Ruņģis, D., Veinberga, I., Voronova-Petrova, A, Daugavietis, M. (2010). Correlation of allelic co... more Ruņģis, D., Veinberga, I., Voronova-Petrova, A, Daugavietis, M. (2010). Correlation of allelic content with tree characteristics in a hybrid alder stand. Mežzinātne | Forest Science 21(54): 56-64.
Vilnis Šķipars 1 *, Tālis Gaitnieks 1 , Dainis Edgars Ruņģis 1 Šķipars, V., Gaitnieks, T., Ruņģis... more Vilnis Šķipars 1 *, Tālis Gaitnieks 1 , Dainis Edgars Ruņģis 1 Šķipars, V., Gaitnieks, T., Ruņģis, D. E. (2011). Evaluation of pigmentation caused by diff erent Heterobasidion annosum (Fr.) Bref. strains aft er under-bark inoculation of Scots pine. Mežzinātne 24(57): 65-77. Kopsavilkums. Lai novērtētu iespējamās atšķirības individuālu koku rezistencē pret Heterobasidion annosum (Fr.) Bref. un dažādu H. annosum izolātu agresivitāti pret saimniekorganismu, deviņi parastās priedes koki inokulēti ar H. annosum izolātu 358, kas raksturots kā agresīvāks H. annosum izolāts, un 20 koki inokulēti ar H. annosum izolātu I Sm 15 92. Izmantota zemmizas inokulācijas metode: 30-40 dienas pēc inokulēšanas novērtēta H. annosum izolāta izraisītā pigmentācija, nosakot vidējo pigmentācijas garumu koksnē uz augšu un uz leju no inokulācijas vietas. Noskaidrots, ka infi cēšanai izmantotais izolāts būtiski (p = 0,001) ietekmējis pigmentācijas garumu. Salīdzinot datus par pigmentācijas garumu dažādu ģimeņu kokos, secināts, ka pastāv būtiska (p = 0,017) atšķirība starp ģimenēm Sm3 un Ja3. Šis ir pirmais pētnieciskais darbs, kurā aprakstīta pieaugušu parastās priedes koku izmantošana H. annosum izolātu agresivitātes pret saimniekorganismu novērtēšanai. Nozīmīgākie vārdi: Heterobasidion annosum, Pinus sylvestris, rezistence, pigmentācija. ••• Šķipars, V. 2 *, Gaitnieks, T. 2 , Ruņģis, D. E. 2
28 pielietošana selekcijā arī paplašina mainības ietvarus, paaugstina augu plastiskumu un izturīb... more 28 pielietošana selekcijā arī paplašina mainības ietvarus, paaugstina augu plastiskumu un izturību pret nelabvēlīgiem biotiskiem un abiotiskiem apstākĜiem. Pētījuma mērėis ir izpētīt un optimizēt poliploīdijas pielietošanas iespējas liliju selekcijā, apstrādājot liliju sīpolu zvīĦlapas ar 0.1, 0.5 un 1 g kg -1 kolhicīna šėīdumu un 0.05, 0.1 un 0.5 g kg -1 orizalīna šėīdumu.
Saussurea esthonica is an endangered species included in the Red Data Book of Latvia and the Red ... more Saussurea esthonica is an endangered species included in the Red Data Book of Latvia and the Red Data Book of the Baltic Region. It is found only in Latvia, Estonia and the Leningrad region of Russia. Genetic diversity and differentiation was studied in two Latvian and two Estonian Saussurea esthonica populations using a retrotransposon-based inter-primer binding site method. Analysis of molecular variation showed that most of the variation was found within populations; variation between populations was 3 to 5% and among regions 10 to 13%. Analysis did not detect low levels of genetic diversity parameters of the Latvian populations, indicating that they are currently genetically robust.
