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PubMed2007

Fast data preprocessing for chromatographic fingerprints of tomato cell wall polysaccharides using chemometric methods.

The variability in the chemistry of cell wall polysaccharides in pericarp tissue of red-ripe tomato fruit (Solanum lycopersicon Mill.) was characterized by chemical methods and enzymatic degradations coupled to high performance anion exchange chromatography (HPAEC) and mass spectrometry analysis. Large fruited line, Levovil (LEV) carrying introgressed chromosome fragments from a cherry tomato line Cervil (CER) on chromosomes 4 (LC4), 9 (LC9), or on chromosomes 1, 2, 4 and 9 (LCX) and containing quantitative trait loci (QTLs) for texture traits, was studied. In order to differentiate cell wall polysaccharide modifications in the tomato fruit collection by multivariate analysis, chromatograms were corrected for baseline drift and shift of the component elution time using an approach derived from image analysis and mathematical morphology. The baseline was first corrected by using a "moving window" approach while the peak-matching method developed was based upon location of peaks as local maxima within a window of a definite size. The fast chromatographic data preprocessing proposed was a prerequisite for the different chemometric treatments, such as variance and principal component analysis applied herein to the analysis. Applied to the tomato collection, the combined enzymatic degradations and HPAEC analyses revealed that the firm LCX and CER genotypes showed a higher proportion of glucuronoxylans and pectic arabinan side chains while the mealy LC9 genotype demonstrated the highest content of pectic galactan side chains. QTLs on tomato chromosomes 1, 2, 4 and 9 contain important genes controlling glucuronoxylan and pectic neutral side chains biosynthesis and/or metabolism.

Acetic Acid↗

PubMed2006

Concomitant replacement of language and mtDNA in South Caspian populations of Iran.

The Gilaki and Mazandarani occupy the South Caspian region of Iran and speak languages belonging to the North-Western branch of Iranian languages . It has been suggested that their ancestors came from the Caucasus region, perhaps displacing an earlier group in the South Caspian . Linguistic evidence supports this scenario, in that the Gilaki and Mazandarani languages (but not other Iranian languages) share certain typological features with Caucasian languages . We analyzed patterns of mtDNA and Y chromosome variation in the Gilaki and Mazandarani. Based on mtDNA HV1 sequences, the Gilaki and Mazandarani most closely resemble their geographic and linguistic neighbors, namely other Iranian groups. However, their Y chromosome types most closely resemble those found in groups from the South Caucasus. A scenario that explains these differences is a south Caucasian origin for the ancestors of the Gilaki and Mazandarani, followed by introgression of women (but not men) from local Iranian groups, possibly because of patrilocality. Given that both mtDNA and language are maternally transmitted, the incorporation of local Iranian women would have resulted in the concomitant replacement of the ancestral Caucasian language and mtDNA types of the Gilaki and Mazandarani with their current Iranian language and mtDNA types. Concomitant replacement of language and mtDNA may be a more general phenomenon than previously recognized.

Chromosomes, Human, Y↗

PubMed2004

Idd1 and Idd3 are necessary but not sufficient for development of type 1 diabetes in NOD mouse.

Type 1 diabetes in the NOD mouse is under polygenic control, with a major susceptibility gene, Idd1, in the major histocompatibility complex (MHC). To investigate the contribution of the NOD MHC to type 1 diabetes susceptibility, a B6.NOD-H-2 congenic strain, in which the NOD MHC was introgressed onto the genetic background of the C57BL/6 strain, was established. Despite possession of the diabetogenic MHC from the NOD mouse, none of the B6.NOD-H-2 mice developed type 1 diabetes, indicating that the NOD MHC alone is not sufficient for type 1 diabetes and that non-MHC genes are also necessary. One of the strongest non-MHC genes is Idd3, and Il2 which encodes interleukin 2, is a candidate gene for Idd3. To test whether a combination of the NOD MHC with the NOD allele of Il2 is sufficient for type 1 diabetes, B6.NOD-H-2 mice were crossed with C3H mice, which possess the NOD allele at Il2, and F2 mice homozygous for NOD alleles at both the MHC and Il2 were produced. None of the F2 mice developed type 1 diabetes, suggesting that NOD alleles at MHC (Idd1) and Il2 (Idd3) are not sufficient for type 1 diabetes in the NOD mouse.

