Displaying publications 141 - 160 of 163 in total

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  1. Fulltext Application of an Effective Statistical Technique for an Accurate and Powerful Mining of Quantitative Trait Loci for Rice Aroma Trait
    Golestan Hashemi FS, Rafii MY, Ismail MR, Mohamed MT, Rahim HA, Latif MA, et al.
    PLoS One, 2015;10(6):e0129069.
    PMID: 26061689 DOI: 10.1371/journal.pone.0129069
    When a phenotype of interest is associated with an external/internal covariate, covariate inclusion in quantitative trait loci (QTL) analyses can diminish residual variation and subsequently enhance the ability of QTL detection. In the in vitro synthesis of 2-acetyl-1-pyrroline (2AP), the main fragrance compound in rice, the thermal processing during the Maillard-type reaction between proline and carbohydrate reduction produces a roasted, popcorn-like aroma. Hence, for the first time, we included the proline amino acid, an important precursor of 2AP, as a covariate in our QTL mapping analyses to precisely explore the genetic factors affecting natural variation for rice scent. Consequently, two QTLs were traced on chromosomes 4 and 8. They explained from 20% to 49% of the total aroma phenotypic variance. Additionally, by saturating the interval harboring the major QTL using gene-based primers, a putative allele of fgr (major genetic determinant of fragrance) was mapped in the QTL on the 8th chromosome in the interval RM223-SCU015RM (1.63 cM). These loci supported previous studies of different accessions. Such QTLs can be widely used by breeders in crop improvement programs and for further fine mapping. Moreover, no previous studies and findings were found on simultaneous assessment of the relationship among 2AP, proline and fragrance QTLs. Therefore, our findings can help further our understanding of the metabolomic and genetic basis of 2AP biosynthesis in aromatic rice.
    Matched MeSH terms: Chromosome Mapping
  2. Fulltext Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism
    Pinheiro MM, Ahmed MA, Millar SB, Sanderson T, Otto TD, Lu WC, et al.
    PLoS One, 2015;10(4):e0121303.
    PMID: 25830531 DOI: 10.1371/journal.pone.0121303
    Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology.
    Matched MeSH terms: Chromosome Mapping
  3. Fulltext The R2R3-MYB gene family in banana (Musa acuminata): Genome-wide identification, classification and expression patterns
    Pucker B, Pandey A, Weisshaar B, Stracke R
    PLoS One, 2020;15(10):e0239275.
    PMID: 33021974 DOI: 10.1371/journal.pone.0239275
    The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a comprehensive, genome-wide analysis of the MYB genes from Musa acuminata DH-Pahang (A genome). A total of 285 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Organ- and development-specific expression patterns were determined from RNA-Seq data. For 280 M. acuminata MYB genes for which expression was found in at least one of the analysed samples, a variety of expression patterns were detected. The M. acuminata R2R3-MYB genes were functionally categorised, leading to the identification of seven clades containing only M. acuminata R2R3-MYBs. The encoded proteins may have specialised functions that were acquired or expanded in Musa during genome evolution. This functional classification and expression analysis of the MYB gene family in banana establishes a solid foundation for future comprehensive functional analysis of MaMYBs and can be utilized in banana improvement programmes.
    Matched MeSH terms: Chromosome Mapping
  4. Fulltext Fine-Scale Mapping at 9p22.2 Identifies Candidate Causal Variants That Modify Ovarian Cancer Risk in BRCA1 and BRCA2 Mutation Carriers
    Vigorito E, Kuchenbaecker KB, Beesley J, Adlard J, Agnarsson BA, Andrulis IL, et al.
    PLoS One, 2016;11(7):e0158801.