There is a long history of flax cultivation in Latvia, and breeding programs were active until 19... more There is a long history of flax cultivation in Latvia, and breeding programs were active until 1970's, when flax breeding in Latvia was halted. Since 1992, the Agriculture Science Centre of Latgale (ASCL) has repatriated Latvian flax germplasm from various genebanks, as well as renewed limited breeding activities in flax. Currently, the ASCL holds a collection of 497 flax accessions, as well as 9865 accessions of various lines and hybrids developed at the LLZC since 1993. To assist in the characterization of this Latvian flax germplasm, we have utilised DNA markers to assess genetic diversity and relatedness, as well as surveying functional polymorphism. We have utilised Simple sequence repeat (SSR) markers developed from both genomic libraries as well as expressed sequences. The results of the DNA marker survey were utilised to determine the genetic polymorphism and relatedness within Latvian flax germplasm, and these results were compared with the analysis of agronomic traits carried out in field trials at the ASCL. The development of DNA markers linked to traits of agronomic importance will assist in the development of a Latvian flax breeding program. The use of DNA marker technology will allow more efficient assessment and rational utilization of Latvian flax germplasm.
Saussurea esthonica Baer ex Rupr. is a species of the genus Saussurea that is found in Estonia, L... more Saussurea esthonica Baer ex Rupr. is a species of the genus Saussurea that is found in Estonia, Latvia and the Leningrad region in Russia. Only two populations have been identified in Latvia, and it is protected at the national level. The taxonomic relationships within this genus are unclear, and the majority of phylogenetic studies of this genus have been undertaken on species found in Asia. The relationship of S. esthonica to the other Saussurea species is equally unclear, with some suggestions that this species should be regarded as a subspecies of S. alpina. Two different molecular marker techniques, iPBS and ITS sequencing, were utilised to investigate the phylogeny of S. esthonica and its relationship with other Saussurea species, including three European species: S. alpina, S. pygmaea and S. discolor. The phylogeny obtained with the iPBS markers was similar to that obtained with the ITS sequences. The phylogenies obtained were broadly consistent with previous morphological classification, with S. alpina, S. esthonica and S. discolor clustering together. S. pulchella, S. albescens and S. candicans also formed one discrete cluster. The taxonomic status of S. esthonica was not unambiguously determined, with Norwegian and Italian S. alpina populations clustering with Latvian and Estonian S. esthonica populations, and the Austrian S. alpina populations clustering with Austrian S. discolor populations.
Mobile genetic elements, or transposable elements, are ubiquitous components of plant genomes, an... more Mobile genetic elements, or transposable elements, are ubiquitous components of plant genomes, and in pine these sequences have been estimated to comprise up to 70 % of the genome. Retrotransposon activity can be a major factor in genome instability, rearrangements and therefore also plasticity of the genome and adaptation to changing environmental conditions. Plant retrotransposons have been shown to be activated under stress conditions. In our study we demonstrate transcriptional activation of many non-specific retrotransposon-like sequences in Scots pine (Pinus sylvestris) after exposure to heat stress. Active retrotransposons have not been described in gymnosperms, one of the most ancient plant groups. Our results suggest the existence of several groups of active retrotransposons in the Scots pine genome, which share different levels of similarity with known retro-elements from other plant species. Further studies of retrotransposon activation in pine are needed to increase understanding of their possible function and evolution.
Ieviņš Ģ. 2010. Preliminary studies on the genetic diversity of an endemic and endangered species... more Ieviņš Ģ. 2010. Preliminary studies on the genetic diversity of an endemic and endangered species Saussurea esthonica Baer ex Rupr. in Latvia. Acta Biol. Univ. Daugavp., 10(1): 37-42. Saussurea esthonica Baer ex Rupr. is a perennial species included in the Red Data Book of Latvia, Red Data Book of the Baltic Region and EU Habitats Directive Annex II. It is important to maintain genetic diversity within and between populations for conservation of this species in Latvia. There are two known populations of S. esthonica in Latvia -in the protected wetlands in the vicinity of Apšuciems and Pope.
