Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp.)

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 923-936 ◽  
Author(s):  
H. Witsenboer ◽  
R. W. Michelmore ◽  
J. Vogel
Keyword(s):  
Lactuca Sativa ◽  
Wild Species ◽  
Polymorphic Locus ◽  
Allelic Diversity ◽  
Pcr Primers ◽  
Null Alleles ◽  
Rflp Markers ◽  
Compound Microsatellite ◽  
In The Wild ◽  
Interspecific Comparisons

Selectively amplified microsatellite polymorphic locus (SAMPL) analysis is a method of amplifying microsatellite loci using generic PCR primers. SAMPL analysis uses one AFLP primer in combination with a primer complementary to microsatellite sequences. SAMPL primers based on compound microsatellite sequences provided the clearest amplification patterns. We explored the potential of SAMPL analysis in lettuce to detect PCR-based codominant microsatellite markers. Fifty-eight SAMPLs were identified and placed on the genetic map. Seventeen were codominant. SAMPLs were dispersed with RFLP markers on 11 of the 12 main linkage groups in lettuce, indicating that they have a similar genomic distribution. Some but not all fragments amplified by SAMPL analysis were confirmed to contain microsatellite sequences by Southern hybridization. Forty-five cultivars of lettuce and five wild species of Lactuca were analyzed to determine the allelic diversity for codominant SAMPLs. From 3 to 11 putative alleles were found for each SAMPL; 2–6 alleles were found within Lactuca sativa and 1–3 alleles were found among the crisphead genotypes, the most genetically homogeneous plant type of L. sativa. This allelic diversity is greater than that found for RFLP markers. Numerous new alleles were observed in the wild species; however, there were frequent null alleles. Therefore, SAMPL analysis is more applicable to intraspecific than to interspecific comparisons. A phenetic analysis based on SAMPLs resulted in a dendrogram similar to those based on RFLP and AFLP markers.Key words: microsatellite, Lactuca sativa, genetic variation, molecular marker.

Molecular mapping of a thermosensitive genetic male sterility gene in rice using bulked segregant analysis

Genome ◽  
1997 ◽  
Vol 40 (2) ◽  
pp. 188-194 ◽  
Author(s):  
P. K. Subudhi ◽  
R. P. Borkakati ◽  
S. S. Virmani ◽  
N. Huang
Keyword(s):  
Male Sterility ◽  
Molecular Mapping ◽  
Bulked Segregant Analysis ◽  
Pcr Primers ◽  
Rflp Markers ◽  
Arbitrary Primers ◽  
Repulsion Phase ◽  
Genetic Male Sterility ◽  
True Breeding ◽  
Efficient Alternative

The thermosensitive genetic male sterility (TGMS) system is considered to be a more efficient alternative to the cytoplasmic male sterility (CMS) system for hybrid rice. An F2 population from a cross between a TGMS mutant line (IR32364TGMS) and IR68 was used to map the TGMS gene tms3(t). Fertile and sterile bulks were constructed following the classification of F2 plants into true breeding sterile, fertile, and segregating fertile plants based on F3 family studies. From the survey of 389 arbitrary primers in bulked segregant analysis, four RAPD markers were identified in which three, OPF182600, OPB19750, and OPAA7550, were linked to tms3(t) in repulsion phase and one, OPAC3640, was linked to tms3(t) in coupling phase. The tms3(t) gene was flanked by OPF182600 and OPAC3640 on one side and by OPAA7550 and OPB19750 on the other side. All four markers were low-copy sequences and two of them (OPF182600 and OPAC3640) detected polymorphism when the markers were used to probe the genomic blots. Subsequently, OPAC3640 was mapped to the short arm of chromosome 6 using a mapping population available at IRRI. However, no RFLP markers from this region showed linkage to tms3(t) owing to the lack of polymorphism between the parents. All RAPD fragments were cloned and partially sequenced from both ends. Thus, PCR primers can be designed to develop PCR markers for marker-assisted breeding to facilitate the transfer of tms3(t) from one genetic background to another.Key words: bulked segregant analysis, gene tagging, marker-assisted selection, RAPD, TGMS.