    PMID: 27463617 DOI: 10.1371/journal.pone.0158801
    Population-based genome wide association studies have identified a locus at 9p22.2 associated with ovarian cancer risk, which also modifies ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. We conducted fine-scale mapping at 9p22.2 to identify potential causal variants in BRCA1 and BRCA2 mutation carriers. Genotype data were available for 15,252 (2,462 ovarian cancer cases) BRCA1 and 8,211 (631 ovarian cancer cases) BRCA2 mutation carriers. Following genotype imputation, ovarian cancer associations were assessed for 4,873 and 5,020 SNPs in BRCA1 and BRCA 2 mutation carriers respectively, within a retrospective cohort analytical framework. In BRCA1 mutation carriers one set of eight correlated candidate causal variants for ovarian cancer risk modification was identified (top SNP rs10124837, HR: 0.73, 95%CI: 0.68 to 0.79, p-value 2× 10-16). These variants were located up to 20 kb upstream of BNC2. In BRCA2 mutation carriers one region, up to 45 kb upstream of BNC2, and containing 100 correlated SNPs was identified as candidate causal (top SNP rs62543585, HR: 0.69, 95%CI: 0.59 to 0.80, p-value 1.0 × 10-6). The candidate causal in BRCA1 mutation carriers did not include the strongest associated variant at this locus in the general population. In sum, we identified a set of candidate causal variants in a region that encompasses the BNC2 transcription start site. The ovarian cancer association at 9p22.2 may be mediated by different variants in BRCA1 mutation carriers and in the general population. Thus, potentially different mechanisms may underlie ovarian cancer risk for mutation carriers and the general population.
    Matched MeSH terms: Chromosome Mapping
  5. Fulltext Vietnam, a Hotspot for Chromosomal Diversity and Cryptic Species in Black Flies (Diptera: Simuliidae)
    Adler PH, Takaoka H, Sofian-Azirun M, Low VL, Ya'cob Z, Chen CD, et al.
    PLoS One, 2016;11(10):e0163881.
    PMID: 27695048 DOI: 10.1371/journal.pone.0163881
    The increasing attention on Vietnam as a biodiversity hotspot prompted an investigation of the potential for cryptic diversity in black flies, a group well known elsewhere for its high frequency of isomorphic species. We analyzed the banding structure of the larval polytene chromosomes in the Simulium tuberosum species group to probe for diversity beyond the morphological level. Among 272 larvae, 88 different chromosomal rearrangements, primarily paracentric inversions, were discovered in addition to 25 already known in the basic sequences of the group in Asia. Chromosomal diversity in Vietnam far exceeds that known for the group in Thailand, with only about 5% of the rearrangements shared between the two countries. Fifteen cytoforms and nine morphoforms were revealed among six nominal species in Vietnam. Chromosomal evidence, combined with available molecular and morphological evidence, conservatively suggests that at least five of the cytoforms are valid species, two of which require formal names. The total chromosomal rearrangements and species (15) now known from the group in Vietnam far exceed those of any other area of comparable size in the world, supporting the country's status as a biodiversity hotspot. Phylogenetic inference based on uniquely shared, derived chromosomal rearrangements supports the clustering of cytoforms into two primary lineages, the Simulium tani complex and the Southeast Asian Simulium tuberosum subgroup. Some of these taxa could be threatened by habitat destruction, given their restricted geographical distributions and the expanding human population of Vietnam.
    Matched MeSH terms: Chromosome Mapping
  6. Fulltext Systematic pharmacogenomics analysis of a Malay whole genome: proof of concept for personalized medicine
    Salleh MZ, Teh LK, Lee LS, Ismet RI, Patowary A, Joshi K, et al.
    PLoS One, 2013;8(8):e71554.
    PMID: 24009664 DOI: 10.1371/journal.pone.0071554
    BACKGROUND: With a higher throughput and lower cost in sequencing, second generation sequencing technology has immense potential for translation into clinical practice and in the realization of pharmacogenomics based patient care. The systematic analysis of whole genome sequences to assess patient to patient variability in pharmacokinetics and pharmacodynamics responses towards drugs would be the next step in future medicine in line with the vision of personalizing medicine.

