Genome-wide screening of candidate genes for improving fertility in Egyptian native Rahmani sheep

Detection of whole genome selection signatures of Pakistani Teddy goat

BACKGROUND

Natural and artificial selection tend to cause variability that contributes to shape the genome of livestock in a way that differentiates them among the animal kingdom. The particular aim here is to identify positive selection signatures with whole genome pooled-sequence data of Pakistani Teddy goat.

METHODS AND RESULTS

Paired-end alignment of 635,357,043 reads of Teddy goat with (ARS1) reference genome assembly was carried out. Pooled-Heterozygosity (Hp) and Tajima's D (TD) are applied for validation and getting better hits of selection signals, while pairwise F_ST statistics is conducted on Teddy vs. Bezoar (wild goat ancestor) for genomic differentiation, moreover annotation of regions under positive selection was also performed. Hp score with - ZHp > 5 detected six windows having highest hits on Chr. 29, 9, 25, 15 and 14 that harbor HRASLS5, LACE1 and AXIN1 genes which are candidate for embryonic development, lactation and body height. Secondly, - ZTD value of > 3.3 showed 4 windows with very strong hits on Chr.5 & 9 which harbor STIM1 and ADM genes related to body mass and weight. Lastly, - ZF_ST < - 5 generated four strong signals on Chr.5 & 12 harbor LOC102183233 gene. Other significant selection signatures encompass genes associated with wool production, prolificacy and coat colors traits in this breed.

CONCLUSIONS

In brief, this study identified the genes under selection in Pakistani Teddy goat that will be helpful to refining the marker-assisted breeding policies and converging required production traits within and across other goat breeds and to explore full genetic potential of this valued species of livestock.

Genome-Wide Analysis for Early Growth-Related Traits of the Locally Adapted Egyptian Barki Sheep

Sheep play a critical role in the agricultural and livestock sector in Egypt. For sheep meat production, growth traits such as birth and weaning weights are very important and determine the supply and income of local farmers. The Barki sheep originates from the northeastern coastal zone of Africa, and due to its good adaptation to the harsh environmental conditions, it contributes significantly to the meat production in these semi-arid regions. This study aimed to use a genome-wide SNP panel to identify genomic regions that are diversified between groups of individuals of Egyptian Barki sheep with high and low growth performance traits. In this context, from a phenotyped population of 140 lambs of Barki sheep, 69 lambs were considered for a genome-wide scan with the Illumina OvineSNP50 V2 BeadChip. The selected lambs were grouped into divergent subsets with significantly different performance for birth weight and weaning weight. After quality control, 63 animals and 40,383 SNPs were used for analysis. The fixation index (F_ST) for each SNP was calculated between the groups. The results verified genomic regions harboring some previously proposed candidate genes for traits related to body growth, i.e., EYA2, GDF2, GDF10, MEF2B, SLC16A7, TBX15, TFAP2B, and TNNC2. Moreover, novel candidate genes were proposed with known functional implications on growth processes such as CPXM2 and LRIG3. Subsequent association analysis showed significant effects of the considered SNPs on birth and weaning weights. Results highlight the genetic diversity associated with performance traits and thus the potential to improve growth traits in the Barki sheep breed.

Genome-Wide SNP Analysis for Milk Performance Traits in Indigenous Sheep: A Case Study in the Egyptian Barki Sheep

Simple Summary

The Barki sheep is one of the three main breeds in Egypt, which is spread mainly throughout the northwestern coastal zone, which has harsh conditions. Considering the harsh, semi-arid habitat of this breed, milk performance traits such as milk yield and milk composition have a very important role in the feeding of newborn lambs and affect their growth during the early stage of life. In this study, rare milk performance data and genomic information of Barki sheep were used to uncover diversified genomic regions that could explain the variability of milk yield and milk quality traits in the studied population of Barki ewes. Genome-wide analysis identified genomic regions harboring interesting candidate genes such as SLC5A8, NUB1, TBC1D1, KLF3 and ABHD5 for milk yield and PPARA and FBLN1 genes for milk quality traits. The findings offer valuable information for obtaining a better understanding of the genetics of milk performance traits and contribute to the genetic improvement of these traits in Barki sheep.

