1
|
Mori H, Ueno S, Ujino-Ihara T, Fujiwara T, Yamashita K, Kanetani S, Endo R, Matsumoto A, Uchiyama K, Yoshida T, Sakai Y, Moriguchi Y, Kusano R, Tsumura Y. Genotype-by-environment interaction and genetic dissection of heartwood color in Cryptomeria japonica based on multiple common gardens and quantitative trait loci mapping. PLoS One 2022; 17:e0270522. [PMID: 35793335 PMCID: PMC9258842 DOI: 10.1371/journal.pone.0270522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/10/2022] [Indexed: 11/19/2022] Open
Abstract
The heartwood color of a major plantation tree Cryptomeria japonica shows high variability among clones and cultivars, and brighter heartwood has higher value in the usage of non-laminated wood such as in traditional construction, which makes heartwood color an important trait in breeding of this species. However, the genetic basis of the interactions between genetics and the environment on heartwood color has been understudied while these are necessary for effective breeding programs in multiple environmental condition. The objectives of the present study were to evaluate the effects of genetics and environments on heartwood color and how they interact in contrasting environments, and to identify genomic regions controlling heartwood color in C. japonica across multiple environments. Heartwood color in terms of L*a*b* color space and spectral reflectance was measured in common gardens established in three contrasting sites. Quantitative trait loci (QTL) that affect heartwood color were identified using previously constructed highly saturated linkage maps. Results found that heartwood color was largely genetically controlled, and genotype-by-environment interaction explained one-third of the total genetic variance of heartwood color. The effect of the environment was small compared to the effect of genetics, whereas environmental effects largely varied among heartwood color traits. QTL analysis identified a large number of QTLs with small to moderate effects (phenotypic variation explained of 6.6% on average). Some of these QTLs were stably expressed in multiple environments or had pleiotropic effects on heartwood color and moisture content. These results indicated that genetic variation in phenotypic plasticity plays an important role in regulating heartwood color and that the identified QTLs would maximize the breeding efficiency of heartwood color in C. japonica in heterogeneous environments.
Collapse
Affiliation(s)
- Hideki Mori
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Tokuko Ujino-Ihara
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Takeshi Fujiwara
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, Japan
| | - Kana Yamashita
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Seiichi Kanetani
- Kyushu Research Center, Forestry and Forest Products Research Institute, Chuo, Kumamoto, Kumamoto, Japan
| | - Ryota Endo
- Forestry Research Institute, Chiba Prefectural Agriculture and Forestry Research Center, Sammu, Chiba, Japan
| | - Asako Matsumoto
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Kentaro Uchiyama
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Takahiro Yoshida
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Yoshimi Sakai
- Kyushu Research Center, Forestry and Forest Products Research Institute, Chuo, Kumamoto, Kumamoto, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, Nishi-ku, Niigata, Japan
| | - Ryouichi Kusano
- Kumamoto Prefecture Forestry Research Center, Kumamoto, Japan
| | - Yoshihiko Tsumura
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| |
Collapse
|
2
|
Liu H, Zhang Y, Wang Z, Su Y, Wang T. Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences. Front Genet 2021; 12:759557. [PMID: 34868238 PMCID: PMC8635753 DOI: 10.3389/fgene.2021.759557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.
Collapse
Affiliation(s)
- Hanjing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuli Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| |
Collapse
|
3
|
Izuno A, Maruyama TE, Ueno S, Ujino-Ihara T, Moriguchi Y. Genotype and transcriptome effects on somatic embryogenesis in Cryptomeria japonica. PLoS One 2020; 15:e0244634. [PMID: 33373415 PMCID: PMC7771663 DOI: 10.1371/journal.pone.0244634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022] Open
Abstract
Somatic embryogenesis (SE), which is in vitro regeneration of plant bodies from somatic cells, represents a useful means of clonal propagation and genetic engineering of forest trees. While protocols to obtain calluses and induce regeneration in somatic embryos have been reported for many tree species, the knowledge of molecular mechanisms of SE development is still insufficient to achieve an efficient supply of somatic embryos required for the industrial application. Cryptomeria japonica, a conifer species widely used for plantation forestry in Japan, is one of the tree species waiting for a secure SE protocol; the probability of normal embryo development appears to depend on genotype. To discriminate the embryogenic potential of embryonal masses (EMs) and efficiently obtain normal somatic embryos of C. japonica, we investigated the effects of genotype and transcriptome on the variation in embryogenic potential. Using an induction experiment with 12 EMs each from six genotypes, we showed that embryogenic potential differs between/within genotypes. Comparisons of gene expression profiles among EMs with different embryogenic potentials revealed that 742 differently expressed genes were mainly associated with pattern forming and metabolism. Thus, we suggest that not only genotype but also gene expression profiles can determine success in SE development. Consistent with previous findings for other conifer species, genes encoding leafy cotyledon, wuschel, germin-like proteins, and glutathione-S-transferases are likely to be involved in SE development in C. japonica and indeed highly expressed in EMs with high-embryogenic potential; therefore, these proteins represent candidate markers for distinguishing embryogenic potential.
Collapse
Affiliation(s)
- Ayako Izuno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Tsuyoshi E. Maruyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| |
Collapse
|
4
|
Geographical Gradients of Genetic Diversity and Differentiation among the Southernmost Marginal Populations of Abies sachalinensis Revealed by EST-SSR Polymorphism. FORESTS 2020. [DOI: 10.3390/f11020233] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than in central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and Methods: A total of 1189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations, namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were genetically differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.