Neimane, U., Veinberga, I., . Phenotypic and genetic aspects of geographical diff erences in Scot... more Neimane, U., Veinberga, I., . Phenotypic and genetic aspects of geographical diff erences in Scots pine populations of Latvia. Mežzinātne / Forest Science 20(53): 3-15.
Extensive genome resources have now been developed for both spruce and pine. However as other tec... more Extensive genome resources have now been developed for both spruce and pine. However as other technologies develop and costs drop, other resources become feasible. One such resource, not yet available in conifers, is collecting complete cDNA sequences (full length messenger RNA transcripts). We describe our approach for obtaining such sequences and the importance of this resource. Second, existing resources and new technologies are allowing new approaches in functional and comparative genomics. In functional genomics, new technologies and the integration of mRNA, protein and metabolite expression profiling promises to improve the identification of gene function, interaction and regulation. In comparative genomics, an apparent slowdown of evolutionary rate in the pine family should allow genome information to be easily transferred between spruce and pine (and other members of the pine family). Ultimately, genomics research should impact practical problems and traits in breeding and management programs. In our own program, we target spruce resistance mechanisms to the spruce weevil, a serious pest in British Columbia.
ABSTRACT Apple cultivars are an integral part of the Latvian State Program for Preservation and S... more ABSTRACT Apple cultivars are an integral part of the Latvian State Program for Preservation and Sustainable Use of Genetic Resources for Food and Agriculture. Latvian apple (n = 109) cultivars of local origin, nominated as National Plant Genetic Resources, were analyzed with eight simple sequence repeat (SSR) markers recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR) Malus/Pyrus working group and a marker for scab resistance gene (Vf). All SSR loci exhibited a high level of polymorphism – 12 to 39 alleles, 18.75 in average, with high observed heterozygosity (Ho) ranging from 0.64 to 0.89 and a mean of 0.78. The gene diversity (polymorphism information content value) varied from 0.79 to 0.90, with an average of 0.86. All cultivars could be distinguished with the tested set of SSR loci, with a high frequency of rare (38%) or unique (26%) alleles. For the Vf gene, all three possible genotypes (VfVf, Vfvf and vfvf) were detected for 1, 6 and 102 varieties, respectively. The analyzed germplasm showed high genetic diversity, particularly landraces, while the modern cultivars clustered mainly into two groups. Cluster analysis did not reveal a clear pattern with well-defined groups, but confirmed some relationships based on known or putative pedigrees, as well as suggesting the possible parentage of some cultivars.
Kopsavilkums: Parastās priedes (Pinus sylvestris L.) populāciju ziedēšanas fenoloģiskās īpatnības... more Kopsavilkums: Parastās priedes (Pinus sylvestris L.) populāciju ziedēšanas fenoloģiskās īpatnības pētītas, 2008. gada pavasarī veicot novērojumus divās priežu sēklu plantācijās -Dravu plantācijā Latvijas rietumdaļā (pārstāvēti 65 Misas populācijas kloni) un Sāvienas plantācijā Latvijas austrumdaļā (pārstāvēti 76 Misas un 86 Smiltenes populācijas kloni). Fenoloģiskie novērojumi veikti 6 reizes laika periodā no 12. maija līdz 3. jūnijam. Katrā novērojumu reizē reģistrēta sievišķo un vīrišķo strobilu ziedēšanas fenoloģiskā fāze. Pēc sievišķo strobilu ziedēšanas kloni klasifi cēti piecās grupās (izteikti vēlu ziedošs, vēlu, vidēji, agri un izteikti agri ziedošs), pēc vīrišķo strobilu ziedēšanas -trīs grupās (vēlu, vidēji, agri ziedošs). Konstatēts, ka pastāv nozīmīgas ziedēšanas fenoloģiskās atšķirības gan starp dažādām populācijām, gan starp vienas populācijas atsevišķiem kokiem. Aptuveni puse klonu pieskaitāmi grupai "vidēji ziedošs". Kopumā apstiprinājies pieņēmums, ka