    METHODS: Genomic DNA obtained from a 55 years old, self-declared healthy, anonymous male of Malay descent was sequenced. The subject's mother died of lung cancer and the father had a history of schizophrenia and deceased at the age of 65 years old. A systematic, intuitive computational workflow/pipeline integrating custom algorithm in tandem with large datasets of variant annotations and gene functions for genetic variations with pharmacogenomics impact was developed. A comprehensive pathway map of drug transport, metabolism and action was used as a template to map non-synonymous variations with potential functional consequences.

    PRINCIPAL FINDINGS: Over 3 million known variations and 100,898 novel variations in the Malay genome were identified. Further in-depth pharmacogenetics analysis revealed a total of 607 unique variants in 563 proteins, with the eventual identification of 4 drug transport genes, 2 drug metabolizing enzyme genes and 33 target genes harboring deleterious SNVs involved in pharmacological pathways, which could have a potential role in clinical settings.

    CONCLUSIONS: The current study successfully unravels the potential of personal genome sequencing in understanding the functionally relevant variations with potential influence on drug transport, metabolism and differential therapeutic outcomes. These will be essential for realizing personalized medicine through the use of comprehensive computational pipeline for systematic data mining and analysis.

    Matched MeSH terms: Chromosome Mapping
  7. Fulltext Fine-Mapping of the 1p11.2 Breast Cancer Susceptibility Locus
    Horne HN, Chung CC, Zhang H, Yu K, Prokunina-Olsson L, Michailidou K, et al.
    PLoS One, 2016;11(8):e0160316.
    PMID: 27556229 DOI: 10.1371/journal.pone.0160316
    The Cancer Genetic Markers of Susceptibility genome-wide association study (GWAS) originally identified a single nucleotide polymorphism (SNP) rs11249433 at 1p11.2 associated with breast cancer risk. To fine-map this locus, we genotyped 92 SNPs in a 900kb region (120,505,799-121,481,132) flanking rs11249433 in 45,276 breast cancer cases and 48,998 controls of European, Asian and African ancestry from 50 studies in the Breast Cancer Association Consortium. Genotyping was done using iCOGS, a custom-built array. Due to the complicated nature of the region on chr1p11.2: 120,300,000-120,505,798, that lies near the centromere and contains seven duplicated genomic segments, we restricted analyses to 429 SNPs excluding the duplicated regions (42 genotyped and 387 imputed). Per-allelic associations with breast cancer risk were estimated using logistic regression models adjusting for study and ancestry-specific principal components. The strongest association observed was with the original identified index SNP rs11249433 (minor allele frequency (MAF) 0.402; per-allele odds ratio (OR) = 1.10, 95% confidence interval (CI) 1.08-1.13, P = 1.49 x 10-21). The association for rs11249433 was limited to ER-positive breast cancers (test for heterogeneity P≤8.41 x 10-5). Additional analyses by other tumor characteristics showed stronger associations with moderately/well differentiated tumors and tumors of lobular histology. Although no significant eQTL associations were observed, in silico analyses showed that rs11249433 was located in a region that is likely a weak enhancer/promoter. Fine-mapping analysis of the 1p11.2 breast cancer susceptibility locus confirms this region to be limited to risk to cancers that are ER-positive.
    Matched MeSH terms: Chromosome Mapping*
  8. rRNA gene restriction patterns of Leptospira: a molecular typing system
    Pérolat P, Grimont F, Regnault B, Grimont PA, Fournié E, Thevenet H, et al.
    Res. Microbiol., 1990 Feb;141(2):159-71.
    PMID: 2189169
    A total of 67 serovar reference strains and 7 isolates belonging to the genus Leptospira were characterized by ribosomal ribonucleic acid (rRNA) gene restriction patterns. Fifty patterns were observed. Strains belonging to different genomic species always gave different patterns. However, genomic species were subdivided into several patterns. Forty-three serovars gave a specific pattern. Some serovars could not be separated by rRNA gene restriction patterns: strains of serovars icterohaemorrhagiae, copenhageni, lai, pyrogenes and jalna gave pattern 1; serovars birkini, mankarso and wolffi gave pattern 4; serovars canicola, gem, hebdomadis, pomona and hardjo (strain hardjoprajitno) gave pattern 12; serovars valbuzzi and zanoni gave pattern 14; serovars jonsis, malaya and sumneri gave pattern 16; serovars arborea, ballum, castellonis and kenya gave pattern 35; and serovars borincana and shermani gave pattern 43. These data provide the bases for a molecular typing system for the genus Leptospira.