Collapse
|
5
|
Climate sensitivity of Cryptomeria japonica in two contrasting environments: Perspectives from QTL mapping. PLoS One 2020; 15:e0228278. [PMID: 31990959 PMCID: PMC6986750 DOI: 10.1371/journal.pone.0228278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/12/2020] [Indexed: 11/30/2022] Open
Abstract
Long-lived forest tree species experience a wide range of environmental conditions throughout their lifespan. Evaluation of the underlying growth and development mechanisms of these species is essential to predict tree growth under climate change. This study investigated climate sensitivity to temperature, precipitation, dry periods, and the associated genomic regions in Cryptomeria japonica, Japan’s most commercially important tree. We used tree rings and common garden experiments with three clonal replicates planted in two contrasting environments in Kyushu (Kumamoto site) and Honshu (Chiba site), Japan. Tree growth showed a significant negative correlation with the dry period (>4 days) in March of the year of tree-ring formation at the Chiba site. In contrast, temperature and precipitation had little influence on tree growth. Quantitative trait locus (QTL) analysis was performed to investigate climate sensitivity to dry periods at the Chiba site, revealing 13 significant QTLs. One QTL showed a substantially large contribution to the overall climate sensitivity, accounting for 12.4% of the total phenotypic variation. The phenotypic variance explained (PVE) by other QTLs ranged from 0.9% to 2.9%, and the total PVE by all QTLs was 35.6%. These findings indicate that the tree population at the Chiba site could be vulnerable to drought in early spring and that the QTL showing the greatest impact on climate sensitivity may be closely related to genes associated with tolerance or adaptation to drought stress. The QTLs identified in this study could be useful for molecular breeding, forest management, and predicting the growth of C. japonica under a changing climate.
Collapse
|
6
|
Ruan X, Wang Z, Wang T, Su Y. Characterization and Application of EST-SSR Markers Developed From the Transcriptome of Amentotaxus argotaenia (Taxaceae), a Relict Vulnerable Conifer. Front Genet 2019; 10:1014. [PMID: 31681436 PMCID: PMC6813739 DOI: 10.3389/fgene.2019.01014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 09/24/2019] [Indexed: 11/13/2022] Open
Abstract
Amentotaxus argotaenia (Taxaceae) is a vulnerable coniferous species with preference for shade and moist environment. Accurate estimation of genetic variation is crucial for its conservation, especially in the context of global warming. In this study, we acquired a transcriptome from A. argotaenia leaves using Illumina sequencing and de novo assembled 62,896 unigenes, of which 5510 EST-SSRs were detected. Twenty-two polymorphic EST-SSRs were successfully developed and further used to investigate genetic variation, linkage disequilibrium, and bottleneck signatures of A. argotaenia. The results showed that A. argotaenia had moderate genetic variation and high genetic differentiation, which may provide raw material to protect against climatic changes and accelerate local adaptation, respectively. No bottlenecks were found to occur in A. argotaenia. Our study not only showed that these EST markers are very effective in population genetic analysis but also lay a solid foundation for further investigating adaptive evolution and conservation strategies of A. argotaenia.
Collapse
Affiliation(s)
- Xiaoxian Ruan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Research Institute of Sun Yat-sen University, Shenzhen, China
| |
Collapse
|
7
|
Yan YD, Li XY, Worth JRP, Lin XY, Ruhsam M, Chen L, Wu XT, Wang MQ, Thomas PI, Wen YF. Development of chloroplast microsatellite markers for Glyptostrobus pensilis (Cupressaceae). APPLICATIONS IN PLANT SCIENCES 2019; 7:e11277. [PMID: 31346509 PMCID: PMC6636616 DOI: 10.1002/aps3.11277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/28/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Glyptostrobus pensilis (Cupressaceae) is a critically endangered conifer native to China, Laos, and Vietnam, with only a few populations remaining in the wild. METHODS AND RESULTS Using a complete chloroplast genome sequence, we designed 70 cpSSR loci and tested them for amplification success and polymorphism in 16 samples. Ten loci were found to be polymorphic and their genetic diversity was characterized using a total of 83 individuals from three populations in China. A total of 43 haplotypes were present, the effective number of haplotypes varied from 4.55 to 13.36, and the haplotypic richness ranged from 8.04 to 16.00. Gene diversity ranged from 0.81 to 0.97 (average 0.89). The number of alleles per locus and population ranged from one to eight, and the effective number of alleles ranged from 1.00 to 3.90. All polymorphic loci were successfully amplified in the related species Cryptomeria japonica var. sinensis, Taxodium distichum, T. ascendens, and Cunninghamia lanceolata. CONCLUSIONS These newly developed chloroplast microsatellites will be useful for population genetic and phylogeographic analyses of G. pensilis and related species.