atšķirīgos augšanas apstākļos vienas populācijas agri un vēlu ziedošie kloni saglabā savas fenoloģiskās īpatnības (Misas kloni Sāvienas un Dravu plantācijās), un vienādos augšanas apstākļos atšķiras dažādu populāciju pēcnācēju ziedēšanas laiks (Misas un Smiltenes kloni Sāvienas plantācijā). Tātad pamatoti uzskatīt, ka šīs īpatnības, vismaz daļēji, ir ģenētiski nosacītas. Ģenētisko atšķirību noskaidrošanai starp dažādām ziedēšanas dinamikas grupām, veikta Misas klonu DNS analīze, izmantojot hloroplastu marķierus: rezultātā ne starp sievišķās, ne vīrišķās ziedēšanas dinamikas grupām atšķirības netika konstatētas, ko varētu skaidrot tādējādi, ka hloroplastu marķieri ir "neitrāli", un tie nav saistīti ar morfoloģiskajām un fenoloģiskajām pazīmēm. Tādēļ turpmākajos fenoloģisko īpatnību pētījumos būtu nosakāma ziedēšanā iesaistīto gēnu ekspresija un alēļu atšķirības.
In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), tw... more In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for EST-SSRs. One database was from "interior spruce" (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.
... Paglia et al. (1998) built another single-tree ge-netic linkage map of Norway spruce using al... more ... Paglia et al. (1998) built another single-tree ge-netic linkage map of Norway spruce using also a panel of 72 megagametophytes with a total of 447 segregat-ing markers [366 AFLPs, 20 selectively amplified mi-crosatellite polymorphic loci (SAMPLs), and 61 SSRs] covering a ...
A single-strand specific (sss) nuclease, found in extracts of celery juice, can be used to digest... more A single-strand specific (sss) nuclease, found in extracts of celery juice, can be used to digest heteroduplex DNA and hence identify heterozygous single nucleotide polymorphism (SNP) sites in PCR products. Here we show this method can be used to map specific genes with relative simplicity and low cost. A particular nucleotide substitution does not need to be identified, and in fact, a priori knowledge of the presence of a SNP is not required, as the entire length of the PCR product is interrogated for the presence of SNPs. This characteristic enables application of this technique to genomes that are not well characterized with regard to SNP polymorphism, and for rapidly placing particular genes onto linkage maps. While this technique is best suited for mapping markers in a backcross configuration, we show that in an F 2 configuration, where alternative homozygotes cannot be discerned by this technique, data are still relatively informative about linkage.
Traditionally, simple sequence repeat (SSR) markers have been developed from libraries of genomic... more Traditionally, simple sequence repeat (SSR) markers have been developed from libraries of genomic DNA. However, the large, repetitive nature of conifer genomes makes development of robust, single-copy SSR markers from genomic DNA difficult. Expressed sequence tags (ESTs), or sequences of messenger RNA, offer the opportunity to exploit single, low-copy, conserved sequence motifs for SSR development. From a 20,275unigene spruce EST set, we identified 44 candidate EST-SSR markers. Of these, 25 amplified and were polymorphic in white, Sitka, and black spruce; 20 amplified in all 23 spruce species tested; the remaining five amplified in all except one species. In addition, 101 previously described spruce SSRs (mostly developed from genomic DNA), were tested. Of these, 17 amplified across white, Sitka, and black spruce. The 25 EST-SSRs had approximately 9% less heterozygosity than the 17 genomicderived SSRs (mean H=0.65 vs 0.72), but appeared to have less null alleles, as evidenced by much lower apparent inbreeding (mean F=0.046 vs 0.126). These robust SSRs are of particular use in comparative studies, and as the EST-SSRs are within the expressed portion of the genome, they are more likely to be associated with a particular gene of interest, improving their utility for quantitative trait loci mapping and allowing detection of selective sweeps at specific genes.
