Development of 12 new SSR markers for genetic diversity and structure analysis in pistachio (Pistacia veraL.)

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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Genetic Diversity and Structure Analysis Assessed by SSR Markers in a Large Collection of Vitis Cultivars from the Island of Crete, Greece

Biochemical Genetics ◽

10.1007/s10528-019-09943-z ◽

2019 ◽

Vol 58 (2) ◽

pp. 294-321 ◽

Cited By ~ 1

Author(s):

Androniki C. Bibi ◽

Evangelos D. Gonias ◽

Andreas G. Doulis

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Structure Analysis ◽

Large Collection ◽

Genetic Diversity And Structure

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Development of transcriptome-wide SSR markers for genetic diversity and structure analysis in Macrotyloma uniflorum (Lam.) Verdc.

Physiology and Molecular Biology of Plants ◽

10.1007/s12298-020-00898-9 ◽

2020 ◽

Vol 26 (11) ◽

pp. 2255-2266

Author(s):

Rahul Kumar ◽

Sumeet Parkash Kaundal ◽

Vikas Sharma ◽

Ashutosh Sharma ◽

Gagandeep Singh ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Structure Analysis ◽

Macrotyloma Uniflorum ◽

Genetic Diversity And Structure

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Genetic Diversity and Structure of Japanese Endemic Genus Thujopsis (Cupressaceae) Using EST-SSR Markers

Forests ◽

10.3390/f11090935 ◽

2020 ◽

Vol 11 (9) ◽

pp. 935

Author(s):

Michiko Inanaga ◽

Yoichi Hasegawa ◽

Kentaro Mishima ◽

Katsuhiko Takata

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Structure Analysis ◽

Expressed Sequence Tag ◽

Distribution Range ◽

Distribution Area ◽

Neighbor Joining ◽

Genetic Population ◽

Distribution Ranges ◽

Genetic Diversity And Structure

The genus Thujopsis (Cupressaceae) comprises monoecious coniferous trees endemic to Japan. This genus includes two varieties: Thujopsis dolabrata (L.f.) Siebold et Zucc. var. dolabrata (southern variety, Td) and Thujopsis dolabrata (L.f.) Siebold et Zucc. var. hondae Makino (northern variety, Th). The aim of this study is to understand the phylogeographic and genetic population relationships of the genus Thujopsis for the conservation of genetic resources and future breeding. A total of 609 trees from 22 populations were sampled, including six populations from the Td distribution range and 16 populations from the Th distribution range. The genotyping results for 19 expressed sequence tag (EST)-based simple sequence repeat (SSR) markers, followed by a structure analysis, neighbor-joining tree creation, an analysis of molecular variance (AMOVA), and hierarchical F statistics, supported the existence of two genetic clusters related to the distribution regions of the Td and Th varieties. The two variants, Td and Th, could be defined by their provenance, in spite of the ambiguous morphological differences between the varieties. The distribution ranges of both variants, which have been defined from their morphology, was confirmed by genetic analysis. The Th populations exhibited relatively uniform genetic diversity, most likely because Th refugia in the glacial period were scattered throughout their current distribution area. On the other hand, there was a tendency for Td’s genetic diversity to decrease from central to southern Honshu island. Notably, the structure analysis and neighbor-joining tree suggest the hybridization of the two varieties in the contact zone. More detailed studies of the genetic structure of Td are required in future analyses.

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Genetic Diversity and Population Structure Analysis of Chinese Wild Grape Using Simple Sequence Repeat Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs05016-20 ◽

2021 ◽

pp. 1-11

Author(s):

Beibei Li ◽

Xiucai Fan ◽

Ying Zhang ◽

Chonghuai Liu ◽

Jianfu Jiang

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Ssr Markers ◽

Structure Analysis ◽

North American ◽

Simple Sequence Repeat ◽

North American Species ◽

Sequence Repeat ◽

Genetic Diversity And Structure ◽

Simple Sequence

Chinese wild Vitis is a useful gene source for resistance to biotic and abiotic stresses, although there is little research on its genetic diversity and structure. In this study, nine simple sequence repeat (SSR) markers were used to assess the genetic diversity and genetic structure among 100 Vitis materials. These materials included 77 indigenous accessions representing 23 of 38 wild Vitis species/cultivars in China, 18 V. vinifera cultivars, and the five North American species V. aestivalis, V. girdiana, V. monticola, V. acerifolia, and V. riparia. The SSR loci used in this study for establishing an international database (Vitis International Variety Catalogue) revealed a total of 186 alleles in 100 Vitis accessions. The mean values for the gene diversity (GD) and polymorphism information content (PIC) per locus were 0.91 and 0.90, respectively, which indicates that the discriminatory power of the markers is high. Based on the genetic distance data, the 100 Vitis accessions were divided into five primary clusters by cluster analysis, and five populations by structure analysis; these results indicate these Chinese wild grapes were more genetically close to European grapes than to North American species. In addition, the clustering patterns of most accessions correlated with the geographic distribution. An analysis of molecular variance (AMOVA) revealed that 3.28%, 3.27%, and 93.46% of the variance occurred between populations, between individuals within populations, and between individuals within the entire population, respectively. In addition, we identified three previously undescribed accessions (Wuzhi-1, MZL-5, and MZL-6) by cluster analysis. Our results reveal a high level of genetic diversity and variability in Vitis from China, which will be helpful in the use of genetic resources in future breeding programs. In addition, our study demonstrates that SSR markers are highly suitable for further genetic diversity analyses of Chinese wild grapes.

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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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