Genetic diversity and structure of improved indica rice germplasm

2014 ◽  
Vol 12 (2) ◽  
pp. 248-254 ◽  
Author(s):  
Kai Wang ◽  
Fulin Qiu ◽  
Madonna Angelita Dela Paz ◽  
Jieyun Zhuang ◽  
Fangming Xie
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Latin American ◽  
Hybrid Rice ◽  
Hybrid Breeding ◽  
Model Based ◽  
Population Structure Analysis ◽  
Wide Range ◽  
Genetic Diversity And Structure ◽  
Breeding Programmes

The characterization of genetic diversity and structure for improved cultivated varieties/elite lines is tremendously important to assist breeders in parental selection for inbred and hybrid breeding and heterotic group construction. In this study, a total of 737 improved indica varieties/lines developed recently and/or widely used by present indica breeding programmes worldwide were genotyped with a 384-single-nucleotide polymorphism assay. Model-based population structure analysis revealed the presence of two major groups with six subgroups (SGs), wherein no clear correlation was found between the groups/SGs and breeding programmes or geographical origin of the accessions. Over half of the accessions (51.8%) appeared to have less than 0.6 memberships assigned to any one of the six model-based groups, highlighting the wide range of gene flow within improved indica varieties/lines and the genetic integration of valuable alleles shared by ancestries among improved high-yielding varieties/lines through germplasm exchanges. Distance-based clustering revealed that Latin-American cultivated indica lines have tended to form their own ecological cline, which could serve as a potential heterotic ecotype for hybrid rice breeding, although they are still closely related to Asian indica lines. African cultivated indica lines, on the other hand, have not yet formed their own ecological cline. It was also observed that the most well-known hybrid rice parents, Zhenshan97B and Minghui63, were unexpectedly clustered in the same SG with a relatively narrow genetic distance, which suggests that a significant genetic distance between parents is not a prerequisite for all elite hybrid rice lines with high heterosis.

scholarly journals Genetic Structure and Core Collection of Olive Germplasm from Albania Revealed by Microsatellite Markers

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 256
Author(s):  
Aida Dervishi ◽  
Jernej Jakše ◽  
Hairi Ismaili ◽  
Branka Javornik ◽  
Nataša Štajner
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Core Collection ◽  
Expressed Sequence Tag ◽  
Fruit Trees ◽  
Ex Situ ◽  
Natural Ecosystems ◽  
Model Based ◽  
Genetic Diversity And Structure

Olive is considered one of the oldest and the most important cultivated fruit trees in Albania. In the present study, the genetic diversity and structure of Albanian olive germplasm is represented by a set of 194 olive genotypes collected in-situ in their natural ecosystems and in the ex-situ collection. The study was conducted using 26 microsatellite markers (14 genomic SSR and 12 Expressed Sequence Tag microsatellites). The identity analysis revealed 183 unique genotypes. Genetic distance-based and model-based Bayesian analyses were used to investigate the genetic diversity, relatedness, and the partitioning of the genetic variability among the Albanian olive germplasm. The genetic distance-based analysis grouped olives into 12 clusters, with an average similarity of 50.9%. Albanian native olives clustered in one main group separated from introduced foreign cultivars, which was also supported by Principal Coordinate Analysis (PCoA) and model-based methods. A core collection of 57 genotypes representing all allelic richness found in Albanian germplasm was developed for the first time. Herein, we report the first extended genetic characterization and structure of olive germplasm in Albania. The findings suggest that Albanian olive germplasm is a unique gene pool and provides an interesting genetic basis for breeding programs.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

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.

scholarly journals Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Ujjal Kumar Nath ◽  
Dhiman Biswas ◽  
Sathishkumar Natarajan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Large Scale ◽  
Polymorphic Information Content ◽  
Pcr Amplification ◽  
Efficient Manner ◽  
Lilium Species ◽  
Population Structure Analysis ◽  
Wide Range ◽  
Functional Molecular Markers