scholarly journals Genetic structure and dispersal patterns of the invasive psocid Liposcelis decolor (Pearman) in Australian grain storage systems

2010 ◽  
Vol 100 (5) ◽  
pp. 521-527 ◽  
Author(s):  
K.M. Mikac ◽  
N.N. FitzSimmons
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Allelic Diversity ◽  
Mantel Test ◽  
Null Alleles ◽  
Dispersal Patterns ◽  
Long Distance ◽  
Population Comparisons ◽  
Low Levels

AbstractMicrosatellite markers were used to investigate the genetic structure among invasive L. decolor populations from Australia and a single international population from Kansas, USA to determine patterns of dispersal. Six variable microsatellites displayed an average of 2.5–4.2 alleles per locus per population. Observed (HO) heterozygosity ranged from 0.12–0.65 per locus within populations; but, in 13 of 36 tests, HO was less than expected. Despite low levels of allelic diversity, genetic structure estimated as θ was significant for all pairwise comparisons between populations (θ=0.05–0.23). Due to suspected null alleles at four loci, ENA (excluding null alleles) corrected FST estimates were calculated overall and for pairwise population comparisons. The ENA-corrected FST values (0.02–0.10) revealed significant overall genetic structure, but none of the pairwise values were significantly different from zero. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2=0.12, P=0.18) and for Australian populations only (r2=0.19, P=0.44), suggesting that IBD does not describe the pattern of gene flow among populations. This study supports a hypothesis of long distance dispersal by L. decolor at moderate to potentially high levels.

scholarly journals Expanding Allelic Diversity of Helicobacter pylori vacA

1998 ◽  
Vol 36 (9) ◽  
pp. 2597-2603 ◽  
Author(s):  
Leen-Jan van Doorn ◽  
Céu Figueiredo ◽  
Ricardo Sanna ◽  
Salvador Pena ◽  
Peter Midolo ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Direct Sequencing ◽  
Allelic Diversity ◽  
Pcr Primers ◽  
Epidemiological Studies ◽  
Sequence Alignments ◽  
Gene Encoding ◽  
The World ◽  
Probe Assay ◽  
H Pylori

The diversity of the gene encoding the vacuolating cytotoxin (vacA) of Helicobacter pylori was analyzed in 98 isolates obtained from different geographic locations. The studies focused on variation in the previously defined s and m regions ofvacA, as determined by PCR and direct sequencing. Phylogenetic analysis revealed the existence of four distinct types of s-region alleles: aside from the previously described s1a, s1b, and s2 allelic types, a novel subtype, designated s1c, was found. Subtype s1c was observed exclusively in isolates from East Asia and appears to be the major s1 allele in that part of the world. Three different allelic forms (m1, m2a, and m2b) were detected in the m region. On the basis of sequence alignments, universal PCR primers that allow effective amplification of the s and m regions from H. pyloriisolates from all over the world were defined. Amplimers were subsequently analyzed by reverse hybridization onto a line probe assay (LiPA) that allows the simultaneous and highly specific hybridization of the different vacA s- and m-region alleles and tests for the presence of the cytotoxin-associated gene (cagA). This PCR-LiPA method permits rapid analysis of the vacA andcagA status of H. pylori strains for clinical and epidemiological studies and will facilitate identification of any further variations.

scholarly journals Assessing the Species in the CARES Preservation Program and the Role of Aquarium Hobbyists in Freshwater Fish Conservation

Fishes ◽  
2019 ◽  
Vol 4 (4) ◽  
pp. 49
Author(s):  
Jose W. Valdez ◽  
Kapil Mandrekar
Keyword(s):  
Freshwater Fish ◽  
Wild Species ◽  
Information Exchange ◽  
Iucn Red List ◽  
Vital Role ◽  
Red List ◽  
Priority List ◽  
In The Wild ◽  
Conservation Organizations

