Joint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids.

Genetic improvement of grain quality is more challenging in hybrid rice than in inbred rice due to additional nonadditive effects such as dominance. Here, we describe a pipeline developed for joint analysis of phenotypes, effects, and generations (JPEG). As a demonstration, we analyze 12 grain quality traits of 113 inbred lines (male parents), five tester lines (female parents), and 565 (113×5) of their hybrids. We sequence the parents for single nucleotide polymorphisms calling and infer the genotypes of the hybrids. Genome-wide association studies with JPEG identify 128 loci associated with at least one of the 12 traits, including 44, 97, and 13 loci with additive effects, dominant effects, and both additive and dominant effects, respectively. These loci together explain more than 30% of the genetic variation in hybrid performance for each of the traits. The JEPG statistical pipeline can help to identify superior crosses for breeding rice hybrids with improved grain quality.

A Comparison of Clinical Characteristics in Overweight/Obese and Normal Weight Patients with Psoriasis Vulgaris: A Bicentric Retrospective Observational Study.

Background: Psoriasis is a chronic, inflammatory skin disease that is often accompanied by multiple comorbidities. Obesity is considered an independent risk factor for the development of psoriasis. However, most of the related data are derived from epidemiological studies conducted in the United States of America and Europe. This study aimed to compare the clinical characteristics of patients with psoriasis who are overweight/obese and patients with psoriasis with normal weight in China. Methods: We reviewed the medical records of 208 patients with psoriasis. Based on their body mass index (BMI), the patients were divided into two groups: patients with psoriasis who were overweight/obese and patients with psoriasis with normal weight. Results: The most patients enrolled in this study were men (77.40%). Patients with psoriasis who were overweight/obese had a higher mean age, longer disease duration, and significantly higher Psoriasis Area and Severity Index (PASI) values (P=0.032). Additionally, the incidence of fatty liver, hyperlipidemia, hyperuricemia, and abnormal liver function was higher among patients with psoriasis who were overweight/obese (P<0.05). Linear regression analysis revealed a linear relationship between PASI values and BMI (P=0.016). Moreover, patients with psoriasis who were overweight/obese had significantly higher levels of serum alanine transaminase (ALT), aspartate transaminase (AST), uric acid (UC), total cholesterol (TC), low-density lipoprotein (LDL), and fasting plasma glucose (FPG) (P<0.05) and lower serum high-density lipoprotein (HDL) levels and absolute lymphocyte count (ALC) (P<0.05). Conclusion: Patients with psoriasis who are overweight/obese have more severe psoriatic lesions and metabolic comorbidities. Detailed assessment of the BMI of patients with psoriasis revealed that weight loss may be necessary for patients who are overweight/obese to reduce the risk of metabolic disorders.

DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis.

Germplasm identification is essential for plant breeding and conservation. In this study, we developed a new method, DT-PICS, for efficient and cost-effective SNP selection in germplasm identification. The method, based on the decision tree concept, could efficiently select the most informative SNPs for germplasm identification by recursively partitioning the dataset based on their overall high PIC values, instead of considering individual SNP features. This method reduces redundancy in SNP selection and enhances the efficiency and automation of the selection process. DT-PICS demonstrated significant advantages in both the training and testing datasets and exhibited good performance on independent prediction, which validates its effectiveness. Thirteen simplified SNP sets were extracted from 749,636 SNPs in 1135 Arabidopsis varieties resequencing datasets, including a total of 769 DT-PICS SNPs, with an average of 59 SNPs per set. Each simplified SNP set could distinguish between the 1135 Arabidopsis varieties. Simulations demonstrated that using a combination of two simplified SNP sets for identification can effectively increase the fault tolerance in independent validation. In the testing dataset, two potentially mislabeled varieties (ICE169 and Star-8) were identified. For 68 same-named varieties, the identification process achieved 94.97% accuracy and only 30 shared markers on average; for 12 different-named varieties, the germplasm to be tested could be effectively distinguished from 1,134 other varieties while grouping extremely similar varieties (Col-0) together, reflecting their actual genetic relatedness. The results suggest that the DT-PICS provides an efficient and accurate approach to SNP selection in germplasm identification and management, offering strong support for future plant breeding and conservation efforts.

Identification and Allele Combination Analysis of Rice Grain Shape-Related Genes by Genome-Wide Association Study.