    Matched MeSH terms: Chromosome Mapping*
  9. Comparison between Pork and wild Boar meat (Sus Scrofa ) by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)
    Sahilah Abu Mutalib, Wan Sakeenah Wan Nazari, Safiyyah Shahimi, Norhayati Yaakob, Norrakiah Abdullah Sani, Aminah Abdullah, et al.
    Sains Malaysiana, 2012;41:199-204.
    A method of PCR-restriction fragment length polymorphism (RFLP) has been utilized to differentiate the mitochondrial genes of pork and wild boar meat (Sus scrofa). The amplification PCR products of 359 bp and 531 bp were successfully amplified from the cyt b gene of these two meats. The amplification product of pork and wild boar using mt-12S rRNA gene successfully produced a single band with molecular size of 456 bp. Three restriction endonucleases (AluI, HindIII and BsaJI) were used to restrict the amplification products of the mitochondrial genes. The restriction enzymes of AluI and BsaJI were identified as potential restriction endonucleases to differentiate those meats. HindIII enzyme was unable to restrict the PCR product of both meats. The genetic differences within the cyt b gene among the two meats were successfully confirmed by PCR-RFLP analysis.
    Matched MeSH terms: Chromosome Mapping
  10. Fulltext Linkage-based genome assembly improvement of oil palm (Elaeis guineensis)
    Ong AL, Teh CK, Kwong QB, Tangaya P, Appleton DR, Massawe F, et al.
    Sci Rep, 2019 04 29;9(1):6619.
    PMID: 31036825 DOI: 10.1038/s41598-019-42989-y
    Meiotic crossovers in outbred species, such as oil palm (Elaeis guineensis Jacq., 2n = 32) contribute to allelic re-assortment in the genome. Such genetic variation is usually exploited in breeding to combine positive alleles for trait superiority. A good quality reference genome is essential for identifying the genetic factors underlying traits of interest through linkage or association studies. At the moment, an AVROS pisifera genome is publicly available for oil palm. Distribution and frequency of crossovers throughout chromosomes in different origins of oil palm are still unclear. Hence, an ultrahigh-density genomic linkage map of a commercial Deli dura x AVROS pisifera family was constructed using the OP200K SNP array, to evaluate the genetic alignment with the genome assembly. A total of 27,890 linked SNP markers generated a total map length of 1,151.7 cM and an average mapping interval of 0.04 cM. Nineteen linkage groups represented 16 pseudo-chromosomes of oil palm, with 61.7% of the mapped SNPs present in the published genome. Meanwhile, the physical map was also successfully extended from 658 Mb to 969 Mb by assigning unplaced scaffolds to the pseudo-chromosomes. A genic linkage map with major representation of sugar and lipid biosynthesis pathways was subsequently built for future studies on oil related quantitative trait loci (QTL). This study improves the current physical genome of the commercial oil palm, and provides important insights into its recombination landscape, eventually unlocking the full potential genome sequence-enabled biology for oil palm.
    Matched MeSH terms: Chromosome Mapping
  11. Fulltext The first draft reference genome of the American mink (Neovison vison)
    Cai Z, Petersen B, Sahana G, Madsen LB, Larsen K, Thomsen B, et al.
    Sci Rep, 2017 Nov 06;7(1):14564.