Collapse
Affiliation(s)
- Ya-Dan Yan
- Central South University of Forestry and Technology Changsha Hunan 410004 People's Republic of China
| | - Xin-Yu Li
- Central South University of Forestry and Technology Changsha Hunan 410004 People's Republic of China
| | - James R P Worth
- Forestry and Forest Products Research Institute Tsukuba Ibaraki 305-8687 Japan
| | - Xue-Ying Lin
- Central South University of Forestry and Technology Changsha Hunan 410004 People's Republic of China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh 20A Inverleith Row Edinburgh EH3 5LR United Kingdom
| | - Lu Chen
- Central South University of Forestry and Technology Changsha Hunan 410004 People's Republic of China
| | - Xing-Tong Wu
- Central South University of Forestry and Technology Changsha Hunan 410004 People's Republic of China
| | - Min-Qiu Wang
- Central South University of Forestry and Technology Changsha Hunan 410004 People's Republic of China
| | - Philip I Thomas
- Royal Botanic Garden Edinburgh 20A Inverleith Row Edinburgh EH3 5LR United Kingdom
| | - Ya-Feng Wen
- Central South University of Forestry and Technology Changsha Hunan 410004 People's Republic of China
| |
Collapse
|
8
|
Ueno S, Uchiyama K, Moriguchi Y, Ujino-Ihara T, Matsumoto A, Wei FJ, Saito M, Higuchi Y, Futamura N, Kanamori H, Katayose Y, Tsumura Y. Scanning RNA-Seq and RAD-Seq approach to develop SNP markers closely linked to MALE STERILITY 1 ( MS1) in Cryptomeria japonica D. Don. BREEDING SCIENCE 2019; 69:19-29. [PMID: 31086480 PMCID: PMC6507728 DOI: 10.1270/jsbbs.17149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 10/01/2018] [Indexed: 06/01/2023]
Abstract
Cryptomeria japonica is a major forestry tree species in Japan. Male sterility of the species is caused by a recessive gene, which shows dysfunction of pollen development and results in no dispersed pollen. Because the pollen of C. japonica induces pollinosis, breeding of pollen-free C. japonica is desired. In this study, single nucleotide polymorphism (SNP) markers located at 1.78 and 0.58 cM to a male sterility locus (MS1) were identified from an analysis of RNA-Seq and RAD-Seq, respectively. SNPs closely linked to MS1 were first scanned by a method similar to MutMap, where a type of index was calculated to measure the strength of the linkage between a marker sequence and MS1. Linkage analysis of selected SNP markers confirmed a higher efficiency of the current method to construct a partial map around MS1. Allele-specific PCR primer pair for the most closely linked SNP with MS1 was developed as a codominant marker, and visualization of the PCR products on an agarose gel enabled rapid screening of male sterile C. japonica. The allele-specific primers developed in this study would be useful for establishing the selection of male sterile C. japonica.
Collapse
Affiliation(s)
- Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization,
1 Matsunosato, Tsukuba, Ibaraki 305-8687,
Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization,
1 Matsunosato, Tsukuba, Ibaraki 305-8687,
Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University,
8050, Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181,
Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization,
1 Matsunosato, Tsukuba, Ibaraki 305-8687,
Japan
| | - Asako Matsumoto
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization,
1 Matsunosato, Tsukuba, Ibaraki 305-8687,
Japan
| | - Fu-Jin Wei
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization,
1 Matsunosato, Tsukuba, Ibaraki 305-8687,
Japan
| | - Maki Saito
- Toyama Prefectural Agricultural Forestry and Fisheries Research Center, Forestry Research Institute,
Yoshimine 3, Tateyama-cho, Nakashinkawagun, Toyama 930-1362,
Japan
| | - Yumi Higuchi
- Niigata Prefectural Forest Research Institute,
2249-5 Unotoro, Murakami, Niigata 958-0264,
Japan (retired)
| | - Norihiro Futamura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization,
1 Matsunosato, Tsukuba, Ibaraki 305-8687,
Japan
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences,
Owashi, Tsukuba, Ibaraki 305-8634,
Japan
| | - Yuichi Katayose
- National Institute of Agrobiological Sciences,
Owashi, Tsukuba, Ibaraki 305-8634,
Japan
| | - Yoshihiko Tsumura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization,
1 Matsunosato, Tsukuba, Ibaraki 305-8687,
Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba,
1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572,
Japan
| |
Collapse
|
9
|
Hasegawa Y, Ueno S, Matsumoto A, Ujino-Ihara T, Uchiyama K, Totsuka S, Iwai J, Hakamata T, Moriguchi Y. Fine mapping of the male-sterile genes (MS1, MS2, MS3, and MS4) and development of SNP markers for marker-assisted selection in Japanese cedar (Cryptomeria japonica D. Don). PLoS One 2018; 13:e0206695. [PMID: 30439978 PMCID: PMC6237302 DOI: 10.1371/journal.pone.0206695] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/17/2018] [Indexed: 11/08/2022] Open
Abstract
Pollinosis caused by Japanese cedar (Cryptomeria japonica) is a widespread social problem in Japan. To date, 23 male-sterile C. japonica trees have been selected in Japan to address pollinosis, from which four male-sterility loci (MS1, MS2, MS3, and MS4) have been identified from test crossing results. For efficient breeding of male-sterile C. japonica trees, more male-sterile individuals and individuals heterozygous for male-sterile genes are required. Therefore, we aimed to develop DNA markers for marker-assisted selection of four types of male-sterile genes from populations without a family structure. First, for four families exhibiting segregation of each male-sterile locus (MS1, MS2, MS3, and MS4), genome-wide single-nucleotide polymorphism and insertion/deletion (indel) genotyping was performed using the Axiom myDesign Targeted Genotyping Array method. Four high-density linkage maps for mapping the MS1, MS2, MS3, and MS4 families were constructed, which included 4923, 1722, 1896, and 2247 markers, respectively. In these maps, 15, 4, 2, and 2 markers were located 0.0, 3.3, 1.1, and 0.0 cM from the MS1, MS2, MS3, and MS4 loci, respectively. Second, for the markers located 0.0 cM from a male-sterile locus (i.e., MS1 and MS4), to clarify the most tightly linked markers, we calculated the prediction rate of male-sterile gene genotypes from marker genotypes for 78 trees. The markers with the highest prediction rates were AX-174127446 (0.95) for MS1 and AX-174121522 (1.00) for MS4. The AX-174121522 marker was considered to be suitable for selecting trees homozygous or heterozygous for the MS4 gene from plus-trees without a pollination test, which requires a large amount of time and effort. The nearest markers to the male-sterile loci found in this study may facilitate the isolation of male-sterile genes in C. japonica via combination with the draft genomic sequence that is currently being collated.
