Isolation, characterizaton, and inheritance of microsatellite loci in alpine larch and western larch

Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 439-448 ◽  
Author(s):  
P D Khasa ◽  
C H Newton ◽  
M H Rahman ◽  
B Jaquish ◽  
B P Dancik
Keyword(s):  
Microsatellite Loci ◽  
Related Species ◽  
Enriched Library ◽  
Larix Occidentalis ◽  
Western Larch ◽  
Repeat Sequences ◽  
Improvement Programs ◽  
Controlled Crosses ◽  
Alpine Larch ◽  
Simple Sequence

Microsatellite loci or simple sequence repeat loci (SSRs) were isolated in alpine larch (Larix lyallii Parl.) and western larch (Larix occidentalis Nutt.). In total, 14 SSR loci were characterized; two [(TCT)4, A7] came from published Larix DNA sequence data, one (CA)17 was obtained from a partial non-enriched alpine larch total genomic DNA library, and the remaining 11 loci were obtained from larch genomic DNAs enriched for (CA)n repeats. The SSR regions in these clones could be divided into three categories: perfect repeat sequences without interruption, imperfect repeat sequences with interruption(s), and compound repeat sequences with adjacent tandem simple dinucleotides. Eight of the 14 loci analyzed were found to be polymorphic and useful markers after silver-staining polyacrylamide gel electrophoresis. In addition, several SSR primers developed for alpine larch were able to successfully amplify polymorphic loci in its related species, western larch, and among other closely related taxa within the Larix genus. The inheritance of microsatellite loci was verified by analysis of haploid megagametophyte and diploid embryo tissues of progeny obtained from controlled crosses between western larch and alpine larch. All microsatellite loci analyzed had alleles that segregated according to expected Mendelian frequencies. Two species-specific markers (UAKLly10a and UAKLla1) allow easy and rapid identification of specific genetic entry of alpine larch and western larch at any stage in the sporophyte phase of the life cycle. Therefore, these markers are efficient in identifying the parental species and to validate controlled crosses between these two closely related species. These results are important in tree improvement programs of alpine larch and western larch aimed at producing genetically improved hybrid stock for reforestation in Western Canada and U.S.A.Key words: database search, enriched library, inheritance, Larix, microsatellites, simple sequence repeats, PCR.

scholarly journals Root Growth Potential and Microsite Effects on Conifer Seedling Establishment in Northern Idaho

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 597
Author(s):  
Jacob A. Reely ◽  
Andrew S. Nelson
Keyword(s):  
Root Growth ◽  
Douglas Fir ◽  
Seedling Quality ◽  
Growth Potential ◽  
Larix Occidentalis ◽  
Root Growth Potential ◽  
Western Larch ◽  
Neighborhood Conditions ◽  
Seedling Performance ◽  
Survival And Growth

Environmental conditions and seedling quality interact to produce complex patterns of seedling survival and growth. Root growth potential (RGP) is one metric of seedling quality that can be rapidly measured prior to planting, but the correlation of RGP and seedling performance is not consistent across studies. Site factors including microsite objects that cast shade and competing vegetation can also influence seedling performance. We examined the effects of RGP, presence/absence of a microsite object, and competition cover on the survival and growth of three native conifers to the Inland Northwest, USA, over 5 years. We found that RGP had no effect on the survival or growth of western larch (Larix occidentalis), Douglas fir (Pseudotsuga menziesii var. glauca), and grand fir (Abies grandis) at a mesic north aspect site and a xeric south aspect site. Comparatively, the presence of a microsite increased the odds of survival by 37% for western larch and 158% for grand fir, while the absence of forb cover increased the odds of survival of western larch by 72% and of grand fir by 26%. Douglas fir was less sensitive to microsites and competition. The strong effects of neighborhood conditions around seedlings help inform silvicultural practices to enhance the establishment of western larch and grand fir, including planting seedlings near shading objects and competition control, while these practices may not be as important for Douglas fir.

scholarly journals Генотипирование сортов винограда селекции Института «Магарач» на основе анализа аллельного полиморфизма SSR локусов