    PMID: 29109430 DOI: 10.1038/s41598-017-15169-z
    The American mink (Neovison vison) is a semiaquatic species of mustelid native to North America. It's an important animal for the fur industry. Many efforts have been made to locate genes influencing fur quality and color, but this search has been impeded by the lack of a reference genome. Here we present the first draft genome of mink. In our study, two mink individuals were sequenced by Illumina sequencing with 797 Gb sequence generated. Assembly yielded 7,175 scaffolds with an N50 of 6.3 Mb and length of 2.4 Gb including gaps. Repeat sequences constitute around 31% of the genome, which is lower than for dog and cat genomes. The alignments of mink, ferret and dog genomes help to illustrate the chromosomes rearrangement. Gene annotation identified 21,053 protein-coding sequences present in mink genome. The reference genome's structure is consistent with the microsatellite-based genetic map. Mapping of well-studied genes known to be involved in coat quality and coat color, and previously located fur quality QTL provide new knowledge about putative candidate genes for fur traits. The draft genome shows great potential to facilitate genomic research towards improved breeding for high fur quality animals and strengthen our understanding on evolution of Carnivora.
    Matched MeSH terms: Chromosome Mapping
  12. Fulltext DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system
    Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M, Halidu J
    Sci Rep, 2021 Jul 15;11(1):14527.
    PMID: 34267249 DOI: 10.1038/s41598-021-93867-5
    As a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized legume, has the capacity to boost food and nutrition security while simultaneously addressing environmental sustainability, food availability, and economic inequalities. A set of 32 ISSRs were screened out of 96 primers based on very sharp, clear, and reproducible bands which detected a total of 510 loci with an average of 97.64% polymorphism. The average calculated value of PIC = 0.243, RP = 5.30, H = 0.285, and MI = 0.675 representing the efficiency of primer set for genetic differentiation among the genotypes. The ISSR primers revealed the number of alleles (Na = 1.97), the effective number of alleles (Ne = 1.38), Nei's genetic diversity (h = 0.248), and a moderate level of gene flow (Nm = 2.26) across the genotypes studied. The estimated Shannon's information index (I = 0.395) indicates a high level of genetic variation exists among the accessions. Based on Nei's genetic dissimilarity a UPMGA phylogenetic tree was constructed and grouped the entire genotypes into 3 major clusters and 6 subclusters. PCA analysis revealed that first principal component extracted maximum variation (PC1 = 13.92%) than second principal component (PC2 = 12.59%). Bayesian model-based STRUCTURE analysis assembled the genotypes into 3 (best ΔK = 3) genetic groups. The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.19 to 0.40) exists within the accessions of these 3 clusters. This investigation specifies the effectiveness of the ISSR primers system for the molecular portrayal of V. subterranea genotypes that could be used for genetic diversity valuation, detection, and tagging of potential genotypes with quick, precise, and authentic measures for this crop improvement through effective breeding schemes.
    Matched MeSH terms: Chromosome Mapping
  13. Fulltext Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs)
    Darabi H, Beesley J, Droit A, Kar S, Nord S, Moradi Marjaneh M, et al.
    Sci Rep, 2016 Sep 07;6:32512.
    PMID: 27600471 DOI: 10.1038/srep32512
    Genome-wide association studies have found SNPs at 17q22 to be associated with breast cancer risk. To identify potential causal variants related to breast cancer risk, we performed a high resolution fine-mapping analysis that involved genotyping 517 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of genotypes for 3,134 SNPs in more than 89,000 participants of European ancestry from the Breast Cancer Association Consortium (BCAC). We identified 28 highly correlated common variants, in a 53 Kb region spanning two introns of the STXBP4 gene, that are strong candidates for driving breast cancer risk (lead SNP rs2787486 (OR = 0.92; CI 0.90-0.94; P = 8.96 × 10(-15))) and are correlated with two previously reported risk-associated variants at this locus, SNPs rs6504950 (OR = 0.94, P = 2.04 × 10(-09), r(2) = 0.73 with lead SNP) and rs1156287 (OR = 0.93, P = 3.41 × 10(-11), r(2) = 0.83 with lead SNP). Analyses indicate only one causal SNP in the region and several enhancer elements targeting STXBP4 are located within the 53 kb association signal. Expression studies in breast tumor tissues found SNP rs2787486 to be associated with increased STXBP4 expression, suggesting this may be a target gene of this locus.