Abstract

Sheep milk yield and milk composition traits play an important role in supplying newborn lambs with essential components such as amino acids, energy, vitamins and immune antibodies and are also of interest in terms of the nutritional value of the milk for human consumption. The aim of this study was to identify genomic regions and candidate genes for milk yield and milk composition traits through genome-wide SNP analyses between high and low performing ewes of the Egyptian Barki sheep breed, which is well adapted to the harsh conditions of North-East Africa. Therefore, out of a herd of 111 ewes of the Egyptian Barki sheep breed (IBD = 0.08), ewes representing extremes in milk yield and milk quality traits (n = 25 for each group of animals) were genotyped using the Illumina OvineSNP50 V2 BeadChip. The fixation index (F_ST) for each SNP was calculated between the diversified groups. F_ST values were Z-transformed and used to identify putative SNPs for further analysis (Z(F_ST) > 10). Genome-wide SNP analysis revealed genomic regions covering promising candidate genes related to milk performance traits such as SLC5A8, NUB1, TBC1D1, KLF3 and ABHD5 for milk yield and PPARA and FBLN1 genes for milk quality trait. The results of this study may contribute to the genetic improvement of milk performance traits in Barki sheep breed and to the general understanding of the genetic contribution to variability in milk yield and quality traits.

Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds

Hu sheep and Small-tailed Han sheep are the most widely raised and most famous maternal sheep breeds in China, which are known for precocious puberty, perennial oestrus and high fecundity (1-6 lambs each parity). Therefore, it is crucial to increase litter size of these two breeds for intensive sheep industry. The objective of this study was to identify potential genetic markers linked with sheep litter size located at ten genes. This study collected blood sample of 537 Hu sheep and 420 Small-tailed Han sheep with litter size of first parity. The average litter sizes in Hu sheep and Small-tailed Han sheep were 2.21 and 1.93. DNA-pooling sequencing method was used for detecting the potential single nucleotide polymorphisms (SNPs) in ten genes related to follicle development and female reproduction. SNPscan® was used for individually genotyping. As a result, a total of 78 putative SNPs in nine out of ten candidate genes (except NOG) were identified. In total, 50 SNPs were successfully genotyped in Hu sheep and Small-tailed Han sheep. After quality control, a total of 42 SNPs in Hu sheep and 44 SNPs in Small-tailed Han sheep were finally used for further analysis. Association analysis revealed that nine SNPs within six genes (KIT: g.70199073A>G, KITLG: g.124520653G>C, ADAMTS1: g.127753565T>C, ADAMTS1: g.127754640G>T, NCOA1: g.31928165C>T, NCOA1: g.32140565G>A, LIFR: g.35862868C>T, LIFR: g.35862947G>T and NGF: g.91795933T>C) were significantly associated with litter size in Hu sheep or Small-tailed Han sheep. A combined haplotypes analysis of the two loci (LIFR: g.35862868C>T and LIFR: g.35862947G>T) revealed that H2H3 (CTTT) combined haplotypes had the largest litter size than the rest combined haplotypes and more than those with either mutation alone in Small-tailed Han sheep. Taken together, our study suggests that nine significant SNPs in six genes can be served as useful genetic markers for MAS in sheep.

Selection signature analysis reveals genes underlying sheep milking performance

Sheep milk is the most important feed resource for newborn lambs and an important food resource for humans. Sheep milk production and ingredients are influenced by genetic and environmental factors. In this study, we implemented selection signature analysis using Illumina Ovine SNP50 BeadChip data of 78 meat Lacaune and 103 milk Lacaune sheep, which have similar genetic backgrounds, from the Sheep HapMap project to identify candidate genes related to ovine milk traits. Since different methods can detect different variation types and complement each other, we used a haplotype-based method (hapFLK) to implement selection signature analysis. The results revealed six selection signature regions showing signs of being selected ( P < 0.001 ): chromosomes 1, 2, 3, 6, 13 and 18. In addition, 38 quantitative trait loci (QTLs) related to sheep milk performance were identified in selection signature regions, which contain 334 candidate genes. Of those, SUCNR1 (succinate receptor 1) and PPARGC1A (PPARG coactivator 1 alpha) may be the most significant genes that affect sheep milking performance, which supply a significant indication for future studies to investigate candidate genes that play an important role in milk production and quality.