Gene flow in three broiler chicken populations in Abeokuta using jackknife procedure

2021 ◽  
Vol 43 (2) ◽  
pp. 1-12
Author(s):  
O. Olowofeso ◽  
M. A. Adeleke ◽  
M. A Azeez ◽  
A. O. Adesegun
Keyword(s):  
Gene Flow ◽  
Microsatellite Markers ◽  
Broiler Chicken ◽  
Natural Populations ◽  
Total Sample ◽  
Chicken Population ◽  
Polymerase Chain ◽  
Polymorphic Microsatellite ◽  
Estimate Gene Flow ◽  
Jackknife Procedure

Jackknife procedure (JP) is a less biased and fascinating method of obtaining gene flow among populations. The purpose of this study was to use JP to eliminate bias associated with indirect estimators of gene flow. With microsatellite markers, it has been possible to estimate gene flow (Nmo ) in natural populations. To quantify Nmo in chicken populations, we used five polymorphic microsatellite markers with 115 genomic deoxyribonucleic acid (DNA) obtained from (dihybrid (DH = 37), trihybrid (TH = 32) and Anak White (AW = 46) broiler chicken populations, respectively. Through polymerase chain reaction, we amplified DNA from the broiler chicken populations, subjected amplicons to electrophoresis, fragment sizes determined and analysed across populations considering selected markers through which standardized genetic variance among sub-populations in total sample depicted as (F)ST was obtained per marker for chicken population pairs. Its average across markers/population pairs was used to infer Nmo  in the chicken population pairs. We used JP which is a mathematical approach that utilizes mean FST across markers to obtain Nmo in the chicken population pairs. Gene flow based on JP in chicken population pairs designated as (Nm)JP were 5.4267 (DH vs. TH), 7.0127 (TH vs. AW) and 11.7405 (DH vs. AW) and among chicken populations, (Nm)JP was 7.1969. Considering these estimates, we concluded that there was JP gene flow among the three broiler chicken populations examined in Abeokuta, Nigeria.

scholarly journals Gene flow in three broiler chicken populations in Abeokuta using jackknife procedure

2021 ◽  
Vol 43 (1) ◽  
pp. 1-12
Author(s):  
O. Olowofeso ◽  
M. A. Adeleke ◽  
M. A. Azeez ◽  
A. O. Adesegun
Keyword(s):  
Gene Flow ◽  
Microsatellite Markers ◽  
Broiler Chicken ◽  
Natural Populations ◽  
Total Sample ◽  
Chicken Population ◽  
Polymerase Chain ◽  
Estimate Gene Flow ◽  
Jackknife Procedure ◽  
Was Gene

Jackknife procedure (JP) is a less biased and fascinating method of obtaining gene slow among populations. The purpose of this study was to use JP to eliminate bias associated with indirect estimators of gene slow, with microsatellite markers, it has been possible to estimate gene flow (Nm) in natural populations. To quantify Nm, in chicken populations, we used five polymorphic microsatellite markers with 115 genomic deoxyribonucleic acid (DNA) obtained from (dihybrid (DH = 37), trihybrid (TH = 32) and Anak White (AW = 46) broiler chicken populations, respectively. Through polymerase chain reaction, we amplified DNA from the broiler chicken populations, subjected amplicons to electrophoresis, fragment sizes determined and analysed across populations considering selected markers through which standardized genetic variance among sub-populations in total sample depicted as (FST) was obtained per marker for chicken population pairs. Its average across markers/population pairs was used to infer Nm, in the chicken population pairs. We used JP which is a mathematical approach that utilizes mean FST, across markers to obtain Nm in the chicken population pairs. Gene flow based on JP in chicken population pairs designated as (Nm)JP were 5.4267 (DH vs. TH), 7.0127 (TH vs. AW) and 11.7405 (DH vs. AW) and among chicken populations, (Nm)JP was 7.1969. Considering these estimates, we concluded that there was gene flow among the three broiler chicken populations examined in Abeokuta, Nigeria.