    Matched MeSH terms: Chromosome Mapping
  14. Fulltext Enterobacter asburiae strain L1: complete genome and whole genome optical mapping analysis of a quorum sensing bacterium
    Lau YY, Yin WF, Chan KG
    Sensors (Basel), 2014;14(8):13913-24.
    PMID: 25196111 DOI: 10.3390/s140813913
    Enterobacter asburiae L1 is a quorum sensing bacterium isolated from lettuce leaves. In this study, for the first time, the complete genome of E. asburiae L1 was sequenced using the single molecule real time sequencer (PacBio RSII) and the whole genome sequence was verified by using optical genome mapping (OpGen) technology. In our previous study, E. asburiae L1 has been reported to produce AHLs, suggesting the possibility of virulence factor regulation which is quorum sensing dependent. This evoked our interest to study the genome of this bacterium and here we present the complete genome of E. asburiae L1, which carries the virulence factor gene virK, the N-acyl homoserine lactone-based QS transcriptional regulator gene luxR and the N-acyl homoserine lactone synthase gene which we firstly named easI. The availability of the whole genome sequence of E. asburiae L1 will pave the way for the study of the QS-mediated gene expression in this bacterium. Hence, the importance and functions of these signaling molecules can be further studied in the hope of elucidating the mechanisms of QS-regulation in E. asburiae. To the best of our knowledge, this is the first documentation of both a complete genome sequence and the establishment of the molecular basis of QS properties of E. asburiae.
    Matched MeSH terms: Chromosome Mapping/methods
  15. Fulltext Haplotype divergence and multiple candidate genes at Rphq2, a partial resistance QTL of barley to Puccinia hordei
    Yeo FK, Wang Y, Vozabova T, Huneau C, Leroy P, Chalhoub B, et al.
    Theor Appl Genet, 2016 Feb;129(2):289-304.
    PMID: 26542283 DOI: 10.1007/s00122-015-2627-5
    Rphq2, a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars.
    Matched MeSH terms: Chromosome Mapping
  16. Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations
    Wong CK, Bernardo R
    Theor Appl Genet, 2008 Apr;116(6):815-24.
    PMID: 18219476 DOI: 10.1007/s00122-008-0715-5
    Oil palm (Elaeis guineensis Jacq.) requires 19 years per cycle of phenotypic selection. The use of molecular markers may reduce the generation interval and the cost of oil-palm breeding. Our objectives were to compare, by simulation, the response to phenotypic selection, marker-assisted recurrent selection (MARS), and genomewide selection with small population sizes in oil palm, and assess the efficiency of each method in terms of years and cost per unit gain. Markers significantly associated with the trait were used to calculate the marker scores in MARS, whereas all markers were used (without significance tests) to calculate the marker scores in genomewide selection. Responses to phenotypic selection and genomewide selection were consistently greater than the response to MARS. With population sizes of N = 50 or 70, responses to genomewide selection were 4-25% larger than the corresponding responses to phenotypic selection, depending on the heritability and number of quantitative trait loci. Cost per unit gain was 26-57% lower with genomewide selection than with phenotypic selection when markers cost US $1.50 per data point, and 35-65% lower when markers cost $0.15 per data point. With population sizes of N = 50 or 70, time per unit gain was 11-23 years with genomewide selection and 14-25 years with phenotypic selection. We conclude that for a realistic yet relatively small population size of N = 50 in oil palm, genomewide selection is superior to MARS and phenotypic selection in terms of gain per unit cost and time. Our results should be generally applicable to other tree species that are characterized by long generation intervals, high costs of maintaining breeding plantations, and small population sizes in selection programs.
