Molecular mapping of the chlorophyll retainer (cl) mutation in pepper (Capsicum spp.) and screening for candidate genes using tomato ESTs homologous to structural genes of the chlorophyll catabolism pathway

Genome ◽  
2005 ◽  
Vol 48 (2) ◽  
pp. 347-351 ◽  
Author(s):  
Ari Efrati ◽  
Yoram Eyal ◽  
Ilan Paran
Keyword(s):  
Expressed Sequence Tag ◽  
Molecular Mapping ◽  
Recessive Gene ◽  
Chromosome 8 ◽  
Chromosome 1 ◽  
Structural Genes ◽  
Chromosome 11 ◽  
Pheophorbide A ◽  
Catabolism Pathway ◽  
Pheophorbide A Oxygenase

The chlorophyll retainer (cl) mutation causes inhibition of chlorophyll degradation during pepper fruit ripening and is controlled by a single recessive gene. The retention of chlorophyll in mature red or yellow fruits produces brown- or green-colored ripe fruits, respectively. We mapped CL on chromosome 1 of pepper corresponding to chromosome 8 in tomato in which a homologous mutation, green flesh, was previously assigned. To test whether known structural genes from the chlorophyll catabolism pathway could correspond to CL, we mapped tomato expressed sequence tag clones corresponding to three loci of CHLOROPHYLLASE and one locus of PHEOPHORBIDE A OXYGENASE in the tomato introgression lines population. The three CHLOROPHYLLASE loci mapped to chromosomes 6, 9, and 12, while PHEOPHORBIDE A OXYGENASE mapped to chromosome 11, indicating that CL may correspond to an as yet unavailable gene from the chlorophyll catabolism pathway or to a regulator of the pathway.Key words: fruit color, pepper, tomato, molecular mapping, chlorophyll catabolism.

Genetic analysis and molecular mapping of a nuclear recessive male sterility gene, ms91(t), in rice

Genome ◽  
2007 ◽  
Vol 50 (9) ◽  
pp. 796-801 ◽  
Author(s):  
Xia Liu ◽  
Songwen Wang ◽  
Yong Wang ◽  
Shu Wei
Keyword(s):  
Male Sterility ◽  
Molecular Mapping ◽  
Recessive Gene ◽  
Chromosome 1 ◽  
Aflp Analysis ◽  
Hybrid Seed Production ◽  
Spontaneous Mutant ◽  
Backcross Population ◽  
Sterility Gene ◽  
Male Sterility Gene

Mutations that result in plant male sterility provide means not only to probe reproductive development but also to facilitate commercial heterosis application and hybrid seed production. In this study, we report a novel male sterility gene, ms91(t), in a spontaneous mutant line (SH38) from a Chinese rice cultivar (Oryza sativa subsp. japonica ‘Jijing14’). The sterility of SH38 was studied by examining its progenies derived from crosses with 6 japonica cultivars. Corresponding F2 populations were obtained by selfing each of the 6 F1s and a backcross population was produced by crossing SH38 to the F1 of SH38 × C18. Our results revealed that SH38 has normal agronomic traits but produces no pollen grains. Segregations of male-sterile and male-fertile progenies in the F2 and backcross populations fit well with ratios of 3:1 and 1:1, respectively, indicating that ms91(t) is a single recessive gene. Amplified fragment length polymorphism (AFLP) analysis of SH38 and Jijing14 plants showed the presence of a unique band in SH38. Simple sequence repeat (SSR) analysis of the bulked and individual progenies of the F2 population of SH38 × C18 showed linkage of ms91(t) with the SSR marker RM5853 on chromosome 1. Subsequently, ms91(t) was fine-mapped to the interval between markers RM7075 (3.75 cM) and RM5638 (3.57 cM). Our results would facilitate the isolation of ms91(t) and male sterility in heterosis application.

