QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps

Abstract Background Melon is a very important horticultural crop produced worldwide with high phenotypic diversity. Fruit size is among the most important domestication and differentiation traits in melon. The molecular mechanisms of fruit size in melon are largely unknown. Results Two high-density genetic maps were constructed by whole-genome resequencing with two F2 segregating populations (WAP and MAP) derived from two crosses (cultivated agrestis × wild agrestis and cultivated melo × cultivated agrestis). We obtained 1,871,671 and 1,976,589 high quality SNPs that show differences between parents in WAP and MAP. A total of 5138 and 5839 recombination events generated 954 bins in WAP and 1027 bins in MAP with the average size of 321.3 Kb and 301.4 Kb respectively. All bins were mapped onto 12 linkage groups in WAP and MAP. The total lengths of two linkage maps were 904.4 cM (WAP) and 874.5 cM (MAP), covering 86.6% and 87.4% of the melon genome. Two loci for fruit size were identified on chromosome 11 in WAP and chromosome 5 in MAP, respectively. An auxin response factor and a YABBY transcription factor were inferred to be the candidate genes for both loci. Conclusion The high-resolution genetic maps and QTLs analyses for fruit size described here will provide a better understanding the genetic basis of domestication and differentiation, and provide a valuable tool for map-based cloning and molecular marker assisted breeding.

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Genetic mapping with Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R.D. Webster Reveals Insights into Spittlebug (Notozulia entreriana Berg) Resistance

10.1101/360594 ◽

2018 ◽

Cited By ~ 1

Author(s):

Rebecca Caroline Ulbricht Ferreira ◽

Letícia Aparecida de Castro Lara ◽

Lucimara Chiari ◽

Sanzio Carvalho Lima Barrios ◽

Cacilda Borges do Valle ◽

...

Keyword(s):

Candidate Genes ◽

Genetic Map ◽

Molecular Breeding ◽

Insect Pest ◽

Genetic Maps ◽

Breeding Cycle ◽

High Quality Snps ◽

Allele Dosage ◽

Urochloa Decumbens ◽

Average Marker Density

AbstractUrochloa decumbens (Stapf) R.D. Webster is one of the most important African forage grasses in Brazilian beef production. Currently available genetic-genomic resources for this species are restricted mainly due to polyploidy and apomixis. Therefore, crucial genomic-molecular studies such as the construction of genetic maps and the mapping of quantitative trait loci (QTLs) are very challenging and consequently affect the advancement of molecular breeding. The objectives of this work were to (i) construct an integrated U. decumbens genetic map for a full-sibling progeny using GBS-based markers with allele dosage information, (ii) detect QTLs for spittlebug (Notozulia entreriana) resistance, and (iii) seek putative candidate genes involved in resistance/defense against pathogens. We used the Setaria viridis genome as reference to align GBS reads and selected 4,240 high-quality SNPs markers with allele dosage information. Of these markers, 1,000 were distributed throughout nine homologous groups with a cumulative map length of 1,335.09 cM and an average marker density of 1.33 cM. We detected QTLs for resistance to spittlebug, an important pasture insect pest, that explained between 4.66% and 6.24% of the phenotypic variation. These QTLs are in regions containing putative candidate genes related to resistance/defense against pathogens. Because this is the first genetic map with SNP autotetraploid dosage data and QTL detection in U. decumbens, it will be useful for future evolutionary studies, genome assembly, and other QTL analyses in Urochloa spp. Moreover, the results might facilitate the isolation of spittlebug-related candidate genes and help clarify the mechanism of spittlebug resistance. These approaches will improve selection efficiency and accuracy in U. decumbens molecular breeding and shorten the breeding cycle.

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High resolution mapping of nucleic acid containing complexes in vitro and in situ

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100162703 ◽

1996 ◽

Vol 54 ◽

pp. 48-49

Author(s):

D. P. Bazett-Jones ◽

M. J. Hendzel

Keyword(s):

Nucleic Acid ◽

High Resolution ◽

Transcription Initiation ◽

Molecular Mechanisms ◽

Heavy Atom ◽

Regulation Of Transcription ◽

High Exposure ◽

Resolution Mapping ◽

Tata Sequence

Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.

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QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Genes ◽

10.3390/genes12040604 ◽

2021 ◽

Vol 12 (4) ◽

pp. 604

Author(s):

Paolo Vitale ◽

Fabio Fania ◽

Salvatore Esposito ◽

Ivano Pecorella ◽

Nicola Pecchioni ◽

...

