scholarly journals Strong Genetic Structure Observed in Primulina danxiaensis, a Small Herb Endemic to Mount Danxia With Extremely Small Populations

2021 ◽  
Vol 12 ◽  
Author(s):  
Sufang Chen ◽  
Wei Guo ◽  
Zaixiong Chen ◽  
Wenbo Liao ◽  
Qiang Fan
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Perennial Grass ◽  
Geographic Distance ◽  
Natural World ◽  
Middle Level ◽  
World Heritage Site ◽  
Grass Species ◽  
Gene Pools ◽  
Unique Type

Danxia landform occurring sporadically in southern China is a unique type of petrographic geomorphology. It has nurtured about 400 rare or threatened plant and animal species, whose diversity, endemism, and conservation have called increasing scientific and public attentions. Among them, Primulina danxiaensis (W. B. Liao, S. S. Lin, and R. J. Shen) W. B. Liao and K. F. Chung is a tiny perennial grass species recorded only in Mount Danxia, a natural World Heritage Site as part of China’s Danxia. In this study, restriction site-associated DNA sequencing (RAD-seq) was performed to investigate genetic diversity among these 12 populations of P. danxiaensis. A total of 432,041 variant sites were detected in 84,779 loci across 94 samples. The expected heterozygosity (HE) ranged from 0.017 to 0.139. Bottleneck signals were detected in most populations, Tajima’s D tests showed that most loci could be under recent positive selection, and one of the six positively selected loci identified by BayeScan was annotated as tRNAGlu, which may contribute to the species’ adaptation to shady environment. STRUCTURE analysis and phylogenetic tree showed that the 12 populations of P. danxiaensis could be divided into four gene pools (clades) corresponding to their geographic locations, and significant correlation was observed between genetic and geographic distances. Our study demonstrated that P. danxiaensis maintained a middle level of genetic diversity and strong population structure; geographic distance could be an important factor limiting gene flow among populations of P. danxiaensis, which were only sporadically recorded in Mount Danxia.

Genetic diversity of bluebunch wheatgrass (Pseudoroegneria spicata) in the Thompson River valley of British Columbia

2006 ◽  
Vol 84 (7) ◽  
pp. 1122-1128 ◽  
Author(s):  
Yong-Bi Fu ◽  
Don Thompson
Keyword(s):  
Genetic Diversity ◽  
British Columbia ◽  
Habitat Restoration ◽  
Expressed Sequence Tag ◽  
Perennial Grass ◽  
Germplasm Conservation ◽  
River Valley ◽  
Grass Species ◽  
Pseudoroegneria Spicata ◽  
Bluebunch Wheatgrass

Bluebunch wheatgrass ( Pseudoroegneria spicata (Pursh) A. Löve) is a cool-season perennial grass native to semi-arid regions of western North America and has been used for habitat restoration. However, the genetic diversity of this species is poorly understood. A total of 172 expressed sequence tag-derived simple sequence repeat (eSSR) primer pairs that had been developed for wheat were characterized for genetic diversity studies of bluebunch wheatgrass. Of these, 12 eSSR primer pairs were found to be informative and were applied to screen 216 plants collected from six locations with two different elevations in the Thompson River valley of British Columbia. These analyses revealed a total of 106 eSSR polymorphic alleles (or bands) scorable for each sample. The number of polymorphic bands per primer pair ranged from 2 to 17 with a mean of 8.8. The frequencies of these bands ranged from 0.005 to 0.995 and averaged 0.146. Most (92.6%) of the eSSR variation detected was present within the 12 populations assessed. The between-population eSSR variability was significantly associated with their geographic distances, but not with their elevations. These findings are useful for genetic diversity and genetic mapping studies of this grass species and should facilitate the sampling and development of bluebunch wheatgrass germplasm for germplasm conservation and habitat restoration.

Hymenachne acutigluma (Steud.) Gilliland in GBS 20:314 - An exceptionally important perennial grass for anatomy and indigenous practice.

