scholarly journals Population structure, inbreeding and admixture in local cattle populations managed by community‐based breeding programs in Burkina Faso

2021 ◽  
Author(s):  
Dominique Ouédraogo ◽  
Salifou Ouédraogo‐Koné ◽  
Bernadette Yougbaré ◽  
Albert Soudré ◽  
Bienvenue Zoma‐Traoré ◽  
...  
Keyword(s):  
Population Structure ◽  
Burkina Faso ◽  
Community Based ◽  
Breeding Programs

scholarly journals Values and Beliefs That Shape Cattle Breeding in Southwestern Burkina Faso

Human Ecology ◽  
2021 ◽  
Author(s):  
Bienvenue Zoma-Traoré ◽  
Salifou Ouédraogo-Koné ◽  
Albert Soudré ◽  
Dominique Ouédraogo ◽  
Bernadette Yougbaré ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Resource Scarcity ◽  
Community Based ◽  
Cattle Breeding ◽  
Breeding Programs ◽  
Rural Livelihood ◽  
Cattle Diseases ◽  
Beliefs And Values ◽  
Values And Beliefs ◽  
Taurine Cattle

AbstractCattle production in southwestern Burkina Faso is under pressure because of resource scarcity, changing climate, and cattle diseases. Well-adapted local breeds, such as Lobi taurine cattle, are increasingly replaced by more productive exotic breeds. Community-based breeding programs (CBBPs) could be a viable option for preserving the breed and improving its productivity. Presuming that CBBPs would succeed only if they align with producers’ beliefs and values, we relied on a combination of conceptual frameworks (theory of basic values, rural livelihood transitions) to explore the values and beliefs of cattle producers. Security was the respondents’ dominant value in their aim to mitigate threats to livelihood, and it was closely linked to achievement in terms of harvest and animal quantity. Livestock-oriented respondents particularly valued conformity with accepted social roles, while achievement and power were more pronounced among crop-oriented respondents. We conclude that CBBPs, to be successful, will need to reduce threats to participants’ livelihood and make benefits of participation immediately visible. We consider the emergence of trusted leadership from the community to be pivotal for creating momentum for novel arrangements in cattle keeping and feeding.

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.

User fees removal and community-based management of undernutrition in Burkina Faso: what effects on children’s nutritional status?

2021 ◽  
pp. 1-12
Author(s):  
David Y Zombré ◽  
Manuela De Allegri ◽  
Valéry Ridde ◽  
Kate Zinszer
Keyword(s):  
Burkina Faso ◽  
Household Survey ◽  
Community Level ◽  
User Fees ◽  
Nutrition Status ◽  
Control Group ◽  
Community Based ◽  
Sahel Region ◽  
Intervention District ◽  
Children Under 5

Abstract Objective: To examine the effect of an intervention combining user fees removal with community-based management of undernutrition on the nutrition status in children under 5 years of age in Burkina Faso. Design: The study was a non-equivalent control group post-test-only design based on household survey data collected 4 years after the intervention onset in the intervention and comparison districts. Additionally, we used propensity score weighting to achieve balance on covariates between the two districts, followed by logistic multilevel modelling. Setting: Two health districts in the Sahel region. Participants: Totally, 1116 children under 5 years of age residing in 41 intervention communities and 1305 from 51 control communities. Results: When comparing children living in the intervention district to children living in a non-intervention district, we determined no differences in terms of stunting (OR = 1·13; 95 % CI 0·83, 1·54) and wasting (OR = 1·21; 95 % CI 0·90, 1·64), nor in severely wasted (OR = 1·27; 95 % CI 0·79, 2·04) and severely stunted (OR = 0·99; 95 % CI 0·76, 1·26). However, we determined that 3 % of the variance of wasting (95 % CI 1·25, 10·42) and 9·4 % of the variance of stunting (95 % CI 6·45, 13·38) were due to systematic differences between communities of residence. The presence of the intervention in the communities explained 2 % of the community-level variance of stunting and 3 % of the community-level variance of wasting. Conclusions: With the scaling-up of the national free health policy in Africa, we stress the need for rigorous evaluations and the means to measure expected changes in order to better inform health interventions.

