Yellow Locus Research Articles

A self-eliminating allelic-drive reverses insecticide resistance in Drosophila leaving no transgene in the population

AbstractInsecticide resistance (IR) poses a significant global challenge to public health and welfare. Here, we develop a locally-acting unitary self-eliminating allelic-drive system, inserted into the Drosophila melanogaster yellow (y) locus. The drive cassette encodes both Cas9 and a single gRNA to bias inheritance of the favored wild-type (1014 L) allele over the IR (1014 F) variant of the voltage-gated sodium ion channel (vgsc) target locus. When enduring a fitness cost, this transiently-acting drive can increase the frequency of the wild-type allele to 100%, depending on its seeding ratio, before being eliminated from the population. However, in a fitness-neutral “hover” mode, the drive maintains a constant frequency in the population, completely converting IR alleles to wild-type, even at low initial seeding ratios.

Yellow Petal locus GaYP promotes flavonol biosynthesis and yellow coloration in petals of Asiatic cotton (Gossypium arboreum)

Yellow Petal locus GaYP is located on chromosome 11 and encodes a Sg6 R2R3-MYB transcription factor, which promotes flavonol biosynthesis and yellow coloration in Asiatic cotton petals. Petal color is pivotal to ornamental value and reproduction of plants. Yellow coloration in plant petals is mainly attributed to colorants including carotenoids, aurones and some flavonols. To date, the genetic regulatory mechanism of flavonol biosynthesis in petals is still to be elucidated. Here, we employed Asiatic cottons with or without deep yellow coloration in petals to address this question. Multi-omic and biochemical analysis revealed significantly up-regulated transcription of flavonol structural genes and increased levels of flavonols, especially gossypetin and 6-hydroxykaempferol, in yellow petals of Asiatic cotton. Furthermore, the Yellow Petal gene (GaYP) was mapped on chromosome 11 by using a recombinant inbred line population. It was found that GaYP encoded a transcriptional factor belonging to Sg6 R2R3-MYB proteins. GaYP could bind to the promoter of flavonol synthase gene (GaFLS) and activate the transcription of downstream genes. Knocking out of GaYP or GaFLS homologs in upland cotton largely eliminated flavonol accumulation and pale yellow coloration in petals. Our results indicated that flavonol synthesis, up-regulated by the R2R3-MYB transcription activator GaYP, was the causative factor for yellow coloration of Asiatic cotton petals. In addition, knocking out of GaYP homologs also led to decrease in anthocyanin accumulation and petal size in upland cotton, suggesting that GaYP and its homologs might modulate developmental or physiological processes beyond flavonol biosynthesis.

RGAP molecular marker for resistance against yellow mosaic disease in ridge gourd [Luffa acutangula (L.) Roxb.

Yellow mosaic disease caused by Tomato leaf curl New Delhi virus (ToLCNDV) causes 100 percent losses in ridge gourd under epidemic conditions, particularly in the tropics and sub-tropics of India. Plant breeding approaches led by the marker-assisted selection have gained increased momentum in virus resistance breeding to hasten the development of resistant varieties. In the present study, an effort has been made to identify molecular markers linked to yellow mosaic disease resistance loci in an F2 population derived from a cross between susceptible ‘Arka Prasan’ and resistant ‘IIHR-Sel-1’ of ridge gourd. All the molecular markers were amplified in parents, and one polymorphic marker clearly distinguished the contrasting parents. The primers LaRGAP 63 produced a polymorphic DNA fragment that co-segregated with yellow mosaic disease reaction phenotypically in the F2 population. The identified marker will be helpful to the breeders for introgression of resistance loci into the elite background.

Marker assisted detection of TYLCV and late blight resistance in tomato (Solanum lycopersicum)

Marker assisted breeding relies on the identification of genetic loci linked to desirable genes/alleles and is beingutilized for selecting desirable traits including disease resistance in a wide variety of crops. The tomato (Solanumlycopersicum L.) production worldwide has lately been threatened by outbreaks of tomato yellow leaf curl virustransmitted by the whitefly (Bemisia tabaci) and late blight caused by oomycete pathogen Phytophthora infestans(Mont.) de Bary. Resistance genes against both pathogens are available and widely used in tomato breeding throughoutthe world. Molecular markers for resistance alleles greatly enhance selection of resistant plants. For effective breedingprogramme, the validation of markers linked to resistance genes in tomato was carried out for tomato improvement.For this purpose, available markers for the tomato yellow leaf curl disease resistance gene loci Ty-2, Ty3, Ty3a andlate blight resistant loci Ph3 were validated. The assay correctly predicted the genotypes of tomato breeding linesharbouring resistance allele at each loci. Further a multiplex assay was also standardized to simultaneously detectthe presence of resistant/susceptible alleles at Ty2,Ty3 and Ty3a loci. The present study carried out in the Division ofVegetable Science, ICAR-IARI, New Delhi, demonstrates the feasibility of combining two SCAR markers (TG0302and P6-25) for detecting simultaneously three important resistance gene loci in tomato genotypes and thereby improvingthe cost and efficiency of the assay.

