Dataset Information

Genetic diversity of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania based on Major Histocompatibility Complex-linked microsatellite LEI0258 marker typing.

ABSTRACT: Unraveling the genetic diversity of livestock species is central to understanding their value and importance for conservation and improvement in diverse production environments. In developing countries, information on genetic attributes of many livestock species is unfortunately scanty to support well-informed decision-making upon relevant management strategies. This study aimed at investigating allelic variability, genetic diversity, and genetic relationships of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania using the Major Histocompatibility Complex-linked LEI0258 marker. A total of 400 DNA samples, 40 per ecotype, were genotyped by capillary electrophoresis. Thirty different alleles with sizes ranging from 197 to 569 bp were determined. The number of alleles ranged from 17 (Itunduma) to 21 (Mbeya), with an average of 19.20 alleles per ecotype. Allelic polymorphism was further evaluated through genotyping by Sanger sequencing. Thirty-three DNA samples with different fragment sizes were re-amplified and their alleles sequenced to depict polymorphism based on a combination of two repeat regions at 12 and 13 bp, respectively, and flanking regions with SNP and indels. The repeat region at 13 bp appeared 1 to 28 times, whereas the region at 12 bp appeared 3 to 19 times in all sequenced fragments. The numbers of indels and SNP determined were 7 and 9, respectively. From capillary electrophoresis, the Chunya and Msimbazi ecotypes exhibited the highest genetic diversity (0.937), whereas the lowest value (0.910) was observed from the Mbarali ecotype, with an average of 0.925. The Namtumbo and Wanging'ombe ecotypes showed high inbreeding coefficients (FIS > 0.05), whereas a high excess heterozygote value (FIS = -0.098) was observed from the Njombe ecotype. Two percent of the genetic diversity was due to differences among ecotypes, and the rest was due to differences among individuals within the ecotypes. Despite the overall low genetic differentiation, both fragment and sequencing analyses depicted a high allelic and genetic variability across 10 chicken ecotypes. These results therefore, underscore the importance of establishing appropriate conservation and management strategies to capitalize on observed variability and maintain genetic flexibility across diverse production environments.

SUBMITTER: Mwambene PL

PROVIDER: S-EPMC6591683 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Genetic diversity of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania based on Major Histocompatibility Complex-linked microsatellite LEI0258 marker typing.

Mwambene Pius L PL Kyallo Martina M Machuka Eunice E Githae Dedan D Pelle Roger R

Poultry science 20190701 7

Unraveling the genetic diversity of livestock species is central to understanding their value and importance for conservation and improvement in diverse production environments. In developing countries, information on genetic attributes of many livestock species is unfortunately scanty to support well-informed decision-making upon relevant management strategies. This study aimed at investigating allelic variability, genetic diversity, and genetic relationships of 10 indigenous chicken ecotypes f ...[more]

PMID: 30877744

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Project description:The poultry industry in Tanzania has grown steadily over the past decade. We surveyed 121 chicken farming households along an intensification gradient from backyard to semi-intensive and intensive production systems based on rearing system and assumed purpose and poultry breed in the Iringa region. About 30% of households had more than one breed and/or rearing system combination. The subdivision of poultry systems was refined by adding the size of the flocks to highlight variation in scale of operations. On this basis we distinguished 3 main types: 1) subsistence small-scale free-range chicken production; 2) market-oriented small to medium scale semi-intensive and 3) small to medium-large scale intensive systems. 'Intensification' involves the transition from keeping indigenous chickens to improved dual-purpose and exotic breeds driven by greater productivity and potential for income generation. The more intensive the production system, the more the intensity and diversity of diseases identified by farmers as their main problem, which was partly attributed to the greater sensitivity of the improved breeds, poor veterinary measures, and the high chicken density facilitating disease spread. Based on the survey we constructed a problem tree to classify the underlying constraints and their interrelations, and to identify common root causes, based on which we propose practical solutions to improve chicken production. Development of medium-large scale systems is particularly constrained by a limited supply of 1-day-old chicks and theft. By contrast, intensification of small-scale systems is constrained by limited access to quality feed, vaccines and medicines, capital, and lack of a reliable market, partly due to the absence of farmer organization. These constraints can be addressed through formation of producer groups and promotion of outgrower and enterprise development models. Enterprise development appears to be the most promising business model for smallholder chicken farmers given that it allows farmers more freedom in decision-making and management while strengthening linkages with input suppliers and output markets to ensure a viable and profitable business.

Project description:BackgroundVarious regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (FST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken.ResultsUsing whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1).ConclusionsOur findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations.

