An official website of the United States government
Abstract As the genetic basis of natural and domesticated variation has been described in recent years, a number of hotspot genes have been repeatedly identified as the targets of selection, Heliconius butterflies display a spectacular diversity of pattern variants in the wild and the genetic basis of these patterns has been well-described. Here, we sought to identify the mechanism behind an unusual pattern variant that is instead found in captivity, the ivory mutant, in which all scales on both the wings and body become white or yellow. Using a combination of autozygosity mapping and coverage analysis from 37 captive individuals, we identify a 78-kb deletion at the cortex wing patterning locus, a gene which has been associated with wing pattern evolution in H. melpomene and 10 divergent lepidopteran species. This deletion is undetected among 458 wild Heliconius genomes samples, and its dosage explains both homozygous and heterozygous ivory phenotypes found in captivity. The deletion spans a large 5′ region of the cortex gene that includes a facultative 5′UTR exon detected in larval wing disk transcriptomes. CRISPR mutagenesis of this exon replicates the wing phenotypes from coding knock-outs of cortex, consistent with a functional role of ivory-deleted elements in establishing scale color fate. Population demographics reveal that the stock giving rise to the ivory mutant has a mixed origin from across the wild range of H. melpomene, and supports a scenario where the ivory mutation occurred after the introduction of cortex haplotypes from Ecuador. Homozygotes for the ivory deletion are inviable while heterozygotes are the targets of artificial selection, joining 40 other examples of allelic variants that provide heterozygous advantage in animal populations under artificial selection by fanciers and breeders. Finally, our results highlight the promise of autozygosity and association mapping for identifying the genetic basis of aberrant mutations in captive insect populations.
more »
« less
Defining a Haplotype Encompassing the LCORL-NCAPG Locus Associated with Increased Lean Growth in Beef Cattle
Numerous studies have shown genetic variation at the LCORL-NCAPG locus is strongly associated with growth traits in beef cattle. However, a causative molecular variant has yet to be identified. To define all possible candidate variants, 34 Charolais-sired calves were whole-genome sequenced, including 17 homozygous for a long-range haplotype associated with increased growth (QQ) and 17 homozygous for potential ancestral haplotypes for this region (qq). The Q haplotype was refined to an 814 kb region between chr6:37,199,897–38,014,080 and contained 218 variants not found in qq individuals. These variants include an insertion in an intron of NCAPG, a previously documented mutation in NCAPG (rs109570900), two coding sequence mutations in LCORL (rs109696064 and rs384548488), and 15 variants located within ATAC peaks that were predicted to affect transcription factor binding. Notably, rs384548488 is a frameshift variant likely resulting in loss of function for long isoforms of LCORL. To test the association of the coding sequence variants of LCORL with phenotype, 405 cattle from five populations were genotyped. The two variants were in complete linkage disequilibrium. Statistical analysis of the three populations that contained QQ animals revealed significant (p < 0.05) associations with genotype and birth weight, live weight, carcass weight, hip height, and average daily gain. These findings affirm the link between this locus and growth in beef cattle and describe DNA variants that define the haplotype. However, further studies will be required to define the true causative mutation.
more »
« less
- Award ID(s):
- 2117272
- PAR ID:
- 10565416
- Publisher / Repository:
- Genes
- Date Published:
- Journal Name:
- Genes
- Volume:
- 15
- Issue:
- 5
- ISSN:
- 2073-4425
- Page Range / eLocation ID:
- 576
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
SUMMARY Self‐incompatibility inPetuniais controlled by the polymorphicS‐locus, which containsS‐RNaseencoding the pistil determinant and 16–20S‐locus F‐box(SLF) genes collectively encoding the pollen determinant. Here we sequenced and assembled approximately 3.1 Mb of theS2‐haplotype of theS‐locus inPetunia inflatausing bacterial artificial chromosome clones collectively containing all 17SLFgenes,SLFLike1, andS‐RNase. TwoSLFpseudogenes and 28 potential protein‐coding genes were identified, 20 of which were also found at theS‐loci of both theS6a‐haplotype ofP. inflataand theSN‐haplotype of self‐compatiblePetunia axillaris, but not in theS‐locus remnants of self‐compatible potato (Solanum tuberosum) and tomato (Solanum lycopersicum). Comparative analyses ofS‐locus sequences of these threeS‐haplotypes revealed potential genetic exchange in the flanking regions ofSLFgenes, resulting in highly similar flanking regions between different types ofSLFand between alleles of the same type ofSLFof differentS‐haplotypes. The high degree of sequence similarity in the flanking regions could often be explained by the presence of similar long terminal repeat retroelements, which were enriched at theS‐loci of all threeS‐haplotypes and in the flanking regions of allS‐locus genes examined. We also found evidence of the association of transposable elements withSLFpseudogenes. Based on the hypothesis thatSLFgenes were derived by retrotransposition, we identified 10F‐boxgenes as putativeSLFparent genes. Our results shed light on the importance of non‐coding sequences in the evolution of theS‐locus, and on possible evolutionary mechanisms of generation, proliferation, and deletion ofSLFgenes.more » « less
-
Abstract Despite awareness of the mutations conferring insecticide resistance in the bed bug, Cimex lectularius L. (Hemiptera: Cimicidae), within the United States few studies address the distribution and frequency of these. Within the United States, studies have focused on collections made along the East Coast and Midwest, documenting the occurrence of two mutations (V419L and L925I) within the voltage-gated sodium channel α-subunit gene shown to be associated with knockdown resistance (kdr) to pyrethroids. Here, the distribution and frequency of the V419L and L925I site variants is reported from infestations sampled within Oklahoma and its immediately adjacent states. Additionally, the presence of a mutation previously undocumented in the United States (I935F) is noted. While novel in the United States, this mutation has previously been reported in Australian and Old World populations. No infestations were found to harbor wild-type individuals, and hence susceptible, at each of the three sites. Instead, ~21% were found to possess the resistant mutation at the L925I site (haplotype B), ~77% had mutations at both the V419L and L925I sites (haplotype C), and 2% possessed the mutation at the L936F site (haplotype Ab). The high frequency of haplotype C corresponds to previous studies in the United States, and contrasts dramatically with those of the Old World and Australia. The data presented here provide insight into the contemporary occurrence of kdr-associated insecticide resistance in the South Central United States, a region for which data have previously been absent. These data suggest that New World and Old World/Australian infestations are likely to have originated from different origins.more » « less
-
In support of Food-Energy-Water Systems (FEWS) analysis to enhance its sustainability for New Mexico (NM), this study evaluated observed trends in beef cattle population in response to environmental and economic changes. The specific goal was to provide an improved understanding of the behavior of NM’s beef cattle production systems relative to precipitation, temperature, rangeland conditions, production of hay and crude oil, and prices of hay and crude oil. Historical data of all variables were available for the 1973–2017 period. The analysis was conducted using generalized autoregressive conditional heteroscedasticity models. The results indicated declining trends in beef cattle population and prices. The most important predictors of beef cattle population variation were hay production, mean annual hay prices, and mean annual temperature, whereas mean annual temperature, cattle feed sold, and crude oil production were the most important predictors for calf population that weigh under 500 lb. Prices of beef cattle showed a strong positive relationship with crude oil production, mean annual hay prices, rangeland conditions, and mean annual precipitation. However, mean annual temperature had a negative relationship with mean annual beef prices. Variation in mean annual calf prices was explained by hay production, mean annual temperature, and crude oil production. This analysis suggested that NM’s beef cattle production systems were affected mainly and directly by mean annual temperature and crude oil production, and to a lesser extent by other factors studied in this research.more » « less
-
Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation – a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/genes15050576