2016 ◽  
Vol 5 (04) ◽  
pp. 4958
Author(s):  
Dulal De
Keyword(s):  
Perennial Grass ◽  
Secondary Growth ◽  
Grass Species ◽  
Stem Anatomy

Hymenachne acutigluma (Steud.) Gilliland, a robust rhizomatous perennial grass spreads on moist and swampy land and also floating in water. Being a grass species, they do not have any cambium for secondary growth. A peculiarity in stem anatomy especially the spongy pith of secondary tissues found in absence of the cambium. The origin and development of the parenchymatous pith tissues has been investigated in the present study. Economically this spongy pith is of very much potent for its high absorbing and filtering capacity and also used as a good fodder.

scholarly journals Global biogeographic sampling of bacterial secondary metabolism

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Zachary Charlop-Powers ◽  
Jeremy G Owen ◽  
Boojala Vijay B Reddy ◽  
Melinda A Ternei ◽  
Denise O Guimarães ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Genome Sequencing ◽  
Geographic Distance ◽  
Gene Clusters ◽  
Natural World ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Road Map ◽  
Two Factors ◽  
Natural Products Discovery

Recent bacterial (meta)genome sequencing efforts suggest the existence of an enormous untapped reservoir of natural-product-encoding biosynthetic gene clusters in the environment. Here we use the pyro-sequencing of PCR amplicons derived from both nonribosomal peptide adenylation domains and polyketide ketosynthase domains to compare biosynthetic diversity in soil microbiomes from around the globe. We see large differences in domain populations from all except the most proximal and biome-similar samples, suggesting that most microbiomes will encode largely distinct collections of bacterial secondary metabolites. Our data indicate a correlation between two factors, geographic distance and biome-type, and the biosynthetic diversity found in soil environments. By assigning reads to known gene clusters we identify hotspots of biomedically relevant biosynthetic diversity. These observations not only provide new insights into the natural world, they also provide a road map for guiding future natural products discovery efforts.

scholarly journals Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

Genetic diversity of the extremely rare Habenaria dentata and the rare Habenaria linearifolia (Orchidaceae) in South Korea: implications for population history and conservation

2018 ◽  
Vol 151 (1) ◽  
pp. 48-60
Author(s):  
Mi Yoon Chung ◽  
Hoa Thi Quynh Le ◽  
Sungwon Son ◽  
Huai Zhen Tian ◽  
Myong Gi Chung
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Geographic Location ◽  
Population History ◽  
Population Variation ◽  
Conservation Strategies ◽  
Ancestral Population ◽  
Allozyme Diversity ◽  
Glacial Origin

Background and aims – Since historical events often leave an indelible mark on levels of genetic diversity of plant populations, one may indirectly infer their evolutionary history with the help of current patterns of genetic diversity. The terrestrial orchid Habenaria dentata, an element of warm-temperate/subtropical vegetation, reaches its northernmost limits in the Korean Peninsula, and thus it is extremely rare there. As H. dentata was absent from the Peninsula during the Last Glacial Maximum (LGM), it is likely to be of post-glacial origin having arrived from either a single refugium or multiple refugia. However, its rare, temperate/boreal congener H. linearifolia might have persisted in situ in either macrorefugia or microrefugia on the Peninsula during the LGM.Methods – To test which hypothesis is most appropriate for each species, we investigated levels of allozyme-based (17 loci) genetic diversity and population genetic structure in the two only known populations of H. dentata and in 12 populations of H. linearifolia.Key results – No allozyme diversity was found in H. dentata (He = 0.000), whereas H. linearifolia exhibited low within-population variation (He = 0.060) and high among-population differentiation (FST = 0.237). We found little association between populations in relation to their geographic location; several populations presented individuals belonging to different clusters.Conclusions – Our results suggest that H. dentata likely originated from a single ancestral population (perhaps from southern Japan or southern China) through post-glacial dispersal, whereas H. linearifolia probably survived the LGM in situ in microrefugia situated at low to mid-elevated regions. We further suggest that separate conservation strategies for each species should be employed, given that the two taxa have different ecological and demographic traits and harbour different levels of genetic diversity.

