Identification of stably expressed quantitative trait loci for cooked rice elongation in non-Basmati varieties

Genome ◽  
2008 ◽  
Vol 51 (2) ◽  
pp. 104-112 ◽  
Author(s):  
L. L. Liu ◽  
X. Y. Yan ◽  
L. Jiang ◽  
W. W. Zhang ◽  
M. Q. Wang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
Basmati Rice ◽  
Eating Quality ◽  
Chromosome 2 ◽  
Elongation Ratio ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Trait Loci

The elongation of the cooked grain determines the cooking and eating quality of Basmati rice. The identification of stable quantitative trait loci (QTLs), especially those from non-Basmati types, will extend the genetic basis of the Basmati type and facilitate the breeding of high-quality varieties. A set of recombinant inbred lines derived from an indica × japonica hybrid was used to identify QTLs controlling the elongation ratio (ER), elongation index (EI), and water absorption (WA) of the cooked grain. Three ER QTLs on chromosomes 2, 4, and 12, two EI QTLs on chromosomes 2 and 5, and two WA QTLs on chromosomes 2 and 6 were detected. Four of these QTLs were validated using a set of established chromosome segment substitution lines. The genetic effect of qER-2 was explored in an analysis of segregating generations, using 8 newly developed simple sequence repeat markers. Two tightly linked loci (qER-2a and qER-2b) were identified on chromosome 2.

scholarly journals Mapping Quantitative Trait Loci Underlying Circadian Light Sensitivity in Drosophila

2017 ◽  
Vol 32 (5) ◽  
pp. 394-405 ◽  
Author(s):  
Adeolu B. Adewoye ◽  
Sergey V. Nuzhdin ◽  
Eran Tauber
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Transcriptome Profiling ◽  
Light Sensitivity ◽  
Significant Advance ◽  
Chromosome 2 ◽  
Light Entrainment ◽  
Trait Loci

Despite the significant advance in our understanding of the molecular basis of light entrainment of the circadian clock in Drosophila, the underlying genetic architecture is still largely unknown. The aim of this study was to identify loci associated with variation in circadian photosensitivity, which are important for the evolution of this trait. We have used complementary approaches that combined quantitative trait loci (QTL) mapping, complementation testing, and transcriptome profiling to dissect this variation. We identified a major QTL on chromosome 2, which was subsequently fine mapped using deficiency complementation mapping into 2 smaller regions spanning 139 genes, some of which are known to be involved in functions that have been previously implicated in light entrainment. Two genes implicated with the clock and located within that interval, timeless and cycle, failed to complement the QTL, indicating that alleles of these genes contribute to the variation in light response. Specifically, we find that the timeless s/ ls polymorphism that has been previously shown to constitute a latitudinal cline in Europe is also segregating in our recombinant inbred lines and is contributing to the phenotypic variation in light sensitivity. We also profiled gene expression in 2 recombinant inbred strains that differ significantly in their photosensitivity and identified a total of 368 transcripts that showed differential expression (false discovery rate < 0.1). Of 131 transcripts that showed a significant recombinant inbred line by treatment interaction (i.e., putative expression QTL), 4 are located within QTL2.

scholarly journals Mapping quantitative trait loci underlying circadian light sensitivity in Drosophila

2017 ◽  
Author(s):  
Adeolu B. Adewoye ◽  
Sergey V. Nuzhdin ◽  
Eran Tauber
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Transcriptome Profiling ◽  
Light Sensitivity ◽  
Significant Advance ◽  
Chromosome 2 ◽  
Light Entrainment ◽  
Trait Loci

AbstractDespite the significant advance in our understanding of the molecular basis of light entrainment of the circadian clock in Drosophila, the underlying genetic architecture is still largely unknown. The aim of this study was to identify loci associated with variation in circadian photosensitivity, which are important for the evolution of this trait. We have used complementary approaches that combined quantitative trait loci (QTL) mapping, complementation testing and transcriptome profiling to dissect this variation.We identified a major QTL on chromosome 2, which was subsequently fine-mapped using deficiency complementation mapping into two smaller regions spanning 139 genes, some of which are known to be involved in functions which have been previously implicated in light entrainment. Two genes implicated with the clock and located within that interval, timeless and cycle, failed to complement the QTL, indicating that alleles of these genes contribute to the variation in light response. Specifically, we find that the timeless s/ls polymorphism that has been previously shown to constitute a latitudinal cline in Europe, is also segregating in our recombinant inbred lines, and is contributing to the phenotypic variation in light sensitivity.We have also profiled gene expression in two recombinant inbred strains that differ significantly in their photosensitivity, and identified a total of 368 transcripts that showed differential expression (FDR < 0.1). Out of 131 transcripts that showed a significant RIL by treatment interaction (i.e. putative expression QTL), four are located within QTL2

Deficiency Mapping of Quantitative Trait Loci Affecting Longevity inDrosophila melanogaster

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1129-1146 ◽  
Author(s):  
Elena G Pasyukova ◽  
Cristina Vieira ◽  
Trudy F C Mackay
Keyword(s):  
Quantitative Trait Loci ◽  
Life Span ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Adult Longevity ◽  
Chromosome 2 ◽  
Recombination Mapping ◽  
Trait Loci ◽  
E Region

AbstractIn a previous study, sex-specific quantitative trait loci (QTL) affecting adult longevity were mapped by linkage to polymorphic roo transposable element markers, in a population of recombinant inbred lines derived from the Oregon and 2b strains of Drosophila melanogaster. Two life span QTL were each located on chromosomes 2 and 3, within sections 33E–46C and 65D–85F on the cytological map, respectively. We used quantitative deficiency complementation mapping to further resolve the locations of life span QTL within these regions. The Oregon and 2b strains were each crossed to 47 deficiencies spanning cytological regions 32F–44E and 64C–76B, and quantitative failure of the QTL alleles to complement the deficiencies was assessed. We initially detected a minimum of five and four QTL in the chromosome 2 and 3 regions, respectively, illustrating that multiple linked factors contribute to each QTL detected by recombination mapping. The QTL locations inferred from deficiency mapping did not generally correspond to those of candidate genes affecting oxidative and thermal stress or glucose metabolism. The chromosome 2 QTL in the 35B–E region was further resolved to a minimum of three tightly linked QTL, containing six genetically defined loci, 24 genes, and predicted genes that are positional candidates corresponding to life span QTL. This region was also associated with quantitative variation in life span in a sample of 10 genotypes collected from nature. Quantitative deficiency complementation is an efficient method for fine-scale QTL mapping in Drosophila and can be further improved by controlling the background genotype of the strains to be tested.

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