Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI

2012 ◽  
Vol 10 (3) ◽  
pp. 186-193 ◽  
Author(s):  
Fangming Xie ◽  
Longbiao Guo ◽  
Guangjun Ren ◽  
Peisong Hu ◽  
Feng Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Indica Rice ◽  
Population Diversity ◽  
Rice Varieties ◽  
Heterotic Groups ◽  
Breeding Lines ◽  
Genetic Diversity And Structure ◽  
Grouping Method ◽  
Genetic Structures

Investigation of genetic diversity and the relationships among varieties and breeding lines is of great importance to facilitate parental selection in the development of inbred and hybrid rice varieties and in the construction of heterotic groups. The technology of single nucleotide polymorphism (SNP) is being advanced for the assessment of population diversity and genetic structures. We characterized 215 widely cultivated indica rice varieties developed in southern China and at the International Rice Research Institute (IRRI) using IRRI-developed SNP oligonucleotide pooled assay (OPA) to provide grouping information of rice mega-varieties for further heterotic pool study. The results revealed that the Chinese varieties were more divergent than the IRRI varieties. Two major subpopulations were clustered for the varieties using a model-based grouping method. The IRRI varieties were closely grouped and separated clearly from the majority of the Chinese varieties. The Chinese varieties were subclustered into three subgroups, but there was no clear evidence to separate the Chinese varieties into subgroups geographically, indicating a great degree of genetic integration of alleles and shared ancestries among those high-yielding modern varieties.

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

Genetic diversity and structure of the noxious alien grass Praxelis clematidea in southern China

2015 ◽  
Vol 59 ◽  
pp. 183-189 ◽  
Author(s):  
Qizhi Wang ◽  
Min Huang ◽  
Stephen R. Downie ◽  
Zhenxi Chen ◽  
Yating Chen
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Genetic Diversity And Structure

Geographic pattern of variation among Asian native rice cultivars (Oryza sativa L.) based on fifteen isozyme loci

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 782-792 ◽  
Author(s):  
J. C. Glaszmann
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Indian Subcontinent ◽  
Indica Rice ◽  
Japonica Rice ◽  
Geographic Pattern ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Himalayan Foothills

The geographic pattern of isozyme variation among rice varieties (Oryza sativa L.) in Asia is described based on an electrophoretic survey of 1688 accessions for 15 loci. The distribution patterns are strongly determined by the existence of several varietal groups that are characterized by contrasting multilocus types with dissimilar environmental and macrogeographic distributions. The two main groups correspond to the indica and japonica subspecies. Other types are frequently found in the Indian subcontinent, especially along the Himalayan foothills. These types are predominant in the Indus River basin. They are differentiated into four groups in the eastern part of the Himalayan foothills. There is variation within the groups. Non-random allele distributions are observed, such as regional clines and narrow localization of alleles. Diversity among indica rice is evenly distributed in whole tropical Asia. Variation among japonica rice shows the hilly part of continental Southeast Asia to be the region of highest genetic diversity and its probable area of origin. All this information provides a guide for further analysis aimed at elucidating the history of cultivated rice in Asia and, subsequently, in other continents.Key words: Asian rice, genetic diversity, isozymes, geographic distributions.

scholarly journals Genetic diversity and structure in fragmented populations of the endangered species Ranunculus cabrerensis (Ranunculaceae): implications for conservation

Biologia ◽  
2013 ◽  
Vol 68 (1) ◽  
Author(s):  
Eduardo Cires ◽  
Candela Cuesta ◽  
José Fernández Prieto
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
Conservation Strategies ◽  
Aflp Analysis ◽  
Issr Primer ◽  
Bayesian Analyses ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Different Populations ◽  
Genetic Structures

AbstractRanunculus cabrerensis is an endemic and endangered species of the Northwestern Iberian Peninsula. The molecular markers AFLP and ISSR were used to investigate the genetic diversity and population structure of four populations across its known distribution. Fifteen selective primer combinations of AFLP and seventeen ISSR primer combinations produced a total of 2830 and 103 unambiguously repeatable fragments respectively, of which 97.57 and 81.38% were polymorphic for both markers. The genetic diversity of R. cabrerensis at species level was high (H E = 0.294 by ISSR and H E = 0.191 by AFLP) and differentiation between sampled locations was also relatively high (G ST = 0.316 and 0.158 by ISSR and AFLP analysis respectively) compared to other studies of endangered and rare species using the same techniques. The analysis of molecular variance (AMOVA) indicated that the main genetic variation was within sampled locations (73% by AFLP; 52% by ISSR), even though the variation among locations was also significant. Principal Coordinates, NeighborNet and Bayesian analyses revealed a weak but significant relationship between the genetic structures of different populations in R. cabrerensis, with gene flow acting as a homogenizing force that prevents stronger differentiation of populations. Finally, suggestions for conservation strategies to preserve the genetic resources of this species are outlined.

scholarly journals Diversity analysis of some selected rice genotypes through SSR- based molecular markers

2016 ◽  
Vol 12 (2) ◽  
pp. 307-311 ◽  
Author(s):  
MH Shahriar ◽  
AHK Robin ◽  
SN Begum ◽  
A Hoque
Keyword(s):  
Genetic Diversity ◽  
Marker Assisted Selection ◽  
Oryza Sativa L ◽  
Diversity Analysis ◽  
Growth Duration ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Early Maturing ◽  
Rice Genotypes