Genome-wide association mapping identifies yellow rust resistance loci in Ethiopian durum wheat germplasm.

Durum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance and combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance using a modified Cobb scale at Meraro, Kulumsa and Chefe Donsa in the 2015 and 2016 main growing seasons. Analysis of the 35K Axiom Array genotyping data of the panel resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. Eleven SNPs significantly associated with yellow rust resistance were identified on four chromosomes (1A, 1B, 2B, and 5A) which defined at least five genomic loci. Six of the SNPs were consistently identified on chromosome 1B singly at each and combined overall environments which explained 62.6-64.0% of the phenotypic variation (R2). Resistant allele frequency ranged from 14.0-71.0%; Zooming in to the identified resistance loci revealed the presence of disease resistance related genes involved in the plant defense system such as the ABC transporter gene family, disease resistance protein RPM1 (NBS-LRR class), Receptor kinases and Protein kinases. This study has provided SNPs for tracking the loci associated with yellow rust resistance and a diversity panel which can be used for association study of other agriculturally important traits in durum wheat.

Genome-wide association study for adult plant resistance to yellow rust in spring bread wheat (Triticum aestivum L.)

Yellow rust, caused by Puccinia striiformis f. sp. tritici, is a common and serious fungal disease of wheat (Triticum aestivum L.) all over the world and particularly in the Central and West Asia and North Africa region. To identify effective yellow rust resistance loci, genome-wide association study (GWAS) was performed using 196 bread wheat genotypes based on 10,477 single nucleotide polymorphisms markers. Adult plants were evaluated under field conditions for resistance to yellow rust for 2 years (2014–2015) at ICARDA station, Marchouch, Morocco. Out of the 196 genotypes, 85 genotypes (43.37%) were resistant, 22 genotypes (11.22%) were moderately resistant, 13 genotypes (6.63%) were moderately susceptible, 48 genotypes (24.49%) were moderately susceptible to susceptible and 28 genotypes (14.29%) were susceptible to Puccinia striiformis f. sp. tritici. GWAS using mixed linear model identified 23 markers on chromosomes 2A, 2B, 2D and 7B significantly associated with adult plant resistance at false discovery rate (FDR-adjusted P ≤ 0.05). Of which, three markers were within 10 wheat functional genes involved in several plant disease resistance and defense mechanism. Five of the reported functional genes are annotated as disease resistance proteins with nucleotide-binding site leucine repeat domains. BLAST analysis confirmed that YrR61 and Yr17 were mostly the candidate genes linked to the marker Tdurum_contig29983_490 on chromosome 2A. Moreover, markers identified on chromosome 7B and Kukri_c12648_434 on 2D were not mapped within any of previously reported gene/QTL region hence, representing novel resistance loci for Pst and needs to be confirmed using an allelism test.

Marker assisted screening of breeding population of wheat segregating for stripe rust resistance using SSR markers

Screening of F2 population from cross WH711 (susceptible parent) and PBW698 (resistant parent) against stripe rust was done on the basis of field reaction of yellow rust and 12 morphlogical traits. The genotyping of parents was done by using 80 SSR markers out of which 11 were found polymorphic. These 11 markers were used to screen 250 individuals of F2 population. Mendelian inheritance was followed by five markers viz. Xgwm631, Cfa2040, Xsps3000, Barc76 and Xgwm 130 which segregated according to expected ratio of 1:2:1 with chisquare values 5.78, 4.23, 2.75, 9.2 and 7.6 respectively. Single marker analysis showed markers Xgwm631, Cfa2040 (Yr2, Yr6), Xsps3000 (Yr10), Xgwm130 (Yr7), Xwmc407 (Lr17), Barc46, Xgwm413 (Yr15), Barc187 (Yr27) and Xgwm273 (YrH52) were linked with yellow rust locus at 0.01% of significance hence these genes may be present in the breeding population. Cfa2040 was found linked with flag leaf area, number of spikelets and Barc181 with spike weight locus. Markers on chromosomes 7A and 1B showed LOD values 6.64 and 6.86 conferring tight linkage with yellow rust locus thus can be used for MAS.

