Genetic Diversity and Population Structure of 93 Rice Cultivars (Lines) (Oryza Sativa Xian Group) in Qinba in China By 3 Types of Genetic Markers

Abstract Background: The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice. Methods: 15 phenotypic traits, a core set of 48 SSR markers as well as SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples.Results: The average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs. Conclusions: The population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.

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Genetic Diversity and Population Structure of 93 Rice Cultivars (Lines) (Oryza Sativa Xian Group) in Qinba in China by 3 Types of Genetic Markers

10.21203/rs.3.rs-1050153/v1 ◽

2021 ◽

Author(s):

Yu Zhang ◽

Yewen Wang ◽

Peijiang Li ◽

Yuexing Wang ◽

Shimao Zheng ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Markers ◽

Ssr Markers ◽

Diversity Index ◽

Indica Rice ◽

Mantel Test ◽

Phenotypic Traits ◽

Phenotypic Analysis

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Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽

10.3390/agronomy11061121 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1121

Author(s):

Hela Chikh-Rouhou ◽

Najla Mezghani ◽

Sameh Mnasri ◽

Neila Mezghani ◽

Ana Garcés-Claver

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Phenotypic Diversity ◽

Diversity Index ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Molecular Data ◽

Mantel Test ◽

Phenotypic Traits ◽

Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

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Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

PeerJ ◽

10.7717/peerj.2504 ◽

2016 ◽

Vol 4 ◽

pp. e2504 ◽

Cited By ~ 1

Author(s):

Katarzyna Bilska ◽

Monika Szczecińska

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Conservation Genetics ◽

Ssr Markers ◽

Full Range ◽

Mantel Test ◽

Evolutionary Potential ◽

Functional Variation ◽

Genetics Research ◽

Outlier Loci

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

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Analysis of genetic diversity and population structure in Saharan maize (Zea mays L.) populations using phenotypic traits and SSR markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-018-0709-3 ◽

2018 ◽

Vol 66 (1) ◽

pp. 243-257 ◽

Cited By ~ 1

Author(s):

Nawel Belalia ◽

Antonio Lupini ◽

Abderrahmane Djemel ◽

Abdelkader Morsli ◽

Antonio Mauceri ◽

...

Keyword(s):

Genetic Diversity ◽

Zea Mays ◽

Population Structure ◽

Ssr Markers ◽

Zea Mays L ◽

Phenotypic Traits

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Assessment of Genetic Diversity and Population Structure in Pea (Pisum sativum L.) Germplasm based on Morphological Traits and SSR Markers

Legume Research - An International Journal ◽

10.18805/lr-4751 ◽

2021 ◽

Author(s):

Shalini Singh ◽

B. Singh ◽

V.R. Sharma ◽

M. Kumar ◽

U. Sirohi

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Morphological Traits ◽

Phenotypic Traits ◽

Pisum Sativum L ◽

New Varieties ◽

Components Analysis ◽

Structure Result ◽

Diversity Estimates

Background: The study was undertaken to assess the genetic diversity and genetic structure among fifty-five pea accessions using morphological traits and SSR markers. Methods: A total of 55 pea accessions were analyzed using eleven phenotypic traits and twenty SSR markers. The data obtained by morphological and molecular profiling was used for the analysis of genetic diversity and for the estimation of genetic diversity estimates, correlation, principal components analysis and population structure. Result: This study reveals that majority of genetic variation was due to variation within population and were clustered into two distinct groups, which reveals a high admixture within individuals. Accessions viz., VRP-82, VRP-320, VRP-194, VRP-375, EC-97280 and EC-8724, showed great diversity as compared to the other accessions based on both morphological and molecular markers. These accessions may assist in developing and planning breeding strategies aimed to produce new varieties in the future.