Genetic characterization of novel polymorphic microsatellite markers for Epilobium nankotaizanense (Onagraceae), an endemic and threatened herb in Taiwan

2021 ◽  
pp. 1-4
Author(s):  
Yu-Wei Tseng ◽  
Chi-Chun Huang ◽  
Chih-Chiang Wang ◽  
Chiuan-Yu Li ◽  
Kuo-Hsiang Hung
Keyword(s):  
Microsatellite Markers ◽  
Natural Populations ◽  
Conservation Strategy ◽  
Sequencing Data ◽  
Germplasm Collections ◽  
The Family ◽  
Conservation Genetic ◽  
Population Sizes ◽  
Polymorphic Microsatellite

Abstract Epilobium belongs to the family Onagraceae, which consists of approximately 200 species distributed worldwide, and some species have been used as medicinal plants. Epilobium nankotaizanense is an endemic and endangered herb that grows in the high mountains in Taiwan at an elevation of more than 3300 m. Alpine herbs are severely threatened by climate change, which leads to a reduction in their habitats and population sizes. However, only a few studies have addressed genetic diversity and population genetics. In the present study, we developed a new set of microsatellite markers for E. nankotaizanense using high-throughput genome sequencing data. Twenty polymorphic microsatellite markers were developed and tested on 30 individuals collected from three natural populations. These loci were successfully amplified, and polymorphisms were observed in E. nankotaizanense. The number of alleles per locus (A) ranged from 2.000 to 3.000, and the observed (Ho) and expected (He) heterozygosities ranged from 0.000 to 0.929 and from 0.034 to 0.631, respectively. The developed polymorphic microsatellite markers will be useful in future conservation genetic studies of E. nankotaizanense as well as for developing an effective conservation strategy for this species and facilitating germplasm collections and sustainable utilization of other Epilobium species.

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

scholarly journals Population Genetics of the Red Rock Lobster,  Jasus edwardsii

2021 ◽  
Author(s):  
◽  
Luke Thomas
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Rocky Reef ◽  
Rock Lobster ◽  
Wide Range ◽  
Jasus Edwardsii ◽  
Polymorphic Microsatellite

<p>Understanding patterns of gene flow across a species range is a vital component of an effective fisheries management strategy. The advent of highly polymorphic microsatellite markers has facilitated the detection of fine-scale patterns of genetic differentiation at levels below the resolving power of earlier techniques. This has triggered the wide-spread re-examination of population structure for a number of commercially targeted species. The aims of thesis were to re-investigate patterns of gene flow of the red rock lobster Jasus edwardsii throughout New Zealand and across the Tasman Sea using novel microsatellite markers. Jasus edwardsii is a keystone species of subtidal rocky reef system and supports lucrative export markets in both Australia and New Zealand. Eight highly polymorphic microsatellite markers were developed from 454 sequence data and screened across a Wellington south coast population to obtain basic diversity indices. All loci were polymorphic with the number of alleles per locus ranging from 6-39. Observed and expected heterozygosity ranged from 0.563-0.937 and 0.583-0.961, respectively. There were no significant deviations from Hardy-Weinberg equilibrium following standard Bonferroni corrections. The loci were used in a population analysis of J. edwardsii that spanned 10 degrees of latitude and stretched 3,500 km across the South Pacific. The analysis rejected the null-hypothesis of panmixia based on earlier mDNA analysis and revealed significant population structure (FST=0.011, RST=0.028) at a wide range of scales. Stewart Island was determined to have the highest levels of genetic differentiation of all populations sampled suggesting a high degree of reproductive isolation and self-recruitment. This study also identified high levels of asymmetric gene flow from Australia to New Zealand indicating a historical source-sink relationship between the two countries. Results from the genetic analysis were consistent with results from oceanographic dispersal models and it is likely that the genetic results reflect historical and contemporary patterns of Jasus edwardsii dispersal and recruitment throughout its range.</p>

Isolation and characterisation via 454 sequencing of microsatellites from the tawny frogmouth, Podargus strigoides (Class Aves, Family Podargidae)