Grain shape is an important agronomic character of rice, which affects the appearance, processing, and the edible quality. Screening and identifying more new genes associated with grain shape is beneficial to further understanding the genetic basis of grain shape and provides more gene resources for genetic breeding. This study has a natural population containing 623 indica rice cultivars. Genome-wide association studies/GWAS of several traits related to grain shape (grain length/GL, grain width/GW, grain length to width ratio/GLWR, grain circumferences/GC, and grain size/grain area/GS) were conducted by combining phenotypic data from four environments and the second-generation resequencing data, which have identified 39 important Quantitative trait locus/QTLs. We analyzed the 39 QTLs using three methods: gene-based association analysis, haplotype analysis, and functional annotation and identified three cloned genes (GS3, GW5, OsDER1) and seven new candidate genes in the candidate interval. At the same time, to effectively utilize the genes in the grain shape-related gene bank, we have also analyzed the allelic combinations of the three cloned genes. Finally, the extreme allele combination corresponding to each trait was found through statistical analysis. This study's novel candidate genes and allele combinations will provide a valuable reference for future breeding work.

Effective identification of varieties by nucleotide polymorphisms and its application for essentially derived variety identification in rice.

BACKGROUND: Plant variety identification is the one most important of agricultural systems. Development of DNA marker profiles of released varieties to compare with candidate variety or future variety is required. However, strictly speaking, scientists did not use most existing variety identification techniques for "identification" but for "distinction of a limited number of cultivars," of which generalization ability always not be well estimated. Because many varieties have similar genetic backgrounds, even some essentially derived varieties (EDVs) are involved, which brings difficulties for identification and breeding progress. A fast, accurate variety identification method, which also has good performance on EDV determination, needs to be developed. RESULTS: In this study, with the strategy of "Divide and Conquer," a variety identification method Conditional Random Selection (CRS) method based on SNP of the whole genome of 3024 rice varieties was developed and be applied in essentially derived variety (EDV) identification of rice. CRS is a fast, efficient, and automated variety identification method. Meanwhile, in practical, with the optimal threshold of identity score searched in this study, the set of SNP (including 390 SNPs) showed optimal performance on EDV and non-EDV identification in two independent testing datasets. CONCLUSION: This approach first selected a minimal set of SNPs to discriminate non-EDVs in the 3000 Rice Genome Project, then united several simplified SNP sets to improve its generalization ability for EDV and non-EDV identification in testing datasets. The results suggested that the CRS method outperformed traditional feature selection methods. Furthermore, it provides a new way to screen out core SNP loci from the whole genome for DNA fingerprinting of crop varieties and be useful for crop breeding.

Effect of Wenshentiaojing Decoction on Hormone Level and Follicular Number in Patients with Menstrual Disorder of Polycystic Ovary Syndrome.

OBJECTIVE: To explore the curative effect of Wenshentiaojing Decoction on the treatment of menstrual disorder caused by PCOS. METHODS: Patients with menstrual disorders caused by PCOS admitted to our department from January 2020 to January 2021 were selected as the research objects and were divided into a control group and observation group according to the random number table method. The control group was treated with Western medicine, and the observation group was treated with Wenshentiaojing Decoction on the basis of Western medicine. The clinical efficacy of the two groups was compared. Before and after treatment, sex hormones (LH, FSH, LH/FSH, and testosterone (T)), ovarian volume, endometrial thickness, cervical mucus score, follicular number, menstrual conditions (menstrual duration, menstrual cycle, and menstrual volume), and other indicators in both groups were recorded. RESULTS: After treatment, the total effective rate of the observation group (91.1% (41/45)) was higher than that of the control group (77.8% (35/45)), and the difference was statistically significant (P < 0.05). After treatment, the LH, LH/FSH, and T levels in the observation group were lower than those in the control group, while the FSH level was higher than that in the control group (P < 0.05). After treatment, the ovarian volume, endometrial thickness, cervical mucus score, and follicle number in the observation group were higher than those in the control group (P < 0.05). After treatment, the menstrual duration and menstrual volume in the observation group were longer than those in the conventional group, and the menstrual cycle was shorter than that in the conventional group (P < 0.05). CONCLUSION: For patients with menstrual disorders caused by PCOS, the treatment effect of Wenshentiaojing Decoction assisted with Western medicine is better, which can effectively improve the level of sex hormones, cervical mucus, and menstrual conditions, increase the ovarian volume, endometrial thickness, and follicle number, and improve the treatment effect, with fewer adverse reactions, which is worthy of further promotion and application.