Keyword(s):

Candidate Genes ◽

Recombinant Inbred Lines ◽

Snp Array ◽

Heading Date ◽

Tiller Number ◽

Genetic Maps ◽

Yield Potential ◽

Adaptation To Climate Change ◽

Map Resolution ◽

Mapping Populations

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

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The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

BMC Plant Biology ◽

10.1186/s12870-021-02858-1 ◽

2021 ◽

Vol 21 (1) ◽

Cited By ~ 1

Author(s):

Ian S. E. Bally ◽

◽

Aureliano Bombarely ◽

Alan H. Chambers ◽

Yuval Cohen ◽

...

Keyword(s):

Candidate Genes ◽

Fruit Quality ◽

De Novo ◽

Mapping Population ◽

Mangifera Indica ◽

Consensus Sequence ◽

Fruit Size ◽

Hybrid Population ◽

High Molecular Weight Dna ◽

Tropical Fruit

Abstract Background Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. Results This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar ‘Tommy Atkins’. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of ‘Tommy Atkins’, supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between ‘Tommy Atkins’ x ‘Kensington Pride’ was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final ‘Tommy Atkins’ genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the ‘Tommy Atkins’ x ‘Kensington Pride’ mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. Conclusions The availability of the complete ‘Tommy Atkins’ mango genome will aid global initiatives to study mango genetics.

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Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese

BMC Genomics ◽

10.1186/s12864-021-07822-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yan Deng ◽

Shenqiang Hu ◽

Chenglong Luo ◽

Qingyuan Ouyang ◽

Li Li ◽

...

Keyword(s):

Molecular Mechanisms ◽

Protein Secondary Structure ◽

Genomic Analysis ◽

Production Performance ◽

Genetic Mechanism ◽

Farm Animals ◽

Practical Significance ◽

Genome Resequencing ◽

Genomic Analyses ◽

Whole Genome Resequencing

Abstract Background During domestication, remarkable changes in behavior, morphology, physiology and production performance have taken place in farm animals. As one of the most economically important poultry, goose owns a unique appearance characteristic called knob, which is located at the base of the upper bill. However, neither the histomorphology nor the genetic mechanism of the knob phenotype has been revealed in geese. Results In the present study, integrated radiographic, histological, transcriptomic and genomic analyses revealed the histomorphological characteristics and genetic mechanism of goose knob. The knob skin was developed, and radiographic results demonstrated that the knob bone was obviously protuberant and pneumatized. Histologically, there were major differences in structures in both the knob skin and bone between geese owing knob (namely knob-geese) and those devoid of knob (namely non-knob geese). Through transcriptome analysis, 592 and 952 genes differentially expressed in knob skin and bone, and significantly enriched in PPAR and Calcium pathways in knob skin and bone, respectively, which revealed the molecular mechanisms of histomorphological differences of the knob between knob- and non-knob geese. Furthermore, integrated transcriptomic and genomic analysis contributed to the identification of 17 and 21 candidate genes associated with the knob formation in the skin and bone, respectively. Of them, DIO2 gene could play a pivotal role in determining the knob phenotype in geese. Because a non-synonymous mutation (c.642,923 G > A, P265L) changed DIO2 protein secondary structure in knob geese, and Sanger sequencing further showed that the AA genotype was identified in the population of knob geese, and was prevalent in a crossing population which was artificially selected for 10 generations. Conclusions This study was the first to uncover the knob histomorphological characteristics and genetic mechanism in geese, and DIO2 was identified as the crucial gene associated with the knob phenotype. These data not only expand and enrich our knowledge on the molecular mechanisms underlying the formation of head appendages in both mammalian and avian species, but also have important theoretical and practical significance for goose breeding.