An experiment was carried out to assess the genetic diversity of advanced rice (Oryza sativa L.) breeding lines using three SSR markers viz., RM147, RM167 and RM215. Thirty T- aman advanced breeding lines at F9 generation along with 4 check varieties were assessed. All three primers showed polymorphism. A total of 29 alleles were detected among the rice genotypes with an average of 9.67 alleles per locus. Polymorphism information content (PIC) ranged from 0.47 to 0.88 with an average of 0.71. A dendrogram was constructed based on total microsatellite polymorphism and 34 genotypes were grouped into four major clusters at 0.36 similarity co-efficient differentiating the early maturing genotypes from the late maturing types. The information about the genetic diversity might be utilized in future breeding programs for developing rice varieties with much shorter growth duration. The results also suggested that microsatellite markers which are linked to genes or QTLs responsible for growth duration properties are suitable tools for marker assisted selection (MAS) to select the rice genotypes of shorter growth duration.J. Bangladesh Agril. Univ. 12(2): 307-311, December 2014

scholarly journals ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China

Biology ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. 2 ◽  
Author(s):  
Weifeng Wu ◽  
Faxing Chen ◽  
Kaiwun Yeh ◽  
Jianjun Chen
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationship ◽  
Phylogenetic Trees ◽  
Southern China ◽  
Morphological Characteristics ◽  
Relationship Analysis ◽  
Genetic Diversity And Structure ◽  
Plum Varieties ◽  
Index Value

Plums (Prunus spp.) are important deciduous fruit crops in the world. China is a major producer of P. salicina Lindl., but the genetic relationship of Chinese plums in key production regions remain unclear. In this study, 14 University of British Columbia (UBC) inter simple sequence repeats (ISSR) primers were used to analyze 33 plum varieties cultivated in Fujian Province to determine their genetic diversity and population structure. A total of 146 bands were generated, of which 130 were polymorphic. Mean percentage of polymorphic bands was 89.04%, Shannon’s information index value was 0.38, and the Nei’s genetic index value was 0.24. Using unrooted trees (Neighbor-Joining method), 33 varieties were classified into four groups. Split graph separated them into two major groups, each with two subgroups. The two phylogenetic trees indicate that environmental or natural selection pressure is an important factor influencing their genetic relationship. Analysis of population structure revealed that they have frequent genetic exchanges among closed subpopulations; thus, genetic variation mainly occurs within the population. Additionally, based on the phylogenetic analysis and unique morphological characteristics of fruits, we propose that the Chinese landrace Nai could contribute significantly to development of the famous variety Wickson.

scholarly journals Population Diversity and Genetic Structure Reveal Patterns of Host Association and Anthropogenic Impact for the Globally Important Fungal Tree Pathogen Ceratocystis manginecans

2021 ◽  
Vol 7 (9) ◽  
pp. 759
Author(s):  
Feifei Liu ◽  
Tuan A. Duong ◽  
Irene Barnes ◽  
Michael J. Wingfield ◽  
Shuaifei Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Fungal Pathogens ◽  
Population Diversity ◽  
Global Distribution ◽  
Host Association ◽  
Genetic Diversity And Structure ◽  
Plant Hosts ◽  
Geographic Regions ◽  
Host Associations

Species in the Ceratocystis manginecans complex are important fungal pathogens of plantation trees globally. The most important hosts include species of Eucalyptus, Acacia, Mangifera, and Punica. Despite their relevance and widespread occurrence, little is known regarding their population genetics and how this might relate to their host associations or geographic regions in which they occur. A global collection of 491 isolates representing the C. manginecans complex, from four different plant hosts and nine countries, were genotyped using microsatellite markers. Population genetic analyses using numerous tools were conducted to interrogate how their genetic diversity and structure might be affected by host or areas of occurrence. Results of genetic diversity studies showed that when grouping isolates into populations based on their host associations, the population on Eucalyptus was most diverse, and it also has a broad global distribution. When considering countries of origin as a basis for defining populations, the gene and genotypic diversity were highest in populations from China, Indonesia, and Brazil. In contrast, populations from Oman and Pakistan collected from Mangifera had the lowest genetic diversity and were clonal. Molecular variance, population differentiation, and network and structure analyses showed that the genetic structure of isolates in the C. manginecans complex is influenced by both host association as well as geographical isolation. Furthermore, the results reflected the movement of genotypes between plant hosts and geographic regions that have implications regarding the broad global distribution of this pathogen.

scholarly journals Genetic Diversity of Main Inbred Indica Rice Varieties Applied in Guangdong Province as Revealed by Molecular Marker

Rice Science ◽  
2015 ◽  
Vol 22 (1) ◽  
pp. 1-8 ◽  
Author(s):  
HUANG Ming ◽  
WU Ya-hui ◽  
TAO Xing-xing ◽  
LIU Yong-zhu ◽  
YANG Gui-li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Indica Rice ◽  
Guangdong Province ◽  
Rice Varieties

Free and bound phenolic profiles and antioxidant activity of milled fractions of different indica rice varieties cultivated in southern China

2014 ◽  
Vol 159 ◽  
pp. 166-174 ◽  
Author(s):  
Huihui Ti ◽  
Qing Li ◽  
Ruifen Zhang ◽  
Mingwei Zhang ◽  
Yuanyuan Deng ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Southern China ◽  
Indica Rice ◽  
Rice Varieties ◽  
Phenolic Profiles
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