Fine mapping of a pistilloid-stamen (PS) gene on the short arm of chromosome 1 in rice

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 1016-1022 ◽  
Author(s):  
Hongfa Luo ◽  
Yunfeng Li ◽  
Zhenglin Yang ◽  
Bingqiang Zhong ◽  
Rong Xie ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Simple Sequence Repeat ◽  
Molecular Mapping ◽  
Oryza Sativa L ◽  
Recessive Gene ◽  
Physical Region ◽  
Floral Organ ◽  
Chromosome 1 ◽  
Sequence Repeat ◽  
Simple Sequence

A novel floral organ mutant of rice (Oryza sativa L. subsp. indica), termed pistilloid-stamen (ps) here, has flowers with degenerated lemma and palea, with some stamens transformed into pistils and pistil–stamen chimeras. Genetic analysis confirmed that the ps trait is controlled by a single recessive gene. F2 and F3 segregation populations derived from PS ps heterozygote crossed with Oryza sativa subsp. indica 'Luhui-17' (PS PS) were used for molecular mapping of the gene using simple sequence repeat (SSR) markers. With 97 recessive individuals from an F2 segregation population, the ps locus was preliminarily mapped 6.2 cM distal to marker RM6324 and 3.1 cM proximal to marker RM6340 in the terminal region of the short arm of chromosome 1. With a large F3 segregation population, the gene was fine-mapped between markers RM6470 and RM1141, at distances of 0.10 and 0.03 cM to each marker, respectively. The position of the ps gene was finally located within a 20 kb physical region containing 3 annotated putative genes. One of them, encoding a protein with a single C2H2 zinc-finger domain, may be the candidate gene for PS.Key words: rice (Oryza sativa L. subsp. indica), pistilloid-stamen mutant (ps mutant), molecular marker, simple sequence repeat (SSR), gene mapping

scholarly journals Underestimation of Heritability across the Molecular Layers of the Gene Expression Process

Processes ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 2144
Author(s):  
Jihye Ryu ◽  
Chaeyoung Lee
Keyword(s):  
Gene Expression ◽  
Mixed Model ◽  
Model Analysis ◽  
Optimal Number ◽  
Chromosome 8 ◽  
Chromosome 1 ◽  
Chromosome 11 ◽  
Translation Speed ◽  
Mixed Model Analysis ◽  
Molecular Layers

We investigated the extent of the heritability underestimation for molecules from an infinitesimal model in mixed model analysis. To this end, we estimated the heritability of transcription, ribosome occupancy, and translation in lymphoblastoid cell lines from Yoruba individuals. Upon considering all genome-wide nucleotide variants, a considerable underestimation in heritability was observed for mRNA transcription (−0.52), ribosome occupancy (−0.48), and protein abundance (−0.47). We employed a mixed model with an optimal number of nucleotide variants, which maximized heritability, and identified two novel expression quantitative trait loci (eQTLs; p < 1.0 × 10−5): rs11016815 on chromosome 10 that influences the transcription of SCP2, a trans-eGene on chromosome 1—whose expression increases in response to MGMT downregulation-induced apoptosis, the cis-eGene of rs11016815—and rs1041872 on chromosome 11 that influences the ribosome occupancy of CCDC25 on chromosome 8 and whose cis-eGene encodes ZNF215, a transcription factor that potentially regulates the translation speed of CCDC25. Our results suggest that an optimal number of nucleotide variants should be used in a mixed model analysis to accurately estimate heritability and identify eQTLs. Moreover, a heterogeneous covariance structure based on gene identity and the molecular layers of the gene expression process should be constructed to better explain polygenic effects and reduce errors in identifying eQTLs.

scholarly journals Novel major QTLs associated with low soil phosphorus tolerance identified from the Indian rice landrace, Wazuhophek

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254526
Author(s):  
Ravindra Ramrao Kale ◽  
Ch. V. Durga Rani ◽  
M. Anila ◽  
H. K. Mahadeva Swamy ◽  
V. P. Bhadana ◽  
...  
Keyword(s):  
Molecular Mapping ◽  
Soil Phosphorus ◽  
Chromosome 8 ◽  
Chromosome 1 ◽  
Total Biomass ◽  
Phenotypic Variance ◽  
Soil P ◽  
Major Qtls ◽  
Shoot Weight ◽  
Genomic Regions