Clinical Value of Serum Thrombospondin-2 Combined with CA19-9 in Early Diagnosis of Gastric Cancer.

Gastric cancer (GC) is a kind of common cancer worldwide. Too late in diagnosis results in poor prognosis of patients with GC. Thrombospondin-2 (THBS2) is a type of secreted protein that has been found to be a diagnostic biomarker in a variety of cancers. Our study aimed to uncover the clinical value of THBS2 in early detection for patients with gastric cancer. THBS2 was upregulated in gastric cancer tissue compared with normal tissue via analyzing data obtained from The Cancer Genome Atlas (TCGA) database. Additionally, the enzyme-linked immunosorbent assay revealed that the level of serum THBS2 and carcinoembryonic antigen, CA19-9, was higher dramatically in patients with early gastric cancer (EGC) than that in healthy control (HC) in addition to patients with benign gastric tumor (BGT), which suggested that THBS2 indeed associated with GC. Receiver operator characteristic (ROC) curve assay was conducted to demonstrate that serum THBS2 was similar to CA19-9 to distinguish patients with early gastric cancer from healthy control and patients with benign gastric tumor and that THBS2 combined with CA19-9 improved the detective performance of THBS2 for early gastric cancer. Furthermore, we applied the gene set enrichment analysis assay to analyze signaling pathways related to THBS2. We found that THBS2 positively controlled MAPK and WNT signaling pathways, which indicated that THBS2 might exert its functions via the pathway mentioned above. Thus, our study expounded that serum THBS2 could serve as a vital early diagnostic marker for patients with gastric cancer.

Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice.

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through "gene-based association analysis, haplotype analysis, and functional annotation", the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential.

Rice yield per plant has a complex genetic architecture, which is mainly determined by its three component traits: the number of grains per panicle (GPP), kilo-grain weight (KGW), and tillers per plant (TP). Exploring ideotype breeding based on selection for genetically less complex component traits is an alternative route for further improving rice production. To understand the genetic basis of the relationship between rice yield and component traits, we investigated the four traits of two rice hybrid populations (575 + 1495 F1) in different environments and conducted meta-analyses of genome-wide association study (meta-GWAS). In total, 3589 significant loci for three components traits were detected, while only 3 loci for yield were detected. It indicated that rice yield is mainly controlled by minor-effect loci and hardly to be identified. Selecting quantitative trait locus/gene affected component traits to further enhance yield is recommended. Mendelian randomization design is adopted to investigate the genetic effects of loci on yield through component traits and estimate the genetic relationship between rice yield and its component traits by these loci. The loci for GPP or TP mainly had a positive genetic effect on yield, but the loci for KGW with different direction effects (positive effect or negative effect). Additionally, TP (Beta = 1.865) has a greater effect on yield than KGW (Beta = 1.016) and GPP (Beta = 0.086). Five significant loci for component traits that had an indirect effect on yield were identified. Pyramiding superior alleles of the five loci revealed improved yield. A combination of direct and indirect effects may better contribute to the yield potential of rice. Our findings provided a rationale for using component traits as indirect indices to enhanced rice yield, which will be helpful for further understanding the genetic basis of yield and provide valuable information for improving rice yield potential.

Palmitic Acid and ß-Hydroxybutyrate Induce Inflammatory Responses in Bovine Endometrial Cells by Activating Oxidative Stress-Mediated NF-κB Signaling.