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens.

Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long-reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome-scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50=37.4Mb, L50=11). We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males (amhr2by+ ) from XX genetic females (amhr2by- ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex-determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance

SummaryGenerally repressed by epigenetic mechanisms, retrotransposons represent around 40% of the murine genome. At the Agouti viable yellow (Avy) locus, an endogenous retrovirus (ERV) of the intracisternal A particle (IAP) class retrotransposed upstream of the agouti coat-color locus, providing an alternative promoter that is variably DNA methylated in genetically identical individuals. This results in variable expressivity of coat color that is inherited transgenerationally. Here, a systematic genome-wide screen identifies multiple C57BL/6J murine IAPs with Avy epigenetic properties. Each exhibits a stable methylation state within an individual but varies between individuals. Only in rare instances do they act as promoters controlling adjacent gene expression. Their methylation state is locus-specific within an individual, and their flanking regions are enriched for CTCF. Variably methylated IAPs are reprogrammed after fertilization and re-established as variable loci in the next generation, indicating reconstruction of metastable epigenetic states and challenging the generalizability of non-genetic inheritance at these regions.

Expanding the genetic toolkit of Tribolium castaneum.

The red flour beetle, Tribolium castaneum, is an important model insect and agricultural pest. However, many standard genetic tools are lacking or underdeveloped in this system. Here, we present a set of new reagents to augment existing Tribolium genetic tools. We demonstrate a new GAL4 driver line that employs the promoter of a ribosomal protein gene to drive expression of a UAS responder in the fat body. We also present a novel dual fluorescent reporter that labels cell membranes and nuclei with different fluorophores for the analysis of cellular morphology. This approach also demonstrates the functionality of the viral T2A peptide for bicistronic gene expression in Tribolium. To facilitate classical genetic analysis, we created lines with visible genetic markers by CRISPR-mediated disruption of the yellow and ebony body color loci with a cassette carrying an attP site, enabling future φC31-mediated integration. Together, the reagents presented here will facilitate more robust genetic analysis in Tribolium and serve as a blueprint for the further development of this powerful model’s genetic toolkit.

English

Data from the snail farm of the University of Calabar, Nigeria were collected and utilized to investigate the distribution and gene frequencies of egg shell colour of two ectotypes of Giant African Land Snails (Archachatina marginata var. saturalis), black skinned (BS) × black skinned mating group, and white skinned (WS) × white skinned mating group. The eggs collected were scored for the presence of yellow (Yp), light yellow (Lp) and milky white (Mp) egg shell colour. The egg shell colour distributions between the two ectotypes (BS × BS and WS × WS) were 46.50 vs. 3.77%, 42.68 vs. 48.11% and 10.83 vs. 48.11% for yellow, light yellow and milky white, respectively. In both ectotypes, the dominant gene for yellow, light yellow and milky white egg shell colour segregated at low frequencies (0.26 vs. 0.02, 0.24 vs. 0.31 and 0.06 vs. 0.31). The lowest value being yellow shell of the white skinned × white skinned mating group with frequency of 0.02, followed by milky white shell of the black skinned × black skinned mating group with frequency of 0.06. These values were much lower than the Mendelian value of 0.75. This is an indication that snails have not been purified through artificial breeding. Estimate of genetic distance between the two ectotypes were 0.060, 0.005 and 0.063 at yellow, light yellow and milky white loci, respectively. This shows that the ectotypes are closely related at the egg shell colour loci. Key words: Genotype, phenotype, snail egg, shell colour, variations.

