Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits

Cheng, Jie; Cao, Xiukai; Hanif, Quratulain; Pi, Li; Hu, Linyong; Huang, Yongzhen; Lan, Xianyong; Lei, Chuzhao; Chen, Hong

doi:10.3389/fgene.2020.00569

Cited by 10 publications

(9 citation statements)

References 43 publications

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“…We found a particularly interesting group of genes for the CSD group in a region of chromosome 6 that distinguishes it from the NRD group. This region harbors different genes related to animal growth and development, such as LCORL [ 35 ], which has been shown to regulate body size in goats and several other mammals, HERC6 [ 36 ], and FAM184B [ 37 ]. A part of this homozygous region and another region that we also found on chromosome 5 for the CSD group were previously described by [ 30 ], who analyzed only the cluster of Sicilian goats.…”

Section: Discussionmentioning

confidence: 99%

Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

et al. 2021

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Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations.

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Section: Discussionmentioning

confidence: 99%

Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

et al. 2021

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“…We looked for: (a) functional category enrichment in CNVRs found in individual breeds (minimum number of individuals per CNVR was equal to two); and (b) CNVRs shared by multiple breeds (CNVR frequency >15% in at least one breed but detected in at least two breeds).Comparison of the CNVRs in Russian sheep to the CNVRs found in other studiesTo estimate the fraction of known CNVRs in our set we compared our data with the combined set of ovine CNVRs reported in several previous studies(Fontanesi et al 2011;Liu et al 2013;Hou et al 2015;Ma et al 2015Ma et al , 2017Jenkins et al 2016;Zhu et al 2016;Yan et al 2017;Yang et al 2018;Di Gerlando et al 2019;Cheng et al 2020;Li et al 2020;Wang et al 2020). A simple overlap with the regions found in other publications has been reported.…”

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Copy number variants in genomes of local sheep breeds from Russia

et al. 2021

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Summary Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed‐specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds.

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“…Here, the five CNVR harboring genes RUNX1 , LOC101104348, LOC105604082, PAG11 and LOC101111988 showed significant pairwise differentiation among HTS, OTS and VTS. RUNX 1 has been reported overlapping with a CNV in Chaka sheep ( Cheng et al, 2020 ). It is well known that RUNX1 plays a crucial role in hematopoiesis, leukemogenesis and neural development.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing

Zhang

et al. 2022

Front. Genet.

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Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.

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Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits

Cited by 10 publications

References 43 publications

Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Copy number variants in genomes of local sheep breeds from Russia

Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing

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