Myanmar mango landraces reveal genetic uniqueness over common cultivars from Florida, India, and Southeast Asia

Genome ◽  
2010 ◽  
Vol 53 (4) ◽  
pp. 321-330 ◽  
Author(s):  
R. Hirano ◽  
Than Htun Oo ◽  
K. N. Watanabe
Keyword(s):  
Genetic Differentiation ◽  
Southeast Asia ◽  
Genetic Background ◽  
Mangifera Indica ◽  
Neighbor Joining ◽  
Large Area ◽  
Principal Coordinates ◽  
Low Degree ◽  
Bayesian Cluster ◽  
Private Alleles

Mango ( Mangifera indica ) is believed to have evolved in a large area spanning northeastern India, Bangladesh, and northwestern Myanmar. We compared the genetic structure of mango accessions from Myanmar with that of mango accessions from Florida, India, and Southeast Asia with 11 SSR markers. The Myanmar accessions exhibited considerable genetic diversity (unbiased heterozygosity, UHe = 0.698) and a high number of private alleles. Despite the low degree of genetic differentiation among accessions (global Fst, θ = 0.123), Myanmar’s accessions were distinguishable from mango accessions from Florida, India, and Southeast Asia in a principal coordinates plot. Genetic differentiation of the Myanmar accessions from other groups was also observed in a Bayesian cluster analysis. No population structure among Myanmar accessions was revealed by a neighbor-joining tree. Our results revealed a broad genetic background and genetic distinctiveness of mango in Myanmar. We discuss the implications for diversification mechanisms based on the embryo type characteristics and provide recommendations for conservation efforts.

scholarly journals Propagation management methods have altered the genetic variability of two traditional mango varieties in Myanmar, as revealed by SSR

2011 ◽  
Vol 9 (3) ◽  
pp. 404-410 ◽  
Author(s):  
R. Hirano ◽  
H. Ishii ◽  
Than Htun Oo ◽  
S. A. Gilani ◽  
A. Kikuchi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Background ◽  
Clonal Propagation ◽  
Mangifera Indica ◽  
Sequence Repeat ◽  
Single Sequence Repeat ◽  
Principal Coordinates ◽  
The Relationship ◽  
Single Sequence ◽  
Cultivation History

Mango (Mangifera indica L.) is an important fruit crop with a long cultivation history in Myanmar. This study evaluated the genetic variation within two economically important traditional varieties, ‘Yin Kwe’ and ‘Sein Ta Lone’, and the relationship between genetic variation and propagation practices. Genetic variation was estimated by genotyping 94 individuals with 12 single sequence repeat markers. ‘Yin Kwe’ (n = 53) showed higher levels of observed heterozygosity (Ho = 0.59) and average genetic distance among individuals (Da = 0.29) than did ‘Sein Ta Lone’ (n = 41; Ho = 0.45; Da = 0.09). The differences between the two varieties at the DNA level were significant (Fst = 0.44). The broader genetic background in ‘Yin Kwe’ compared with ‘Sein Ta Lone’ was also demonstrated by neighbour-joining and principal coordinates analyses. Differences in variety uses and propagation practices were determined by interviewing local specialists in Lower Myanmar (southern Myanmar). ‘Yin Kwe’ was often used as a rootstock for ‘Sein Ta Lone’. Clonal propagation by grafting was observed frequently for ‘Sein Ta Lone’ but never for ‘Yin Kwe’. The differences in genetic variation between these two varieties might have been caused by the propagation practices for each variety, which result from their respective uses.

scholarly journals Genetic and Ecological Relationships of Anastrepha ludens (Diptera: Tephritidae) Populations in Southern Mexico

Insects ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 815
Author(s):  
Lorena Ruiz-Montoya ◽  
Rodrigo Verónica Vallejo ◽  
David Haymer ◽  
Pablo Liedo
Keyword(s):  
Sexual Selection ◽  
Genetic Differentiation ◽  
Host Plants ◽  
Control Strategies ◽  
Mangifera Indica ◽  
Random Mating ◽  
Management Strategies ◽  
Fruit Fly ◽  
Anastrepha Ludens ◽  
Southern Mexico

