Assessing the Genetic Diversity and Population Structure of World Germplasm Collection of Erianthus arundinaceus (Retz.) Jeswiet Using Sequence-Related Amplified Polymorphic Markers

Sugar Tech ◽  
2021 ◽  
Author(s):  
R. Valarmathi ◽  
H. K. Mahadevaswamy ◽  
V. Ulaganathan ◽  
C. Appunu ◽  
S. Karthigeyan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Polymorphic Markers ◽  
Erianthus Arundinaceus

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

scholarly journals Genetic diversity and population structure of a mini-core subset from the world cowpea (Vigna unguiculata (L.) Walp.) germplasm collection

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Christian Fatokun ◽  
Gezahegn Girma ◽  
Michael Abberton ◽  
Melaku Gedil ◽  
Nnanna Unachukwu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Vigna Unguiculata ◽  
Germplasm Collection ◽  
Core Subset ◽  
The World

Genetic diversity, population structure and association analysis in coconut (Cocos nucifera L.) germplasm using SSR markers

2017 ◽  
Vol 16 (2) ◽  
pp. 156-168 ◽  
Author(s):  
S. Geethanjali ◽  
J. Anitha Rukmani ◽  
D. Rajakumar ◽  
P. Kadirvel ◽  
P.L. Viswanathan
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Association Analysis ◽  
Gene Diversity ◽  
Cocos Nucifera ◽  
Germplasm Collection ◽  
Yield Component ◽  
Chromosome 1 ◽  
Genetic Structuring ◽  
Model Based Clustering

AbstractA world-wide coconut germplasm collection (79 genotypes) was analyzed for genetic diversity and population structure based on 48 simple sequence repeat (SSR) loci. The genotypes displayed moderately high amount of genetic diversity, which was strongly structured according to geographical origins. Number of SSR alleles ranged from 2 to 7 with an average of 4.1 per locus. Gene diversity (expected heterozygosity) estimates ranged from 0.162 to 0.811 with a mean of 0.573. Polymorphism information content values ranged from 0.149 to 0.785 with an average of 0.522. Hierarchical clustering analysis grouped the genotypes into two major clusters with two sub-groups in each, which corresponded with the geographic origins. The first cluster comprised of ‘Tall’ genotypes originated from Indo-Atlantic and South Asia regions. The second cluster comprised mostly of ‘Dwarf’ genotypes and some Tall genotypes which originated from Indo-Pacific and South-East Asia regions. Model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations (K = 2) and four sub-populations (K = 4). The proportion of SSR locus-pairs in linkage disequilibrium was low (2.4%). Association analysis in a subset of 44 genotypes detected a single SSR locus, CnCir73 (chromosome 1) putatively associated with fruit yield component traits, which corresponded with a previously mapped quantitative trait locus in coconut.

scholarly journals Genetic Diversity and Population Structure of Cowpea [Vigna unguiculata (L.) Walp.] Germplasm Collected from Togo Based on DArT Markers

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1451
Author(s):  
Kodjo M. Gbedevi ◽  
Ousmane Boukar ◽  
Haruki Ishikawa ◽  
Ayodeji Abe ◽  
Patrick O. Ongom ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Improvement ◽  
Agricultural Research ◽  
Polymorphic Information Content ◽  
Germplasm Collection ◽  
Mean Value ◽  
Economic Life ◽  
Dart Markers ◽  
Crop Genetic Diversity

Crop genetic diversity is a sine qua non for continuous progress in the development of improved varieties, hence the need for germplasm collection, conservation and characterization. Over the years, cowpea has contributed immensely to the nutrition and economic life of the people in Togo. However, the bulk of varieties grown by farmers are landraces due to the absence of any serious genetic improvement activity on cowpea in the country. In this study, the genetic diversity and population structure of 255 cowpea accessions collected from five administrative regions and the agricultural research institute of Togo were assessed using 4600 informative diversity array technology (DArT) markers. Among the regions, the polymorphic information content (PIC) ranged from 0.19 to 0.27 with a mean value of 0.25. The expected heterozygosity (He) varied from 0.22 to 0.34 with a mean value of 0.31, while the observed heterozygosity (Ho) varied from 0.03 to 0.07 with an average of 0.05. The average inbreeding coefficient (FIS) varied from 0.78 to 0.89 with a mean value of 0.83, suggesting that most of the accessions are inbred. Cluster analysis and population structure identified four groups with each comprising accessions from the six different sources. Weak to moderate differentiation was observed among the populations with a genetic differentiation index varying from 0.014 to 0.117. Variation was highest (78%) among accessions within populations and lowest between populations (7%). These results revealed a moderate level of diversity among the Togo cowpea germplasm. The findings of this study constitute a foundation for genetic improvement of cowpea in Togo.

scholarly journals Genetic diversity and population structure of castor (Ricinus communis L.) germplasm within the US collection assessed with EST-SSR markers

Genome ◽  
2017 ◽  
Vol 60 (3) ◽  
pp. 193-200 ◽  
Author(s):  
M.L. Wang ◽  
M. Dzievit ◽  
Z. Chen ◽  
J.B. Morris ◽  
J.E. Norris ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Acid Composition ◽  
Ssr Markers ◽  
Oil Content ◽  
Germplasm Collection ◽  
Germplasm Management ◽  
The Us