Collapse
Affiliation(s)
- Yoichi Hasegawa
- Graduate School of Science and Technology, Niigata University, Niigata, Niigata, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Asako Matsumoto
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Satoko Totsuka
- Niigata Prefectural Forest Research Institute, Murakami, Niigata, Japan
| | - Junji Iwai
- Niigata Prefectural Forest Research Institute, Murakami, Niigata, Japan
| | - Tetsuji Hakamata
- Forestry and Forest Products Research Center, Shizuoka Prefectural Research Institute of Agriculture and Forestry, Hamamatsu, Shizuoka, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, Niigata, Niigata, Japan
| |
Collapse
|
10
|
Zeng J, Chen J, Kou Y, Wang Y. Application of EST-SSR markers developed from the transcriptome of Torreya grandis (Taxaceae), a threatened nut-yielding conifer tree. PeerJ 2018; 6:e5606. [PMID: 30258714 PMCID: PMC6151121 DOI: 10.7717/peerj.5606] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/17/2018] [Indexed: 02/04/2023] Open
Abstract
Torreya grandis (Taxaceae) is an ancient conifer species endemic to southeast China. Because of its nutrient-rich and delicious seeds, this species has been utilized for centuries by the Chinese. However, transcriptome data and transcriptome-derived microsatellite markers for population genetics studies are still insufficient for understanding of this species’ genetic basis. In this study, a transcriptome from T. grandis leaves was generated using Illumina sequencing. A total of 69,920 unigenes were generated after de novo assembly, and annotated by searching against seven protein databases. In addition, 2,065 expressed sequence tag–simple sequence repeats (EST-SSRs) were detected, with the distribution frequency of 2.75% of total unigenes and average number of 0.03 SSRs per unigene. Among these EST-SSRs, 1,339 primer pairs were successfully designed, and 106 primer pairs were randomly selected for the development of potential molecular markers. Among them, 11 EST-SSR markers revealed a moderate level of genetic diversity, and were used to investigate the population structure of T. grandis. Two different genetic groups within this species were revealed using these EST-SSR markers, indicating that these markers developed in this study can be effectively applied to the population genetic analysis of T. grandis.
Collapse
Affiliation(s)
- Jun Zeng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jie Chen
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, China
| | - Yujin Wang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| |
Collapse
|
11
|
Mishima K, Hirao T, Tsubomura M, Tamura M, Kurita M, Nose M, Hanaoka S, Takahashi M, Watanabe A. Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don). BMC Genomics 2018; 19:277. [PMID: 29685102 PMCID: PMC5914023 DOI: 10.1186/s12864-018-4581-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/06/2018] [Indexed: 11/30/2022] Open
Abstract
Background Japanese cedar (Cryptomeria japonica) is an important tree for Japanese forestry. Male-sterile marker development in Japanese cedar would facilitate selection of male-sterile plus trees, addressing the widespread social problem of pollinosis and facilitating the identification of heterozygotes, which are useful for breeding. Results This study used next-generation sequencing for single-nucleotide polymorphism discovery in libraries constructed from several organs, including male-sterile and male-fertile strobili. The single-nucleotide polymorphisms obtained were used to construct a high-density linkage map, which enabled identification of a locus on linkage group 9 strongly correlated with male-sterile trait. Expressed sequence tags corresponding to 11 marker loci from 5 isotigs were associated with this locus within 33.4-34.5 cM. These marker loci explained 100% of the phenotypic variation. Several homologs of these sequences are associated with male sterility in rice or Arabidopsis, including a pre-mRNA splicing factor, a DEAD-box protein, a glycosyl hydrolase, and a galactosyltransferase. These proteins are thus candidates for the causal male-sterile gene at the ms-1 locus. After we used a SNaPshot assay to develop markers for marker-assisted selection (MAS), we tested F2 progeny between male-sterile and wild-type plus trees to validate the markers and extrapolated the testing to a larger plus-tree population. We found that two developed from one of the candidates for the causal gene were suitable for MAS. Conclusions More than half of the ESTs and SNPs we collected were new, enlarging the genomic basis for genetic research on Japanese cedar. We developed two SNP markers aimed at MAS that distinguished individuals carrying the male-sterile trait with 100% accuracy, as well as individuals heterozygous at the male-sterile locus, even outside the mapping population. These markers should enable practical MAS for conifer breeding. Electronic supplementary material The online version of this article (10.1186/s12864-018-4581-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Tomonori Hirao
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Miho Tamura
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Manabu Kurita
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Mine Nose
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - So Hanaoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Makoto Takahashi
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Atsushi Watanabe
- Department of Forest Environmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan.