Ruņģis, D., Veinberga, I., Voronova-Petrova, A, Daugavietis, M. (2010). Correlation of allelic co... more Ruņģis, D., Veinberga, I., Voronova-Petrova, A, Daugavietis, M. (2010). Correlation of allelic content with tree characteristics in a hybrid alder stand. Mežzinātne | Forest Science 21(54): 56-64.
Vilnis Šķipars 1 *, Tālis Gaitnieks 1 , Dainis Edgars Ruņģis 1 Šķipars, V., Gaitnieks, T., Ruņģis... more Vilnis Šķipars 1 *, Tālis Gaitnieks 1 , Dainis Edgars Ruņģis 1 Šķipars, V., Gaitnieks, T., Ruņģis, D. E. (2011). Evaluation of pigmentation caused by diff erent Heterobasidion annosum (Fr.) Bref. strains aft er under-bark inoculation of Scots pine. Mežzinātne 24(57): 65-77. Kopsavilkums. Lai novērtētu iespējamās atšķirības individuālu koku rezistencē pret Heterobasidion annosum (Fr.) Bref. un dažādu H. annosum izolātu agresivitāti pret saimniekorganismu, deviņi parastās priedes koki inokulēti ar H. annosum izolātu 358, kas raksturots kā agresīvāks H. annosum izolāts, un 20 koki inokulēti ar H. annosum izolātu I Sm 15 92. Izmantota zemmizas inokulācijas metode: 30-40 dienas pēc inokulēšanas novērtēta H. annosum izolāta izraisītā pigmentācija, nosakot vidējo pigmentācijas garumu koksnē uz augšu un uz leju no inokulācijas vietas. Noskaidrots, ka infi cēšanai izmantotais izolāts būtiski (p = 0,001) ietekmējis pigmentācijas garumu. Salīdzinot datus par pigmentācijas garumu dažādu ģimeņu kokos, secināts, ka pastāv būtiska (p = 0,017) atšķirība starp ģimenēm Sm3 un Ja3. Šis ir pirmais pētnieciskais darbs, kurā aprakstīta pieaugušu parastās priedes koku izmantošana H. annosum izolātu agresivitātes pret saimniekorganismu novērtēšanai. Nozīmīgākie vārdi: Heterobasidion annosum, Pinus sylvestris, rezistence, pigmentācija. ••• Šķipars, V. 2 *, Gaitnieks, T. 2 , Ruņģis, D. E. 2
28 pielietošana selekcijā arī paplašina mainības ietvarus, paaugstina augu plastiskumu un izturīb... more 28 pielietošana selekcijā arī paplašina mainības ietvarus, paaugstina augu plastiskumu un izturību pret nelabvēlīgiem biotiskiem un abiotiskiem apstākĜiem. Pētījuma mērėis ir izpētīt un optimizēt poliploīdijas pielietošanas iespējas liliju selekcijā, apstrādājot liliju sīpolu zvīĦlapas ar 0.1, 0.5 un 1 g kg -1 kolhicīna šėīdumu un 0.05, 0.1 un 0.5 g kg -1 orizalīna šėīdumu.
Saussurea esthonica is an endangered species included in the Red Data Book of Latvia and the Red ... more Saussurea esthonica is an endangered species included in the Red Data Book of Latvia and the Red Data Book of the Baltic Region. It is found only in Latvia, Estonia and the Leningrad region of Russia. Genetic diversity and differentiation was studied in two Latvian and two Estonian Saussurea esthonica populations using a retrotransposon-based inter-primer binding site method. Analysis of molecular variation showed that most of the variation was found within populations; variation between populations was 3 to 5% and among regions 10 to 13%. Analysis did not detect low levels of genetic diversity parameters of the Latvian populations, indicating that they are currently genetically robust.
