Comparative analysis of genetic diversity between Qinghai-Tibetan wild and Chinese landrace barley

Genome ◽  
2009 ◽  
Vol 52 (10) ◽  
pp. 849-861 ◽  
Author(s):  
Xue Gong ◽  
Sharon Westcott ◽  
Chengdao Li ◽  
Guijun Yan ◽  
Reg Lance ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Analysis ◽  
Ssr Markers ◽  
Wild Barley ◽  
Production Systems ◽  
Barley Accession ◽  
Tibetan Wild Barley ◽  
Ssr Loci ◽  
Chinese Landrace ◽  
Barley Germplasm

Fifty-two SSR markers were used to evaluate the genetic diversity of 33 Qinghai-Tibetan wild barley accessions, 56 landraces collected primarily from other parts of China, and 1 Israeli wild barley accession. At the 52 SSR loci, 206 alleles were detected for the 90 accessions, among which 111 were common alleles. The number of alleles per locus ranged from 1 to 9, with an average of 4.0. Polymorphism information content (PIC) values ranged from 0 to 0.856 among all the markers, with an average of 0.547. The PIC value of Qinghai-Tibetan wild barley varied from 0 to 0.813 with an average of 0.543, while in landraces, the markers showed a range of 0 to 0.790 with an average of 0.490. The SSR markers could clearly differentiate the Qinghai-Tibetan wild barley from the landraces. Twenty-four unique alleles were observed in Qinghai-Tibetan wild barley, and the frequency of unique alleles in Qinghai-Tibetan wild barley was about 2.1 times higher than that in the landraces, on average. Five of the 7 chromosomes had more unique alleles in the Qinghai-Tibetan wild barley, but chromosome 2H had more unique alleles in the landraces. The presence of many unique alleles may reflect the adaptation of this barley germplasm to diverse environments and production systems.

Genetic Diversity Analysis of Tibetan Wild Barley Using SSR Markers

2006 ◽  
Vol 33 (10) ◽  
pp. 917-928 ◽  
Author(s):  
Zong-Yun FENG ◽  
Xian-Jun LIU ◽  
Yi-Zheng ZHANG ◽  
Hong-Qing LING
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Wild Barley ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis ◽  
Tibetan Wild Barley

Comparative Analysis of Genetic Diversity and Structure in Rice Using ILP and SSR Markers

Rice Science ◽  
2010 ◽  
Vol 17 (4) ◽  
pp. 257-268 ◽  
Author(s):  
Ming HUANG ◽  
Fang-min XIE ◽  
Li-yun CHEN ◽  
Xiang-qian ZHAO ◽  
L. JOJEE ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Analysis ◽  
Ssr Markers ◽  
Genetic Diversity And Structure

scholarly journals Genetic Differentiation in Moroccan Opuntia ficus-indica Cultivars Using Simple Sequence Repeat (SSR) Markers

2016 ◽  
Vol 8 (3) ◽  
pp. 380-385 ◽  
Author(s):  
Aissam EL FINTI ◽  
Driss TALIBI ◽  
Mouhamed SIDKI ◽  
Abdelhamid E. MOUSADIK
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Opuntia Ficus Indica ◽  
Distance Analysis ◽  
Reference Collection ◽  
Ssr Loci ◽  
Set Up ◽  
Genetic Distance Analysis ◽  
Simple Sequence

Estimation of genetic parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources. In this study, 13 Opuntia ficus-indica cultivars were analyzed using 10 SSR markers selected for studying the genetic diversity among these chosen cultivars. Over the 10 SSR markers, a total of 45 reproducible bands were scored with an average of 4.5 alleles/locus, while the observed heterozygosity (Ho) values of amplified loci ranged from 0.15 (SSR1) to 0.92 (SSR2 and SSR 11). Genetic distance analysis of the 13 cultivars showed a large genetic differentiation (GST = 0.47) and high number of different groups. Most of the accessions were not found to be clustered according to their eco-geographical origin. In addition, each cultivar was characterized by its own multiallelic combination between loci. The results revealed the usefulness of SSR in understanding of genetic diversity in Moroccans Barbary fig cultivars, thus being helpful to set up rational decisions concerning the establishment of a national reference collection.

Assessment of genetic diversity among Jordanian wild barley (Hordeum spontaneum) genotypes revealed by SSR markers

2015 ◽  
Vol 63 (5) ◽  
pp. 813-822 ◽  
Author(s):  
Y. Shakhatreh ◽  
M. Baum ◽  
N. Haddad ◽  
M. Alrababah ◽  
S. Ceccarelli
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Wild Barley ◽  
Hordeum Spontaneum

Mosaic microecological differential stress causes adaptive microsatellite divergence in wild barley, Hordeum spontaneum, at Neve Yaar, Israel

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1216-1229 ◽  
Author(s):  
Qingyang Huang ◽  
Alex Beharav ◽  
Youchun Li ◽  
Valery Kirzhner ◽  
Eviatar Nevo
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Wild Barley ◽  
Permutation Test ◽  
Balancing Selection ◽  
Real Data ◽  
Hordeum Spontaneum ◽  
Data Sets ◽  
Total Genetic Diversity ◽  
Ssr Loci