Unique hue loci differ with methodology

Studies investigating the effect of rods on unique hue loci in the peripheral retina generally obtain measures at two time points associated with the dark adaptation function - the cone plateau and the rod plateau. In comparison, this study used a color-naming procedure to identify the loci of unique green and unique yellow as a function of time associated with the entire dark adaptation function. The unique hue loci derived by this procedure were then compared to those obtained directly with a staircase procedure. Hue-scaling functions were obtained for monochromatic stimuli for four observers using the '4 + 1' procedure. Data were collected every 4 min following extinction of a bleaching stimulus. These hue-scaling functions were then converted to uniform appearance diagrams (UADs) to derive unique green and unique yellow loci. Unique green and unique yellow loci were also obtained from the same observers via a staircase procedure at 4-9 min post-bleach (minimal rod input) and after 28 min dark adaptation (maximal rod input). Measurements were made in the peripheral retina at 10° temporal retinal eccentricity and at the fovea. Unique green loci derived from UADs are at longer wavelengths compared to those measured directly with the staircase procedure. In addition, unique green loci derived from UADs show a progressive shift to longer wavelengths as time post-bleach increases; whereas, unique green loci obtained from the staircase procedure differ little between the rod-bleach and no-bleach conditions. Unique yellow loci are similar across both experimental procedures. Unique green loci derived from UADs are not the same as those measured with traditional psychophysical procedures. These differences may be due to the different response criteria used by observers in the color-naming and staircase procedures. The unique green loci obtained from UADs indicate that rod signals shift unique green loci to longer wavelengths as time post-bleach increases. More direct methods need to be employed to determine if this rod effect is valid.

A composite six bp in-frame deletion in the melanocortin 1 receptor (MC1R) gene is associated with the Japanese brindling coat colour in rabbits (Oryctolagus cuniculus)

BackgroundIn the domestic rabbit (Oryctolagus cuniculus), classical genetic studies have identified five alleles at the Extension locus: ED (dominant black), ES (steel, weaker version of ED), E (wild type, normal extension of black), eJ(Japanese brindling, mosaic distribution of black and yellow) and e (non-extension of black, yellow/red with white belly). Sequencing almost the complete coding sequence (CDS) of the rabbit MC1R gene, we recently identified two in-frame deletions associated with dominant black (c.280_285del6; alleles ED or ES) and recessive red (c.304_333del30; allele e) coat colours. It remained to characterize the eJallele whose phenotypic effect is similar to the Orange and Sex-linked yellow loci of cat and Syrian hamster.ResultsWe sequenced the whole CDS in 25 rabbits of different coat colours including 10 Japanese and 10 Rhinelander (tricolour) rabbits and identified another 6 bp-in frame deletion flanked by a G > A transition in 5' (c.[124G>A;125_130del6]) that was present in all animals with Japanese brindling coat colour and pattern. These mutations eliminate two amino acids in the first transmembrane domain and, in addition, cause an amino acid substitution at position 44 of the wild type sequence. Genotyping 371 rabbits of 31 breeds with different coat colour this allele (eJ) was present in homozygous state in Japanese, Rhinelander and Dutch tricolour rabbits only (except one albino rabbit). Rabbits with eJ/eJ genotype were non fixed at the non-agouti mutation we previously identified in the ASIP gene. Segregation in F1 and F2 families confirmed the order of dominance already determined by classical genetic experiments with a possible dose effect evident comparing eJ/eJ and eJ/e animals. MC1R mRNA was expressed in black hair skin regions only.ConclusionsThe c.[124A;125_130del6] allele may be responsible for a MC1R variant determining eumelanin production in the black areas. However, the mechanism determining the presence of both red and black hairs in the same animal seems more complex. Expression analyses of the c.[124A;125_130del6] allele suggest that MC1R transcription may be regulated epigenetically in rabbits with the Japanese brindling phenotype. Further studies are needed to clarify this issue.

Active promoters and insulators are marked by the centrosomal protein 190

For the compact Drosophila genome, several factors mediating insulator function, such as su(Hw) and dCTCF, have been identified. Recent analyses showed that both these insulator-binding factors are functionally dependent on the same cofactor, CP190. Here we analysed genome-wide binding of CP190 and dCTCF. CP190 binding was detected at CTCF, su(Hw) and GAF sites and unexpectedly at the transcriptional start sites of actively transcribed genes. Both insulator and transcription start site CP190-binding elements are strictly marked by a depletion of histone H3 and, therefore, a loss of nucleosome occupancy. In addition, CP190/dCTCF double occupancy was seen at the borders of many H3K27me3 'islands'. As before, these sites were also depleted of H3. Loss of either dCTCF or CP190 causes an increase of H3 and H3K27 trimethylation at these sites. Thus, for both types of cis-regulatory elements, domain borders and promoters, the chromatin structure is dependent on CP190.