Abstract Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

scholarly journals Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255418
Author(s):  
Siou Ting Gan ◽  
Chin Jit Teo ◽  
Shobana Manirasa ◽  
Wei Chee Wong ◽  
Choo Kien Wong
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Oil Palm ◽  
Core Collection ◽  
Elaeis Guineensis ◽  
Germplasm Conservation ◽  
Ex Situ ◽  
Fixation Index ◽  
Core Set ◽  
Genetic Diversity And Structure

Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright’s fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei’s genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.

scholarly journals Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3842 ◽  
Author(s):  
Daniela Lazo-Cancino ◽  
Selim S. Musleh ◽  
Cristian E. Hernandez ◽  
Eduardo Palma ◽  
Enrique Rodriguez-Serrano
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Isolation By Distance ◽  
Landscape Fragmentation ◽  
Native Forest ◽  
Least Cost Path ◽  
Natural Habitats ◽  
Forest Patches ◽  
Genetic Diversity And Structure ◽  
Oligoryzomys Longicaudatus

Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between full growth native forest remnants is mediated by the presence of dense shrublands and native forest corridors. In this sense, our results are important because they show how native forest patches and associated routes act as source of vector species in silvoagropecuary landscape, increasing the infection risk on human population. This study is the first approach to understand the epidemiological spatial context of silvoagropecuary risk of Hantavirus emergence. Further studies are needed to elucidate the effects of landscape fragmentation in order to generate new predictive models based on vector intrinsic attributes and landscape features.

scholarly journals MORPHO-AGRONOMIC CHARACTERIZATION AND GENETIC DIVERSITY IN PEPPERS (Capsicum spp.)

2021 ◽  
Vol 34 (3) ◽  
pp. 505-513
Author(s):  
MAYARA RODRIGUES E SILVA ◽  
RAIMUNDO NONATO OLIVEIRA SILVA
Keyword(s):  
Genetic Diversity ◽  
Block Design ◽  
Randomized Block Design ◽  
Wide Range ◽  
Significant Difference ◽  
Conservation Of Genetic Resources ◽  
Bell Peppers ◽  
Capsicum Spp ◽  
Breeding Programmes ◽  
Fruit Wall

ABSTRACT Peppers and bell peppers (Capsicum spp.) are vegetables that have wide genetic variability, as well as a wide range of applications. Studies on genetic diversity help to understand the existing variability and the conservation of genetic resources, allowing breeders to select superior genotypes that meet the needs of breeding programmes. This study aimed to evaluate the genetic diversity among 15 Capsicum genotypes based on morpho-agronomic descriptors and through the Ward-MLM (Modified Location Model) procedure, as well as to indicate the most promising genotypes for breeding programmes. The research was conducted in an experimental area using a randomized block design, with three replications, using nine qualitative descriptors and ten quantitative descriptors. Analysis of variance was performed, and means were subsequently grouped by Scott-Knott’s method. There was a significant difference between genotypes for all traits evaluated, making it possible to select promising genotypes. According to the Scott-Knott grouping test, the number of seeds per fruit had the largest number of groups, with eight distinct groups, while plant height had only two groups. The genotypes GEN18 and GEN21 had the highest average values for fruit wall thickness and thus are indicated for the preparation of sauces. The genotypes GEN14 and GEN16 were the most promising for use for ornamental purposes. The Ward-MLM method made it possible to differentiate C. annuum L., C. baccatum L., C. chinense Jacq., and C. frutescens L. into different groups, and is thus a useful tool to detect genetic divergence.

Assessment of genetic diversity in advanced breeding lines derived from intraspecific crosses of garden pea (Pisum sativum L.)

