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1. A large deletion at the cortex locus eliminates butterfly wing patterning

   https://doi.org/10.1093/g3journal/jkac021  

   Hanly, Joseph J; Livraghi, Luca; Heryanto, Christa; McMillan, W Owen; Jiggins, Chris D; Gilbert, Lawrence E; Martin, Arnaud (January 2022, G3 Genes|Genomes|Genetics)

   Oliver, B (Ed.)

   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. 

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2. Sequence analysis of the Petunia inflata S‐locus region containing 17 S‐Locus F‐Box genes and the S‐RNase gene involved in self‐incompatibility

   https://doi.org/10.1111/tpj.15005  

   Wu, Lihua; Williams, Justin S.; Sun, Linhan; Kao, Teh‐Hui (October 2020, The Plant Journal)

   null (Ed.)

   Self‐incompatibility in Petunia is controlled by the polymorphic S‐locus, which contains S‐RNase encoding the pistil determinant and 16–20 S‐locus F‐box (SLF) genes collectively encoding the pollen determinant. Here we sequenced and assembled approximately 3.1 Mb of the S2‐haplotype of the S‐locus in Petunia inflata using bacterial artificial chromosome clones collectively containing all 17 SLF genes, SLFLike1, and S‐RNase. Two SLF pseudogenes and 28 potential protein‐coding genes were identified, 20 of which were also found at the S‐loci of both the S6a‐haplotype of P. inflata and the SN‐haplotype of self‐compatible Petunia axillaris, but not in the S‐locus remnants of self‐compatible potato (Solanum tuberosum) and tomato (Solanum lycopersicum). Comparative analyses of S‐locus sequences of these three S‐haplotypes revealed potential genetic exchange in the flanking regions of SLF genes, resulting in highly similar flanking regions between different types of SLF and between alleles of the same type of SLF of different S‐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 the S‐loci of all three S‐haplotypes and in the flanking regions of all S‐locus genes examined. We also found evidence of the association of transposable elements with SLF pseudogenes. Based on the hypothesis that SLF genes were derived by retrotransposition, we identified 10 F‐box genes as putative SLF parent genes. Our results shed light on the importance of non‐coding sequences in the evolution of the S‐locus, and on possible evolutionary mechanisms of generation, proliferation, and deletion of SLF genes. 

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3. Knockdown Resistance-Associated Mutations Dominate Populations of the Common Bed Bug (Hemiptera: Cimicidae) Across the South Central United States

   https://doi.org/10.1093/jme/tjz105  

   Holleman, Jeffrey G; Robison, Grant A; Bellovich, Ian J; Booth, Warren; Severson, David (June 2019, Journal of Medical Entomology)

   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. 

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4. Biochemical Characterization of Disease-Associated Variants of Human Ornithine Transcarbamylase

   https://doi.org/10.1021/acschembio.5c00043  

   Micheloni, Emily; Watson, Samantha S; Beuning, Penny J; Ondrechen, Mary Jo (May 2025, ACS Chemical Biology)

   Human Ornithine Transcarbamylase Deficiency (OTCD) is the most common ureagenesis disorder in the world. OTCD is an X-linked genetic deficiency in which patients experience hyperammonemia to varying degrees depending on the severity of the genetic mutation. More than two-thirds of the known mutations are caused by single nucleotide substitutions. In this paper, Partial Order Optimum Likelihood (POOL), a machine learning method, is used to analyze single nucleotide substitutions in OTC with varying disease phenotypes and predicted catalytic efficiencies. Specifically, we used a computed metric, μ4, a measure of the degree of coupling between an ionizable residue and its neighbors, calculated for the catalytic residues, to identify which protein variants were most likely to have impacted catalytic activities. From this analysis, 17 disease-associated variants were selected plus one additional variant, representing a range of μ4 values and POOL ranks. Then μ4 predictions were compared with established bioinformatics tools, SIFT, PolyPhen-2, Provean, FATHMM, and MutPred2. The bioinformatics tools predicted that most of these mutations are deleterious. The variants were biochemically characterized using kinetics assays, size exclusion chromatography, and differential scanning fluorimetry. POOL combined with μ4 analysis was able to predict correctly which variants were catalytically hindered in vitro for 17 out of 18 variants. Then by expressing a subset of these proteins in cell culture, mechanisms for disease were proposed. Analysis using μ4 is a complementary method to the sequence-based bioinformatics tools for predicting the effects of mutation on catalytic function. 

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5. An Evaluation of Historical Trends in New Mexico Beef Cattle Production in Relation to Climate and Energy

   https://doi.org/10.3390/su11236840  

   Zaied, Ashraf; Geli, Hatim; Holechek, Jerry; Cibils, Andres; Sawalhah, Mohammed; Gard, Charlotte (December 2019, Sustainability)

   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. 

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