Potential effects of climate change on the Chinese Bulbul (Pycnontus sinensis) in China

Biologia ◽  
2014 ◽  
Vol 69 (11) ◽  
Author(s):  
Longying Wen ◽  
Huigen He ◽  
Yong Wang ◽  
Jimmy Gorimar ◽  
Mark Liu
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Literature Review ◽  
Range Expansion ◽  
Human Disturbance ◽  
Southern China ◽  
Distribution Range ◽  
Population Increase ◽  
Increased Temperature

AbstractThe Chinese Bulbul (Pycnontus sinensis) has an extensive distribution throughout southern China. Investigators have reported that the species has expanded its distribution range northward since 1995. We performed a literature review and analysis to examine the relationships between the range expansion of the species and the changes of climate and habitat. We found that the northward range expansion was associated with the increased temperature and human created habitat. We believe that the combination of the increased temperature and the ability to utilize human created habitat while maintaining genetic diversity resulted in the population increase and range expansion of the species. We suggest that increased temperature and human disturbance could lead to evolutionary and distributional changes of some species such as the Chinese Bulbul, therefore possibly making these species indicators of climate change.

scholarly journals Genetic diversity and selection of genotypes to enhance Zn and Fe content in common bean

2010 ◽  
Vol 90 (1) ◽  
pp. 49-60 ◽  
Author(s):  
Z I Talukder ◽  
E Anderson ◽  
P N Miklas ◽  
M W Blair ◽  
J Osorno ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Allelic Variation ◽  
Gene Pools ◽  
Gene Sequences ◽  
Mineral Contents ◽  
Discriminatory Ability ◽  
Fe Content ◽  
Mapping Populations ◽  
Selection Of

Common bean (Phaseolus vulgaris L.) is an important source of dietary protein and minerals worldwide. Genes conditioning variability for mineral contents are not clearly understood. Our ultimate goal is to identify genes conditioning genetic variation for Zn and Fe content. To establish mapping populations for this objective, we tested mineral content of 29 common bean genotypes. Chemical analyses revealed significant genetic variability for seed Zn and Fe contents among the genotypes. Genetic diversity was evaluated with 49 primer pairs, of which 23 were simple sequence repeats (SSR), 16 were developed from tentative consensus (TC) sequences, and 10 were generated from common bean NBS-LRR gene sequences. The discriminatory ability of molecular markers for identifying allelic variation among genotypes was estimated by polymorphism information content (PIC) and the genetic diversity was measured from genetic similarities between genotypes. Primers developed from NBS-LRR gene sequences were highly polymorphic in both PIC values and number of alleles (0.82 and 5.3), followed by SSRs (0.56 and 3.0), and markers developed from TC (0.39 and 2.0). genetic similarity values between genotypes ranged from 14.0 (JaloEEP558 and DOR364) to 91.4 (MIB152 and MIB465). Cluster analysis clearly discriminated the genotypes into Mesoamerican and Andean gene pools. Common bean genotypes were selected to include in crossing to enhance seed Zn and Fe content based on genetic diversity and seed mineral contents of the genotypes. Key words: Common bean, genetic diversity, mineral nutrients, breeding

Genetic Structure and Diversity among Species of Salacia: An Endangered Medicinal Herb of Western Ghats, India

2019 ◽  
Vol 9 (1) ◽  
pp. 23-33
Author(s):  
Chandrashekhar G Patil ◽  
Sheetal Ganapati Kamat ◽  
R Vasudeva
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Issr Marker ◽  
Group Method ◽  
Population Genetic Differentiation ◽  
Expected Heterozygosity ◽  
Marker Analysis ◽  
Endangered Medicinal Herb ◽  
High Level ◽  
Genetic Structure And Diversity

