Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing

Abstract

Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout (Oncorhynchus mykiss), an important aquaculture species of cold freshwater. The objectives of this study were 1) to identify and validate high-confidence SVs in rainbow trout using whole-genome re-sequencing; and 2) to examine the contribution of transposable elements (TEs) to SVs in rainbow trout. A total of 96 rainbow trout, including 11 homozygous lines and 85 outbred fish from three breeding populations, were whole-genome sequenced with an average genome coverage of 17.2×. Putative SVs were identified using the program Smoove which integrates LUMPY and other associated tools into one package. After rigorous filtering, 13,863 high-confidence SVs were identified. Pacific Biosciences long-reads of Arlee, one of the homozygous lines used for SV detection, validated 98% (3,948 of 4,030) of the high-confidence SVs identified in the Arlee homozygous line. Based on principal component analysis, the 85 outbred fish clustered into three groups consistent with their populations of origin, further indicating that the high-confidence SVs identified in this study are robust. The repetitive DNA content of the high-confidence SV sequences was 86.5%, which is much higher than the 57.1% repetitive DNA content of the reference genome, and is also higher than the repetitive DNA content of Atlantic salmon SVs reported previously. TEs thus contribute substantially to SVs in rainbow trout as TEs make up the majority of repetitive sequences. Hundreds of the high-confidence SVs were annotated as exon-loss or gene-fusion variants, and may have phenotypic effects. The high-confidence SVs reported in this study provide a foundation for further rainbow trout SV studies.

A 104-bp Structural Variation of the ADPRHL1 Gene Is Associated With Growth Traits in Chickens

“…Growth and development are important processes that affect different body parts of all animals in different life stages, and are affected by many factors, including genetics, nutrient absorption and environmental conditions (Hui et al, 2020;De Robertis and Gurdon, 2021;Liu et al, 2021). We found that a significant association between 104-bp indel and growth characteristics occurred in the early stage of chicken growth.…”

“…For example, the 18-bp indel in the porcine SOX9 5 -UTR is of functional importance and may therefore indeed be a causative variation in SOX9 associated traits (Brenig et al, 2015). Genome SVs is a major source of genetic and phenotypic variation and has received increasing attention (Liu et al, 2021). Some researchers have made some progress through the role of SVs in evolution and the mechanism of SVs in promoting pig phenotypic variation (Du et al, 2021).…”

A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques

“…In addition, two recent whole-genome sequencing projects in Atlantic salmon and rainbow trout have documented 242 and six small to medium-sized CIs, respectively ( i.e. , <1.5 MB; Bertolotti et al 2020 ; Liu et al 2021 ). Although the function of these inversions has not yet been determined, many of the CIs reported in Atlantic salmon are known to span multiple protein-coding genes and therefore are likely to influence traits subjected to selection ( Bertolotti et al 2020 ).…”

“…Although such methods will not give false positives, we do believe that RAD-seq will bias detection of inversions to those greater than several MB in size. However, with the continued decrease in sequencing costs, it is likely that more studies will employ low-coverage whole-genome sequencing approaches which should lead to an increase in detection of CIs and other SVs ( Bertolotti et al 2020 ; Liu et al 2021 ). Indeed, a draft genome of the Atlantic silverside ( Menidia menidia ) describes the presence of 29 inversions including 5 greater than 5 MB ( Tigano et al 20 21).…”

“…Other SVs in salmonids have been documented in chum salmon ( Oncorhynchus keta ) where an inversion on the sex chromosome has been found in samples across western Alaska ( McKinney et al 2020 ), and in Atlantic salmon where multiple chromosomal translocations and fusions have occurred in different populations ( Lehnert et al 2019 ). In addition, two recent studies utilizing whole-genome sequencing have documented many types of SVs (including CIs) in Atlantic salmon and rainbow trout ( Bertolotti et al 2020 ; Liu et al 2021 , respectively).…”