Ketosis is a nutritional metabolic disease in dairy cows, and researches indicated that ketonic cows always accompany reproductive problems. When ketosis occurs, the levels of non-esterified fatty acids (NEFAs) and ß-hydroxybutyrate (BHBA) in the blood increase significantly. Palmitic acid (PA) is a main component of saturated fatty acids composing NEFA. The aim of this study was to investigate whether high levels of PA and BHBA induce inflammatory responses and regulatory mechanisms in bovine endometrial cells (BEND). Using an enzyme-linked immunosorbent assay, quantitative real-time PCR, and western blotting, we evaluated oxidative stress, pro-inflammatory factors, and the nuclear factor (NF)-κB pathway in cultured BEND cells treated with different concentrations of PA, BHBA, pyrrolidinedithiocarbamate (PDTC, an NF-κB pathway inhibitor), and N-acetylcysteine (NAC, an antioxidant). The content of malondialdehyde was significantly higher, the content of glutathione was lower, and antioxidant activity-glutathione peroxidase, superoxide dismutase, catalase, and total antioxidant capacity-was lower in treated cells compared with control cells. PA- and BHBA-induced oxidative stress activated the NF-κB signaling pathway and upregulated the release of pro-inflammatory factors. Moreover, PA- and BHBA-induced activation of NF-κB-mediated inflammatory responses was inhibited by PDTC and NAC. High concentrations of PA and BHBA induce inflammatory responses in BEND cells by activating oxidative stress-mediated NF-κB signaling.

Proanthocyanidins Protect against ß-Hydroxybutyrate-Induced Oxidative Damage in Bovine Endometrial Cells.

Metabolic diseases, such as ketosis, are closely associated with decreased reproductive performance (such as delayed estrus and decreased pregnancy rate) in dairy cows. The change of ß-hydroxybutyrate (BHBA) concentration in dairy cattle is an important mechanism leading to ketosis, and its blood concentration in ketotic cows is always significantly higher than in nonketotic cows. Many studies indicated that BHBA can induce oxidative damage in liver and other organs. Proanthocyanidins (PCs) have gained substantial attention in the last decade as strong antioxidative substances. This study aimed to demonstrate a protective effect of PCs against BHBA-induced oxidative stress damage in bovine endometrial (BEND) cells by activating the nuclear erythroid2-related factor2 (Nrf2) signaling pathway. Our research show that PCs could significantly increase activities of catalase (CAT) and glutathione peroxidase (GSH-PX), glutathione (GSH) content, and antioxidant capacity (T-AOC), while significantly decreasing malondialdehyde (MDA) content in BEND cells. Both mRNA and protein expression levels of Nrf2 were significantly increased in BEND cells, and glutamate⁻cysteine ligase catalytic subunit (GCLC), heme oxygenase 1 (HO-1), manganese superoxide dismutase (Mn-SOD), and NAD(P)H quinone dehydrogenase 1 (NQO-1) were also significantly increased. These results indicate that PCs can antagonize BHBA-induced oxidative damage by activating the Nrf2 signaling pathway to exert an antioxidant effect.

Correction: Genetic dissection of main and epistatic effects of QTL based on augmented triple test cross design.

[This corrects the article DOI: 10.1371/journal.pone.0189054.].

Genetic dissection of main and epistatic effects of QTL based on augmented triple test cross design.

The use of heterosis has considerably increased the productivity of many crops; however, the biological mechanism underpinning the technique remains elusive. The North Carolina design III (NCIII) and the triple test cross (TTC) are powerful and popular genetic mating design that can be used to decipher the genetic basis of heterosis. However, when using the NCIII design with the present quantitative trait locus (QTL) mapping method, if epistasis exists, the estimated additive or dominant effects are confounded with epistatic effects. Here, we propose a two-step approach to dissect all genetic effects of QTL and digenic interactions on a whole genome without sacrificing statistical power based on an augmented TTC (aTTC) design. Because the aTTC design has more transformation combinations than do the NCIII and TTC designs, it greatly enriches the QTL mapping for studying heterosis. When the basic population comprises recombinant inbred lines (RIL), we can use the same materials in the NCIII design for aTTC-design QTL mapping with transformation combination Z1, Z2, and Z4 to obtain genetic effect of QTL and digenic interactions. Compared with RIL-based TTC design, RIL-based aTTC design saves time, money, and labor for basic population crossed with F1. Several Monte Carlo simulation studies were carried out to confirm the proposed approach; the present genetic parameters could be identified with high statistical power, precision, and calculation speed, even at small sample size or low heritability. Additionally, two elite rice hybrid datasets for nine agronomic traits were estimated for real data analysis. We dissected the genetic effects and calculated the dominance degree of each QTL and digenic interaction. Real mapping results suggested that the dominance degree in Z2 that mainly characterize heterosis showed overdominance and dominance for QTL and digenic interactions. Dominance and overdominance were the major genetic foundations of heterosis in rice.

Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement.

