Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria

Uganda chicken genetic resources: II. genetic diversity and population demographic history inferred from mitochondrial DNA D-loop sequences

The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA) D-loop sequences among 12 Ugandan chicken populations was evaluated. Twenty-eight polymorphic sites, accounting for 4.26% of the total analyzed loci of 658 bp, defined 32 haplotypes. The haplotype diversity (Hd) was 0.437, with a nucleotide diversity (π) of 0.0169, while the average number of nucleotide differences (k) was 0.576, indicating a population that is moderately genetically diverse. Analysis of molecular variance found 98.39% (ρ < 0.01) of the total sequence variation among the chicken haplotypes within populations, 1.08% (ρ < 0.05) among populations, and 0.75% (ρ > 0.05) among populations within regions. This revealed subtle genetic differentiation among the populations, which appeared to be influenced by population fragmentation, probably due to neutral mutation, random genetic drift, and/or balancing selection. All the haplotypes showed affinity exclusively to the haplogroup-E mtDNA phylogeny, with haplotype UGA01 signaling an ancestral haplotype in Uganda. Neutrality tests Tajima's D (-2.320) and Fu's Fs (-51.369), augmented with mismatch distribution to measure signatures of recent historical demographic events, supported a population expansion across the chicken populations. The results show one matrilineal ancestry of Ugandan chickens from a lineage widespread throughout the world that began in the Indian subcontinent. The lack of phylogeographic signals is consistent with recent expansion events with extensive within-country genetic intermixing among haplotypes. Thus, the findings in this study hold the potential to guide conservation strategies and breeding programs in Uganda, given that higher genetic diversity comes from within the chicken population.

Impact of broiler breeder hens' age and egg storage on egg quality, embryonic development, and hatching traits of FUNAAB-alpha chickens

This study aimed to determine the impact of the age of breeder hens and egg storage on egg quality, embryonic development, hatching events and chick quality in FUNAAB-alpha chickens. The study involved the use of 500 hatching eggs each collected from 32-wk and 60-wk-old of FUNAAB-alpha broiler breeder hens at the Animal Breeding and Genetic Unit of the Federal University of Agriculture, Abeokuta, Nigeria and subjected to 5 storage periods (0, 3, 7, 11, and 15 d). The quality traits of the eggs were recorded and incubated using the conventional protocol. Data were collected on the internal and external egg characteristics, embryonic development, hatching events, and chick quality. The data collected were laid out in 2 by 5 factorial design. The results showed that eggs from 32-wk-old breeder hens had higher albumen height and Haugh unit (HU) value than those from 60-wk-old breeders. The albumen height and HU decreased progressively with storage length in the 2 age groups. Extended storage duration linearly increased (P < 0.01) egg weight loss and decreased (P < 0.01) yolk height. The eggs from both breeder ages had increasing blastodermal diameters at oviposition up until d 11 of storage but decreased on d 15 of storage in eggs from 32 wk breeders. Eggs of 32-wk-old FUNAAB-alpha breeder hens had larger diameters at oviposition compared with 60-wk-old breeders. The chicks from 60-wk breeder had late internal pipping (469.06 h), early external pipping (474.46 h) and a shorter time lag between both pips (9.00 h) compared to chicks from 32 wk breeder. The highest fertility was recorded in eggs stored for 3 d (80.7% and 79.6%), while the lowest fertility was in eggs stored for 15 d (53.4% and 47.7%) in both 32-wk and 60-wk-old breeders, respectively. Chicks from young breeder hens stored for 3 d had better quality scores (100%) compared to 0, 7, 11, and 15-d storage duration and in 60-wk-old breeders across all storage duration. It was concluded that both egg storage duration and age of breeder affected egg quality, hatching events and hatchling quality of FUNAAB-alpha chickens and the interaction effects of both factors was recorded for some of these traits. However, extended storage beyond 7 d had a larger negative impact on egg quality and hatchability of eggs from an old breeder (60 wk) than on eggs of a young breeder (32 wk).

Population structure and evolutionary history of the greater cane rat (Thryonomys swinderianus) from the Guinean Forests of West Africa

Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (FST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.

An exploratory study on differences in maternal care between two ecotypes of Nigerian indigenous chicken hens

The Yoruba (YRE) and Fulani (FLE) are the two notable indigenous chicken ecotypes in Nigeria. They exhibit broodiness and post-hatch care of their chicks. Studies on welfare, productivity, and maternal behaviors of these two ecotypes are scarce, hence the need for this study. Separate flocks of these ecotypes were housed intensively and hens that showed broodiness (ten YRE and five FLE) were monitored. Brooding behaviors were monitored for 3 days in the 1st and 2nd weeks of brooding and daily in the 3rd week of brooding for 6 h/day (07:00–09:00 h, 11:00–13:00 h, and 15:00–17:00 h). During brooding, surface body temperatures (eye, brood patch and under the wings), egg temperature and body weight of the hens were measured. Chicks hatched (44 chicks from the YRE and 24 chicks from the FLE) by these hens were subjected to tonic immobility tests on the 7th, 14th, and 21st days post-hatch and to a simulated predator test on the 8th, 15th, and 22nd days post-hatch to determine their level of fear. In each ecotype, brooding behaviors did not change over the three weeks, but the YRE hens spent longer time sitting on their eggs at the 2nd (U = 5.000, z = −2.454, P = 0.014) and 3rd (U = 9.000, z = −1.961, P = 0.050) week of brooding. The surface body temperatures of both ecotypes, egg temperature, and relative weekly weight loss were similar over the brooding period, but relative weekly weight loss was greater (P < 0.05) at the 3rd than 1st and 2nd week of brooding. The surface body temperatures were positively correlated (P < 0.01) with egg temperature. In both ecotypes, attempts to induce and duration of tonic immobility were similar over the test periods but on the 7th day post-hatch, the duration of tonic immobility was longer (U = 323.000, z = −2.632, P = 0.008) and on the 14th day post-hatch, the number of attempts to induce tonic immobility was less (U = 332.000, z = −2.630, P = 0.009) in the YRE chicks. In conclusion, YRE hens sat more on the eggs and their chicks were more fearful.