Combining QTL mapping and gene co-expression network analysis for prediction of candidate genes and molecular network related to yield in wheat

BACKGROUND

Wheat (Triticum aestivum L.) is an important cereal crop. Increasing grain yield for wheat is always a priority. Due to the complex genome of hexaploid wheat with 21 chromosomes, it is difficult to identify underlying genes by traditional genetic approach. The combination of genetics and omics analysis has displayed the powerful capability to identify candidate genes for major quantitative trait loci (QTLs), but such studies have rarely been carried out in wheat. In this study, candidate genes related to yield were predicted by a combined use of linkage mapping and weighted gene co-expression network analysis (WGCNA) in a recombinant inbred line population.

RESULTS

QTL mapping was performed for plant height (PH), spike length (SL) and seed traits. A total of 68 QTLs were identified for them, among which, 12 QTLs were stably identified across different environments. Using RNA sequencing, we scanned the 99,168 genes expression patterns of the whole spike for the recombinant inbred line population. By the combined use of QTL mapping and WGCNA, 29, 47, 20, 26, 54, 46 and 22 candidate genes were predicted for PH, SL, kernel length (KL), kernel width, thousand kernel weight, seed dormancy, and seed vigor, respectively. Candidate genes for different traits had distinct preferences. The known PH regulation genes Rht-B and Rht-D, and the known seed dormancy regulation genes TaMFT can be selected as candidate gene. Moreover, further experiment revealed that there was a SL regulatory QTL located in an interval of about 7 Mbp on chromosome 7A, named TaSL1, which also involved in the regulation of KL.

CONCLUSIONS

A combination of QTL mapping and WGCNA was applied to predicted wheat candidate genes for PH, SL and seed traits. This strategy will facilitate the identification of candidate genes for related QTLs in wheat. In addition, the QTL TaSL1 that had multi-effect regulation of KL and SL was identified, which can be used for wheat improvement. These results provided valuable molecular marker and gene information for fine mapping and cloning of the yield-related trait loci in the future.

Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq

Bread wheat (Triticum aestivum L.) is an allohexaploid, and the transcriptional characteristics of the wheat embryo and endosperm during grain development remain unclear. To analyze the transcriptome, we performed isoform sequencing (Iso-Seq) for wheat grain and RNA sequencing (RNA-Seq) for the embryo and de-embryonated kernels. The differential regulation between the embryo and de-embryonated kernels was found to be greater than the difference between the two time points for each tissue. Exactly 2264 and 4790 tissue-specific genes were found at 14 days post-anthesis (DPA), while 5166 and 3784 genes were found at 25 DPA in the embryo and de-embryonated kernels, respectively. Genes expressed in the embryo were more likely to be related to nucleic acid and enzyme regulation. In de-embryonated kernels, genes were rich in substance metabolism and enzyme activity functions. Moreover, 4351, 4641, 4516, and 4453 genes with the A, B, and D homoeoloci were detected for each of the four tissues. Expression characteristics suggested that the D genome may be the largest contributor to the transcriptome in developing grain. Among these, 48, 66, and 38 silenced genes emerged in the A, B, and D genomes, respectively. Gene ontology analysis showed that silenced genes could be inclined to different functions in different genomes. Our study provided specific gene pools of the embryo and de-embryonated kernels and a homoeolog expression bias model on a large scale. This is helpful for providing new insights into the molecular physiology of wheat.

Clinical diagnostic value of free body of reduced iron protoporphyrin in uterus epithelial cells on cervical carcinoma and precancerous lesion

OBJECTIVE

Cervical cancer is a common malignant tumor in women with increased incidence and younger onset age. As a curable tumor, timely diagnosis and early intervention are critical. Based on the golden standard of cervical tissues pathology examination, we investigated the value of free body of reduced iron protoporphyrin (FH) in uterus epithelial cells for the diagnosis of cervical cancer and precancerous lesions, aiming to provide novel methods for early screening of cervical cancer.

PATIENTS AND METHODS

A total of 574 women who were screened for cervical cancer according to golden standard of pathology as the reference, were recruited for the analysis of authenticity, reliability, and predictive values of FH. The diagnostic value of FH on cervical carcinoma and precancerous lesion diagnosis was further analyzed.

RESULTS

340 individuals had normal cervical or benign lesion by pathology examination, while 155 people had precancerous lesion, among which 79 cases presented early infiltration and infiltrative cancer. In FH screening, 361 and 213 people had negative and positive results, respectively. No significant differences in the results were observed between the two methods in screening cancer and precancerous lesion (p>0.05). FH showed 93.55% sensitivity and 81.94% specificity in diagnosing precancerous lesion, while the sensitivity and specificity for cervical cancer diagnosis were 93.53% and 81.01%, respectively.

CONCLUSIONS

FH assay was demonstrated to have advantages of high diagnostic value for cervical cancer and precancerous lesion, and might be used for early screening.