Amino Acid Sequence↗

PubMed2005

Nanos (nos) genes of the vector mosquitoes, Anopheles gambiae, Anopheles stephensi and Aedes aegypti.

A number of genetics-based strategies for the control of vector-borne diseases require the development of genetic drive systems for introgressing antipathogen effector genes into wild populations of insects. Modified transposons whose mobilization is controlled by the DNA elements of developmentally regulated genes offer a potential solution for introducing effector genes into mosquitoes. Such elements could exhibit sex-, stage- and species-specific transposition, thus mitigating some of the concerns associated with autonomous transposition. Hybridizations in situ show that the transcription products of the nanos orthologous genes of Anopheles gambiae (Anga nos), An. stephensi (Anst nos) and Aedes aegypti (Aeae nos) accumulate in developing oocytes in adult females and localize to the posterior pole in early embryos. These features make nos genes promising candidates for donating control sequences to modified transposons.

Aedes↗

PubMed2006

Functional characterization of the promoter of the vitellogenin gene, AsVg1, of the malaria vector, Anopheles stephensi.

Some genetic strategies for controlling transmission of mosquito-borne diseases call for the introgression of antipathogen effector genes into vector populations. Endogenous mosquito promoter and other cis-acting DNA sequences are needed to direct the expression of the effector molecules to maximize their efficacy. Vitellogenin (Vg)-encoding gene control sequences are candidates for driving tissue-, stage- and sex-specific expression of exogenous genes. One of the Anopheles stephensi Vg genes, AsVg1, was cloned and a full-length cDNA, as well as 850 base pairs adjacent to the 5'-end, were sequenced and characterized. Expression of AsVg1 is restricted to the fat body tissues of blood-fed females, and the amino acid sequence of the conceptual translation product is >85% identical to those of other anopheline Vgs. These characteristics support the conclusion that AsVg1 is a Vg-encoding gene. Functional analyses of the AsVg1 putative cis-regulatory sequences were performed using transgenic mosquitoes. The results showed that DNA fragments encompassing the 850 base pairs immediately adjacent to the 5'-end of the gene and the 3'-end untranslated region are sufficient to direct sex-, stage- and tissue-specific expression of a reporter gene. These data indicate that the AsVg1 promoter is a good candidate for controlling the expression of anti-pathogen effector molecules in this malaria vector mosquito.

Animals↗

PubMed2026

Beyond the salt barrier: CRISPR-mediated DNA reprogramming to uncouple yield from tolerance in Rice: A review.

Rice (Oryza sativa L.) feeds half of humanity, yet its cultivation is increasingly threatened by soil salinization, which now affects 1.4 billion hectares globally. Decades of breeding and engineering have focused on Na+ exclusion, principally through the Saltol QTL and the xylem-unloading transporter OsHKT1;5, yet this strategy has reached a physiological ceiling. Excluder genotypes survive salinity but fail to fill grain, because the ATP-intensive cost of continuous ion extrusion starves reproductive sinks, while ABA-mediated stomatal closure imposes chronic carbon limitation. The resulting "survival-yield gap" exposes a fundamental flaw in single-trait approaches to a polygenic stress. In this review, we argue that durable, yield-stable salt tolerance requires a coordinated systems-level intervention spanning five mechanistic tiers: (i) CRISPR/Cas9-mediated removal of negative regulatory brakes (OsRR22, RST1, PC1) that suppress plant's latent stress-adaptive capacity; (ii) reinforcement of actin-myosin cytoskeletal transport to sustain SOS1, NHX1, and HKT1;5 delivery under ionic stress; (iii) importation of halophyte design principles from Oryza coarctata, including salt gland architecture and superior Na+ compartmentalization; (iv) recalibration of the ROS-photosynthesis axis via the DHHC09-STRK1-CatC molecular switch and stomatal density engineering; and (v) pyramiding these modules into a "Salt-Shield Rice" genotype through multiplex editing, marker-assisted introgression, speed breeding, and genomic selection. We propose a phased ten-year roadmap that integrates synthetic biology circuit design with conventional breeding to deliver field-ready, multi-module varieties with greater than 70% yield stability at 8-10 dS m-1. This remains an aspirational design target rather than a demonstrated outcome, as three of the five tiers-halophyte-derived structural traits, cytoskeletal reinforcement, and full multi-module pyramiding-remain unvalidated in rice.