Rice breeding has achieved great productivity improvements by semi-dwarf varieties and hybrid vigour. Due to poor understanding of genetic basis of elite backbone varieties, the continuous increasing in rice yield still faces great challenges. Here, 52 elite rice varieties from three historical representative pedigrees were re-sequenced with 10.1× depth on average, and ~6.5 million single nucleotide polymorphisms (SNPs) were obtained. We identified thousands of low-diversity genomic regions and 0-diversity genes during breeding. Using pedigree information, we also traced SNP transmission patterns and observed breeding signatures in pedigree. These regions included the larger number of key well-known functional genes. Besides, 35 regions spanning 0.16% of the rice gnome had been differentially selected between conventional and restorer pedigrees. These genes identified here will be useful to the further pedigree breeding. Our study provides insights into the genetic basis of backbone varieties and will have immediate implications for performing genome-wide breeding by design.

Overall condition improvement in a rat model of nephrotic syndrome treated with CellCept nanoliposomes.

Purpose To investigate the effect of CellCept nanoliposomes on Adriamycin-induced nephrotic syndrome in rats. Methods To model nephrotic syndrome, rats were injected with 6.5 mg/kg of Adriamycin in the tail vein. The rats were randomly divided into three groups, including a control group, a free mycophenolate mofetil (MMF)-treated group, and a liposome-encapsulated MMF-treated group. Five weeks after the Adriamycin treatment, the free MMF-treated group received CellCept while the liposome-encapsulated MMF-treated group received the CellCept nanoliposomes for 2 weeks. The general condition of the animals was observed, which included urine volume over 24 h, urine protein levels, and serum biochemical indexes. Renal morphology was also observed. Results The level of urine protein over 24 h was increased in the control group, while plasma albumin (ALB) was decreased. The total cholesterol (TC) and triacylglycerol (TG) levels increased significantly (P < 0.05, P < 0.01). The pathological examination of the kidneys showed some abnormalities. In contrast, these parameters were improved significantly in the free mycophenolate mofetil (MMF)-treated and liposome-contained mycophenolate mofetil (MMF)-treated groups. Conclusion The CellCept nanoliposomes have a good therapeutic effect on Adriamycin-induced nephrotic syndrome in rats.

Informative gene selection and the direct classification of tumors based on relative simplicity.

BACKGROUND: Selecting a parsimonious set of informative genes to build highly generalized performance classifier is the most important task for the analysis of tumor microarray expression data. Many existing gene pair evaluation methods cannot highlight diverse patterns of gene pairs only used one strategy of vertical comparison and horizontal comparison, while individual-gene-ranking method ignores redundancy and synergy among genes. RESULTS: Here we proposed a novel score measure named relative simplicity (RS). We evaluated gene pairs according to integrating vertical comparison with horizontal comparison, finally built RS-based direct classifier (RS-based DC) based on a set of informative genes capable of binary discrimination with a paired votes strategy. Nine multi-class gene expression datasets involving human cancers were used to validate the performance of new method. Compared with the nine reference models, RS-based DC received the highest average independent test accuracy (91.40%), the best generalization performance and the smallest informative average gene number (20.56). Compared with the four reference feature selection methods, RS also received the highest average test accuracy in three classifiers (Naïve Bayes, k-Nearest Neighbor and Support Vector Machine), and only RS can improve the performance of SVM. CONCLUSIONS: Diverse patterns of gene pairs could be highlighted more fully while integrating vertical comparison with horizontal comparison strategy. DC core classifier can effectively control over-fitting. RS-based feature selection method combined with DC classifier can lead to more robust selection of informative genes and classification accuracy.

Genomewide mapping reveals a combination of different genetic effects causing the genetic basis of heterosis in two elite rice hybrids.