Genetic diversity at 38 microsatellite (short sequence repeats (SSRs)) loci was studied in a sample of 54 plants representing a natural population of wild barley, Hordeum spontaneum, at the Neve Yaar microsite in Israel. Wild barley at the microsite was organized in a mosaic pattern over an area of 3180 m2 in the open Tabor oak forest, which was subdivided into four microniches: (i) sun–rock (11 genotypes), (ii) sun–soil (18 genotypes), (iii) shade–soil (11 genotypes), and (iv) shade–rock (14 genotypes). Fifty-four genotypes were tested for ecological–genetic microniche correlates. Analysis of 36 loci showed that allele distributions at SSR loci were nonrandom but structured by ecological stresses (climatic and edaphic). Sixteen (45.7%) of 35 polymorphic loci varied significantly (p < 0.05) in allele frequencies among the microniches. Significant genetic divergence and diversity were found among the four subpopulations. The soil and shade subpopulations showed higher genetic diversities at SSR loci than the rock and sun subpopulations, and the lowest genetic diversity was observed in the sun–rock subpopulation, in contrast with the previous allozyme and RAPD studies. On average, of 36 loci, 88.75% of the total genetic diversity exists within the four microniches, while 11.25% exists between the microniches. In a permutation test, GST was lower for 4999 out of 5000 randomized data sets (p < 0.001) when compared with real data (0.1125). The highest genetic distance was between shade-soil and sun–rock (D = 0.222). Our results suggest that diversifying natural selection may act upon some regulatory regions, resulting in adaptive SSR divergence. Fixation of some loci (GMS61, GMS1, and EBMAC824) at a specific microniche seems to suggest directional selection. The pattern of other SSR loci suggests the operation of balancing selection. SSRs may be either direct targets of selection or markers of selected haplotypes (selective sweep).Key words: natural selection, genetic diversity, microsatellites, adaptation, Hordeum spontaneum, wild barley, microsite divergence.

Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers

2011 ◽  
Vol 39 (4) ◽  
pp. 3637-3647 ◽  
Author(s):  
Jihong Hu ◽  
Lei Pan ◽  
Honggao Liu ◽  
Shuzhen Wang ◽  
Zhihua Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Analysis ◽  
Ssr Markers ◽  
Nelumbo Nucifera ◽  
Sacred Lotus

A SSR kit to study genetic diversity in chickpea (Cicer arietinum L.)

2014 ◽  
Vol 12 (S1) ◽  
pp. S118-S120 ◽  
Author(s):  
Rajeev Varshney ◽  
Mahendar Thudi ◽  
Hari Upadhyaya ◽  
Sangam Dwivedi ◽  
Sripada Udupa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Ssr Markers ◽  
Quality Criteria ◽  
Specific Information ◽  
Wide Range ◽  
Ssr Loci ◽  
Polymerase Chain ◽  
Diversity Studies

A chickpea simple sequence repeat (SSR) marker reference kit has been developed based on the genotyping of the global chickpea composite collection (3,000 accessions) with 35 SSR markers. The kit consists of three pools of chickpea accessions along with supporting documentation on the SSR markers, polymerase chain reaction and detection conditions, and the expected allele sizes for each of the 35 SSR loci. These markers were selected based on quality criteria, genome coverage and locus-specific information content. Other important SSR selection criteria were quality of amplification products, locus complexity, polymorphism information content and well-dispersed location on a chickpea genetic map. The developed SSR kit has a wide range of applications, especially for genetic diversity studies in chickpea. Using the markers and reference accessions in the kit, scientists in other laboratories will be able to compare the genotypic data that they obtain for their germplasm with that obtained using the global composite collection.

scholarly journals Genome-wide development of lncRNA-derived-SSR markers for Dongxiang wild rice (Oryza rufipogon Griff.)

2021 ◽  
Author(s):  
Wanling Yang ◽  
Yuanwei Fan ◽  
Yong Chen ◽  
Gumu Ding ◽  
Hu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Stress Responses ◽  
Wild Rice ◽  
Diversity Index ◽  
Oryza Rufipogon ◽  
Coding Sequences ◽  
Genome Wide ◽  
Ssr Loci ◽  
Dongxiang Wild Rice

AbstractDongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost distributed common wild rice found in the world. It contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in crop breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice materials. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content (PIC) values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research, including genetic diversity analysis, QTL mapping, and molecular breeding programs, to make good use of the elite lncRNA genes from DXWR.

scholarly journals Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259146
Author(s):  
Venugopal Vidya ◽  
Duraisamy Prasath ◽  
Mohandas Snigdha ◽  
Ramasamy Gobu ◽  
Charles Sona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Zingiber Officinale ◽  
Eastern India ◽  
Coding Sequences ◽  
North Eastern ◽  
Ssr Primers ◽  
Ssr Loci ◽  
North Eastern India

Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies at the molecular level in ginger is limited due to limited availability of genetic and genomic information. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger. We obtained 16,790 EST-SSR loci from 78987 unigenes, and 4597 SSR loci in the predicted 76929 coding sequences from RNA-Seq assembled contigs of ginger through Illumina paired-end sequencing. Gene ontology results indicate that the unigenes with SSR loci participate in various biological processes such as metabolism, growth, and development in ginger. One hundred and twenty-five primer pairs were designed from unigenes and coding sequences. These primers were tested for PCR optimization, characterization, and amplification and identified 12 novel EST-SSR markers. Twelve flanking polymorphic EST-SSR primers were validated using 48 ginger genotypes representing North-Eastern India and different eco-geographical adaptations by PCR amplification and allele sizing through capillary electrophoresis. Twelve EST-SSR primers generated a total of 111 alleles with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp. This study implies that the SSR markers designed from transcriptome sequences provides ample EST-SSR resources, which are helpful for genetic diversity analysis of Zingiberaceae species and molecular verification of ginger genotypes.

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