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Contrasting effects of geographical separation on the genetic population structure of sympatric species of mites in avocado orchards

Bulletin of Entomological Research ◽

10.1017/s0007485314000388 ◽

2014 ◽

Vol 104 (5) ◽

pp. 610-621 ◽

Cited By ~ 4

Author(s):

S. Guzman-Valencia ◽

M.T. Santillán-Galicia ◽

A.W. Guzmán-Franco ◽

H. González-Hernández ◽

M.G. Carrillo-Benítez ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Sequence Data ◽

Mite Species ◽

Mantel Test ◽

Sequence Information ◽

Genetic Population ◽

Nucleotide Sequence Data ◽

Geographical Separation

AbstractOligonychus punicae and Oligonychus perseae (Acari: Tetranychidae) are the most important mite species affecting avocado orchards in Mexico. Here we used nucleotide sequence data from segments of the nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes to assess the phylogenetic relationships between both sympatric mite species and, using only ITS sequence data, examine genetic variation and population structure in both species, to test the hypothesis that, although both species co-occur, their genetic population structures are different in both Michoacan state (main producer) and Mexico state. Phylogenetic analysis showed a clear separation between both species using ITS and COI sequence information. Haplotype network analysis done on 24 samples of O. punicae revealed low genetic diversity with only three haplotypes found but a significant geographical population structure confirmed by analysis of molecular variance (AMOVA) and Kimura-2-parameter (K2P) analyses. In addition, a Mantel test revealed that geographical isolation was a factor responsible for the genetic differentiation. In contrast, analyses of 22 samples of O. perseae revealed high genetic diversity with 15 haplotypes found but no geographical structure confirmed by the AMOVA, K2P and Mantel test analyses. We have suggested that geographical separation is one of the most important factors driving genetic variation, but that it affected each species differently. The role of the ecology of these species on our results, and the importance of our findings in the development of monitoring and control strategies are discussed.

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Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

10.21203/rs.2.17640/v1 ◽

2019 ◽

Author(s):

Xiu Yang ◽

Ling Xi ◽

Binwen Tan ◽

Wei Zhu ◽

Lili Xu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Common Wheat ◽

Diversity Index ◽

Genotyping By Sequencing ◽

Cost Effective ◽

Wheat Breeding ◽

Snp Markers ◽

Next Generation Sequencing Technology

Abstract Background Availability of information on the genetic diversity and population structure of germplasm facilitates its use in wheat breeding programs. Recently, with the development of next-generation sequencing technology, genotyping-by-sequencing (GBS) has been used as a high-throughput and cost-effective molecular tool for examination of the genetic diversity of wheat breeding lines. In this study, GBS was used to characterize a population of 180 accessions of common wheat originating from Asia and Europe between the latitudes 30° and 45°N.Results In total, 24,767 high-quality single-nucleotide polymorphism (SNP) markers were used for analysis of genetic diversity and population structure. The B genome contained the highest number of SNPs, followed by the A and D genomes. The polymorphism information content ranged from 0.1 to 0.4, with an average of 0.26. The distribution of SNPs markers on the 21 chromosomes ranged from 243 on chromosome 4D to 2,337 on chromosome 3B. Structure and cluster analyses divided the panel of accessions into two subgroups (G1 and G2). G1 principally consisted of European and partial Asian accessions, and G2 comprised mainly accessions from the Middle East and partial Asia. Molecular analysis of variance showed that the genetic variation was greater within groups (99%) than between groups (1%). Comparison of the two subgroups indicated that G1 and G2 contained a high level of genetic diversity. The genetic diversity of G2 was higher as indicated by the Shannon’s information index ( I ) = 0.512, diversity index ( h ) = 0.334, observed heterozygosity ( H o ) = 0.226, and unbiased diversity index (uh) = 0.338.Conclusion The present results will not only help breeders to understand the genetic diversity of wheat germplasm on the Eurasian continent between the latitudes of 30° and 45°N, but also provide valuable information for wheat genetic improvement through introgression of novel genetic variation in this region.

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ISSR markers and morphometry determine genetic diversity and population structure in Hedera helix L.

Czech Journal of Genetics and Plant Breeding ◽

10.17221/93/2021-cjgpb ◽

2021 ◽

Author(s):