With an objective of mapping novel low soil P (Phosphorus) tolerance loci in the non-Pup1 type donor rice line, Wazuhophek, we screened a recombinant inbred line (RIL) mapping population consisting of 330 lines derived from the cross Wazuhophek x Improved Samba Mahsuri (which is highly sensitive to low soil P) in a plot with low soil P for tolerance associated traits. Molecular mapping with SSR markers revealed a total of 16 QTLs (seven major and nine minor QTLs), which are associated with low soil P tolerance related traits. Interestingly, a QTL hotspot, harbouring 10 out of 16 QTLs were identified on the short arm of chromosome 8 (flanked by the makers RM22554 and RM80005). Five major QTLs explaining phenotypic variance to an extent of 15.28%, 17.25%, 21.84%, 20.23%, and 18.50%, associated with the traits, plant height, shoot length, the number of productive tillers, panicle length and yield, respectively, were located in the hotspot. Two major QTLs located on chromosome 1, associated with the traits, total biomass and root to shoot ratio, explaining 15.44% and 15.44% phenotypic variance, respectively were also identified. Complex epistatic interactions were observed among the traits, grain yield per plant, days to 50% flowering, dry shoot weight, and P content of the seed. In-silico analysis of genomic regions flanking the major QTLs revealed the presence of key putative candidate genes, possibly associated with tolerance.

scholarly journals Identification and Molecular Mapping of a Gene Conferring Resistance to Pyrenophora tritici-repentis Race 3 in Tetraploid Wheat

2006 ◽  
Vol 96 (8) ◽  
pp. 885-889 ◽  
Author(s):  
P. K. Singh ◽  
J. L. Gonzalez-Hernandez ◽  
M. Mergoum ◽  
S. Ali ◽  
T. B. Adhikari ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Molecular Mapping ◽  
Recombinant Inbred Lines ◽  
Tetraploid Wheat ◽  
Recessive Gene ◽  
Tan Spot ◽  
Substitution Lines ◽  
Disease Reaction ◽  
Pyrenophora Tritici Repentis ◽  
The Cross

Race 3 of the fungus Pyrenophora tritici-repentis, causal agent of tan spot, induces differential symptoms in tetraploid and hexaploid wheat, causing necrosis and chlorosis, respectively. This study was conducted to examine the genetic control of resistance to necrosis induced by P. tritici-repentis race 3 and to map resistance genes identified in tetraploid wheat (Triticum turgidum). A mapping population of recombinant inbred lines (RILs) was developed from a cross between the resistant genotype T. tur-gidum no. 283 (PI 352519) and the susceptible durum cv. Coulter. Based on the reactions of the Langdon-T. dicoccoides (LDN[DIC]) disomic substitution lines, chromosomal location of the resistance genes was determined and further molecular mapping of the resistance genes for race 3 was conducted in 80 RILs of the cross T. turgidum no. 283/Coulter. Plants were inoculated at the two-leaf stage and disease reaction was assessed 8 days after inoculation based on lesion type. Disease reaction of the LDN(DIC) lines and molecular mapping on the T. turgidum no. 283/Coulter population indicated that the gene, designated tsn2, conditioning resistance to race 3 is located on the long arm of chromosome 3B. Genetic analysis of the F2 generation and of the F4:5 and F6:7 families indicated that a single recessive gene controlled resistance to necrosis induced by race 3 in the cross studied.

scholarly journals Computational Mining and Genome Wide Distribution of Microsatellite in Fusarium oxysporum f. sp. lycopersici

2012 ◽  
Vol 4 (4) ◽  
pp. 127-131 ◽  
Author(s):  
Sudheer KUMAR ◽  
Deepak MAURYA ◽  
Shalini RAI ◽  
Prem Lal KASHYAP ◽  
Alok Kumar SRIVASTAVA
Keyword(s):  
Fusarium Oxysporum ◽  
Genomic Analysis ◽  
Wide Distribution ◽  
Chromosome 1 ◽  
Coding Region ◽  
Chromosome 11 ◽  
High Throughput Analysis ◽  
Genome Wide ◽  
Baseline Information ◽  
Simple Sequence