CRISPR/Cas9↗

PubMed2025

Genomic insights into the population history of fat-tailed sheep and identification of two mutations that contribute to fat tail adipogenesis.

INTRODUCTION: Since their domestication, domestic sheep (Ovis aries) have been culturally and economically significant farming animals worldwide. Fat-tailed sheep serve as a unique genetic resource for understanding adipogenesis and adaptive evolution in livestock. OBJECTIVES: Several genomic analyses have been conducted on various sheep breeds to elucidate the genome and regulation mechanism of the fat tail trait, prior genomic studies have failed to reconcile conflicting evidence about the genetic basis of tail morphology, particularly regarding the roles of PDGFD and BMP2. METHODS: Here, we conducted whole-genome resequencing of 283 sheep, encompassing 66 domestic breeds and 5 wild ovine species, to investigate the domestication history and selection signatures of fat-tailed sheep. Additionally, we performed transcriptome sequencing on adipose tissue to identify differentially expressed genes and cellular assays to validate these results. RESULTS: Demographic analysis revealed that domestic sheep descended from Asiatic mouflon and fat-tailed sheep began to diverge from thin-tailed sheep approximately 4.4-7.5 thousand years ago in East Asia. Chinese indigenous sheep were classified into Mongolian, Kazakh, Tibetan, and Yunnan populations. The Yunnan population may have experienced more recent genetic introgression from wild species, rather than an independent domestication event. Moreover, many potential regions associated with the fat-tailed phenotype (DDI1, PDGFD, and BMP2) were identified by selective sweep and genome-wide association analyses. Additionally, a fine-scale analysis of fat-tailed and thin-tailed sheep revealed two novel mutations: a G/A missense variant of PDGFD (Chr15: 3900312) and a C/T missense variant of BMP2 (Chr13: 48462350), both of which were significantly associated with tail adiposity. Functional validation demonstrated that mutant A-PDGFD significantly activated PFGFD expression and reduced fat deposition compared to wildtype. The C-BMP2 mutant activated BMP2 expression and promoted preadipocyte fat deposition. CONCLUSION: Our study provides the first evidence that these genes jointly regulate fat tail development through complementary mechanisms: PDGFD promotes adipose expansion, whereas BMP2 modulates energy partitioning. These findings offer new insights into the evolutionary history of fat-tailed sheep and identify potential targets for precision breeding in small ruminants.

Animals↗

PubMed2005

Photoperiod-sensitive developmental delay in facet mutants of the drosophilid fly, Chymomyza costata and the genetic interaction with timeless.

Previously, we demonstrated that the biological clock gene, timeless (tim), is potentially involved in photoperiodic diapause induction in the larvae of the drosophilid fly Chymomyza costata. Suppression of tim transcription was inevitably associated with the loss of diapause induction even under diapause-promoting short-day conditions. In the present paper, I report a novel gene, facet (fa), which may genetically interact with tim in photoperiodically controlled larval development in this species. I demonstrated the effect of photoperiod on the development of fa morphological mutants. Developmental delay was remarkable in fa larvae under a diapause-preventing photoperiod, 16 h light: 8 h dark/day, in which the wild-type individuals showed normal and synchronous development. The delay was recovered by extension of the light phase of daily light/dark cycles or the introgression of a deficient tim allele.

Animals↗

PubMed2005

Comparative analysis of genomic sequences suggests that Trypanosoma cruzi CL Brener contains two sets of non-intercalated repeats of satellite DNA that correspond to T. cruzi I and T. cruzi II types.

Approximately 10% of the Trypanosoma cruzi genome is formed by a satellite DNA, composed by 195-bp repeats organized in 30+/-10 kb clusters in some, but not all chromosomes. Here, the satellite DNA of six representative T. cruzi strains was sequenced and used for phylogenetic inference. The results show that CL Brener contains satellite repeats from T. cruzi I and T. cruzi II strains, although type II sequences are more abundant. The presence of types I and II sequences extends previous propositions that genetic exchange between the two major T. cruzi lineages have occurred in CL Brener, although our data accommodate alternative scenarios of hybridization within T. cruzi II, as proposed by others. Altogether, present data suggest a complex origin for CL Brener. Sequence analysis of satellites isolated from chromosomal bands indicates that satellite DNA sequences are not chromosome specific. Neighbor analysis of in tandem satellite DNAs containing up to five repeats shows that each cluster contains only one type of sequence. Consequently, clusters with intercalated types I and II repeats were not found. We propose that the CL Brener genome contains large pieces of satellite DNA originated mainly from chromosomes of T. cruzi II with introgression of T. cruzi I lineage.

