AFLP-based genetic diversity of wild orchardgrass germplasm collections from Central Asia and Western China, and the relation to environmental factors

Abstract Background Due to the environmental heterogeneity along elevation gradients, alpine ecosystems are ideal study objects for investigating how ecological variables shape the genetic patterns of natural species. The highest region in the world, the Qinghai-Tibetan Plateau, is a hotspot for the studies of evolutionary processes in plants. Many large rivers spring from the plateau, providing abundant habitats for aquatic and amphibious organisms. In the present study, we examined the genetic diversity of 13 Ranunculus subrigidus populations distributed throughout the plateau in order to elucidate the relative contribution of geographic distance and environmental dissimilarity to the spatial genetic pattern. Results A relatively low level of genetic diversity within populations was found. No spatial genetic structure was suggested by the analyses of molecular variance, Bayesian clustering analysis and Mantel tests. Partial Mantel tests and multiple matrix regression analysis showed a significant influence of the environment on the genetic divergence of the species. Both climatic and water quality variables contribute to the habitat heterogeneity of R. subrigidus populations. Conclusions Our results suggest that historical processes involving long-distance dispersal and local adaptation may account for the genetic patterns of R. subrigidus and current environmental factors play an important role in the genetic differentiation and local adaptation of aquatic plants in alpine landscapes.

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Variations in rare earth elements with environmental factors in lake surface sediments from 17 lakes in western China

Journal of Mountain Science ◽

10.1007/s11629-020-6040-4 ◽

2021 ◽

Vol 18 (7) ◽

pp. 1811-1822

Author(s):

Ding-ding Du ◽

Liu-qin Chen ◽

Yong-hui Bai ◽

Hai-ping Hu

Keyword(s):

Rare Earth ◽

Environmental Factors ◽

Rare Earth Elements ◽

Surface Sediments ◽

Western China ◽

Lake Surface

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Effect of Environmental Factors on the Germination and Emergence of Drunken Horse Grass (Achnatherum inebrians)

Weed Science ◽

10.1017/wsc.2020.81 ◽

2020 ◽

pp. 1-29

Author(s):

Yonghuan Yue ◽

Guili Jin ◽

Weihua Lu ◽

Ke Gong ◽

Wanqiang Han ◽

...

Keyword(s):

Seed Germination ◽

Environmental Factors ◽

Abiotic Factors ◽

Seedling Emergence ◽

Management Strategies ◽

Germination Percentage ◽

Western China ◽

Burial Depth ◽

Achnatherum Inebrians ◽

Water Ph

Abstract Drunken horse grass [Achnatherum inebrians (Hance) Keng] is a perennial poisonous weed in western China. A comprehensive understanding of the ecological response of A. inebrians germination to environmental factors would facilitate the formulation of better management strategies for this weed. Experiments were conducted under laboratory conditions to assess the effects of various abiotic factors, including temperature, light, water, pH and burial depth, on the seed germination and seedling emergence of A. inebrians. The seeds germinated at constant temperatures of 15, 20, 25, 30, 35°C and in alternating-temperature regimes of 15/5, 20/10, 25/15, 30/20, 35/25, 40/30°C, and the seed germination percentages under constant and alternating temperatures ranged from 51% to 94% and 15% to 93%, respectively. Maximum germination occurred at a constant temperature of 25°C, and germination was prevented at 45/35°C. Light did not appear to affect seed germination. The germination percentage of seeds was more than 75% in the pH range of 5 to 10, with the highest germination percentage at pH 6. The seeds germinated at osmotic potentials of 0 MPa to -1.0 MPa, but decreasing osmotic potential inhibited germination, with no germination at -1.2MPa. After 21 d of low osmotic stress, the seeds that did not germinate after rehydration had not lost their vitality. The seedling emergence percentage was highest (90%) when seeds were buried at 1 cm but declined with increasing burial depth and no emergence at 9 cm. Deep tillage may be effective in limiting the seed germination and emergence of this species. The results of this study provide useful information on the conditions necessary for A. inebrians germination and provide a theoretical basis for science-based prediction, prevention and control of this species.

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Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach

Frontiers in Genetics ◽

10.3389/fgene.2021.740437 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sanjaya Gyawali ◽

Gehendra Bhattarai ◽

Ainong Shi ◽

Chris Kik ◽

Lindsey J. du Toit

Keyword(s):

Genetic Diversity ◽

Central Asia ◽

Selective Sweep ◽

Spinacia Oleracea ◽

Genomic Region ◽

Day Length ◽

Mountain Range ◽

Nucleotide Polymorphisms ◽

Selective Sweeps ◽

Genetic Diversity And Structure

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica group. Likewise, the S. oleracea Q1 group had a smaller Fst (0.008) with the Q2 group than with the Q3 group (Fst = 0.012), and a greater gene flow (Nm = 30.13) with the Q2 group than with the Q3 group (Nm = 21.83). The Q2 accessions originated primarily from Uzbekistan while the Q3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q2 and Q3 groups of S. turkestanica. Accessions with admixtures of Q2 and Q3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.