There is a long history of flax cultivation in Latvia, and breeding programs were active until 19... more There is a long history of flax cultivation in Latvia, and breeding programs were active until 1970's, when flax breeding in Latvia was halted. Since 1992, the Agriculture Science Centre of Latgale (ASCL) has repatriated Latvian flax germplasm from various genebanks, as well as renewed limited breeding activities in flax. Currently, the ASCL holds a collection of 497 flax accessions, as well as 9865 accessions of various lines and hybrids developed at the LLZC since 1993. To assist in the characterization of this Latvian flax germplasm, we have utilised DNA markers to assess genetic diversity and relatedness, as well as surveying functional polymorphism. We have utilised Simple sequence repeat (SSR) markers developed from both genomic libraries as well as expressed sequences. The results of the DNA marker survey were utilised to determine the genetic polymorphism and relatedness within Latvian flax germplasm, and these results were compared with the analysis of agronomic traits carried out in field trials at the ASCL. The development of DNA markers linked to traits of agronomic importance will assist in the development of a Latvian flax breeding program. The use of DNA marker technology will allow more efficient assessment and rational utilization of Latvian flax germplasm.
Saussurea esthonica Baer ex Rupr. is a species of the genus Saussurea that is found in Estonia, L... more Saussurea esthonica Baer ex Rupr. is a species of the genus Saussurea that is found in Estonia, Latvia and the Leningrad region in Russia. Only two populations have been identified in Latvia, and it is protected at the national level. The taxonomic relationships within this genus are unclear, and the majority of phylogenetic studies of this genus have been undertaken on species found in Asia. The relationship of S. esthonica to the other Saussurea species is equally unclear, with some suggestions that this species should be regarded as a subspecies of S. alpina. Two different molecular marker techniques, iPBS and ITS sequencing, were utilised to investigate the phylogeny of S. esthonica and its relationship with other Saussurea species, including three European species: S. alpina, S. pygmaea and S. discolor. The phylogeny obtained with the iPBS markers was similar to that obtained with the ITS sequences. The phylogenies obtained were broadly consistent with previous morphological classification, with S. alpina, S. esthonica and S. discolor clustering together. S. pulchella, S. albescens and S. candicans also formed one discrete cluster. The taxonomic status of S. esthonica was not unambiguously determined, with Norwegian and Italian S. alpina populations clustering with Latvian and Estonian S. esthonica populations, and the Austrian S. alpina populations clustering with Austrian S. discolor populations.
Mobile genetic elements, or transposable elements, are ubiquitous components of plant genomes, an... more Mobile genetic elements, or transposable elements, are ubiquitous components of plant genomes, and in pine these sequences have been estimated to comprise up to 70 % of the genome. Retrotransposon activity can be a major factor in genome instability, rearrangements and therefore also plasticity of the genome and adaptation to changing environmental conditions. Plant retrotransposons have been shown to be activated under stress conditions. In our study we demonstrate transcriptional activation of many non-specific retrotransposon-like sequences in Scots pine (Pinus sylvestris) after exposure to heat stress. Active retrotransposons have not been described in gymnosperms, one of the most ancient plant groups. Our results suggest the existence of several groups of active retrotransposons in the Scots pine genome, which share different levels of similarity with known retro-elements from other plant species. Further studies of retrotransposon activation in pine are needed to increase understanding of their possible function and evolution.
Ieviņš Ģ. 2010. Preliminary studies on the genetic diversity of an endemic and endangered species... more Ieviņš Ģ. 2010. Preliminary studies on the genetic diversity of an endemic and endangered species Saussurea esthonica Baer ex Rupr. in Latvia. Acta Biol. Univ. Daugavp., 10(1): 37-42. Saussurea esthonica Baer ex Rupr. is a perennial species included in the Red Data Book of Latvia, Red Data Book of the Baltic Region and EU Habitats Directive Annex II. It is important to maintain genetic diversity within and between populations for conservation of this species in Latvia. There are two known populations of S. esthonica in Latvia -in the protected wetlands in the vicinity of Apšuciems and Pope.