2019 ◽  
pp. 289-293
Author(s):  
Svetlana Gorislavets ◽  
Vitalii Volodin ◽  
Gennadii Spotar ◽  
Valentina Risovannaya ◽  
Yakov Alekseev
Keyword(s):  
Genetic Variation ◽  
Simple Sequence Repeats ◽  
Microsatellite Loci ◽  
Molecular Genetic ◽  
Information Value ◽  
International Standards ◽  
Agricultural Crops ◽  
Ssr Analysis ◽  
Short Period ◽  
Simple Sequence

Обязательными условиями успешного сохранения и использования различных сортов сельскохозяйственных культур является идентификация и контроль генетической изменчивости сортов, для изучения которой используются различные методы, в том числе методы молекулярно-генетического анализа. В связи с быстрым развитием селекции, ежегодно появляются десятки новых сортов винограда, требующих паспортизации. Молекулярные маркеры могут способствовать подбору родительских пар для скрещивания, повышению точности и ускорению селекционного процесса, так как идентификация исходного материала с использованием молекулярных маркеров и анализ результатов скрещивания могут быть выполнены в достаточно короткий период. К наиболее информативным молекулярным маркерам относятся микросателлитные маркеры, основанные на анализе простых повторяющихся повторов (simple sequence repeats, SSR). Анализ полиморфизма SSR локусов позволяет изучить генетическую изменчивость сельскохозяйственных культур на уровне генома. Цель нашего исследования - генотипирование, оценка аллельного разнообразия и ДНК-паспортизация ряда сортов винограда селекции Института «Магарач» на основе SSR анализа. Основной метод, использованный в работе, - полимеразная цепная реакция (ПЦР) и фрагментный анализ продуктов ПЦР на генетическом анализаторе ABI 3130. В результате фрагментного анализа были генотипированы 8 селекционных сортов Института «Магарач» по 9 ядерным микросателлитным локусам (nSSR). Размеры аллелей оценены с помощью программы Gene Mapper v. 4.0. Полиморфизм микросателлитных локусов и генетическое разнообразие рассчитано с использованием программы Popgene (v. 1.32). Сравнительный анализ nSSR профилей ДНК изученных сортов позволил установить, что все сорта имеют уникальные профили. Всего идентифицировано 69 аллелей, среднее число аллелей - 7,67 аллелей/локус. На основании размеров аллелей составлены индивидуальные молекулярно-генетические паспорта в соответствии с международными стандартами.Identification and control of genetic variation of different varieties of agricultural crops enter as prerequisites for their efficient conservation and use. Genetic variation is investigated by means of a wide set of methods, including those relying on molecular-genetic analysis. Every year, dozens of new breedings of grapevine come into being, and their passportization is necessary. Molecular markets can promote selection of parent pairs for crossing, improve efficiency of breeding and accelerate the process as enable both identification of the initial material and analysis of crossing results to be done in a sufficiently short period of time. The highest information value is associated with microsatellite markers consisting of simple sequence repeats (SSR). Analysis of polymorphism of SSR loci allows to investigate genetic variation of agricultural crops at the level of genome. The goals of the study were to conduct genotyping of a number of grape breedings developed by the Institute Magarach, to assess their allelic diversity and to achieve DNA passportization based on SSR analysis. Polymerase chain reaction (PCR) and fragment analysis of PCR products with the use of a genetic analizer ABI 3130 were the main methods the study relied upon. As a result of the aforesaid analysis, eight new breedings of the Institute were genotyped for nine nuclear microsatellite loci (nSSR). The sizes of alleles were assessed using Gene Mapper v. 4.0 software. Popgene (v. 1.32) software was used to calculate polymorphism of microsatellite loci and genetic diversity. A comparative nSSR-analysis of DNA-profiles of the study varieties indicated that all of them had unique profiles. A total of 69 alleles were identified, with 7.67 alleles per locus on an average. Based on the sizes of the alleles, individual molecular-genetic passports of the varieties were made, in accordance with international standards.