Castor is an important oilseed crop and although its oil is inedible, it has multiple industrial and pharmaceutical applications. The entire US castor germplasm collection was previously screened for oil content and fatty acid composition, but its genetic diversity and population structure has not been determined. Based on the screening results of oil content, fatty acid composition, and country origins, 574 accessions were selected and genotyped with 22 polymorphic EST-SSR markers. The results from cluster analysis, population structure, and principal component analysis were consistent, and partitioned accessions into four subpopulations. Although there were certain levels of admixtures among groups, these clusters and subpopulations aligned with geographic origins. Both divergent and redundant accessions were identified in this study. The US castor germplasm collection encompasses a moderately high level of genetic diversity (pairwise dissimilarity coefficient = 0.53). The results obtained here will be useful for choosing accessions as parents to make crosses in breeding programs and prioritizing accessions for regeneration to improve germplasm management. A subset of 230 accessions was selected and will be planted in the field for establishing a core collection of the US castor germplasm. Further evaluation of the US castor germplasm collection is also discussed.

scholarly journals Genetic variation and population structure in China summer maize germplasm

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guoping Shu ◽  
Gangqiang Cao ◽  
Niannian Li ◽  
Aifang Wang ◽  
Fang Wei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Germplasm Collection ◽  
Genotyping By Sequencing ◽  
Inbred Lines ◽  
Summer Maize ◽  
Heterotic Groups ◽  
Breeding Germplasm

AbstractMaize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.

scholarly journals Genetic Diversity and Population Structure of Job’s Tears(Coix lacryma-jobi L.) Germplasm Based on ISSR Marker

2021 ◽  
Author(s):  
Gang Shen ◽  
Lingling Yang ◽  
Teerayoot Girdthai ◽  
Fanzhi Liu ◽  
Yuhua Fu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Population Structure ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Germplasm Collection ◽  
Issr Markers ◽  
Issr Primer ◽  
Upgma Cluster ◽  
Job’S Tears

Abstract Background: Job's tears（Coix lachryma-jobi L.）is a minor cereal and an important food item in some parts of Asia. It has also been used in the traditional Chinese medicine for relieving various ailments, therefore, it plays an important role in our lives. Lack of excellent new varieties hinders the development of coix as a sustainable crop, and it is urgent to provide new cultivars with excellent trait in Chinese Coix industry. Results: ISSR markers were used to assess the genetic diversity and population structure of 8 populations of Job’s tears in China. A genotyping analysis that utilized ten ISSR primer pairs resulted in the production of 116 bands, of which 98 were polymorphic. The Guizhou population (PPB = 81.90%, h = 0.3113, I = 0.4589) was the most genetically diverse, while the lowest was observed in the Hebei population (PPB = 46.55%, h = 0.1842, I = 0.2701). Genetic differentiation analyses including GST and AMOVA illustrated that genetic variation was most prevalent within populations while only minor variations were observed among populations. Genetic distance coefficients ranged from 0.0095 to 0.0948 for the 8 populations; the genetic relationship between the Guizhou and Chongqing populations was the closest, while the most distant genetic relationship occurred between the Hubei and Hunan populations. The results of an UPGMA cluster analysis that investigated genetic diversity among the populations were consistent with the genetic distance results. The results of a STRUCTURE analysis suggested that 94 Job’s tears accessions could be grouped into two subpopulations. Moreover, according to a cluster analysis based on the UPGMA for individuals of Job’s tears, accessions were divided into two major clusters. The results of the Bayesian cluster and UPGMA cluster analyses were largely consistent despite minor differences. There was no significant correlation between genetic distance and geographic distance (r = 0.055, p = 0.782). Conclusions: Our study was undertaken to systematically analyze genetic diversity and population structure in 94 Job’s tears accessions using ISSR markers. And this study provides us with valuable information pertaining to germplasm collection, genetic improvement, and systematic utilization of Job’s tears.

scholarly journals On genetic diversity in caraway: Genotyping of a large germplasm collection

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244666
Author(s):  
Daniel von Maydell ◽  
Heike Lehnert ◽  
Thomas Berner ◽  
Evelyn Klocke ◽  
Wolfram Junghanns ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genome Size ◽  
Phylogenetic Trees ◽  
Germplasm Collection ◽  
Genotyping By Sequencing ◽  
Gene Pools ◽  
History Of ◽  
Winter Annual ◽  
Neighbor Network

Caraway (Carum carvi) is a widespread and frequently used spice and medicinal plant with a long history of cultivation. However, due to ongoing climatic changes, the cultivation is becoming increasingly risky. To secure caraway cultivation in future, timely breeding efforts to develop adapted material are necessary. Analysis of genetic diversity can accompany this process, for instance, by revealing untapped gene pools. Here, we analyzed 137 accessions using genotyping by sequencing (GBS). Hence, we can report a broad overview of population structure and genetic diversity of caraway. Population structure was determined using a principal coordinate analysis, a Bayesian clustering analysis, phylogenetic trees and a neighbor network based on 13,155 SNPs. Genotypic data indicate a clear separation of accessions into two subpopulations, which correlates with the flowering type (annual vs. biennial). Four winter-annual accessions were closer related to biennial accessions. In an analysis of molecular variance, genetic variation between the two subpopulations was 7.84%. In addition, we estimated the genome size for 35 accessions by flow cytometry. An average genome size of 4.282 pg/2C (± 0.0096 S.E.) was estimated. Therefore, we suggest a significantly smaller genome size than stated in literature.

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