Neimane, U., Veinberga, I., . Phenotypic and genetic aspects of geographical diff erences in Scot... more Neimane, U., Veinberga, I., . Phenotypic and genetic aspects of geographical diff erences in Scots pine populations of Latvia. Mežzinātne / Forest Science 20(53): 3-15.
Extensive genome resources have now been developed for both spruce and pine. However as other tec... more Extensive genome resources have now been developed for both spruce and pine. However as other technologies develop and costs drop, other resources become feasible. One such resource, not yet available in conifers, is collecting complete cDNA sequences (full length messenger RNA transcripts). We describe our approach for obtaining such sequences and the importance of this resource. Second, existing resources and new technologies are allowing new approaches in functional and comparative genomics. In functional genomics, new technologies and the integration of mRNA, protein and metabolite expression profiling promises to improve the identification of gene function, interaction and regulation. In comparative genomics, an apparent slowdown of evolutionary rate in the pine family should allow genome information to be easily transferred between spruce and pine (and other members of the pine family). Ultimately, genomics research should impact practical problems and traits in breeding and management programs. In our own program, we target spruce resistance mechanisms to the spruce weevil, a serious pest in British Columbia.
ABSTRACT Apple cultivars are an integral part of the Latvian State Program for Preservation and S... more ABSTRACT Apple cultivars are an integral part of the Latvian State Program for Preservation and Sustainable Use of Genetic Resources for Food and Agriculture. Latvian apple (n = 109) cultivars of local origin, nominated as National Plant Genetic Resources, were analyzed with eight simple sequence repeat (SSR) markers recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR) Malus/Pyrus working group and a marker for scab resistance gene (Vf). All SSR loci exhibited a high level of polymorphism – 12 to 39 alleles, 18.75 in average, with high observed heterozygosity (Ho) ranging from 0.64 to 0.89 and a mean of 0.78. The gene diversity (polymorphism information content value) varied from 0.79 to 0.90, with an average of 0.86. All cultivars could be distinguished with the tested set of SSR loci, with a high frequency of rare (38%) or unique (26%) alleles. For the Vf gene, all three possible genotypes (VfVf, Vfvf and vfvf) were detected for 1, 6 and 102 varieties, respectively. The analyzed germplasm showed high genetic diversity, particularly landraces, while the modern cultivars clustered mainly into two groups. Cluster analysis did not reveal a clear pattern with well-defined groups, but confirmed some relationships based on known or putative pedigrees, as well as suggesting the possible parentage of some cultivars.
Kopsavilkums: Parastās priedes (Pinus sylvestris L.) populāciju ziedēšanas fenoloģiskās īpatnības... more Kopsavilkums: Parastās priedes (Pinus sylvestris L.) populāciju ziedēšanas fenoloģiskās īpatnības pētītas, 2008. gada pavasarī veicot novērojumus divās priežu sēklu plantācijās -Dravu plantācijā Latvijas rietumdaļā (pārstāvēti 65 Misas populācijas kloni) un Sāvienas plantācijā Latvijas austrumdaļā (pārstāvēti 76 Misas un 86 Smiltenes populācijas kloni). Fenoloģiskie novērojumi veikti 6 reizes laika periodā no 12. maija līdz 3. jūnijam. Katrā novērojumu reizē reģistrēta sievišķo un vīrišķo strobilu ziedēšanas fenoloģiskā fāze. Pēc sievišķo strobilu ziedēšanas kloni klasifi cēti piecās grupās (izteikti vēlu ziedošs, vēlu, vidēji, agri un izteikti agri ziedošs), pēc vīrišķo strobilu ziedēšanas -trīs grupās (vēlu, vidēji, agri ziedošs). Konstatēts, ka pastāv nozīmīgas ziedēšanas fenoloģiskās atšķirības gan starp dažādām populācijām, gan starp vienas populācijas atsevišķiem kokiem. Aptuveni puse klonu pieskaitāmi grupai "vidēji ziedošs". Kopumā apstiprinājies pieņēmums, ka atšķirīgos augšanas