2012 ◽  
Vol 60 (2) ◽  
pp. 133
Author(s):  
Fiona E. Hogan ◽  
Marian Weaving ◽  
Gregory R. Johnston
Keyword(s):  
Population Genetics ◽  
Gene Flow ◽  
Microsatellite Markers ◽  
Reproductive Ecology ◽  
454 Sequencing ◽  
Urban Environments ◽  
Shotgun Sequencing ◽  
Target Species ◽  
Single Population ◽  
Polymorphic Microsatellite

We isolated 24 novel polymorphic microsatellite markers from the tawny frogmouth, a nocturnal bird endemic to Australia, which has successfully adapted to urban environments. Initially, 454 shotgun sequencing was used to identify 733 loci with primers designed. Of these, we trialled 30 in the target species of which all amplified a product of expected size. Subsequently, all 30 of these loci were screened for variation in 25 individuals, from a single population in Melbourne, Victoria, Australia. Twenty-eight loci were polymorphic with observed heterozygosity ranging from 0.03 to 0.96 (mean 0.58) and the number of alleles per locus ranged from 2 to 18 (average of 6.5); we confirmed that 24 loci conformed to Hardy–Weinberg expectations. The 24 loci identified here will be sufficient to unequivocally identify individuals and will be useful in understanding the reproductive ecology, population genetics and the gene flow amongst localities in urban environments where this bird thrives.

scholarly journals SSR Markers for Analysing South American Nothofagus Species

2004 ◽  
Vol 53 (1-6) ◽  
pp. 240-243 ◽  
Author(s):  
M. M. Azpilicueta ◽  
H. Caron ◽  
C. Bodénès ◽  
L. A. Gallo
Keyword(s):  
Gene Flow ◽  
Genetic Mapping ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Natural Populations ◽  
South American ◽  
Sample Sizes ◽  
Polymorphic Ssrs ◽  
The Cross ◽  
Qualitative Confirmation

Summary11 newly discovered microsatellites were used to identify SSR markers for characterising South American Nothofagus species. This was carried out in six species. The sample sizes used were between four and six individuals per species. The cross-genera transferability of 34 Quercus SSRs was also essayed. Out of the 11 new microsatellite markers, three proved to be polymorphic (NnBIO 11, NgBIO 13 and NgBIO 14). The qualitative confirmation of the inheritance of these markers could also be verified. Polymorphism was also observed in five of the cross-genera transferred SSRs (QrBIO7, quru-GA-0A01, quru-GA-0C11, quru-GA-0I01, quru-GA-0M07). The number of alleles per locus found range between 1 and 6 per species. The eight polymorphic SSRs identified in this study will constitute a valuable tool in the gene flow studies that are currently being carried out in natural populations of South American Nothofagus species. The confirmation of crossspecies and cross-genera transferability opens the way for the use of SSRs as bridge markers in genetic mapping.

Development and characterization of polymorphic microsatellite markers for Spathoglottis plicata (Orchidaceae)

2018 ◽  
Vol 16 (6) ◽  
pp. 572-575
Author(s):  
Chiuan-Yu Li ◽  
Chi-Chun Huang ◽  
Chaur-Tzuhn Chen ◽  
Kuo-Hsiang Hung
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Primers ◽  
Wild Populations ◽  
Terrestrial Orchid ◽  
Chain Reaction ◽  
Expected Heterozygosity ◽  
Genetic Patterns ◽  
Polymerase Chain ◽  
Polymorphic Microsatellite

AbstractWe developed novel and polymorphic microsatellite primers for Spathoglottis plicata, a tropical and subtropical terrestrial orchid, to investigate the genetic patterns and population structure among wild populations, and also to identify the varieties and hybrids of S. plicata in horticultural industry. The 12 novel microsatellites from S. plicata were developed by using polymerase chain reaction (PCR)-based isolation of microsatellite arrays. These markers that were successfully PCR amplified exhibited polymorphisms in S. plicata. The number of alleles, observed heterozygosity, expected heterozygosity and polymorphism information content values across loci ranged from 2.000 to 8.000, 0.000 to 0.756, 0.208 to 0.813 and 0.405 to 0.805 in total populations, respectively. The newly developed microsatellite markers exhibited variation in S. plicata. These markers can be used as a tool to further investigate the genetic diversity, conservation genetics and variety/hybrid identification of S. plicata.

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

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