| |
Collapse
|
12
|
Ujino-Ihara T, Ueno S, Uchiyama K, Futamura N. Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica. PLoS One 2018. [PMID: 29529051 PMCID: PMC5846777 DOI: 10.1371/journal.pone.0193665] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Deep sequencing of small RNAs (sRNAs) in developing male strobili of second-generation offspring originating from a nuclear genic male sterile tree of Cryptomeria japonica were performed to characterize sRNA populations in the male strobili at early pollen developmental stages. Comparing to sequences of microRNA (miRNA) families of plant species and sRNAs expressed in the reproductive organs of representative vascular plants, 37 conserved miRNA families were detected, of which eight were ubiquitously expressed in the reproductive organs of land plant species. In contrast, miR1083 was common in male reproductive organs of gymnosperm species but absent in angiosperm species. In addition to conserved miRNAs, 199 novel miRNAs candidates were predicted. The expression patterns of the obtained sRNAs were further investigated to detect the differentially expressed (DE) sRNAs between genic male sterile and fertile individuals. A total of 969 DE sRNAs were obtained and only three known miRNA families were included among them. These results suggest that both conserved and species-specific sRNAs contribute to the development of male strobili in C. japonica.
Collapse
Affiliation(s)
- Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| | - Norihiro Futamura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan
| |
Collapse
|
13
|
Molecular Markers in Whole Genome Evolution of Brachypodium. Methods Mol Biol 2017. [PMID: 29039008 DOI: 10.1007/978-1-4939-7278-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Molecular markers play more and more important role in population genetic and phylogenetic studies; choice of marker systems for a particular study has become a serious problem. These marker systems have different advantages and disadvantages, so it is imperative to keep in mind all the pros and cons of the technique while selecting one for the problem to be addressed.Here, we concisely introduced three molecular marker techniques, namely SSR, ISSR, and RFLP. We elaborated their properties such as reliability, simplicity, cost-effectiveness, and speed, in addition to data analysis of genetic diversity. We have outlined here the whole methodology of these techniques.
Collapse
|
14
|
Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.). Sci Rep 2017; 7:41124. [PMID: 28120935 PMCID: PMC5264649 DOI: 10.1038/srep41124] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/14/2016] [Indexed: 11/18/2022] Open
Abstract
With the aim of identifying sex determinants of fig, we generated the first draft genome sequence of fig and conducted the subsequent analyses. Linkage analysis with a high-density genetic map established by a restriction-site associated sequencing technique, and genome-wide association study followed by whole-genome resequencing analysis identified two missense mutations in RESPONSIVE-TO-ANTAGONIST1 (RAN1) orthologue encoding copper-transporting ATPase completely associated with sex phenotypes of investigated figs. This result suggests that RAN1 is a possible sex determinant candidate in the fig genome. The genomic resources and genetic findings obtained in this study can contribute to general understanding of Ficus species and provide an insight into fig’s and plant’s sex determination system.
Collapse
|
15
|
Jia H, Yang H, Sun P, Li J, Zhang J, Guo Y, Han X, Zhang G, Lu M, Hu J. De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila. Sci Rep 2016; 6:39591. [PMID: 27995985 PMCID: PMC5171774 DOI: 10.1038/srep39591] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 11/25/2016] [Indexed: 12/27/2022] Open
Abstract
Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE 0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST = 0.006-0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST = 0.045-0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila.
Collapse
Affiliation(s)
- Huixia Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Haifeng Yang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, 010019, China
| | - Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jianbo Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yinghua Guo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Guosheng Zhang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, 010019, China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| |
Collapse
|
16
|
Li CY, Chiang TY, Chiang YC, Hsu HM, Ge XJ, Huang CC, Chen CT, Hung KH. Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing. Molecules 2016; 21:67. [PMID: 26751439 PMCID: PMC6273106 DOI: 10.3390/molecules21010067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 01/02/2023] Open
Abstract
Amentotaxus, a genus of Taxaceae, is an ancient lineage with six relic and endangered species. Four Amentotaxus species, namely A. argotaenia, A. formosana, A. yunnanensis, and A. poilanei, are considered a species complex because of their morphological similarities. Small populations of these species are allopatrically distributed in Asian forests. However, only a few codominant markers have been developed and applied to study population genetic structure of these endangered species. In this study, we developed and characterized polymorphic expressed sequence tag-simple sequence repeats (EST-SSRs) from the transcriptome of A. formosana. We identified 4955 putative EST-SSRs from 68,281 unigenes as potential molecular markers. Twenty-six EST-SSRs were selected for estimating polymorphism and transferability among Amentotaxus species, of which 23 EST-SSRs were polymorphic within Amentotaxus species. Among these, the number of alleles ranged from 1-4, the polymorphism information content ranged from 0.000-0.692, and the observed and expected heterozygosity were 0.000-1.000 and 0.080-0.740, respectively. Population genetic structure analyses confirmed that A. argotaenia and A. formosana were separate species and A. yunnanensis and A. poilanei were the same species. These novel EST-SSRs can facilitate further population genetic structure research of Amentotaxus species.
Collapse
Affiliation(s)
- Chiuan-Yu Li
- Taiwan Endemic Species Research Institute, Nantou 552, Taiwan.
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng-Kung University, Tainan 701, Taiwan.