scholarly journals Developing Microsatellite DNA Markers in Pecan

2003 ◽  
Vol 128 (3) ◽  
pp. 374-380 ◽  
Author(s):  
L.J. Grauke ◽  
Muhammad J. Iqbal ◽  
Avutu S. Reddy ◽  
Tommy E. Thompson
Keyword(s):  
Dna Markers ◽  
Microsatellite Dna ◽  
Southern Hybridization ◽  
Genomic Library ◽  
Carya Illinoinensis ◽  
Enriched Library ◽  
Microsatellite Dna Markers ◽  
Ssr Primers ◽  
Nucleotide Repeats ◽  
Simple Sequence

A microsatellite-enriched library was developed from `Halbert', a native pecan [Carya illinoinensis (Wangenh.) K. Koch] selection from Coleman County, Texas. A genomic library enriched for simple sequence repeats (SSR) containing 6144 clones was archived in 384 well plates for screening. In total, 439 clones were identified after Southern hybridization using di- and tri-nucleotide repeats as probes. In total, 125 positive clones were sequenced and primers were designed for 24 repeats. The SSR markers chosen for analysis include di-(CT and GA) and tri-nucleotide repeats (CTT, GAA and GAT). Of the 24 primer pairs tested, 19 successfully amplified microsatellites from `Halbert'. DNA was isolated from 48 pecan and hickory accessions selected to strategically represent the genetic diversity of the National Clonal Germplasm Repository (NCGR) Carya collections. The 19 SSR primers that produced good amplification products in `Halbert' were used to evaluate the collection, with 11 revealing polymorphism. The number of fragments amplified with different primer combinations ranged from 4 to 32 in the 48 genotypes tested. Evaluation of the data confirms the utility of the microsatellites in delimiting known relationships.

scholarly journals Genomically Intact Endogenous Feline Leukemia Viruses of Recent Origin

2004 ◽  
Vol 78 (8) ◽  
pp. 4370-4375 ◽  
Author(s):  
Alfred L. Roca ◽  
Jill Pecon-Slattery ◽  
Stephen J. O'Brien
Keyword(s):  
Long Terminal Repeat ◽  
Related Species ◽  
Germ Line ◽  
Open Reading Frames ◽  
Domestic Cats ◽  
Repeat Sequences ◽  
Recent Origin ◽  
Leukemia Viruses ◽  
Feline Leukemia Viruses ◽  
Reading Frames

ABSTRACT We isolated and sequenced two complete endogenous feline leukemia viruses (enFeLVs), designated enFeLV-AGTT and enFeLV-GGAG. In enFeLV-AGTT, the open reading frames are reminiscent of a functioning FeLV genome, and the 5′ and 3′ long terminal repeat sequences are identical. Neither endogenous provirus is genetically fixed in cats but polymorphic, with 8.9 and 15.2% prevalence for enFeLV-AGTT and enFeLV-GGAG, respectively, among a survey of domestic cats. Neither provirus was found in the genomes of related species of the Felis genus, previously shown to harbor enFeLVs. The absence of mutational divergence, polymorphic incidence in cats, and absence in related species suggest that these enFeLVs may have entered the germ line more recently than previously believed, perhaps coincident with domestication, and reopens the question of whether some enFeLVs might be replication competent.

Black Bear Damage to Thinned Timber Stands in Northwest Montana

1989 ◽  
Vol 4 (1) ◽  
pp. 10-13 ◽  
Author(s):  
Andrew C. Mason ◽  
David L. Adams
Keyword(s):  
Pinus Contorta ◽  
Black Bear ◽  
Tsuga Heterophylla ◽  
Thuja Plicata ◽  
Abies Lasiocarpa ◽  
Pinus Monticola ◽  
Larix Occidentalis ◽  
Western Larch ◽  
Engelmann Spruce ◽  
Northwest Montana