2018 ◽  
Author(s):  
Bhallan Singh Sekhon ◽  
Akhilesh Sharma ◽  
Viveka Katoch . ◽  
Rakesh K. Kapila ◽  
V. K. Sood
Keyword(s):  
Genetic Diversity ◽  
Hybrid Breeding ◽  
Internodal Length ◽  
Garden Pea ◽  
Breeding Lines ◽  
Pisum Sativum L ◽  
Breeding Programmes ◽  
Pedigree Selection ◽  
Direct Use ◽  
Intraspecific Hybrid

An intraspecific hybrid breeding program involving six crosses, Palam Sumool (PS) × Palam Priya, PS × Pb-89, PS × Azad P-1, PS × Palam Triloki and VRPMR10 × Sugar Giant, Green Pearl × DPP-9411 was initiated in 2006 onwards followed by pedigree selection, resulted in isolation of 45 genotypes with desirable attributes. These progenies along with five recommended varieties were evaluated during 2014-15 to assess degree of divergence. A considerable genetic diversity was observed among genotypes, dispersed in 18 diverse clusters. Of these, 17 were monogenotypic while cluster I had maximum genotypes. Internodal length contributed maximum towards total genetic divergence followed by nodes per plant, protein content and average pod weight. Superior performing genotypes viz., ‘DPP-2011-SP-7’, ‘DPP-2011-SP-17’, and ‘DPP-2011-SP-24’ from cluster I and ‘DPP-2011-SP-6’, ‘DPP-2011-SP-22’ ‘DPPMR-09-1’, ‘DPPMR-09-2’, ‘DPP-2011-SN-5’ and ‘Palam Triloki’ from monogenotypic clusters offer promise for their direct use as varieties and as potential parents in future breeding programmes.

scholarly journals The Genetic Diversity and Structure of Tomato Landraces from the Campania Region (Southern Italy) Uncovers a Distinct Population Identity

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 564
Author(s):  
Martina Caramante ◽  
Youssef Rouphael ◽  
Giandomenico Corrado
Keyword(s):  
Genetic Diversity ◽  
Southern Italy ◽  
Molecular Profile ◽  
Campania Region ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure ◽  
Conservation Actions ◽  
Regional Population ◽  
Regional Brand ◽  
The Individual

Italy is one of the main producers and processors of tomato and it is considered a secondary center of diversity. In some areas, such as the Campania region (Southern Italy), a range of traditional tomato landraces is still cultivated. The distinction of this heritage germplasm is often based only on folk taxonomy and a more comprehensive definition and understanding of its genetic identity is needed. In this work, we compared a set of 15 local landraces (representative of traditional fruit types) to 15 widely used contemporary varieties, using 14 fluorescent Simple Sequence Repeat (SSR) markers. Each of the accessions possessed a unique molecular profile and overall landraces had a genetic diversity comparable to that of the contemporary varieties. The genetic diversity, multivariate, and population structure analysis separated all the genotypes according to the pre-defined groups, indicating a very reduced admixture and the presence of a differentiated (regional) population of landraces. Our work provides solid evidence for implementing conservation actions and paves the way for the creation of a premium regional brand that goes beyond the individual landrace names of the Campania region known throughout the world.

scholarly journals Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 340
Author(s):  
Muhammad Massub Tehseen ◽  
Deniz Istipliler ◽  
Zakaria Kehel ◽  
Carolina P. Sansaloni ◽  
Marta da Silva Lopes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Distance ◽  
Bread Wheat ◽  
Structure Analysis ◽  
Geographic Origin ◽  
Climatic Conditions ◽  
Population Structure Analysis ◽  
North Eastern ◽  
Wheat Landraces

Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high-yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north-eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping-by-sequencing of studied landraces after quality control provided 4897 high-quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using model-based STRUCTURE analysis and cluster-based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub-populations compared with the variation observed as a whole between sub-populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro-climatic conditions prevalent within the north-eastern agro-ecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro-climatic conditions within the agro-climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north-eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses.

scholarly journals Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv.

Forests ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1282
Author(s):  
Yu Wang ◽  
Zhongyi Jiao ◽  
Jiwei Zheng ◽  
Jie Zhou ◽  
Baosong Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Management Strategies ◽  
Natural Populations ◽  
Snp Markers ◽  
Fixation Index ◽  
Landscape Genomics ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure ◽  
Chosenia Arbutifolia

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

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