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan.
| | - Hsin-Mei Hsu
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Xue-Jun Ge
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | | | - Chaur-Tzuhn Chen
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| |
Collapse
|
17
|
Ranade SS, Lin YC, Van de Peer Y, García-Gil MR. Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda). BMC Genet 2015; 16:149. [PMID: 26706685 PMCID: PMC4691297 DOI: 10.1186/s12863-015-0304-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/10/2015] [Indexed: 11/24/2022] Open
Abstract
Background Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1–6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies. We carried out a comparative study of perfect SSR loci belonging to class I (≥20) and class II (≥12 and <20 bp) types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to retrieve SSRs from the full length CDS of predicted genes in both species. Results Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich motifs, within class II SSRs in both the species (P-values = 10−9 and 0). With reference to class I SSRs, AT-rich and GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005). Conclusions Our study gives a comparative overview of the genome SSRs composition based on high confidence genes in the two recently sequenced and economically important conifers and, also provides information on functional molecular markers that can be applied in genetic studies in Pinus and Picea species. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0304-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden.
| | - Yao-Cheng Lin
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. .,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028, South Africa. .,Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium.
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden.
| |
Collapse
|
18
|
Ueno S, Wen Y, Tsumura Y. Development of EST-SSR markers for Taxus cuspidata from publicly available transcriptome sequences. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.09.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
19
|
de Miguel M, Bartholomé J, Ehrenmann F, Murat F, Moriguchi Y, Uchiyama K, Ueno S, Tsumura Y, Lagraulet H, de Maria N, Cabezas JA, Cervera MT, Gion JM, Salse J, Plomion C. Evidence of intense chromosomal shuffling during conifer evolution. Genome Biol Evol 2015; 7:2799-2809. [PMID: 26400405 PMCID: PMC4684699 DOI: 10.1093/gbe/evv185] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Although recent advances have been gained on genome evolution in angiosperm lineages, virtually nothing is known about karyotype evolution in the other group of seed plants, the gymnosperms. Here, we used high-density gene-based linkage mapping to compare the karyotype structure of two families of conifers (the most abundant group of gymnosperms) separated around 290 Ma: Pinaceae and Cupressaceae. We propose for the first time a model based on the fusion of 20 ancestral chromosomal blocks that may have shaped the modern karyotpes of Pinaceae (with n = 12) and Cupressaceae (with n = 11). The considerable difference in modern genome organization between these two lineages contrasts strongly with the remarkable level of synteny already reported within the Pinaceae. It also suggests a convergent evolutionary mechanism of chromosomal block shuffling that has shaped the genomes of the spermatophytes.
Collapse
Affiliation(s)
- Marina de Miguel
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Jérôme Bartholomé
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - François Ehrenmann
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Florent Murat
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Yoshinari Moriguchi
- Niigata University, Graduate School of Science and Technology, 8050, Igarashi 2-Nocho, Nishi-ku, Niigata 950-2181, Japan
| | - Kentaro Uchiyama
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tsukuba, Ibaraki 305-8687, Japan
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tsukuba, Ibaraki 305-8687, Japan
| | - Yoshihiko Tsumura
- University of Tsukuba, Faculty of Life & Environmental Sciences, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hélène Lagraulet
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Nuria de Maria
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - José-Antonio Cabezas
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - Maria-Teresa Cervera
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - Jean Marc Gion
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France CIRAD, UMR AGAP, F-33612 Cestas, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Christophe Plomion
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| |
Collapse
|
20
|
Takeuchi T, Yamaguchi M, Tanaka R, Dayi M, Ogura N, Kikuchi T. Development and validation of SSR markers for the plant-parasitic nematode Subanguina moxae using genome assembly of Illumina pair-end reads. NEMATOLOGY 2015. [DOI: 10.1163/15685411-00002885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Subanguina moxae, belonging to the subfamily Anguininae, is an obligate parasite of Artemisia plants, which are widely used as cooking herbs and in traditional medicine in East Asia. Because the nematode is distributed throughout East Russia and East Asia, there is concern about the potential for significant damage to commercial farming; however, details about its biology remain unclear. To investigate the genetic diversity of S. moxae, we developed 2243 simple sequence repeat (SSR) markers using Illumina short reads of the genomic DNA. We validated 100 randomly selected markers indicating their robustness and examined polymorphisms among nematode populations sampled from four different locations in Japan. These SSR markers will be a useful tool for understanding the population structure and transmission patterns of this parasitic nematode.
Collapse
Affiliation(s)
- Tomoaki Takeuchi
- Laboratory of Plant Nematology, Department of Agriculture, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Madoka Yamaguchi
- Laboratory of Plant Nematology, Department of Agriculture, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Ryusei Tanaka
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Mehmet Dayi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Forest Entomology and Protection Unit, Faculty of Forestry, Duzce University, Duzce, 81620, Turkey
| | - Nobuo Ogura
- Laboratory of Plant Nematology, Department of Agriculture, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| |
Collapse
|
21
|
Kimura MK, Uchiyama K, Nakao K, Moriguchi Y, San Jose-Maldia L, Tsumura Y. Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica. ANNALS OF BOTANY 2014; 114:1687-1700. [PMID: 25355521 PMCID: PMC4649686 DOI: 10.1093/aob/mcu197] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/26/2014] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Distribution shifts and natural selection during past climatic changes are important factors in determining the genetic structure of forest species. In particular, climatic fluctuations during the Quaternary appear to have caused changes in the distribution ranges of plants, and thus strongly affected their genetic structure. This study was undertaken to identify the responses of the conifer Cryptomeria japonica, endemic to the Japanese Archipelago, to past climatic changes using a combination of phylogeography and species distribution modelling (SDM) methods. Specifically, this study focused on the locations of refugia during the last glacial maximum (LGM). METHODS Genetic diversity and structure were examined using 20 microsatellite markers in 37 populations of C. japonica. The locations of glacial refugia were assessed using STRUCTURE analysis, and potential habitats under current and past climate conditions were predicted using SDM. The process of genetic divergence was also examined using the approximate Bayesian computation procedure (ABC) in DIY ABC to test the divergence time between the gene pools detected by the STRUCTURE analysis. KEY RESULTS STRUCTURE analysis identified four gene pools: northern Tohoku district; from Chubu to Chugoku district; from Tohoku to Shikoku district on the Pacific Ocean side of the Archipelago; and Yakushima Island. DIY ABC analysis indicated that the four gene pools diverged at the same time before the LGM. SDM also indicated potential northern cryptic refugia. CONCLUSIONS The combined evidence from microsatellites and SDM clearly indicates that climatic changes have shaped the genetic structure of C. japonica. The gene pool detected in northern Tohoku district is likely to have been established by cryptic northern refugia on the coast of the Japan Sea to the west of the Archipelago. The gene pool in Yakushima Island can probably be explained simply by long-term isolation from the other gene pools since the LGM. These results are supported by those of SDM and the predicted divergence time determined using ABC analysis.