apstākļos vienas populācijas agri un vēlu ziedošie kloni saglabā savas fenoloģiskās īpatnības (Misas kloni Sāvienas un Dravu plantācijās), un vienādos augšanas apstākļos atšķiras dažādu populāciju pēcnācēju ziedēšanas laiks (Misas un Smiltenes kloni Sāvienas plantācijā). Tātad pamatoti uzskatīt, ka šīs īpatnības, vismaz daļēji, ir ģenētiski nosacītas. Ģenētisko atšķirību noskaidrošanai starp dažādām ziedēšanas dinamikas grupām, veikta Misas klonu DNS analīze, izmantojot hloroplastu marķierus: rezultātā ne starp sievišķās, ne vīrišķās ziedēšanas dinamikas grupām atšķirības netika konstatētas, ko varētu skaidrot tādējādi, ka hloroplastu marķieri ir "neitrāli", un tie nav saistīti ar morfoloģiskajām un fenoloģiskajām pazīmēm. Tādēļ turpmākajos fenoloģisko īpatnību pētījumos būtu nosakāma ziedēšanā iesaistīto gēnu ekspresija un alēļu atšķirības.
In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), tw... more In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for EST-SSRs. One database was from "interior spruce" (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.
... Paglia et al. (1998) built another single-tree ge-netic linkage map of Norway spruce using al... more ... Paglia et al. (1998) built another single-tree ge-netic linkage map of Norway spruce using also a panel of 72 megagametophytes with a total of 447 segregat-ing markers [366 AFLPs, 20 selectively amplified mi-crosatellite polymorphic loci (SAMPLs), and 61 SSRs] covering a ...
A single-strand specific (sss) nuclease, found in extracts of celery juice, can be used to digest... more A single-strand specific (sss) nuclease, found in extracts of celery juice, can be used to digest heteroduplex DNA and hence identify heterozygous single nucleotide polymorphism (SNP) sites in PCR products. Here we show this method can be used to map specific genes with relative simplicity and low cost. A particular nucleotide substitution does not need to be identified, and in fact, a priori knowledge of the presence of a SNP is not required, as the entire length of the PCR product is interrogated for the presence of SNPs. This characteristic enables application of this technique to genomes that are not well characterized with regard to SNP polymorphism, and for rapidly placing particular genes onto linkage maps. While this technique is best suited for mapping markers in a backcross configuration, we show that in an F 2 configuration, where alternative homozygotes cannot be discerned by this technique, data are still relatively informative about linkage.
Traditionally, simple sequence repeat (SSR) markers have been developed from libraries of genomic... more Traditionally, simple sequence repeat (SSR) markers have been developed from libraries of genomic DNA. However, the large, repetitive nature of conifer genomes makes development of robust, single-copy SSR markers from genomic DNA difficult. Expressed sequence tags (ESTs), or sequences of messenger RNA, offer the opportunity to exploit single, low-copy, conserved sequence motifs for SSR development. From a 20,275unigene spruce EST set, we identified 44 candidate EST-SSR markers. Of these, 25 amplified and were polymorphic in white, Sitka, and black spruce; 20 amplified in all 23 spruce species tested; the remaining five amplified in all except one species. In addition, 101 previously described spruce SSRs (mostly developed from genomic DNA), were tested. Of these, 17 amplified across white, Sitka, and black spruce. The 25 EST-SSRs had approximately 9% less heterozygosity than the 17 genomicderived SSRs (mean H=0.65 vs 0.72), but appeared to have less null alleles, as evidenced by much lower apparent inbreeding (mean F=0.046 vs 0.126). These robust SSRs are of particular use in comparative studies, and as the EST-SSRs are within the expressed portion of the genome, they are more likely to be associated with a particular gene of interest, improving their utility for quantitative trait loci mapping and allowing detection of selective sweeps at specific genes.
Uploads
Papers by Dainis Rungis