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Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers

PeerJ ◽

10.7717/peerj.8038 ◽

2019 ◽

Vol 7 ◽

pp. e8038

Author(s):

Yanli Xiong ◽

Wenhui Liu ◽

Yi Xiong ◽

Qingqing Yu ◽

Xiao Ma ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Western China ◽

Tibet Plateau ◽

Group Method ◽

Breeding Strategies ◽

Population Genetic Differentiation ◽

Principal Coordinates ◽

Geographical Regions ◽

Genetic Diversity And Structure

Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread Elymus species. Elymus excelsus Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of E. excelsus germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of E. excelsus from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei’s genetic diversity (H) and Shannon’s diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of E. excelsus germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (Fst = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (He = 0.197) was greater than that of the GSC (He = 0.176) and XJC (He = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that E. excelsus accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable E. excelsus germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.

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Genetic Diversity of Rhubarb Cultivars

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.133.4.587 ◽

2008 ◽

Vol 133 (4) ◽

pp. 587-592 ◽

Cited By ~ 7

Author(s):

Joseph C. Kuhl ◽

Veronica L. DeBoer

Keyword(s):

Genetic Diversity ◽

Central Asia ◽

Length Polymorphism ◽

Genetic Relationship ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

18Th Century ◽

Pedigree Information ◽

Aflp Analysis ◽

Fingerprint Analysis

The genus Rheum L., commonly known as rhubarb, is composed of ≈60 species, primarily distributed throughout northern and central Asia. Rhubarb species have been used for medicinal purposes for thousands of years; however, it was not until the 18th century that the culinary use of petioles was first reported. Although the origin(s) of culinary rhubarb is not clear, it is thought that they originated from hybridization of rhubarb species originally brought to Europe for medicinal purposes. Most rhubarb cultivars lack pedigree information, and the genetic relationship among cultivars is largely unknown. Amplified fragment length polymorphism (AFLP) markers were generated for fingerprint analysis of 37 cultivars and four putative Rheum species accessions. Ten EcoRI and MseI primer combinations were analyzed for a total of 1400 scored polymorphisms, with an average of 140 polymorphisms per primer combination. Results show at least two clusters of related cultivars, as well as distantly related accessions. This study provides an estimate of rhubarb cultivar genetic diversity using AFLP analysis.

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Single Nucleotide Polymorphisms and Indel Markers from the Transcriptome of Garlic

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.141.1.62 ◽

2016 ◽

Vol 141 (1) ◽

pp. 62-65 ◽

Cited By ~ 6

Author(s):

Michael J. Havey ◽

Yul-Kyun Ahn

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Single Nucleotide Polymorphisms ◽

Nucleotide Polymorphisms ◽

Phenotypic Characteristics ◽

Single Nucleotide ◽

Germplasm Collections ◽

Indel Markers ◽

Production Environments ◽

Culinary Uses

Garlic (Allium sativum) is cultivated worldwide and appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great morphological variation and adaptability to diverse production environments. Molecular markers and phenotypic characteristics have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid (DH) of onion (Allium cepa). Single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) events were identified in 4355 independent garlic assemblies. A sample of the indels was verified using the original complementary DNA (cDNA) library and genomics DNAs from diverse garlics, and segregations confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.

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ROADS OF CENTRAL ASIA. THE NEW INTERNATIONAL TRANSIT PROJECTS

Eastern Analytics ◽

10.31696/2227-5568-2020-03-051-060 ◽

2020 ◽

pp. 51-60

Author(s):

Ekaterina Borisova ◽

Keyword(s):

Central Asia ◽

Western Europe ◽

Western China ◽

State Budget ◽

Mountain Ranges ◽

Relevant Today ◽

Central Asian ◽

International Transport ◽

Political Background ◽

Central Asian Republics

The development of international trade implies the use of the territory of Central Asia as a transit zone, through which the routes China–Europe, China – the middle East should be laid. The existing communication capabilities are not enough, so new directions are being developed (Railways “China–Kazakhstan – Turkmenistan–Iran”, “Turkmenistan– Afghanistan–Tajikistan”, ”China–Kyrgyzstan–Uzbekistan”; multimodal transit corridors” Lazurit”,” TRANS – Caspian international transport route”; such highways as “Western China– Western Europe”). However, paved roads, both rail and road, do not always meet expectations in terms of the volume of cargo passing through them (projects “China – Kazakhstan – Turkmenistan – Iran” and the Lapis lazuli corridor). Their loading is delayed “until better times” either due to the unstable political background, or due to the lack of necessary commodity flows in both directions. In some cases, there is a lack of political will to make appropriate decisions. Finished projects are unprofitable. None of the international transit projects announced or even completed over the past 20 years through the Central Asian republics has been fully operational. Meanwhile, international transit allows not only to fill the state budget, but also to solve issues of internal connectivity of territories. This task is most relevant today for Kyrgyzstan and Tajikistan, which have become hostages of their own geography, with localities separated by impassable mountain ranges.