Animals↗

PubMed2026

A cis-regulatory allele of ZmNPR1I spatially uncouples flowering from stalk-rot resistance in maize.

Pleiotropic effects of adaptive genes frequently constrain crop improvement by coupling beneficial traits with unfavorable trade-offs. In maize, ZmCCT10 confers strong stalk-rot resistance but causes delayed flowering under long-day conditions, limiting its deployment in temperate breeding. Here, we identify qPss3 as a cis-regulatory locus that governs its downstream target gene, ZmNPR1I. The ZmNPR1I protein represses ZmCCT10 transcription and, together with ZmNPR1-3, facilitates ZmCCT10 protein degradation. The favorable qPss3A5 allele reduces ZmNPR1I expression in leaves, relieving repression of ZmCCT10, ZmSPL32, and ID1, which collectively enhance ZCN8 expression to accelerate flowering. In roots, however, pathogen-induced activation of the resistant ZmCCT10H5 allele largely bypasses qPss3 regulation, thereby preserving stalk-rot resistance. Introgression of qPss3A5 into ZmCCT10H5-containing maize germplasm restores flowering adaptation without compromising disease resistance, improving yield stability under disease pressure. Our work reveals a tissue-specific qPss3A5-ZmNPR1I regulatory module that uncouples the developmental and immune functions of a pleiotropic adaptive gene, providing a general strategy for optimizing beneficial alleles in crop breeding.

flowering time↗

PubMed2005

Advances in plant chromosome identification and cytogenetic techniques.

Recent developments that improve our ability to distinguish slightly diverged genomes from each other, as well as to distinguish each of the nonhomologous chromosomes within a genome, add a new dimension to the study of plant genomics. Differences in repetitive sequences among different species have been used to develop multicolor fluorescent in situ hybridization techniques that can define the components of allopolyploids in detail and reveal introgression between species. Bacterial artificial chromosome probes and repetitive sequence arrays have been used to distinguish each of the nonhomologous somatic chromosomes within a species. Such karyotype analysis opens new avenues for the study of chromosomal variation and behavior, as well as for the localization of individual genes and transgenes to genomic position.

Chromosomes, Plant↗

PubMed2004

Salt preference of congenic strains derived from the spontaneously hypertensive rat.

Previous studies using reciprocal crosses between the spontaneously hypertensive rat (SHR) and the normotensive Wistar-Kyoto (WKY) strain suggested a role for the Y chromosome in the SHR's exaggerated preference for saline solutions. We have reexamined the role of the Y chromosome in the salt preference of the SHR using a consomic strain derived from SHR and Brown Norway (BN-Lx) progenitors. We also studied congenic lines in which regions of BN-Lx chromosomes 8 and 20 had been introgressed into the SHR genome. Animals were given a choice of water and 0.9% saline to drink over a period of 7 days and their total fluid intake (TFI; water plus saline) and saline preference (proportion of the TFI taken as saline) calculated. SHR bearing the BN-Lx Y chromosome had a significantly reduced saline preference when compared to progenitor SHR. Evidence was also found for the existence of a region on chromosome 8, which influences fluid intake in the SHR. The causative genes involved in these effects however remain to be determined.

Animals↗

PubMed2006

Phylogenetic fragrance patterns in Nicotiana sections Alatae and Suaveolentes.