Expression of T-lymphoma invasion and metastasis factor on the occurrence of oral squamous cell carcinoma

In recent years, many studies have found that tumor metastasis-related gene T-lymphoma invasion and metastasis-inducing factor 1 (TIAM1) had abnormal high expression in a variety of tumor cells; however, there are few studies regarding its expression in oral squamous cell carcinoma (OSCC). This study aimed to observe the expression of TIAM1 in OSCC and investigated its clinical significance. The expression of TIAM1 in tissues from 120 cases of OSCC and oral mucosa from 40 normal cases was detected by immunohistochemistry, and the relationship between the expression of TIAM1 and the clinicopathological parameters of OSCC was analyzed. The positive expression rate of TIAM1 in the OSCC tissues was significantly higher than that in the normal oral mucosa (92.5% vs 0%). With the decrease of histological differentiation of OSCC, the increase of tumor node metastasis (TNM) stage and the occurrence of lymph node metastasis, the TIAM1 staining positive rate was gradually increased, and the difference was statistically significant (P less than 0.05). However, the expression of TIAM1 in the OSCC tissues was in no correlation with the gender and age of the patients. The expression of TIAM1 is closely related to the occurrence, development and metastasis of OSCC, and it can be used as a new marker for reflecting its biological behaviors.

Factors influencing QTL mapping accuracy under complicated genetic models by computer simulation

The accuracy of quantitative trait loci (QTLs) identified using different sample sizes and marker densities was evaluated in different genetic models. Model I assumed one additive QTL; Model II assumed three additive QTLs plus one pair of epistatic QTLs; and Model III assumed two additive QTLs with opposite genetic effects plus two pairs of epistatic QTLs. Recombinant inbred lines (RILs) (50-1500 samples) were simulated according to the Models to study the influence of different sample sizes under different genetic models on QTL mapping accuracy. RILs with 10-100 target chromosome markers were simulated according to Models I and II to evaluate the influence of marker density on QTL mapping accuracy. Different marker densities did not significantly influence accurate estimation of genetic effects with simple additive models, but influenced QTL mapping accuracy in the additive and epistatic models. The optimum marker density was approximately 20 markers when the recombination fraction between two adjacent markers was 0.056 in the additive and epistatic models. A sample size of 150 was sufficient for detecting simple additive QTLs. Thus, a sample size of approximately 450 is needed to detect QTLs with additive and epistatic models. Sample size must be approximately 750 to detect QTLs with additive, epistatic, and combined effects between QTLs. The sample size should be increased to >750 if the genetic models of the data set become more complicated than Model III. Our results provide a theoretical basis for marker-assisted selection breeding and molecular design breeding.

Relationship between anal occult blood and hepatobiliary pancreatic carcinoma screening

Cotton swab anal smear instead of stool occult blood test can not only be used as a mass screening method for colorectal cancer, but is an auxiliary way to screen hepatobiliary pancreatic carcinoma. Two hundred and twenty-three cases of hepatobiliary pancreatic carcinoma patients received anal occult blood test, of which 121 were positive (54.3%). The screening test was performed in 14,645 healthy people aged 40-60 years; 511 persons (3.4%) were positive for anal blood. Among these, six cases of digestive tract cancer were found (one oesophageal carcinoma, one gastric cardia carcinoma, two gastric carcinomas, two liver carcinomas). This suggests that when anal occult blood is positive, the patient should be scanned by ultrasonic means to rule out hepatobiliary pancreatic tumour.

New concept for cancer screening

Prevention of cancer mortality can be achieved by two main routes: (1) detection of precancerous lesions and preventing their progression to cancer, and (2) detecting cancers at an early stage when they are still amenable to curative treatment. Early detection of cancer is dependent on the population being well-informed about cancer, and about how to carry out self-examination as a preliminary screen (followed by a full clinical examination in the event of suspicious symptoms). In this paper the warning signs that the population should be taught to look out for are discussed. Superficial observation and palpation can be used for surface tumours (which comprise 10-15% of the total). A further 60-70% of tumours are of the digestive tract, respiratory tract or urogenital tract. For these, it is argued that a simple occult blood test could be used as a self-administered screening test. Data are presented to show that this is a practicable way for the general population to detect early signs of cancer or pre-cancer, with a high yield of clinically significant results in the occult blood positive persons.

Screening of esophageal and gastric cancer by occult blood bead detector

A previously described bead method used to detect blood is simple, cheap, and effective; it can be repeated periodically. In 11 provinces in China, 233,825 persons (age range, 30-70 years) were screened. A positive occult blood test result was found in 28,557 persons (12%). Of these, 16,918 underwent a gastroscopy, resulting in the detection of 581 cancers that were located in similar frequencies in the esophagus, gastric cardia, and gastric body; 70% of the lesions were in an early or moderately advanced stage. Among 119 patients with early-stage cancer, the 3-year survival rate was 98.3%. After preliminary screening of cancer, the 4-year follow-up found a mortality rate in the group with negative occult blood test results that was only 25% of that of the positive group. Preliminary yearly screening would detect more early cancers and fewer advanced cancers. The mortality rate of esophageal and gastric cancer might be reduced drastically.