Abstract Bear damage was at least five times higher in thinned blocks than in adjacent unthinned blocks of western larch (Larix occidentalis), lodgepole pine (Pinus contorta), and Engelmann spruce (Picea engelmannii) on the Kootenai National Forest in northwest Montana. Western larch suffered the greatest damage (63% of all trees damaged and 92% of the trees killed). Damaged larch ranged from 4 to 13 in. dbh; the 4 to 8-in. dbh class accounted for 85% of the damage. Douglas-fir (Pseudotsuga menziesii), western redcedar (Thuja plicata), subalpine fir (Abies lasiocarpa), western white pine (Pinus monticola), and western hemlock (Tsuga heterophylla) were not damaged. Stand projections showed up to a 17% reduction in board-foot yield from bear damage, after 50 years, compared with hypothetical undamaged stands. West. J. Appl. For. 4(1):10-13, January 1989.

scholarly journals Analysis of genetic diversity and population structure in Asparagus species using SSR markers

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Manish Kapoor ◽  
Pooja Mawal ◽  
Vikas Sharma ◽  
Raghbir Chand Gupta
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Mean Value ◽  
Discrete Groups ◽  
Base Pairs ◽  
High Genetic Diversity ◽  
Pharmaceutical Industries ◽  
Improvement Programs ◽  
Northwest India ◽  
Simple Sequence

Abstract Background Various Asparagus species constitute the significant vegetable and medicinal genetic resource throughout the world. Asparagus species serve as important commodity of food and pharmaceutical industries in India. A diverse collection of Asparagus species from different localities of Northwest India was investigated for its genetic diversity using simple sequence repeat (SSR) markers. Results Polymorphic SSR markers revealed high genetic diversity. Primer SSR-15 amplified maximum of 8 fragments while 3 primers, namely, SSR-43, SSR-63, and AGA1 amplified minimum of 3 fragments. Collectively, 122 alleles were amplified in a range between 3 and 8 with an average of 5 alleles per marker. The size of the amplified alleles ranged between 90 and 680 base pairs. Polymorphism information content (PIC) value varied from a highest value of 0.499 in primer AGA1 to a lowest value of 0.231 in primer SSR-63 with a mean value of 0.376 showing considerable SSR polymorphism. Dendrogram developed on the basis of Jaccard’s similarity coefficient and neighbor-joining tree segregated all the studied Asparagus species into two discrete groups. Structure analysis based on Bayesian clustering allocated different accessions to two independent clusters and exhibited low level of individual admixture. Conclusions The genetic diversity analysis showed a conservative genetic background for maximum species of asparagus. Only Accessions of Asparagus adscendens were split into two diverse clusters suggesting a wide genetic base of this species as compared to other species. Overall genetic diversity was high, and this germplasm of Asparagus can be used in future improvement programs. The findings of current research on Asparagus germplasm can make a momentous contribution to initiatives of interbreeding, conservation, and improvement of Asparagus in future.

scholarly journals Larch Seed Trees Sustain Arboreal Lichens and Encourage Recolonization of Regenerating Stands

2007 ◽  
Vol 22 (2) ◽  
pp. 94-98 ◽  
Author(s):  
Fred L. Bunnell ◽  
Trevor Goward ◽  
Isabelle Houde ◽  
Curtis Björk
Keyword(s):  
Pinus Contorta ◽  
Lodgepole Pine ◽  
Road Dust ◽  
Larix Occidentalis ◽  
Western Larch ◽  
Source Tree ◽  
Winter Food ◽  
The Difference

Abstract In many areas Bryoria lichen is a major winter food for deer and caribou. We examined the role of western larch (Larix occidentalis) seed trees in retaining arboreal lichens and encouraging recolonization of regenerating stands by Bryoria. Although exposed to desiccation, Bryoria was sustained in significant amounts in larch seed trees. Other than a reduction near roads, apparently by alkaline road dust, arboreal forage lichens were relatively uniformly distributed throughout the regenerating stands. There was little difference in abundance up to 135 m from the source tree. The sorediate form of the lichens did better on lodgepole pine (Pinus contorta), and larger, nonsorediate fragments were more abundant on western larch. We attribute the difference to bark pH. Scattered western larch seed trees were effective at retaining lichens and facilitating recolonization of the regenerating stand.

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