Salacia is one of the medicinally valuable genus, distributed throughout tropical areas which include India, Sri Lanka, Southern China and other Southern Asian Countries. The genus Salacia is represented by 21 species in India, among them eight species are recorded from the state of Karnataka in the Southern part of India. Despite its pharmaceutical importance, very little information exists about the genetic diversity of Salacia at molecular level. Hence the present study was carried out to evaluate the genetic among six species of Salacia namely S. chinensis, S. malabarica, S. oblonga, S. macrosperma, S. reticulata and S. gambleana with the help of ISSR marker analysis. Dendrogram and genetic distance were generated adopting Unweighted Paired Group Method with Arithmetic mean (UPGMA) in the NTSYS-pc software. Basic genetic parameters were calculated by analysing the genetic data with Pop gene 1.32 and GenAlEx 6.2 software. The overall polymorphism across the ten primers screened revealed 26 % polymorphism. A 60% polymorphism was scored for the primer UBC 841, whereas, no polymorphism was observed for primer UBC 840 and ISSR 6. The average observed heterozygosity was more than expected heterozygosity. Observed heterozygosity (Ho) ranged from 0.15 (UBC 841) to 0.38 (ISSR 6) with an average of 0.25, whereas expected heterozygosity (He) ranged from 0.10 (UBC 843) to 0.35 (ISSR 6) with an average of 0.23 for Salacia species. The higher heterozygosity pointed towards increased genetic diversity amongst the species. ISSR marker analysis showed high level of inter and intra population genetic differentiation.

The germinable soil seedbank of Eucalyptus victrix grassy woodlands at Roy Hill station, Pilbara district, Western Australia

2004 ◽  
Vol 26 (1) ◽  
pp. 17 ◽  
Author(s):  
R. A. Graham ◽  
S. K. Florentine ◽  
J. E. D. Fox ◽  
T. M. Luong
Keyword(s):  
Species Composition ◽  
Western Australia ◽  
Perennial Grass ◽  
Summer Rainfall ◽  
Distribution Patterns ◽  
Grass Species ◽  
Surface Areas ◽  
Hill Station ◽  
Soil Seedbank ◽  
Germinable Seed

The paper reports soil seedbank species composition, of Eucalyptus victrix grassy woodlands, of the upper Fortescue River in the Pilbara District, Western Australia. In this study, our objectives were to investigate germinable soil seedbanks and species composition in response to three simulated seasons, using emergence. Variation in seed density from three depths was tested. Four field sites were sampled. Thirty samples were collected in late spring, after seed rain and before summer rainfall. From each sample spot, three soil depths (surface, 1–5, and 6–10 cm) were segregated from beneath surface areas of 100 cm2. Samples were later incubated in a glasshouse to simulate three different seasonal conditions (autumn, winter and spring). Germinating seedlings were recorded on emergence and grown until identified. Forty-one species germinated, comprising 11 grasses (7 annuals and 4 perennials), 25 annual herbs and 5 perennial herbs. Distribution patterns of germinable seed in both the important annual grass Eragrostis japonica and the perennial Eragrostis setifolia (a preferred cattle fodder species), suggest that seedbank accumulation differs among species and between sites. In part, this may be associated with the absence of grazing. Species with most total germinable seed were E. japonica (Poaceae; 603/m2), and the annual herbs Calotis multicaulis (Asteraceae; 346/m2), and Mimulus gracilis (Scrophulariaceae; 168/m2). Perennial grass seed was sparse. Spring simulation gave most germination (1059), followed by autumn (892) and winter (376) sets. Greatest species diversity was produced from the spring simulation (33 species), followed by autumn (26), and winter (22). Of the total germination, 92% came from 17 species that were represented in all three simulations. Of the 1227 grass seedlings counted, most were recruited from the surface soil (735), followed by the 5 (310) and 10 (182) cm depths. Marginally more grass seedlings germinated from the spring simulation (558) than the autumn set (523). Only 11.9% of grass germinants came from the winter simulation. All grass species recruited from the soil seedbanks had a C4 photosynthetic pathway. Except for Cenchrus ciliaris all grass species are native to Australia. Of the four sites sampled, one fenced to exclude cattle five years earlier had significantly more germination than the three unfenced sites. Seedbank sampling produced several new records for plants in the areas sampled.

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