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Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens

Scientific Reports ◽

10.1038/s41598-021-86176-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Juniper A. Lake ◽

Jack C. M. Dekkers ◽

Behnam Abasht

Keyword(s):

Candidate Genes ◽

Broiler Chickens ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Specific Protein ◽

Chromosome 11 ◽

A Genome ◽

White Striping ◽

Commercial Broiler ◽

Wooden Breast

AbstractWooden breast (WB) and white striping (WS) are highly prevalent and economically damaging muscle disorders of modern commercial broiler chickens characterized respectively by palpable firmness and fatty white striations running parallel to the muscle fiber. High feed efficiency and rapid growth, especially of the breast muscle, are believed to contribute to development of such muscle defects; however, their etiology remains poorly understood. To gain insight into the genetic basis of these myopathies, a genome-wide association study was conducted using a commercial crossbred broiler population (n = 1193). Heritability was estimated at 0.5 for WB and WS with high genetic correlation between them (0.88). GWAS revealed 28 quantitative trait loci (QTL) on five chromosomes for WB and 6 QTL on one chromosome for WS, with the majority of QTL for both myopathies located in a ~ 8 Mb region of chromosome 5. This region has highly conserved synteny with a portion of human chromosome 11 containing a cluster of imprinted genes associated with growth and metabolic disorders such as type 2 diabetes and Beckwith-Wiedemann syndrome. Candidate genes include potassium voltage-gated channel subfamily Q member 1 (KCNQ1), involved in insulin secretion and cardiac electrical activity, lymphocyte-specific protein 1 (LSP1), involved in inflammation and immune response.

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Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis

BMC Plant Biology ◽

10.1186/s12870-020-02739-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Massimiliano Trenti ◽

Silvia Lorenzi ◽

Pier Luigi Bianchedi ◽

Daniele Grossi ◽

Osvaldo Failla ◽

...

Keyword(s):

Drought Stress ◽

Stomatal Conductance ◽

Candidate Genes ◽

Water Deficit ◽

Genetic Basis ◽

Phenotypic Diversity ◽

Snp Array ◽

A Genome ◽

Raffinose Synthase ◽

Response To Water

Abstract Background Understanding the complexity of the vine plant’s response to water deficit represents a major challenge for sustainable winegrowing. Regulation of water use requires a coordinated action between scions and rootstocks on which cultivars are generally grafted to cope with phylloxera infestations. In this regard, a genome-wide association study (GWAS) approach was applied on an ‘ad hoc’ association mapping panel including different Vitis species, in order to dissect the genetic basis of transpiration-related traits and to identify genomic regions of grape rootstocks associated with drought tolerance mechanisms. The panel was genotyped with the GrapeReSeq Illumina 20 K SNP array and SSR markers, and infrared thermography was applied to estimate stomatal conductance values during progressive water deficit. Results In the association panel the level of genetic diversity was substantially lower for SNPs loci (0.32) than for SSR (0.87). GWAS detected 24 significant marker-trait associations along the various stages of drought-stress experiment and 13 candidate genes with a feasible role in drought response were identified. Gene expression analysis proved that three of these genes (VIT_13s0019g03040, VIT_17s0000g08960, VIT_18s0001g15390) were actually induced by drought stress. Genetic variation of VIT_17s0000g08960 coding for a raffinose synthase was further investigated by resequencing the gene of 85 individuals since a SNP located in the region (chr17_10,497,222_C_T) was significantly associated with stomatal conductance. Conclusions Our results represent a step forward towards the dissection of genetic basis that modulate the response to water deprivation in grape rootstocks. The knowledge derived from this study may be useful to exploit genotypic and phenotypic diversity in practical applications and to assist further investigations.

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ZnWO4 Nanoparticle Scintillators for High Resolution X-ray Imaging

Nanomaterials ◽

10.3390/nano10091721 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1721

Author(s):

Heon Yong Jeong ◽

Hyung San Lim ◽

Ju Hyuk Lee ◽

Jun Heo ◽

Hyun Nam Kim ◽

...

Keyword(s):

Particle Size ◽

Zinc Oxide ◽

High Resolution ◽

Tungsten Oxide ◽

Spatial Resolution ◽

High Spatial Resolution ◽

X Ray ◽

X Ray Imaging ◽

Average Size ◽

And Tungsten

The effect of scintillator particle size on high-resolution X-ray imaging was studied using zinc tungstate (ZnWO4) particles. The ZnWO4 particles were fabricated through a solid-state reaction between zinc oxide and tungsten oxide at various temperatures, producing particles with average sizes of 176.4 nm, 626.7 nm, and 2.127 μm; the zinc oxide and tungsten oxide were created using anodization. The spatial resolutions of high-resolution X-ray images, obtained from utilizing the fabricated particles, were determined: particles with the average size of 176.4 nm produced the highest spatial resolution. The results demonstrate that high spatial resolution can be obtained from ZnWO4 nanoparticle scintillators that minimize optical diffusion by having a particle size that is smaller than the emission wavelength.

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