Knowledge of the influence of evolutionary factors that promote either the differentiation or cohesion of pest insect populations is critical for the improvement of control strategies. Here, we explore the extent to which genetic differentiation occurs between populations of the Mexican fruit fly, Anastrepha ludens, in association with four plant hosts (Citrus sinensis, C. paradisi, Mangifera indica and Casimiroa edulis) in the Soconusco region of Chiapas (Mexico). Using variants from six enzymatic loci, we obtained measures of genetic diversity for three sample arrangements: (1) by sex per locality, (2) by locality and (3) by host. The extent of genetic differentiation in populations was assessed using the Analyses of Molecular Variance (AMOVA) method for each array of samples, and moderate to high levels of genetic variation were observed between the sexes, as well as among localities and host plants. A Bayesian approach was then used to assess any population structure underlying the genetic data we obtained, but this analysis showed no significant structuring due to locality or host plant. We also considered whether the observed genotypic frequencies in male and females matched those expected under a hypothesis of random mating. Here we found significant deviations from expected genotypic frequencies, suggesting that sexual selection is acting on these populations. Overall, our results indicate that sexual selection, along with the presence of some heterogeneity in environments provided by both geographical factors and availability of host plants, has influenced the evolution of pest populations in this region of Mexico. Implications for area-wide pest management strategies are discussed.

scholarly journals Genetic differentiation of Ganaspis brasiliensis (Hymenoptera: Figitidae) from East and Southeast Asia

2017 ◽  
Vol 52 (3) ◽  
pp. 429-437 ◽  
Author(s):  
Fumiaki Y. Nomano ◽  
Nazuki Kasuya ◽  
Akira Matsuura ◽  
Awit Suwito ◽  
Hideyuki Mitsui ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Southeast Asia ◽  
East And Southeast Asia

scholarly journals Genetic Structure of Colletotrichum gloeosporioides sensu lato Isolates Infecting Papaya Inferred by Multilocus ISSR Markers

2013 ◽  
Vol 103 (2) ◽  
pp. 182-189 ◽  
Author(s):  
Sephra N. Rampersad
Keyword(s):  
Cluster Analysis ◽  
Genetic Differentiation ◽  
Colletotrichum Gloeosporioides ◽  
Gene Diversity ◽  
Polymorphic Loci ◽  
Bayesian Cluster Analysis ◽  
The Mean ◽  
Bayesian Cluster ◽  
Group 1 ◽  
Issr Primers

Colletotrichum gloeosporioides sensu lato is widely distributed throughout temperate and tropical regions and causes anthracnose disease in numerous plant species. Development of effective disease management strategies is dependent on, among other factors, an understanding of pathogen genetic diversity and population stratification at the intraspecific level. For 132 isolates of C. gloeosporioides sensu lato collected from papaya in Trinidad, inter-simple-sequence repeat-polymerase chain reaction (ISSR-PCR) generated 121 polymorphic loci from five ISSR primers selected from an initial screen of 22 ISSR primers. The mean percentage of polymorphic loci was 99.18%. Bayesian cluster analysis inferred three genetic subpopulations, where group 1 consisted exclusively of isolates collected in the southern part of Trinidad whereas groups 2 and 3, although genetically distinct, were mixtures of isolates collected from both the northern and southern parts of Trinidad. Principal coordinates analysis and unweighted pair-group method with arithmetic mean phylogeny were concordant with Bayesian cluster analysis and supported subdivision into the three subpopulations. Overall, the total mean gene diversity was 0.279, the mean within-population gene diversity was 0.2161, and genetic differentiation for the Trinidad population was 0.225. Regionally, northern isolates had a lower gene diversity compared with southern isolates. Nei's gene diversity was highest for group 1 (h = 0.231), followed by group 2 (h = 0.215) and group 3 (h = 0.202). Genotypic diversity was at or near maximum for all three subpopulations after clone correction. Pairwise estimates of differentiation indicated high and significant genetic differentiation among the inferred subpopulations (Weir's θ of 0.212 to 0.325). Pairwise comparisons among subpopulations suggested restricted gene flow between groups 1 and 2 and groups 1 and 3 but not between groups 2 and 3. The null hypothesis of random mating was rejected for all three inferred subpopulations. These results suggest that pathogen biology and epidemiology as well as certain evolutionary factors may play an important role in population substructuring of C. gloeosporioides sensu lato isolates infecting papaya in Trinidad.

scholarly journals Genetic diversity analysis of a Flax (Linum usitatissimum L.) global collection