Collapse
Affiliation(s)
- Megumi K Kimura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| | - Kentaro Uchiyama
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| | - Katsuhiro Nakao
- Department of Forest Vegetation, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, 8050, Igarashi 2-Nocho, Nishi-ku Niigata 950-2181, Japan
| | - Lerma San Jose-Maldia
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoshihiko Tsumura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan
| |
Collapse
|
22
|
Genetic differentiation and evolutionary adaptation in Cryptomeria japonica. G3-GENES GENOMES GENETICS 2014; 4:2389-402. [PMID: 25320072 PMCID: PMC4267934 DOI: 10.1534/g3.114.013896] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Local adaptation of plant species is a central issue for survival during global climate change, especially for long-lived forest trees, with their lengthy regeneration time and spatially limited gene flow. Identification of loci and/or genomic regions associated with local adaptation is necessary for knowledge of both evolution and molecular breeding for climate change. Cryptomeria japonica is an important species for forestry in Japan; it has a broad natural distribution and can survive in a range of different environments. The genetic structure of 14 natural populations of this species was investigated using 3930 SNP markers. Populations on the Pacific Ocean side of Japan are clearly different from those on the Japan Sea side, as discussed in previous studies. Structure analysis and population network trees show that peripheral populations, including the most northerly and southerly ones, have unique features. We found that the genetic differentiation coefficient is low, FST = 0.05, although it must account for the presence of important genes associated with adaptation to specific environments. In total, 208 outlier loci were detected, of which 43 were associated with environmental variables. Four clumped regions of outlier loci were detected in the genome by linkage analysis. Linkage disequilibrium (LD) was quite high in these clumps of outlier loci, which were found in linkage groups (LGs) 2, 7, 10, and 11, especially between populations of two varieties, and when interchromosomal LD was also detected. The LG7 region is characteristic of the Yakushima population, which is a large, isolated, peripheral population occupying a specific environment resulting from isolation combined with volcanic activity in the region. The detected LD may provide strong evidence for selection between varieties.
Collapse
|
23
|
Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, García-Gil MDR. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC PLANT BIOLOGY 2014; 14:220. [PMID: 25143005 PMCID: PMC4160553 DOI: 10.1186/s12870-014-0220-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/05/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). RESULTS Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. CONCLUSIONS Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
Collapse
Affiliation(s)
- Sonali Sachin Ranade
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
| | - Yao-Cheng Lin
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Andrea Zuccolo
- />Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy
- />Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
| | - Yves Van de Peer
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- />Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa
| | - María del Rosario García-Gil
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
| |
Collapse
|
24
|
Gene discovery through transcriptome sequencing for the invasive mussel Limnoperna fortunei. PLoS One 2014; 9:e102973. [PMID: 25047650 PMCID: PMC4105566 DOI: 10.1371/journal.pone.0102973] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/24/2014] [Indexed: 11/22/2022] Open
Abstract
The success of the Asian bivalve Limnoperna fortunei as an invader in South America is related to its high acclimation capability. It can inhabit waters with a wide range of temperatures and salinity and handle long-term periods of air exposure. We describe the transcriptome of L. fortunei aiming to give a first insight into the phenotypic plasticity that allows non-native taxa to become established and widespread. We sequenced 95,219 reads from five main tissues of the mussel L. fortunei using Roche’s 454 and assembled them to form a set of 84,063 unigenes (contigs and singletons) representing partial or complete gene sequences. We annotated 24,816 unigenes using a BLAST sequence similarity search against a NCBI nr database. Unigenes were divided into 20 eggNOG functional categories and 292 KEGG metabolic pathways. From the total unigenes, 1,351 represented putative full-length genes of which 73.2% were functionally annotated. We described the first partial and complete gene sequences in order to start understanding bivalve invasiveness. An expansion of the hsp70 gene family, seen also in other bivalves, is present in L. fortunei and could be involved in its adaptation to extreme environments, e.g. during intertidal periods. The presence of toll-like receptors gives a first insight into an immune system that could be more complex than previously assumed and may be involved in the prevention of disease and extinction when population densities are high. Finally, the apparent lack of special adaptations to extremely low O2 levels is a target worth pursuing for the development of a molecular control approach.
