IDENTIFICATION OF DIVERSIFIED SELECTIVE SWEEPS USING HIGH DENSITY SNP ARRAY IN SAHIWAL CATTLE
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Date
2022
Authors
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Journal ISSN
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Publisher
ICAR-NDRI, KARNAL
Abstract
Both natural and artificial selection have resulted in cattle breeds that are
specialized for particular uses. Several specific genomic regions have been under
selection pressure, and it is widely accepted that these genomic sequences, or
selection signatures, control or affect key phenotypes that are involved in some
traits. Positive selection pressure can reduce or even eliminate the frequency of
negative alleles in the offspring’s genome. Therefore, selection signatures in a
population could provide genomic information to facilitate selection and provide
insights into evolutionary history. The estimation of the population structure and
genetic relatedness between individuals is important for uncovering the
demographic history of the population under study. We analyzed 735636
autosomal single nucleotide polymorphisms (SNPs) which were shared by 48
randomly sampled individuals to determine the genetic structure of Sahiwal herd.
STRUCTURE reported maximum LnK (Mean of. Ln prob of data) at k=2 also
confirmed by minimum ADMIXTURE cross validation error at same k value. Thus
appropriate k value for Sahiwal herd is 2 indicating farm born animals and
purchased animals. The effective population size was estimated to be 54 at one
generation ago using GONE and 75 using SNeP 13 generations ago. Estimates
from SNeP, built on equation, were lower than GONE estimates with the genetic
algorithm both utilizing linkage disequilibrium data. In addition, the most rapid
decline of population size was observed between 8 and 12 generations ago which
suggests that the reduction in the population of Sahiwal cattle breeds began with
herd formation at NDRI. We scanned the genome of Sahiwal cattle for selection
signatures with 777 K SNP panel. A total of 284 extreme iHS values exceeded the
empirical threshold level of 3 were calculated, with highest value at BTA 9
(iHS=4.26). Annotating the regions harboring clustered iHS signals revealed a
panel of interesting candidate genes like NOL10,CXCL8,PDIA6, ATP6V1C2 and
HPCAL1, in the context of Oxidative phosphorylation, IL-17 signaling, RIG-I-like
receptor signaling and Synaptic vesicle cycle. The QTL present in iHS regions
include Milk kappa-casein percentage, Milk yield, Milk fat percentage, luteal
activity and clinical mastitis. By performing LASSI (Likelihood-based Approach for
Selective Sweep Inference) a composite likelihood ratio statistic, we compiled a
list of 561 selection sweeps described across 29 cattle autosome, which we
subsequently grouped according to number of sweeping haplotype “m” with “m” =
1 indicating hard sweep (198) and “m”> 1 indicating soft sweep (363).For each
selective sweep, we performed a candidate gene survey that identified 102 genes
within the hard sweeps and 273 genes within soft sweeps regions. Genes
identified were linked to milk fat yield, Immunoglobulin G level, Milk betalactoglobulin
percentage and Milk protein yield in hard sweeps and Milk yield,
triglyceride level, feed conversion ratio, age at first calving in soft sweeps. A
complementary functional enrichment analysis of the selective sweep candidates
highlighted other genes related to pathways underlying behavior, immune
response, and reproductive traits.