North Carolina design III (NCIII) is one of the most powerful and widely used mating designs for understanding the genetic basis of heterosis. However, the quantitative trait mapping (QTL) conducted in previous studies with this design was mainly based on analysis of variance (ANOVA), composite interval or multiple interval mapping methods. These methodologies could not investigate all kinds of genetic effects, especially epistatic effects, simultaneously on the whole genome. In this study, with a statistical method for mapping epistatic QTL associated with heterosis using the recombinant inbred line (RIL)-based NCIII design, we conducted QTL mapping for nine agronomic traits of two elite hybrids to characterize the mode of gene action contributing to heterosis on a whole genomewide scale. In total, 23 main-effect QTL (M-QTL) and 23 digenic interactions in IJ (indica x japonica) hybrids, 11 M-QTL and 82 digenic interactions in II (indica x indica) hybrid QTLs were identified in the present study. The variation explained by individual M-QTL or interactions ranged from 2.3 to 11.0%. The number of digenic interactions and the total variation explained by interactions of each trait were larger than those of M-QTL. The augmented genetic effect ratio of most M-QTL and digenic interactions in (L1 - L2) data of two backcross populations (L1 and L2) showed complete dominance or overdominance, and in (L1 + L2) data showed an additive effect. Our results indicated that the dominance, overdominance and epistatic effect were important in conditioning the genetic basis of heterosis of the two elite hybrids. The relative contributions of the genetic components varied with traits and the genetic basis of the two hybrids was different.

Binary matrix shuffling filter for feature selection in neuronal morphology classification.

A prerequisite to understand neuronal function and characteristic is to classify neuron correctly. The existing classification techniques are usually based on structural characteristic and employ principal component analysis to reduce feature dimension. In this work, we dedicate to classify neurons based on neuronal morphology. A new feature selection method named binary matrix shuffling filter was used in neuronal morphology classification. This method, coupled with support vector machine for implementation, usually selects a small amount of features for easy interpretation. The reserved features are used to build classification models with support vector classification and another two commonly used classifiers. Compared with referred feature selection methods, the binary matrix shuffling filter showed optimal performance and exhibited broad generalization ability in five random replications of neuron datasets. Besides, the binary matrix shuffling filter was able to distinguish each neuron type from other types correctly; for each neuron type, private features were also obtained.

Informative gene selection and direct classification of tumor based on Chi-square test of pairwise gene interactions.

In efforts to discover disease mechanisms and improve clinical diagnosis of tumors, it is useful to mine profiles for informative genes with definite biological meanings and to build robust classifiers with high precision. In this study, we developed a new method for tumor-gene selection, the Chi-square test-based integrated rank gene and direct classifier (χ(2)-IRG-DC). First, we obtained the weighted integrated rank of gene importance from chi-square tests of single and pairwise gene interactions. Then, we sequentially introduced the ranked genes and removed redundant genes by using leave-one-out cross-validation of the chi-square test-based Direct Classifier (χ(2)-DC) within the training set to obtain informative genes. Finally, we determined the accuracy of independent test data by utilizing the genes obtained above with χ(2)-DC. Furthermore, we analyzed the robustness of χ(2)-IRG-DC by comparing the generalization performance of different models, the efficiency of different feature-selection methods, and the accuracy of different classifiers. An independent test of ten multiclass tumor gene-expression datasets showed that χ(2)-IRG-DC could efficiently control overfitting and had higher generalization performance. The informative genes selected by χ(2)-IRG-DC could dramatically improve the independent test precision of other classifiers; meanwhile, the informative genes selected by other feature selection methods also had good performance in χ(2)-DC.

QTL mapping for combining ability in different population-based NCII designs: a simulation study.

The NCII design (North Carolina mating design II) has been widely applied in studies of combining ability and heterosis. The objective of our research was to estimate how different base populations, sample sizes, testcross numbers and heritability influence QTL analyses of combining ability and heterosis. A series of Monte Carlo simulation experiments with QTL mapping were then conducted for the base population performance, testcross population phenotypic values and the general combining ability (GCA), specific combining ability (SCA) and Hmp (midparental heterosis) datasets. The results indicated that: (i) increasing the number of testers did not necessarily enhance the QTL detection power for GCA, but it was significantly related to the QTL effect. (ii) The QTLs identified in the base population may be different from those from GCA dataset. Similar phenomena can be seen from QTL detected in SCA and Hmp datasets. (iii) The QTL detection power for GCA ranked in the order of DH(RIL) based > F2 based > BC based NCII design, when the heritability was low. The recombinant inbred lines (RILs) (or DHs) allows more recombination and offers higher mapping resolution than other populations. Further, their testcross progeny can be repeatedly generated and phenotyped. Thus, RIL based (or DH based) NCII design was highly recommend for combining ability QTL analysis. Our results expect to facilitate selecting elite parental lines with high combining ability and for geneticists to research the genetic basis of combining ability.