parallel pyrosequencing of two pepper varieties, the highly pungent, Saengryeg 211, and the non-pungent, Saengryeg 213, including de novo transcriptome assembly, functional annotation, and in silico discovery of potential molecular markers is described. We performed 454 GS-FLX Titanium sequencing of polyA-selected and normalized cDNA libraries generated from a single pool of transcripts obtained from mature fruits of two pepper varieties. RESULTS A single 454 pyrosequencing run generated 361,671 and 274,269 reads totaling 164.49 and 124.60 Mb of sequence data (average read length of 454 nucleotides), which assembled into 23,821 and 17,813 isotigs and 18,147 and 15,129 singletons for both varieties, respectively. These reads were organized into 20,352 and 15,781 'isogroups' for both varieties. Assembled sequences were functionally annotated based on homology to genes in multiple public databases and assigned with Gene Ontology (GO) terms. Sequence variants analyses identified a total of 3,766 and 2,431 potential (Simple Sequence Repeat) SSR motifs for microsatellite analysis for both varieties, where trinucleotide was the most common repeat unit (84%), followed by di (9.9%), hexa (4.1%) and pentanucleotide repeats (2.1%). GAA repeat (8.6%) was the most frequent repeat motif, followed by TGG (7.2%), TTC (6.5%), and CAG (6.2%). CONCLUSIONS High-throughput transcriptome assembly, annotation and large scale of SSR marker discovery has been achieved using next generation sequencing (NGS) of two pepper varieties. These valuable informations for functional genomics resource shall help to further improve the pepper breeding efforts with respect to genetic linkage maps, QTL mapping and marker-assisted trait selection.
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Affiliation(s)
- Yul-Kyun Ahn
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Swati Tripathi
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Young-Il Cho
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Jeong-Ho Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Jong-Gyu Woo
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Myeong-Cheoul Cho
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
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