Searching for genetic factors of fatty liver in SMXA-5 mice by quantitative trait loci analysis under a high-fat diet

AbstractSeveral nonparametric bootstrap methods are tested to obtain better confidence intervals for the quantitative trait loci (QTL) positions, i.e., with minimal width and unbiased coverage probability. Two selective resampling schemes are proposed as a means of conditioning the bootstrap on the number of genetic factors in our model inferred from the original data. The selection is based on criteria related to the estimated number of genetic factors, and only the retained bootstrapped samples will contribute a value to the empirically estimated distribution of the QTL position estimate. These schemes are compared with a nonselective scheme across a range of simple configurations of one QTL on a one-chromosome genome. In particular, the effect of the chromosome length and the relative position of the QTL are examined for a given experimental power, which determines the confidence interval size. With the test protocol used, it appears that the selective resampling schemes are either unbiased or least biased when the QTL is situated near the middle of the chromosome. When the QTL is closer to one end, the likelihood curve of its position along the chromosome becomes truncated, and the nonselective scheme then performs better inasmuch as the percentage of estimated confidence intervals that actually contain the real QTL's position is closer to expectation. The nonselective method, however, produces larger confidence intervals. Hence, we advocate use of the selective methods, regardless of the QTL position along the chromosome (to reduce confidence interval sizes), but we leave the problem open as to how the method should be altered to take into account the bias of the original estimate of the QTL's position.

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Chromosomes I and X Harbor Consistent Genetic Factors Associated with the Anthocyanin Variation in Potato

Agronomy ◽

10.3390/agronomy9070366 ◽

2019 ◽

Vol 9 (7) ◽

pp. 366 ◽

Cited By ~ 3

Author(s):

María-Angélica Parra-Galindo ◽

Clara Piñeros-Niño ◽

Johana Carolina Soto-Sedano ◽

Teresa Mosquera-Vasquez

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genetic Factors ◽

Germplasm Collection ◽

Potato Tubers ◽

High Positive Correlation ◽

A Genome ◽

Trait Loci ◽

Nutritional Compounds ◽

Genomic Regions

Potatoes are an important staple food worldwide and are the third main source of antioxidants in the human diet. One of the most important antioxidant compounds in potatoes is the anthocyanin pigments. Some reports indicate a high positive correlation between color intensity, anthocyanins content, and antioxidant level in potato tubers. The variation in anthocyanins composition and content in potato tubers among diverse germplasm sources has important nutritional and health implications and constitutes an interesting trait for potato breeding programs focused on enhancing the anthocyanin and antioxidant contents of potato materials. We identified and quantified five anthocyanidins (delphinidin, cyanidin, petunidin, pelargonidin, and peonidin) on tubers from the Colombian germplasm collection of Solanum tuberosum L. Group Phureja. The phenotypic data were merged into a genome-wide association study in order to identify genomic regions associated with the nutritional compounds’ variation in potatoes. The association was conducted using a 7520 single nucleotide polymorphisms markers matrix. Seven quantitative trait loci were identified. Chromosomes I and X harbored the most stable quantitative trait loci (QTL). Three quantitative trait loci were identified close to previously reported genes involved in the regulation of anthocyanins in potato tubers. The genomic regions of these QTL reveal presumptive candidate genes as genetic factors that are the basis for a better understanding of the genetic architecture of the regulation of nutritional compounds in potatoes.

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ROLE OF GENETIC FACTORS IN REGULATING CADMIUM UPTAKE, TRANSPORT AND ACCUMULATION MECHANISMS AND QUANTITATIVE TRAIT LOCI MAPPING IN RICE. A REVIEW

Applied Ecology and Environmental Research ◽

10.15666/aeer/1803_40054023 ◽

2020 ◽

Vol 18 (3) ◽

pp. 4005-4023

Author(s):

A. RASHEED ◽

S. FAHAD ◽

M. AAMER ◽

M.U. HASSAN ◽

M.M. TAHIR ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genetic Factors ◽

Cadmium Uptake ◽

Quantitative Trait Loci Mapping ◽

Trait Loci

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Quantitative trait loci for starch-corrected chip color after harvest, cold storage and after reconditioning mapped in diploid potato

Molecular Genetics and Genomics ◽

10.1007/s00438-019-01616-1 ◽

2019 ◽

Vol 295 (1) ◽

pp. 209-219 ◽

Cited By ~ 1

Author(s):

Dorota Sołtys-Kalina ◽

Katarzyna Szajko ◽

Iwona Wasilewicz-Flis ◽

Dariusz Mańkowski ◽

Waldemar Marczewski ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Cold Storage ◽

Quantitative Trait ◽

Genetic Factors ◽

Starch Content ◽

Chip Color ◽

Diploid Potato ◽

Trait Loci ◽

On Chip ◽

Variance Explained

Abstract The objective of this study was to map the quantitative trait loci (QTLs) for chip color after harvest (AH), cold storage (CS) and after reconditioning (RC) in diploid potato and compare them with QTLs for starch-corrected chip color. Chip color traits AH, CS, and RC significantly correlated with tuber starch content (TSC). To limit the effect of starch content, the chip color was corrected for TSC. The QTLs for chip color (AH, CS, and RC) and the starch-corrected chip color determined with the starch content after harvest (SCAH), after cold storage (SCCS) and after reconditioning (SCRC) were compared to assess the extent of the effect of starch and the location of genetic factors underlying this effect on chip color. We detected QTLs for the AH, CS, RC and starch-corrected traits on ten potato chromosomes, confirming the polygenic nature of the traits. The QTLs with the strongest effects were detected on chromosomes I (AH, 0 cM, 11.5% of variance explained), IV (CS, 43.9 cM, 12.7%) and I (RC, 49.7 cM, 14.1%). When starch correction was applied, the QTLs with the strongest effects were revealed on chromosomes VIII (SCAH, 39.3 cM, 10.8% of variance explained), XI (SCCS, 79.5 cM, 10.9%) and IV (SCRC, 43.9 cM, 10.8%). Applying the starch correction changed the landscape of QTLs for chip color, as some QTLs became statistically insignificant, shifted or were refined, and new QTLs were detected for SCAH. The QTLs on chromosomes I and IV were significant for all traits with and without starch correction.

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