Development and Characterization of Novel EST-SSRs from Larix gmelinii and Their Cross-Species Transferability
10
Citation
25
Reference
10
Related Paper
Citation Trend
Abstract:
A set of 899 L. gmelinii expression sequence tags (ESTs), available at the National Center of Biotechnology Information (NCBI), was employed to address the feasibility on development of simple sequence repeat (SSR) markers for Larch species. Totally, 634 non-redundant unigenes including 145 contigs and 489 singletons were finally identified and mainly involved in biosynthetic, metabolic processes and response to stress according to BLASTX results, gene ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) maps. Approximately 11.7% (74) unigenes contained 90 candidate SSRs, which were mainly trinucleotides (29, 32.2%) and dinucleotides (26, 28.9%). A relatively high frequency of SSRs was respectively found in the Open Reading Frame (ORF, about 54.4%) and 5′-untranslated region (5′-UTR, 31.2%), while a low frequency was observed in the 3′-untranslated region (3′-UTR, about 14.4%). Of the 45 novel EST-SSRs markers, nine were found to be polymorphic at two L. gmelinii populations. The number of alleles per locus (Na) ranged from two to four, and the observed (Ho) and expected (He) heterozygosity values were 0.200–0.733 and 0.408–0.604, respectively. The inbreeding coefficients (FIS) for all loci were more than zero except Lg41. Most of these 9EST-SSR markers were transferable to its related species L. kaempferi, L. principis-rupprechtii and L. olgensis. These novel EST-SSRs will be useful for further research on comparative genomics, genetic resources conservation and molecular breeding in larch trees.Keywords:
KEGG
Transferability
Breakpoint
Candidate gene
Sequence-tagged site
Cite
Citations (1)
Breakpoint
Candidate gene
Cite
Citations (0)
Pine wood nematodes were inoculated on 2-year-old seedlings of a non-selected susceptible and one of the strongest resistant breed variety, respectively. The five samples were harvested at every 7 days and counted the nematode numbers of the samples. They are also stored at -80°C for RNA extraction. The nematodes were collected by Baermann funnel technique and counted under a stereomicroscope to judge the resistance. RNAs were extracted from the resistant and susceptible stems judged at the stage when the nematodes had just started to propagate, by Quagen RNeasy Plant Mini Kit with minor modification. The cDNAs obtained from the resistant and susceptible breed varieties, were differentially screened by Megasort beads technology. The 1507 and 1329 cDNAs, or ESTs, from the respective breed varieties, were effectively sequenced and assembled as the contigs. They were subjected to Blast retrieval against various public databases for their assignments. The data sets obtained were analyzed in silico. Results and conclusions A contig sequence is composed of ESTs, and it approximates an expressed gene species, while the numbers of ESTs in a contig approximate the expressed level of the gene. Comprehensive expression analyses show that the contig numbers, i.e. gene species, were more abundant in a resistant breed variety than those in a susceptible one. The contigs expressed more than 4 ESTs, being composed of 803 ESTs, were three times abundant in the resistant variety than in the susceptible one. The defense response might be triggered by the nematode invasion in a resistant variety but not in a susceptible one. Alternatively, it may be caused by the suppressed gene expression in the susceptible one. The latter is
Cite
Citations (15)
We performed random sequencing of cDNAs from nine biologically or industrially important cultures of the industrially valuable fungus Aspergillus oryzae to obtain expressed sequence tags (ESTs). Consequently, 21 446 raw ESTs were accumulated and subsequently assembled to 7589 non-redundant consensus sequences (contigs). Among all contigs, 5491 (72.4%) were derived from only a particular culture. These included 4735 (62.4%) singletons, i.e. lone ESTs overlapping with no others. These data showed that consideration of culture grown under various conditions as cDNA sources enabled efficient collection of ESTs. BLAST searches against the public databases showed that 2953 (38.9%) of the EST contigs showed significant similarities to deposited sequences with known functions, 793 (10.5%) were similar to hypothetical proteins, and the remaining 3843 (50.6%) showed no significant similarity to sequences in the databases. Culture-specific contigs were extracted on the basis of the EST frequency normalized by the total number for each culture condition. In addition, contig sequences were compared with sequence sets in eukaryotic orthologous groups (KOGs), and classified into the KOG functional categories.