Polymorphism of yellow locus in Drosophila melanogaster mutants from natural populations

We studied molecular characteristics of yellow (y; 1-0.0) locus, which determines the body coloration of phenotypically wild-type and mutant alleles isolated from geographically distant populations of Drosophila melanogaster in different years. According to Southern data, restrictions map of yellow locus of all studied strains differ from each other as well as from that of Oregon stock. FISH analysis shows that in the neighborhood of yellow locus in X chromosome neither P nor hobo elements are found in y1-775 stock, while only hobo is found there in y1-859 and y1-866 stocks, only P element in y+sn849 stock, and both elements in y1-719 stock. Thus, all studied mutant variants of yellow are of independent origin. Yellow locus residing at the very end of X chromosome (region 1A5-8 of cytologic map) carries significantly more transposon than retrotransposon-induced mutations, as compared to white locus (regions 3C2). It is possible that transposons are more active than retrotransposons at the chromosomal ends of D. melanogaster.

Yr10 gene polymorphism in bread wheat varieties

Yellow rust resistance locus Yr10 located on chromosome 1B in Moro and originated from the Turkish line PI178383 was investigated in terms of polymorphism in seven winter type bread wheat cvs. (Triticum aestivum ssp. Aestivum) Altay2000, zgi2001, Sonmez2001 (yellow rust resistant), Aytýn98, ES14, Harmankaya99 (yellow rust susceptible) and PI178383 as control. Exon 1 (1 - 833 bp) and Exon 2 (1989 - 3630 bp) parts of Yr10 were amplified with three primers. Amplification was not observed with E2A primers in Harmankaya99, zgi2001 and Sonmez2001 cvs, while amplification products were observable at all tested varieties with the other primers. PCR results showed that E2A reverse primer is not able to anneal to the three varieties mentioned above. Sequence analysis and bioinformatics analysis proved that there has been single nucleotide changes especially in the second exon. The most similar sequences to the first exon of Harmankaya99, zgi01 and Sonmez2001 are AF509535 (Aegilops tauschii NBS-LRR-like gene), AF509534 (A. tauschii NBS-LRR-like gene sequence) and AF509534, respectively. These results could be helpful in revealing divergence between resistant and susceptible varieties.

The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species

Understanding the mechanisms underlying the morphological divergence of species is one of the central goals of evolutionary biology. Here, we analyze the genetic and molecular bases of the divergence of body pigmentation patterns between Drosophila yakuba and its sister species Drosophila santomea. We found that loss of pigmentation in D. santomea involved the selective loss of expression of the tan and yellow pigmentation genes. We demonstrate that tan gene expression was eliminated through the mutational inactivation of one specific tan cis-regulatory element (CRE) whereas the Tan protein sequence remained unchanged. Surprisingly, we identify three independent loss-of-function alleles of the tan CRE in the young D. santomea lineage. We submit that there is sufficient empirical evidence to support the general prediction that functional evolutionary changes at pleiotropic loci will most often involve mutations in their discrete, modular cis-regulatory elements.

Persistent locus-specific instability of yellow 2-717 and Notch Uc-1 in Drosophila melanogaster coincides with hobo multiplication

According to FISH data the presence of multiple hobo element copies in the unstable yellow and Notch loci in y(2-717) and Uc-1 Drosophila melanogaster stocks, respectively, was found. Locus-specific instability in these strains is caused by hobo multiplication in the respective loci and its subsequent recombination with neighboring hobo copies rather than its insertion-excision.

Drosophila gypsy insulator and yellow enhancers regulate activity of yellow promoter through the same regulatory element

There is ample evidence that the enhancers of a promoterless yellow locus in one homologous chromosome can activate the yellow promoter in the other chromosome where the enhancers are inactive or deleted, which is indicative of a high specificity of the enhancer-promoter interaction in yellow. In this paper, we have found that the yellow sequence from -100 to -69 is essential for stimulation of the heterologous eve (TATA-containing) and white (TATA-less) promoters by the yellow enhancers from a distance. However, the presence of this sequence is not required when the yellow enhancers are directly fused to the heterologous promoters or are activated by the yeast GAL4 activator. Unexpectedly, the same promoter proximal region defines previously described promoter-specific, long-distance repression of the yellow promoter by the gypsy insulator on the mod(mdg4) ( u1 ) background. These finding suggest that proteins bound to the -100 to -69 sequence are essential for communication between the yellow promoter and upstream regulatory elements.

Ty-3, a begomovirus resistance locus near the Tomato yellow leaf curl virus resistance locus Ty-1 on chromosome 6 of tomato

Ty-3, a begomovirus resistance locus near the Tomato yellow leaf curl virus resistance locus Ty-1 on chromosome 6 of tomato