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Incidence, geographical distribution and genetic diversity of sugarcane striate virus in Saccharum species in China

Plant Disease ◽

10.1094/pdis-10-20-2307-re ◽

2021 ◽

Author(s):

Yinfu Lin ◽

Niyaz Ali ◽

M. R. Hajimorad ◽

Lijuan Zhang ◽

Xiaohang Qi ◽

...

Keyword(s):

Genetic Diversity ◽

Geographical Distribution ◽

Phylogenetic Trees ◽

Full Length ◽

Leaf Sample ◽

Local Varieties ◽

Saccharum Spp ◽

Saccharum Species ◽

Germplasm Collections ◽

Virus Incidence

A novel virus of the genus Mastrevirus, family Geminivirdae, was recently reported in sugarcane germplasm collections in Florida, Guadeloupe and Réunion, and was named sugarcane striate virus (SStrV). Although the full-length sequence of a SStrV isolate from China was obtained in 2015, the incidence, geographical distribution, and genetic diversity of this virus remained unclear. A single leaf sample from 2,368 sugarcane plants from main sugarcane producing regions of China and germplasm collections were tested for SStrV by polymerase chain reaction (PCR). Average virus incidence was 25.1% for field collected samples and SStrV was detected in most Saccharum species and two sugarcane-related species with the highest incidence in S. officinarum (44.1%) followed by Saccharum spp. local varieties (33.3%) grown for chewing cane for a long time. The virus incidence was much lower (6.8%) in modern commercial cultivars (Saccharum spp. hybrids). Phylogenetic trees based on full-length genomes of 157 SStrV isolates revealed that Chinese isolates comprised strains A and B, but not C and D that were reported in Florida, USA. SStrV strain A was the most prominent (98.7%) and widespread strain in China and was further divided into eight sub-groups. Almost half (45.6%) of the SStrV-positive samples from S. officinarum and Saccharum spp. local varieties were co-infected with sugarcane mosaic disease viruses or sugarcane yellow leaf virus. Interestingly, most of the plants infected by strain A of SStrV were asymptomatic. SStrV appears to be widespread in China, and its influence on chewing cane deserves further investigation.

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Analisis Keragaman Genetik 28 Nomor Koleksi Kakao (Theobroma cacao L.) Berdasarkan Marka SSR

Jurnal Tanaman Industri dan Penyegar ◽

10.21082/jtidp.v4n1.2017.p13-22 ◽

2017 ◽

Vol 4 (1) ◽

pp. 13 ◽

Cited By ~ 1

Author(s):

Ilham Nur ardhi Wicaksono ◽

Rubiyo Rubiyo ◽

Dewi Sukma ◽

Sudarsono Sudarsono

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Plant Molecular Biology ◽

Average Value ◽

Germplasm Collections ◽

Ctab Method ◽

Parental Lines ◽

Biology Laboratory ◽

Superior Clones ◽

Selection Of

<em>Analysis of genetic diversity of cacao germplasm collections using molecular markers has an important role in the assembly of new superior clones. The availability of commercial and superior local clones could increase the success of new superior clones’ assembly. Hence, the genetic diversity analysis of these materials needs to be done. The study was aimed to analyze genetic diversity of 28 cacao collections based on SSR markers that would be useful for selection of parental lines. The research was conducted in the Integrated Laboratory, Indonesian Industrial and Beverage Crops Research Institute, Sukabumi, and Plant Molecular Biology laboratory, Bogor Agricultural University, from November 2015 to May 2016.</em> <em>Analysis of genetic diversity was conducted using 28 cacao clones (13 superior local clones and 15 commercial clones). DNA was extraction using CTAB method, which then amplified by PCR technique using 20 SSR primers. The result showed that all SSR markers used in this study were polymorphic with an average value of PIC was high (57%). Phylogenetic tree constructed using DARwin program version 6.05 is divided into 3 major groups, which placed commercial and superior local clones together in each group. Superior local clones observed herein might have close relationships with commercial clones that have long been cultivated in Indonesia. Furthermore, some cacao clones could potentially be parental lines because they had high genetic distance. The results showed that SSR markers are powerful tools to determine potential parental lines, which is expected to increase the chances of heterosis in their progenies.</em>

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