Unraveling the Genetic Diversity and Population Structure of Bangladeshi Indigenous Cattle Populations Using 50K SNP Markers

Simple Summary

Indigenous cattle have extraordinary adaptation capability to diverse environments under low input production system. However, the population size is declining rapidly in Bangladesh due to massive imports of high yielding dairy breeds. The genetic diversity measures are important for assessing population architecture as well as for development of conservation strategies. The aim of this study was to investigate genetic variability and population structure of indigenous cattle genetic resources of Bangladesh using Illumina Bovine SNP50K BeadChip genotyped data. Similar to other zebu populations, low genetic diversity measures were found in Bangladeshi cattle populations. Our findings revealed their distinct genetic structure but showed low levels of genetic differentiation among the six indigenous cattle populations. Moreover, admixture and phylogenetic analysis highlighted historical gene flow among the studied populations. Altogether, our findings provide a comprehensive genomic information on indigenous cattle populations of Bangladesh that could be utilized in their future conservation and breeding research.

Abstract

Understanding the genetic basis of locally adapted indigenous cattle populations is essential to design appropriate strategies and programs for their genetic improvement and conservation. Here, we report genetic diversity measures, population differentiation, and structure of 218 animals sampled from six indicine cattle populations of Bangladesh. Animals were genotyped with Illumina Bovine SNP50K BeadChip along with genotyped data of 505 individuals included from 19 zebu and taurine breeds worldwide. The principal component analysis (PCA) showed clear geographic separation between taurine and indicine lineages where Bangladeshi indigenous cattle clustered with South Asian zebu populations. However, overlapped clusters in PCA, heterozygosity estimates, and Neighbor-Joining phylogenetic tree analysis revealed weak genetic differentiation among the indigenous cattle populations of Bangladesh. The admixture analysis at K = 5 and 9 suggests distinct genetic structure of the studied populations along with 1 to 4% of taurine ancestry. The effective population size suggested a limited pool of ancestors particularly for Sahiwal and North Bengal Grey cattle. In conclusion, these findings shed insights into the genetic architecture of six indigenous cattle populations of Bangladesh for the first time and suggested as distinct gene pools without potential admixture with zebu or taurine populations.

Large-scale genomic analysis reveals the genetic cost of chicken domestication

BACKGROUND

Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.

RESULTS

We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.

CONCLUSION

This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

863 genomes reveal the origin and domestication of chicken

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh

In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (F_IS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (F_ST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

Prevalence of sub-clinical mastitis in high yielding crossbred cows using Draminski mastitis detector

The subclinical mastitis (SCM) causes great economical loss in dairy farms due to reduction in milk production. The objectives of the study were to know the prevalence of subclinical mastitis in lactating cows using Draminski mastitis detector and to evaluate the efficacy of intramammary infusion against SCM in lactating dairy cows. The study was conducted in crossbred dairy cattle in peri-urban dairy production system within seven kilometers around the artificial insemination Centre, Bangladesh Agricultural University, Mymensingh during April, 2011 to May, 2012. The overall prevalence of SCM in lactating cows was 55.1%. The highest prevalence of SCM was 84.4% in more than 7 years old cows. The prevalence of SCM was significantly (p<0.001) increasing with the advancement of the age. The prevalence of SCM was significantly (p<0.05) higher (73.7%) in cows producing more than 15 liters of milk. Cows with 75% Holstein Friesian genotype experienced more SCM (63.0%) than other genotypes. An increased prevalence of SCM with increased number of parity in cows was also observed. The prevalence of SCM was significantly (p<0.001) higher in cows with parity more than five. The highest prevalence of SCM was recorded in left hind quarter (32.3%) but the difference was not significant (p>0.05) statistically. The efficacy of Neomastipra-JR5® as intra mammary infusion against SCM in lactating cows was 78.2%. Draminski mastitis detector could be a potential candidate for the diagnosis of SCM in dairy animals in Bangladesh context. But before introducing this machine in the field it should be validated either by comparing with a gold standard test like somatic cell counter or by using latent class evaluation in a multi-test approach. DOI: http://dx.doi.org/10.3329/bjvm.v11i1.17731 Bangl. J. Vet. Med. (2013). 11 (1): 37-41

Genetic diversity and maternal origin of Bangladeshi chicken

Local domestic chicken populations are of paramount importance as a source of protein in developing countries. Bangladesh possesses a large number of native chicken populations which display a broad range of phenotypes well adapted to the extreme wet and hot environments of this region. This and the fact that wild jungle fowls (JFs) are still available in some regions of the country, it urges to study the present genetic diversity and relationships between Bangladeshi autochthonous chicken populations. Here, we report the results of the mitochondrial DNA (mtDNA) sequence polymorphisms analyses to assess the genetic diversity and possible maternal origin of Bangladeshi indigenous chickens. A 648-bp fragment of mtDNA control region (D-loop) was analyzed in 96 samples from four different chicken populations and one red JF population. Sequence analysis revealed 39 variable sites that defined 25 haplotypes. Estimates of haplotype and nucleotide diversities ranged from 0.745 to 0.901 and from 0.011 to 0.016, respectively. The pairwise differences between populations ranged from 0.091 to 1.459 while most of the PhiST (ΦST) values were significant. Furthermore, AMOVA analysis revealed 89.16 % of the total genetic diversity was accounted for within population variation, indicating little genetic differentiation among the studied populations. The median network analysis from haplotypes of Bangladeshi chickens illustrated five distinct mitochondrial haplogroups (A, D, E, F and I). Individuals from all Bangladeshi chicken populations were represented in the major clades D and E; those maternal origins are presumed to be from Indian Subcontinent and Southeast Asian countries, more particularly from South China, Vietnam, Myanmar and Thailand. Further, phylogenetic analysis between indigenous chicken populations and sub-species of red JFs showed G. g. gallus and G. g. spadiceus shared with almost all haplogroups and had major influence than G. g. murghi in the origin of indigenous chicken of Bangladesh. These results suggest that Bangladeshi indigenous chickens still have abundant genetic diversity and have originated from multiple maternal lineages, and further conservation efforts are warranted to maintain the diversity.

Ovarian Response to Different Dose Levels of Follicle Stimulating Hormone (FSH) in Different Genotypes of Bangladeshi Cattle

The experiment was conducted under the Department of Animal Breeding and Genetics, Bangladesh Agricultural University (BAU), Mymensingh from June, 2001 to December, 2005 in two different locations (Central Cattle Breeding and Dairy Farm and Bangladesh Livestock Research Institute in Savar, Dhaka) to observe ovarian response to different doses of FSH in three different genotypes of cattle- indigenous Local, Pabna cattle and Friesian×Local cross. Five different dose levels used were 200, 240, 280, 320 and 360 mg. Ovarian response as corpus luteum (CL), recovered embryo (RE) and of transferable embryos (TE) count in Local were significant for 320, 280 and 280 mg respectively. In Pabna cattle CL, RE and TE count were found significant for 360, 320 and 320 mg respectively. In Friesian×Local cross CL, RE and TE count were found significant for 360, 320 and 320 mg respectively. The excellent quality embryos showed significantly the highest yield (1.80±0.20) in the 240 and 280 mg FSH levels in Local genotype. In Pabna cattle, the highest yield (2.00±0.32) was found at FSH level 320 mg. In Friesian×Local, the highest yield (2.20±0.20) was found at FSH level 280 mg.