Freshwater fish represent half of all fish species and are the most threatened vertebrate group. Given their considerable passion and knowledge, aquarium hobbyists can play a vital role in their conservation. CARES is made up of many organizations, whose purpose is to encourage aquarium hobbyists to devote tank space to the most endangered and overlooked freshwater fish to ensure their survival. We found the CARES priority list contains nearly six hundred species from twenty families and two dozen extinct-in-the-wild species. The major families were typically those with the largest hobbyist affiliations such as killifish, livebearers, and cichlids, the latter containing half of CARES species. CARES included every IUCN threatened species of Pseudomugilidae and Valenciidae, but only one percent of threatened Characidae, Cobitidae, and Gobiidae species. No Loricariidae in CARES were in the IUCN red list as they have not been scientifically described. Tanzania and Mexico contained the largest amount of species, with the latter containing the most endemics. Many species were classified differently than the IUCN, including a third of extinct-in-the-wild species classified as least concern by the IUCN. This vast disconnect exemplifies the importance of future collaboration and information exchange required between hobbyists, the scientific community, and conservation organizations.

Significant increase of oleic acid level in the wild species Lepidium campestre through direct gene silencing

2016 ◽  
Vol 35 (10) ◽  
pp. 2055-2063 ◽  
Author(s):  
Emelie Ivarson ◽  
Annelie Ahlman ◽  
Ida Lager ◽  
Li-Hua Zhu
Keyword(s):  
Oleic Acid ◽  
Gene Silencing ◽  
Wild Species ◽  
Acid Level ◽  
Direct Gene ◽  
In The Wild ◽  
Lepidium Campestre

The high fruit soluble sugar content in wild Lycopersicon species and their hybrids with cultivars depends on sucrose import during ripening rather than on sucrose metabolism

2006 ◽  
Vol 33 (3) ◽  
pp. 279 ◽  
Author(s):  
María E. Balibrea ◽  
Cristina Martínez-Andújar ◽  
Jesús Cuartero ◽  
María C. Bolarín ◽  
Francisco Pérez-Alfocea
Keyword(s):  
Wild Species ◽  
Sugar Content ◽  
Soluble Sugar ◽  
Sucrose Metabolism ◽  
F1 Hybrids ◽  
Metabolic Parameter ◽  
Wild Relative ◽  
Soluble Sugar Content ◽  
Total Soluble Sugar ◽  
In The Wild

Soluble sugar content has been studied in relation to sucrose metabolism in the hexose-accumulating cultivated tomato Lycopersicon esculentum Mill, the wild relative species Lycopersicon cheesmanii Riley, in the sucrose-accumulating wild relative species Lycopersicon chmielewskii Rick, Kesicky, Fobes & Holle. and in two hexose-accumulating interspecific F1 hybrids (L. esculentum × L. cheesmanii; L. esculentum × L. chmielewskii), cultivated under two irrigation regimes (control: EC = 2.1 and saline: EC = 8.4 dS m–1). Under control conditions the total soluble sugar content (as hexose equivalents) in the ripe fruits of L. cheesmanii was 3-fold higher than in L. esculentum, while L. chmielewskii and both F1 hybrids contained twice as much as the cultivar. With the exception of L. esculentum × L. cheesmanii, salinity increased the sugar content by 1.3 (wild species) and 1.7 times (cultivar and L. esculentum × L. chmielewskii) with respect to control fruits. Wild germplasm or salinity provided two different mechanisms for the increases in fruit sugar content. The hexoses accumulated in ripe fruits were strongly influenced by those accumulated at the start of ripening, but the hydrolysed starch before start of ripening only partially explained the final hexose levels and especially the increase under salinity. The early cell wall acid invertase and the late neutral invertase activities appeared to be related to the amount of hexoses accumulated in ripe fruits. However, no metabolic parameter was positively related to the amount of sugar accumulated (including sucrose). The major differences between genotypes appeared in ripe fruits, in which up to 50% of the total amount of sugars accumulated in the wild species (mainly in L. cheesmanii) and hybrids cannot be explained by the sugars accumulated and the starch hydrolysed before the start of ripening stage. As a consequence, the higher fruit quality of the wild species compared with L. esculentum may depend more on the continuation of sucrose import during ripening than on osmotic or metabolic particularities such as the hexose / sucrose-accumulator character or specific enzyme activities.