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation

2014 ◽  
Vol 127 (4) ◽  
pp. 995-1004 ◽  
Author(s):  
Hiroshi Shinada ◽  
Toshio Yamamoto ◽  
Eiji Yamamoto ◽  
Kiyosumi Hori ◽  
Junichi Yonemaru ◽  
...  
Keyword(s):  
Population Structure ◽  
Rice Cultivation ◽  
Rice Breeding ◽  
Breeding Programs ◽  
Historical Changes

scholarly journals Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

2020 ◽  
Author(s):  
R. H. Sammour ◽  
M. A. Karam ◽  
Y. S. Morsi ◽  
R. M. Ali
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Rapa ◽  
Phylogenetic Relationships ◽  
Fixation Index ◽  
Distribution Area ◽  
Enzyme Analysis ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

scholarly journals Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Sirlene Viana de Faria ◽  
Leandro Tonello Zuffo ◽  
Wemerson Mendonça Rezende ◽  
Diego Gonçalves Caixeta ◽  
Hélcio Duarte Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Breeding Program ◽  
Tropical Maize ◽  
Maize Breeding ◽  
Breeding Programs ◽  
The Public ◽  
Maize Inbred Lines

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

scholarly journals GENOTYPIC DIVERSITY IN 291 MAIZE LINES FROM CIMMYT AND PHENOTYPIC CHARACTERIZATION IN SOUTHERN CORDOBA, ARGENTINA

2019 ◽  
Vol 30 (1) ◽  
pp. 25-33
Author(s):  
E.A. Rossi ◽  
M. Ruiz ◽  
M. Di Renzo ◽  
N.C. Bonamico
Keyword(s):  
Population Structure ◽  
Morphological Traits ◽  
Phenotypic Diversity ◽  
Genotypic Diversity ◽  
Inbred Lines ◽  
Environmental Adaptation ◽  
Procrustes Analysis ◽  
Phenotypic Characterization ◽  
Breeding Programs ◽  
Maize Inbred Lines

CIMMYT maize inbred lines (CMLs) are freely distributed to breeding programs around the world. Better information on phenotypic and genotypic diversity may provide guidance to breeders on how to use more efficiently the CMLs in their breeding programs. In this study a group of 291 CIMMYT maize inbred lines, was phenotyped by nine agro-morphological traits in south Córdoba, Argentina and genotyped using 18,082 SNPs. Based on the geographic information and the environmental adaptation, 291 CMLs were classified into eight subgroups. Anthesis-silking interval (IAE) was the trait with higher phenotypic diversity. A 40% of maize inbred lines, with IAE less than five days, show a good adaptation to growing conditions in south Córdoba, Argentina. The low phenotypic variation explained by environmental adaptation subgroups indicates that population structure is only a minor factor contributing to phenotypic diversity in this panel. Principal component analysis (ACP) allowed us to obtain phenotypic and genotypic orderings. Generalized procrustes analysis (APG) indicated a 60% consensus between both data type from the total panel of maize lines. In each environmental adaptation subgroup, the APG consensus was higher. This result, which might indicate linkage disequilibrium between SNPs markers and the genes controlling these agro-morphological traits, is promising and could be used as an initial tool in the identification of Quantitative Trait Loci (QTL). Information on genetic diversity, population structure and phenotypic diversity in local environments will help maize breeders to better understand how to use the current CIMMYT maize inbred lines group. Key words: broad-sense heritability, multivariate analysis, SNPs, agro-morphological traits.

scholarly journals Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2025
Author(s):  
Shyryn Almerekova ◽  
Yuliya Genievskaya ◽  
Saule Abugalieva ◽  
Kazuhiro Sato ◽  
Yerlan Turuspekov
Keyword(s):  
Population Structure ◽  
Heading Date ◽  
Snp Markers ◽  
Principal Coordinate Analysis ◽  
Neighbor Joining ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Polymorphic Snps ◽  
Ancestral Node

The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.

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