    Matched MeSH terms: Chromosome Mapping*
  17. Fulltext Whole gene transcriptomic analysis of PCB/biphenyl degrading Rhodococcus jostii RHA1
    Sha'arani S, Hara H, Araie H, Suzuki I, Mohd Noor MJM, Akhir FNM, et al.
    J Gen Appl Microbiol, 2019 Sep 14;65(4):173-179.
    PMID: 30686798 DOI: 10.2323/jgam.2018.08.003
    This study gives the first picture of whole RNA-Sequencing analysis of a PCB-degrading microbe, Rhodococcus jostii RHA1. Genes that were highly expressed in biphenyl-grown cells, compared with pyruvate-grown cells, were chosen based on the Reads Per Kilobase Million (RPKM) value and were summarized based on the criteria of RPKM ≥100 and fold change ≥2.0. Consequently, 266 total genes were identified as genes expressed particularly for the degradation of biphenyl. After comparison with previous microarray data that identified highly-expressed genes, based on a fold change ≥2.0 and p-value ≤0.05, 62 highly-expressed genes from biphenyl-grown cells were determined from both analytical platforms. As these 62 genes involve known PCB degradation genes, such as bph, etb, and ebd, the genes identified in this study can be considered as essential genes for PCB/biphenyl degradation. In the 62 genes, eleven genes encoding hypothetical proteins were highly expressed in the biphenyl-grown cells. Meanwhile, we identified several highly-expressed unannotated DNA regions on the opposite strand. In order to verify the encoded proteins, two regions were cloned into an expression vector. A protein was successfully obtained from one region at approximately 25 kDa from the unannotated strand. Thus, the genome sequence with transcriptomic analysis gives new insight, considering re-annotation of the genome of R. jostii RHA1, and provides a clearer picture of PCB/biphenyl degradation in this strain.
    Matched MeSH terms: Chromosome Mapping
  18. Variation in the genome of rice tungro bacilliform virus: molecular characterization of six isolates
    Fan Z, Dahal G, Dasgupta I, Hay J, Hull R
    J Gen Virol, 1996 May;77 ( Pt 5):847-54.
    PMID: 8609480
    The DNA genomes of isolates of rice tungro bacilliform virus from Bangladesh, India, Indonesia, Malaysia and Thailand were cloned and compared with that of the type isolate from the Philippines. Restriction endonuclease maps revealed differences between the isolates and cross-hybridization showed that they fell into two groups, those from the Indian subcontinent and those from south-east Asian countries. The genomes of isolates from the Indian subcontinent contained a deletion of 64 bp when compared with those from south-east Asia. The implications of this variation are discussed.
    Matched MeSH terms: Chromosome Mapping
  19. The chromosomes of four species of the nasuta complex of Drosophila. I. Chromosome maps and inversion polymorphism
    Lambert DM
    J Hered, 1976 3 1;67(2):92-8.
    PMID: 5483
    The salivary chromosomes of four species of the nasuta complex of Drosophila, D. sulfurigaster albostrigata, D, kohkoa, D. albomicans, and D. kepulauana were studied and chromosome maps of each species are presented; the maps of the latter three species are based on the map of D. sulfurigaster albostrigata. Three of the species D. sulfurigaster albostrigata, D. albomicans, and D. kohkoa were shown to be highly polymorphic for chromosomal inversions while the available evidence indicated that D. kepulauana is much less polymorphic. These facts are correlated with the geographic distribution of the species. Transitional homoselection has not been complete in the evolution of three of the species since D. sulfurigaster albostrigata, D. kohkoa, and D. albomicans have a number of naturally occurring polymorphisms in common.
    Matched MeSH terms: Chromosome Mapping
  20. Fulltext Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs
    Graham NS, Hammond JP, Lysenko A, Mayes S, O Lochlainn S, Blasco B, et al.
    Plant Cell, 2014 Jul;26(7):2818-30.
    PMID: 25082855 DOI: 10.1105/tpc.114.128603
    Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca(2+) transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca(2+) transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization.
    Matched MeSH terms: Chromosome Mapping
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