Allozyme variation of the endangered Florida torreya (Torreyataxifolia)

1993 ◽  
Vol 23 (12) ◽  
pp. 2598-2602 ◽  
Author(s):  
Mark W. Schwartz
Keyword(s):  
Genetic Variation ◽  
Spatial Pattern ◽  
Genetic Information ◽  
Allelic Variation ◽  
Polymorphic Locus ◽  
Allozyme Variation ◽  
Soil Types ◽  
In The Wild ◽  
Apalachicola River ◽  
The 1950S

Torreyataxifolia Arn. is an endangered conifer restricted to ravine slopes along the Apalachicola River in northern Florida. The species began a decline in the 1950s that has resulted in fewer than 1500 trees remaining extant in the wild. Allelic variation was examined for 189 trees throughout its range. The species is characterized by low overall levels of genetic variation: seven of 20 loci were variable; each polymorphic locus had no more than two alleles; mean heterozygosity (He) was 0.064. Over 78% of this measured genetic variation was found within populations; no spatial pattern was detected in the remaining variation between populations within drainage regions, across drainage regions, or across soil types. This genetic information was used to plan tissue collection for a permanent offsite population.

scholarly journals SPECIFIC FEATURES OF THE TRACE ELEMENT COMPOSITION OF THE CULTIVATED FLAX AND SOME OF ITS WILD RELATIVES

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
I. Poliakova ◽  
N. Sinyaeva ◽  
V. Lyakh
Keyword(s):  
Trace Elements ◽  
Wild Species ◽  
Unsaturated Fatty Acids ◽  
Mineral Elements ◽  
Trace Element Composition ◽  
Wild Relatives ◽  
In The Wild ◽  
Flax Seeds ◽  
Cereal Plants ◽  
Cultivated Flax

Controlling the content of trace elements in human food is a major problem. Lack of them, as well as their excess, can seriously affect a person’s health. Commonly, people do not receive enough minerals they need. Though these minerals are found in products of both animal and plant origin, many ethnic groups have a significant preference for plant food, which is very often obtained from cereal plants. Not infrequently, though, these plants are poor in mineral elements, or a specific processing technology depletes a product of minerals. This article shows the content of such trace elements important for people as zinc, copper, cobalt, and nickel in the seeds and leaves of cultivated flax (L. usitatissimum) and its three wild perennial relatives (L. austriacum, L. hirsutum, and L. thracicum). We focus on flax, because, besides containing valuable trace elements, it is also a source of unsaturated fatty acids which are no less important for the human body. To date, there is but little information on the content of certain trace elements in the seeds of cultivated flax, and practically nothing is known about their content in its wild relatives, which are used mainly as decorative verdure. It has been established that the seeds contain 37.1-64.2 mg/kg of zinc, 5.3-9.3mg/kg of copper, 2.9-7.3mg/kg of nickel, and 1.4-3.3mg/kg of cobalt. In the leaves, these trace elements are present in far smaller amounts (1.1-4.3mg/kg). The highest in these trace elements is the wild species L. thracicum, and the lowest is L. austriacum. It has been found that in the plant material of cultivated flax, the ratio of the microelements under study was similar to that in the wild species. Zinc predominates in the flax seeds, but in the leaves, it exceeds other elements only insignificantly. Generally, both cultivated flax and its three wild relatives can be viewed as valuable and worthwhile sources of zinc, cobalt, copper, and nickel.

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