2020 ◽  
Author(s):  
Ahasanul Hoque ◽  
Jason D. Fiedler ◽  
Mukhlesur Rahman
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Genetic Differentiation ◽  
Genetic Gain ◽  
Mantel Test ◽  
Snp Markers ◽  
Breeding Program ◽  
Neighbor Joining ◽  
Breeding Lines ◽  
The North

Abstract Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6,200 SNP markers Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise F st comparison revealed a great degree of divergence ( F st > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r= 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest ( F st > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree assists to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.

scholarly journals Microsatellite Characterization of Malaysian Mahseer (Tor spp.) for Improvement of Broodstock Management and Utilization

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2633
Author(s):  
Poh Chiang Chew ◽  
Annie Christianus ◽  
Jaapar M. Zudaidy ◽  
Md Yasin Ina-Salwany ◽  
Chou Min Chong ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Relatedness ◽  
Genetic Distances ◽  
Group Method ◽  
Genetic Management ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Geographical Regions

In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei’s genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.

scholarly journals GENETIC DIFFERENTIATION AMONG POPULATIONS OF Chromobotia macracanthus BLEEKER FROM SUMATRA AND KALIMANTAN BASED ON SEQUENCING GENE OF MTDNA CYTOCHROME B AND NUCLEUS DNA RAG2

2008 ◽  
Vol 3 (2) ◽  
pp. 107 ◽  
Author(s):  
Sudarto Sudarto ◽  
Kafi Hidonis ◽  
Emmanuel Paradis
Keyword(s):  
Genetic Differentiation ◽  
Genetic Distance ◽  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Population Group ◽  
Fish Population ◽  
Neighbor Joining ◽  
R Language ◽  
Estimation Of Time ◽  
Two Populations

Research on genetic differentiation among populations of Chromobotia macracanthus Bleeker from Sumatra, based on sequencing gene of mtDNA Cytochrome b and nucleus DNA RAG2 has been done. The objectives of the study were to obtain the representation of genetic differentiation among population of clown loach fishes or botia (Chromobotia macracanthus) from Sumatra and Kalimantan and to estimate the time divergence of both population group of botia. Samples of botia population were taken from 3 rivers in Sumatra namely Batanghari, Musi, and Tulang Bawang and one river from Kalimantan namely Kapuas. The genetic analysis was based on the sequencing of mtDNA Cytochrome b and nucleus DNA RAG2. The statistical analysis was done by using APE package on R language. The parameters observed were: nucleotide diversity, genetic distance, and neighbor-joining tree. The result showed that the highest nucleotide diversity was fish population of Musi, while the other two populations, Tulang Bawang (Sumatra) and Kapuas (Kalimantan), were considered as the lowest genetic diversity especially based on nucleus DNA RAG2 sequencing. Based on mtDNA Cytochrome-b sequencing, the most distinct population among those populations based on genetic distance were fish populations of Musi and Kapuas. According to the result of neighbor-joining tree analysis, the populations of botia were classified into two groups namely group of Sumatra and group of Kalimantan. The estimation of time divergence among group of population of Sumatra and Kalimantan based on mtDNA Cytochrome b was about 9.25—9.46 million years (Miocene era). The high genetic differences between groups of Sumatra and Kalimantan suggested that the effort of restocking botia from Sumatra into Kalimantan has to be done carefully, because it may disturb the gene originality of both botia populations.

scholarly journals State formation on China’s southern frontier: Vietnam as a shadow empire and hegemon

HumaNetten ◽  
2016 ◽  
pp. 39
Author(s):  
Tuong Vu
Keyword(s):  
Nineteenth Century ◽  
Southeast Asia ◽  
State Formation ◽  
Driving Force ◽  
Dyadic Interactions ◽  
Large Area ◽  
Early Nineteenth Century ◽  
Communist State ◽  
Vietnamese History ◽  
Mainland Southeast Asia

State formation in Vietnam followed an imperial pattern, namely, a process of conquests and annexations typical of an empire. At its peak in the early nineteenth century, the frontier of the Vietnamese empire encompassed much of today’s Cambodia and Laos. This imperial pattern was the basis on which the French built their Indochinese colony and the Vietnamese communist state built its modern hegemony. By re-examining Vietnamese history as that of an empire and hegemon, this paper challenges the nationalist historiography’s assumption about Vietnam’s need for survival from China as the driving force of Vietnamese history. In contrast, I argue that the threat to Vietnamese survival has come less from China than from other states on China’s southern frontier. Vietnam has in fact benefited from a positive synergy with China in much of its premodern and modern history. By situating Vietnamese state formation in the context of mainland Southeast Asia, I hope to correct the tendency in many studies that focus exclusively on Sino-Vietnamese dyadic interactions and that posit the two as opposites. Treating Vietnam as an empire or hegemon over a large area of mainland Southeast Asia also is essential to understand why Vietnamese sometimes did not automatically accept Chinese superiority despite the obvious “asymmetry” between them.