Simple sequence repeat (SSR) is currently the most preferred molecular marker system owing to their highly desirable properties viz., abundance, hyper-variability, and suitability for high-throughput analysis. Hence, in present study an attempt was made to mine and analyze microsatellite dynamics in whole genome of Fusarium oxysporum f. sp. lycopersici. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of tetra-nucleotide (3837) repeats followed by tri-nucleotide (3367) repeats. Maximum frequency distribution in coding region was shown by mono-nucleotide SSR motifs (34.8%), where as minimum frequency is observed for penta-nucleotide SSR (0.87%). Highest relative abundance (1023 SSR/Mb) and density of SSRs (114.46 bp/Mb) were observed on chromosome 1, while least density of SSR motifs was recorded on chromosome 11 (7.40 bp/Mb) and 12 (7.41 bp/Mb), respectively. Maximum trinucleotide (34.24%) motifs code for glutamic acid (GAA) while GT/CT were the most frequent repeat of dinucleotide SSRs. Most common and highly repeated SSR motifs were identified as (A)64, (T)48, (GT)24, (GAA)31, (TTTC)24, (TTTCT)28 and (AACCAG)27. Overall, the generated information may serve as baseline information for developing SSR markers that could find applications in genomic analysis of F. oxysporum f. sp. lycopersici for better understanding of evolution, diversity analysis, population genetics, race identification and acquisition of new virulence.

scholarly journals Genome-wide analysis of over 106 000 individuals identifies 9 neuroticism-associated loci

2016 ◽  
Vol 21 (6) ◽  
pp. 749-757 ◽  
Author(s):  
D J Smith ◽  
V Escott-Price ◽  
G Davies ◽  
M E S Bailey ◽  
L Colodro-Conde ◽  
...  
Keyword(s):  
Medical Research ◽  
Genetic Correlation ◽  
Meta Analysis ◽  
Small Sample ◽  
Chromosome 8 ◽  
Chromosome 17 ◽  
Chromosome 1 ◽  
Eysenck Personality Questionnaire ◽  
Uk Biobank ◽  
Genome Wide

Abstract Neuroticism is a personality trait of fundamental importance for psychological well-being and public health. It is strongly associated with major depressive disorder (MDD) and several other psychiatric conditions. Although neuroticism is heritable, attempts to identify the alleles involved in previous studies have been limited by relatively small sample sizes. Here we report a combined meta-analysis of genome-wide association study (GWAS) of neuroticism that includes 91 370 participants from the UK Biobank cohort, 6659 participants from the Generation Scotland: Scottish Family Health Study (GS:SFHS) and 8687 participants from a QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute (QIMR) cohort. All participants were assessed using the same neuroticism instrument, the Eysenck Personality Questionnaire-Revised (EPQ-R-S) Short Form’s Neuroticism scale. We found a single-nucleotide polymorphism-based heritability estimate for neuroticism of ∼15% (s.e.=0.7%). Meta-analysis identified nine novel loci associated with neuroticism. The strongest evidence for association was at a locus on chromosome 8 (P=1.5 × 10−15) spanning 4 Mb and containing at least 36 genes. Other associated loci included interesting candidate genes on chromosome 1 (GRIK3 (glutamate receptor ionotropic kainate 3)), chromosome 4 (KLHL2 (Kelch-like protein 2)), chromosome 17 (CRHR1 (corticotropin-releasing hormone receptor 1) and MAPT (microtubule-associated protein Tau)) and on chromosome 18 (CELF4 (CUGBP elav-like family member 4)). We found no evidence for genetic differences in the common allelic architecture of neuroticism by sex. By comparing our findings with those of the Psychiatric Genetics Consortia, we identified a strong genetic correlation between neuroticism and MDD and a less strong but significant genetic correlation with schizophrenia, although not with bipolar disorder. Polygenic risk scores derived from the primary UK Biobank sample captured ∼1% of the variance in neuroticism in the GS:SFHS and QIMR samples, although most of the genome-wide significant alleles identified within a UK Biobank-only GWAS of neuroticism were not independently replicated within these cohorts. The identification of nine novel neuroticism-associated loci will drive forward future work on the neurobiology of neuroticism and related phenotypes.

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