Project description:BackgroundUse of skilled health provider (SBA) during and after childbirth has been reported to reduce maternal and newborn deaths; and is one of the key indicators monitored in Sustainable Development Goals (SDGs). Progress, levels and factors influencing utilization of SBA differ within and between countries. In Tanzania, SBA coverage stands at 64% while the national target is 80%; with wide variability between regions (42-96%). This study aimed at determining factors associated with utilization of skilled births providers during childbirth in Mbeya Region, Southern highlands, Tanzania.MethodsThis was a cross-sectional analytical study conducted in December 2015 to January 2016, in Mbeya Region. A total of 2844 women of reproductive age were enrolled, but only 1777 women who reported a live birth 5 years prior to the survey were included in this analysis. Multilevel logistic regression analyses were used to determine independent factors influencing utilization of SBA during childbirth. Random effects logistic model was used to assess the variability between clusters on the odds of using skilled birth attendants during delivery.ResultsIn this setting, 81% of the women reported utilization of skilled births attendants during childbirth. ANC visits four times or more (aOR = 1.63-95% CI = 1.26, 2.10; p < 0.001) and having secondary education or higher (aOR = 2.16; 95% CI = 1.19-3.90; p = 0.011) were associated with increased SBA use during childbirth whereas having two (aOR = 0.51; 95% CI: 0.33-0.79; p = 0.003) or three children (aOR = 0.37; 95% CI: 0.27-0.58; p < 0.001) relative to one child, 30 to 60 min walking distance to the health facility (aOR = 0.66; 95% CI: 0.48-0.92; p = 0.012) and more than 1 h walking distance to the health facility (aOR = 0.43; 95% CI: 0.32-0.57; p < 0.001) compared to < 30 min; were associated with decreased SBA use during childbirth.ConclusionThe proportion of births attended by skilled births attendants was high, but 19% of the women are still left behind. Concentrated efforts to improve utilization of SBA should be targeted to women with low education, with higher number of children, and with low frequency of ANC attendance. Furthermore, community and facility interventions addressing transport for pregnant women are needed. Qualitative study to explore the barriers of SBA use among the 19% who are not using skilled assistance during childbirth is needed.

Project description:Animals have been identified as the potential reservoirs of rotavirus group A (RVA) for human infection. However, very little is known regarding the genotype and genomic profiles of circulating RVA in Tanzanian piglets. The rotavirus genetic diversity and genome analysis was assessed among piglets from Southern highlands and Eastern Tanzania. A total of 241 faecal samples were collected from piglets in the regions of Mbeya, Iringa, and Morogoro. RVA was detected and genotyped using reverse transcription polymerase chain reaction (RT-PCR). Sanger dideoxynucleotide cycle sequencing of the viral protein (VP) 4 and VP7 genes was afterwards performed to confirm the RT-PCR results. Selected genotypes were subjected to whole genome sequencing. The overall prevalence of RVA was 35.26% (85/241) in piglets (30.58% in Mbeya, 43.75% in Iringa and 31.16% in Morogoro). Upon genotyping, the G genotypes were G4 (26), G9 (10), G3 (6), G5 (3) and the remaining 40 were untypeable, while the P genotype, were P[6] (35), P[13] (3) and the remaining 47 were untypeable. The G4P[6] were the predominant genotype followed by G3P[6], G3P[13], G4P[13] and G5P[13] were most common genotypes combinations. On phylogenetic analysis, G4 was grouped to lineage V, sublineages VIIa and VIIc, G9 to lineage I, G5 to lineage II, G3 to lineage IV, P[6] to lineage V and sublineage Ic and the P[13] to lineage IV. We revealed amino acid differences between the circulating G4 and the G4 in the ProSystems RCE vaccine used in pigs. The whole genome reveals genomic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1, G5-P[x]-I5-R1-C1-M1-A8-N1-Tx-E1-H1, G3/G4-P[13]/P[6]-Ix-R1-C1-M1-A8-N1-T1-E1-H1, G3-P[6]-Ix-R1-C1-M1-A8-N1-Tx-E1-H1 and G9-P[x]-Ix-R1-C1-M1-Ax-N1-Tx-E1-H1. The VP7 gene of G9, the VP4 gene of P[6] and NSP4 (E1) gene of some genotypes clustered together and closely related to humans origin or porcine-human reassortant strains with nucleotide similarities ranging from 97.90% to 99.74% from neighboring countries, implying possibility intragenogroup reassortment and interspecies transmission. The higher strain diversity observed within the gene segments highlight the importance of genomic analysis and continuous monitoring of RVA genotypes. Further research is needed to determine the risk factors associated with RVA infection in Tanzanian pigs in order to properly design a control program.

Dataset Information

Genetic diversity of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania based on Major Histocompatibility Complex-linked microsatellite LEI0258 marker typing.

Publications

Genetic diversity of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania based on Major Histocompatibility Complex-linked microsatellite LEI0258 marker typing.

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