EVIDENCE FOR EXTENSIVE GENETIC DIFFERENTIATION BETWEEN THE SEX-RATIO AND THE STANDARD ARRANGEMENT OF DROSOPHILA PSEUDOOBSCURA AND D. PERSIMILIS AND IDENTIFICATION OF HYBRID STERILITY FACTORS

Genetics ◽  
1983 ◽  
Vol 105 (1) ◽  
pp. 71-86
Author(s):  
Chung-I Wu ◽  
Andrew T Beckenbach
Keyword(s):  
Sex Ratio ◽  
Genetic Differentiation ◽  
Genetic Background ◽  
Hybrid Sterility ◽  
Strong Support ◽  
Meiotic Drive ◽  
Complete Loss ◽  
Drosophila Pseudoobscura ◽  
Drosophila Persimilis ◽  
Standard Arrangement

ABSTRACT This study deals with sex-ratio genes tightly linked within the Sex-Ratio inversion. By taking advantage of the fact that the Sex-Ratio chromosome of Drosophila persimilis [SR(B)] is homosequential to the Standard chromosome of D. pseudoobscura [ST(A)], we carried out two reciprocal introgression experiments. Individual segments of SR(B) or ST(A) were introgressed into the genome of D. pseudoobscura or D. persimilis, respectively. Males possessing a hybrid SR(B)-ST(A) X chromosome and a genetic background derived from either of the two species were tested for fertility and sex-ratio expression.—It was found that, in terms of the meiotic drive genes, the Sex-Ratio chromosome differs extensively from the Standard chromosome. Because recombinations of these genes result in a complete loss of sex-ratio expression, this finding lends strong support to the hypothesis of gene coadaptation. Coadaptation, in this context, is the advantage of being transmitted preferentially. In light of this finding, the evolution of the sex-ratio system in these two sibling species is discussed.—Introgression experiments also yielded information about hybrid sterility. With reciprocal introgression, sterility interactions were found to be "asymmetric." The asymmetry is fully expected from the viewpoint of evolution of postmating reproductive isolation.

Eriophyoid mites (Acari: Prostigmata) in Southeast Asia: a synopsis of 104 genera, with an illustrated key to genera and checklist of species

Zootaxa ◽  
2009 ◽  
Vol 2257 (1) ◽  
pp. 1-128 ◽  
Author(s):  
XIAO-FENG XUE ◽  
ZHI-QIANG ZHANG
Keyword(s):  
New Species ◽  
Southeast Asia ◽  
Jatropha Curcas ◽  
Mangifera Indica ◽  
Identification Key ◽  
New Combinations ◽  
Eriophyoid Mites ◽  
Croton Oblongifolius ◽  
A New Species

This paper provides a synopsis of 104 genera of eriophyoid mites in Southeast Asia, with an identification key to families and genera, and a checklist of 325 species. A new species—Paniculatus curcasis sp. nov. on Jatropha curcas (Euphorbiaceae) from Java, Indonesia—was described. Four new combinations were proposed—Cosella crotoni (Boczek & Chandrapatya, 2000), comb. nov. on Croton oblongifolius (Euphorbiaceae) from Thailand; Paraphytoptus binarius (Keifer, 1977), comb. nov. on Peltophorum pterocarpum (Fabaceae) from Thailand; Leipothrix mangiferae (Chandrapatya, 1997), comb. nov. on Mangifera indica (Anacardiaceae) from Thailand; and Levonga caseariae (Chandrapatya, 1997) comb. nov. on Casearia grewiaefolia (Flacourtiaceae) from Thailand. Four new names were proposed for junior homonyms—Quadriporca samphran nom. nov. on Mangifera indica (Anacardiaceae) from Thailand; Knorella blumcanae nom. nov. on Bambusa blumcana (Poaceae) from Thailand; Rhombacus bangkoki nom. nov. on Eucalyptus sp. (Myrtaceae) from Thailand; and Tetra stipularisis nom. nov. on Bridelia stipularis (Euphorbiaceae) from Thailand.

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