Collapse
|
25
|
Li X, Luo J, Yan T, Xiang L, Jin F, Qin D, Sun C, Xie M. Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome. PLoS One 2013; 8:e85480. [PMID: 24392013 PMCID: PMC3877369 DOI: 10.1371/journal.pone.0085480] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/27/2013] [Indexed: 12/13/2022] Open
Abstract
Cymbidium ensifolium is a Chinese Cymbidium with an elegant shape, beautiful appearance, and a fragrant aroma. C. ensifolium has a long history of cultivation in China and it has excellent commercial value as a potted plant and cut flower. The development of C. ensifolium genomic resources has been delayed because of its large genome size. Taking advantage of technical and cost improvement of RNA-Seq, we extracted total mRNA from flower buds and mature flowers and obtained a total of 9.52 Gb of filtered nucleotides comprising 98,819,349 filtered reads. The filtered reads were assembled into 101,423 isotigs, representing 51,696 genes. Of the 101,423 isotigs, 41,873 were putative homologs of annotated sequences in the public databases, of which 158 were associated with floral development and 119 were associated with flowering. The isotigs were categorized according to their putative functions. In total, 10,212 of the isotigs were assigned into 25 eukaryotic orthologous groups (KOGs), 41,690 into 58 gene ontology (GO) terms, and 9,830 into 126 Arabidopsis Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 9,539 isotigs into 123 rice pathways. Comparison of the isotigs with those of the two related orchid species P. equestris and C. sinense showed that 17,906 isotigs are unique to C. ensifolium. In addition, a total of 7,936 SSRs and 16,676 putative SNPs were identified. To our knowledge, this transcriptome database is the first major genomic resource for C. ensifolium and the most comprehensive transcriptomic resource for genus Cymbidium. These sequences provide valuable information for understanding the molecular mechanisms of floral development and flowering. Sequences predicted to be unique to C. ensifolium would provide more insights into C. ensifolium gene diversity. The numerous SNPs and SSRs identified in the present study will contribute to marker development for C. ensifolium.
Collapse
Affiliation(s)
- Xiaobai Li
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Jie Luo
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Tianlian Yan
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Lin Xiang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Feng Jin
- College of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Dehui Qin
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Chongbo Sun
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Ming Xie
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| |
Collapse
|
26
|
Liu SR, Li WY, Long D, Hu CG, Zhang JZ. Development and characterization of genomic and expressed SSRs in citrus by genome-wide analysis. PLoS One 2013; 8:e75149. [PMID: 24204572 PMCID: PMC3810390 DOI: 10.1371/journal.pone.0075149] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/10/2013] [Indexed: 12/26/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are one of the most popular sources of genetic markers and play a significant role in plant genetics and breeding. In this study, we identified citrus SSRs in the genome of Clementine mandarin and analyzed their frequency and distribution in different genomic regions. A total of 80,708 SSRs were detected in the genome with an overall density of 268 SSRs/Mb. While di-nucleotide repeats were the most frequent microsatellites in genomic DNA sequence, tetra-nucleotides, which had more repeat units than any other SSR types, had the highest cumulative sequence length. We identified 6,834 transcripts as containing 8,989 SSRs in 33,929 Clementine mandarin transcripts, among which, tri-nucleotide motifs (36.0%) were the most common, followed by di-nucleotide (26.9%) and hexa-nucleotide motifs (15.1%). The motif AG (16.7%) was most abundant among these SSRs, while motifs AAG (6.6%), AAT (5.0%), and TAG (2.2%) were most common among tri-nucleotides. Functional categorization of transcripts containing SSRs revealed that 5,879 (86.0%) of such transcripts had homology with known proteins, GO and KEGG annotation revealed that transcripts containing SSRs were those implicated in diverse biological processes in plants, including binding, development, transcription, and protein degradation. When 27 genomic and 78 randomly selected SSRs were tested on Clementine mandarin, 95 SSRs revealed polymorphism. These 95 SSRs were further deployed on 18 genotypes of the three generas of Rutaceae for the genetic diversity assessment, genomic SSRs generally show low transferability in comparison to SSRs developed from expressed sequences. These transcript-markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in citrus, such as diversity study, QTL mapping, molecular breeding, comparative mapping and other genetic analyses.
Collapse
Affiliation(s)
- Sheng-Rui Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Wen-Yang Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Dang Long
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
- * E-mail:
| |
Collapse
|
27
|
Gao C, Ren X, Mason AS, Li J, Wang W, Xiao M, Fu D. Revisiting an important component of plant genomes: microsatellites. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:645-661. [PMID: 32481138 DOI: 10.1071/fp12325] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/16/2013] [Indexed: 06/11/2023]
Abstract
Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals.
Collapse
Affiliation(s)
- Caihua Gao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaodong Ren
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Annaliese S Mason
- Centre for Integrative Legume Research and School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Qld, Australia
| | - Jiana Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Wei Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Meili Xiao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| |
Collapse
|
28
|
Du FK, Xu F, Qu H, Feng S, Tang J, Wu R. Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to develop and characterize new EST-SSR markers and construct an EST-SSR database. PLoS One 2013; 8:e61337. [PMID: 23593466 PMCID: PMC3623821 DOI: 10.1371/journal.pone.0061337] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/08/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Microsatellite markers or Simple Sequence Repeats (SSRs) are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries. METHODOLOGY/PRINCIPAL FINDINGS A total of 94,090 non-redundant Expressed Sequence Tags (ESTs) from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37%) and hexanucleotides (33%) repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs) and selected 673 of these pairs at random for further validation. 575 pairs (85%) gave successful amplification, of which, 464 (80.7%) were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html). CONCLUSIONS The large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.
Collapse
Affiliation(s)
- Fang K. Du
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Fang Xu
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hong Qu
- Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
| | - Sisi Feng
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jijun Tang
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, United States of America
| | - Rongling Wu
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| |
Collapse
|