Abdul Shakoor ◽

Gul Zaib ◽

Fang Zhao ◽

Wuyang Li ◽

Xincan Lan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Similarity ◽

Diversity Index ◽

Morphological Characteristics ◽

Principal Component ◽

Mantel Test ◽

Hedera Helix ◽

Plant Populations ◽

High Genetic Diversity

Hedera helix L. is an invasive, but medicinally important plant. In Iran, there is no available study on the H. helix population to reveal the genetic diversity and population structure. Fifty-six individual plants belonging to nine geographical populations were collected in four provinces of Iran. High genetic diversity, polymorphisms, and a Shannon diversity index of 0.269 were detected in Mazandaran, Kandovan (Population 3). Analysis of the molecular variance indicated 40% of total genetic variation of the whole population was present in the subpopulation. A high genetic similarity (0.922) between plant Populations 5 (Kermanshah; Islamabad) and 6 (Kermanshah; Paveh) was noted. On the other hand, a low genetic similarity was observed between plant Populations 1 (Tehran; Darband) and 8 (Ardabil; Hur). The Mantel test revealed a correlation between the genetic and geographical distances. Furthermore, it demonstrated the isolation mechanism responsible for the population structure in the H. helix plant populations. The principal component analysis explained the majority of the variation in the morphological characteristics. Three components explained 87% of the variation, and the first component explained 60% of the variation. For instance, the leaf morphology showed a correlation of > 0.7 between leaf morphological and floral characters. The plant leaves and quantitative flower characteristics separated the plant populations according to the differences in length. The current results have implications for plant conservation and management.

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Assessing Genetic Variability and Population Structure of Ziziphus Nummularia as Characterized by Phenotypic Traits and SSR Markers with Climatic Distribution

10.21203/rs.3.rs-432958/v1 ◽

2021 ◽

Author(s):

Nisar Uddin ◽

Noor Muhammad ◽

Niaz Ali ◽

Muhammad Khalil Ullah Khan ◽

Muhammad Nisar ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Ssr Markers ◽

Gene Diversity ◽

Important Variable ◽

Phenotypic Traits ◽

Migration Routes ◽

Precipitation Seasonality ◽

Ziziphus Nummularia

Abstract Genus of Ziziphus (family Rhamnaceae), approximately 170 species of prodigious economic and ecological importance. Studies on the genetic diversity within Pakistani Ziziphus species are limited, and to date, no single report on the application of DNA barcoding attempt for identification of Ziziphus species is available in the literature. Therefore, the current study was designed to biogeographic distribution, to assess diversity based on phenotypic traits, SSRs markers, and relationships among Ziziphus nummularia (Burm.f.) Wight & Arn. genotypes. For the first time we use ArcGIS modeling, and their cartographic function for the identification of diversity in climatic variables such as temperature, mean diurnal, humidity, precipitation, and precipitation seasonality and the using of these techniques to determine the important variable which is responsible for the recent distribution of the Ziziphus species. A total of 11 phenotypic traits were noted and have significant phenotypic variation among the traits. The study has used 40 simple sequence repeats (SSR) markers for gaining insights into the genetic diversity within 180 genotypes of Z. nummularia. Successful amplification was achieved with 27 SSRs and was applied for understanding the population structure and relationships among the genotypes. A total of 120 alleles were amplified from Z. nummularia genotypes collected from three districts of the Malakand division, alleles per locus ranged from 2 to 6, averaging 4.4286. whereas polymorphism information content (PIC) from 0.332 to 0.794 in locus JSSR-490 and JSSR-97, within mean value was 0.671 per locus, expected heterozygosity (He), was 0.575, observed heterozygosity (Ho), 0.6618 and average gene diversity 0.494. Flow estimates (6.415) indicated frequent gene flow within Z. nummularia genotypes. Analysis of molecular variance (AMOVA) revealed high genetic variability (80%). The genetic relationship inferred from the neighbor-joining (NJ) phylogeny separate genotypes into three clusters and Bayesian model-based STRUCTURE analyses and PCoA analysis resolved all genotypes and indicted that the KP, populations, Swat and Buner, represent excesses of two different migration routes, with one designated from Swat and Dir (L). The overall results indicated the prevalence of genetic variability and relationships among Z. nummularia across geographical boundaries has retained unique alleles and this may facilitate the development of agronomically desirable and genetically improved Ziziphus cultivars and collections that can help achieve efficient conservation.

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Genetic diversity and population structure of Populus yunnanensis revealed by SSR markers

Pakistan Journal of Botany ◽

10.30848/pjb2020-6(21) ◽

2020 ◽

Vol 52 (6) ◽

Author(s):

Anpei Zhou ◽

Dan Zong ◽

Peihua Gan ◽

Yao Zhang ◽

Dan Li ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers

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