Aspergillus oryzae
Sequence (biology)
Cite
Citations (73)
Reciprocal cross pollinations between western larch (Larixoccidentalis Nutt.) and alpine larch (L. lyallii Parl.) were done in Spring, 1991. The cross to alpine larch females was highly successful; 63% of the seeds developed mature embryos and 79% germinated. However, the cross to western larch females resulted in only 4% filled seed of which 68% germinated. Open-pollinated western larch and alpine larch averaged 26 and 32% filled seed with 48 and 44% germination, respectively. Less than 1% of the alpine larch hypocotyls were reddish in color; most of them were green. About 15% of the western larch and about 17% of the hybrids from alpine larch females had reddish hypocotyls, whereas hybrids from western larch females were intermediate between western larch and alpine larch. Hybrid seed began germinating before the parental types and initial height growth exceeded that of the parental types. However, 4 months following germination, western larch seedlings were ca. four times taller than the hybrids and 10 times taller than alpine larch. Stems of hybrids were significantly thicker than those of either western larch or alpine larch. Hybrid seedlings are robust, stocky, and may be useful in revegetating cold, moist sites between the elevational ranges of alpine and western larch.
Larix kaempferi
Cite
Citations (9)
Larix gmelinii
Cite
Citations (0)
Primer (cosmetics)
Cite
Citations (9)
The modern literature on dendrology recognizes and describes 3 species of larch: Gmelin (Daurian) larch (L. gmelinii (Rupr) Rupr), Kayander larch (L. cajanderi Mayr.) and Olginsky larch (Larix olgensis A. Henry). However, Far Eastern foresters-researchers believe that the Lyubarsky larch, described in 1931 by V.N. Sukachev, grows on the territory of Primorsky Krai. The article presents research data on the current state of the Olginskaya larch (Lyubarsky larch) biogroups on the territory of the Borisov Plateau in Primorsky Krai. The Olginsky larch vegetation area and the grass cover of the territory is described in detail. The characteristics of the stand are given according to taxation indicators: origin, composition divided into stories (by weight and number of trees), age, forest density, average height and diameter, bonus, sum of cross-sectional areas, stock. The measurement results of 100 larch trees (diameter and height) were processed in the Exel STATISTIKA program. The age of the stand was determined, the influence of the average annual temperature and the annual amount of precipitation on the growth of larch in diameter was analyzed. The dynamics of the growth of model trees in diameter is analyzed. It has been established that the Olginskaya larch under the conditions of the Borisov Plateau shows negative growth rates in diameter with a lack and excess of moisture, and also at high temperatures the growth rates decrease. The analysis showed that in the conditions of the Borisov plateau there is a general dependence of the increments in diameter on climatic factors. Larch trees growing in the same micro-conditions showed completely different growth rates, which is obviously explained by genetic differences.
Larix gmelinii
Cite
Citations (0)
Different hybridized combinations between intraspecies and interspecies of larches showed different heterosis,and genetic characteristics could be maintained by asexual propagation.The results of experiments on growth and cuttings of superior families of hybrid larches in 3 successive years indicated that the best hybridized combinations were Korean Larch 14×Japanese Larch and Korean Larch 4c×Japanese Larch,the rooting rates of cuttings and development of root systems were increased compared with maternal plants,which indicated that hybridization of Korean Larch with Japanese Larch increased not only growth but also rooting characteristics.Japanese Larch yong8×Korean Larch increased not only growth but also rooting characteristics compared with maternal plants.However, the number of roots and the length of the longest root were lower than Korean Larch×Japanese Larch compared with hybridized combinations of Korean Larch ×Japanese Larch except for growth of 3 years was higher and the rooting rates were lower than Korean Larch 14×Japanese Larch and Korean Larch 4c×Japanese Larch.So much emphasis should be put on higher rooting rates in selection of superior clones.Propagation of cuttings of hybrid larches could bring the inheritance potentials into full play.The heritability for most characteristics was much higher except for lower heritability of one-side rooting percentage,thus stability of superior genetic characteristics of maternal plants were maintained.
Cutting
Vegetative reproduction
Cite
Citations (0)
A cDNA library from the amur grape(Vitis amurensis Rupr.) was constructed by using Creator~(TM) SMART~(TM) cDNA Library Construction protocol.The library capacity was 1.001×10~6 with a recombinant rate of 94.11%and the inserted cDNA fragments ranged from 0.25 to 1.9 kb.935 available ESTs through random sequencing were obtained,and 636 unigenes which including 98 contigs and 201 singlets were generated after clustering.This study is propitious to gene cloning and functional genomic research of amur grape.
Cloning (programming)
Cite
Citations (0)