We analyzed floral volatiles from eight tobacco species (Nicotiana; Solanaceae) including newly discovered Brazilian taxa (Nicotiana mutabilis and "Rastroensis") in section Alatae. Eighty-four compounds were found, including mono- and sesquiterpenoids, nitrogenous compounds, benzenoid and aliphatic alcohols, aldehydes and esters. Floral scent from recent accessions of Nicotiana alata, Nicotiana bonariensis and Nicotiana langsdorffii differed from previously published data, suggesting intraspecific variation in scent composition at the level of biosynthetic class. Newly discovered taxa in Alatae, like their relatives, emit large amounts of 1,8-cineole and smaller amounts of monoterpenes on a nocturnal rhythm, constituting a chemical synapomorphy for this lineage. Fragrance data from three species of Nicotiana sect. Suaveolentes, the sister group of Alatae, (two Australian species: N. cavicola, N. ingulba; one African species: N. africana), were compared to previously reported data from their close relative, N. suaveolens. Like N. suaveolens, N. cavicola and N. ingulba emit fragrances dominated by benzenoids and phenylpropanoids, whereas the flowers of N. africana lacked a distinct floral scent and instead emitted only small amounts of an aliphatic methyl ester from foliage. Interestingly, this ester also is emitted from foliage of N. longiflora and N. plumbaginifolia (both in section Alatae s.l.), which share a common ancestor with N. africana. This result, combined with the synapomorphic pattern of 1,8 cineole emission in Alatae s.s., suggests that phylogenetic signal explains a major component of fragrance composition among tobacco species in sections Alatae and Suaveolentes. At the intraspecific level, interpopulational scent variation is widespread in sect. Alatae, and may reflect edaphic specialization, introgression, local pollinator shifts, genetic drift or artificial selection in cultivation. Further studies with genetically and geographically well-defined populations are needed to distinguish between these possibilities.

Cyclohexanols↗

PubMed2005

Gene drive systems in mosquitoes: rules of the road.

Population replacement strategies for controlling transmission of mosquito-borne diseases call for the introgression of antipathogen effector genes into vector populations. It is anticipated that these genes, if present at high enough frequencies, will impede transmission of the target pathogens and result in reduced human morbidity and mortality. Recent laboratory successes in the development of virus- and protozoan-resistant mosquito strains make urgent research of gene drive systems capable of moving effector genes into wild populations. A systematic approach to developing safe and effective gene drive systems that includes defining the requirements of the system, identifying naturally occurring or synthetic genetic mechanisms for gene spread upon which drive systems can be based and the successful adaptation of a mechanism to a drive system, should mitigate concerns about using genetically engineered mosquitoes for disease control.

Animals↗

PubMed2005

Single base hits score a home run in wheat.

Finding a way to identify point mutants for a genome in which there are six copies of every gene seems a daunting task, however this has recently been reported. In this research, the redundancy in the wheat genome proved a help instead of a hindrance and the results suggest a promising approach in functional genomics of polyploid crop species. It is now feasible to generate point mutations in all the homologs for a particular gene directly in a polypoid commercial crop variety and then combine them, thus avoiding undesirable, linked traits that often complicate introgressing traits into crops from wild relatives.

Genome, Plant↗

PubMed2006

Wild sex in the grasses.

To date, alien introgression of agronomically important traits into bread wheat (Triticum aestivum) from wild relatives has not been readily achievable through traditional breeding practices. However, this door might now be unlocked. The insightful research published recently by Graham Moore and his team delivers a likely candidate in the form of a cdc2-kinase-related gene family for the Ph1 locus--a chromatin region located on chromosome 5B that is responsible for homologous chromosome pairing integrity in bread wheat.

Chromosomes, Plant↗

PubMed2006

Identification, isolation and pyramiding of quantitative trait loci for rice breeding.

Many agronomically important traits are governed by several genes known as quantitative trait loci (QTLs). The identification of important, QTL-controlled agricultural traits has been difficult because of their complex inheritance; however, completion of the rice genomic sequence has facilitated the cloning of QTLs and their pyramiding for breeding. Because QTLs are derived from natural variation, the use of a wider range of variations such as that found in wild species is important. In addition, Introgression Lines (ILs) developed from wild species in combination with Marker Assisted Selection should facilitate efficient gene identification. This review describes recent developments in rice QTL analysis including mapping, cloning and pyramiding QTLs.

Breeding↗

PubMed2005

Genes invading new populations: a risk assessment perspective.

One of the concerns raised over the introduction of genetically modified crops is that transgenes will invade populations of wild relatives, causing ecologically significant changes in fitness. In recent years, this has given rise to several studies estimating hybridization rates and the fitness of crop-wild relative hybrids. These studies have established that transgenes are likely to move to F1 hybrids, albeit at low frequency. Hybridization, however, is not synonymous with introgression, and questions remain as to whether particular transgenes will cause ecologically significant changes in recipient plant populations. Research effort should now focus on estimating any changes in the fitness of a population as a consequence of having a transgene, understanding genotype x environment interactions, and deducing the extent to which pathogens and herbivores (transgene targets) regulate wild relative populations. This will involve a combination of manipulative experiments and empirically motivated mathematical models.

Journal Article↗