Combining meta-QTL with RNA-seq data to identify candidate genes of kernel row number trait in maize

Kernel row number is an important component of grain yield in maize. With development of classical quantitative trait loci (QTL) mapping and modern RNA-seq, numerous QTL and tissue-specific gene expression data were accumulated in previous studies. In this paper, a total of initial 373 QTL for grain yield (GY) and kernel row number (KRN) were collected based on 29 previous literatures. Fifty-four meta-QTL (MQTL) were detected via the meta-analysis method with IBM2 2008 Neighbors as a reference map, including 19 for GY and 35 for KRN. These MQTL were unevenly distributed on all 10 chromosomes. Chromosome 1 harbored the most initial QTL and MQTL, and chromosome 7 contained the least. Three MQTL for KRN have been overlapped with MQTL for GY on chromosomes 1 and 3. A total of 1,588 (46.07%) out of 3,447 genes located in the KRN MQTL regions were identified by gene expression data, and categorized into 101 significant GO terms. Meanwhile, six candidate genes were identified from MQTL regions, which are homologous to three functionally characterized genes found to participate in plant inflorescence development. The identified MQTL could be applied to marker-assisted selection (MAS) to facilitate yield architecture, QTL fine mapping and gene cloning in the maize community. Furthermore, the identified candidate genes could enhance the selection efficiency by MAS directly, and could illuminate molecular mechanisms of grain yield in maize

New Phytol

Fruit development is a complex process that is regulated not only by plant hormones and transcription factors, but also requires epigenetic modifications. Epigenetic modifications include DNA methylation, histone post-translational modifications, chromatin remodeling and noncoding RNAs. Together, these epigenetic modifications, which are controlled during development and in response to the environment, determine the chromatin state of genes and contribute to the transcriptomes of an organism. Recent studies have demonstrated that epigenetic regulation plays an important role in fleshy fruit ripening. Dysfunction of a DNA demethylase delayed ripening in tomato, and the application of a DNA methylation inhibitor altered ripening process in the fruits of several species. These studies indicated that manipulating the epigenome of fruit crops could open new ways for breeding in the future. In this review, we highlight recent progress and address remaining questions and challenges concerning the epigenetic regulation of fruit development and ripening

Fruit development and epigenetic modifications

Fruit development is a complex process that is regulated not only by plant hormones and transcription factors, but also requires epigenetic modifications. Epigenetic modifications include DNA methylation, histone post-translational modifications, chromatin remodeling and noncoding RNAs. Together, these epigenetic modifications, which are controlled during development and in response to the environment, determine the chromatin state of genes and contribute to the transcriptomes of an organism. Recent studies have demonstrated that epigenetic regulation plays an important role in fleshy fruit ripening. Dysfunction of a DNA demethylase delayed ripening in tomato, and the application of a DNA methylation inhibitor altered ripening process in the fruits of several species. These studies indicated that manipulating the epigenome of fruit crops could open new ways for breeding in the future. In this review, we highlight recent progress and address remaining questions and challenges concerning the epigenetic regulation of fruit development and ripening

Intrapulmonary lymph node metastasis is common in clinically staged IA adenocarcinoma of the lung

Background Intrapulmonary lymph nodes (LNs, stations 11–14) are usually omitted in postoperative pathological examination. Some non‐small cell lung cancer (NSCLC) patients with intrapulmonary LN metastasis are incorrectly diagnosed as N0 cases. Furthermore, underestimation of intrapulmonary LN involvement in clinically early stage NSCLC may lead to the incorrect choice of surgical procedure: lobectomy or sublobar resection. This study was conducted to determine the status of intrapulmonary LN involvement in clinically staged IA (c‐T1N0M0) peripheral adenocarcinoma of the lung. Methods Seventy‐five lobectomy specimens of c‐T1N0M0 peripheral adenocarcinoma of the lung were carefully dissected to find intrapulmonary LNs. The longest diameter of each intrapulmonary LN was measured and sent for pathological examination, together with hilar and mediastinal LNs, to investigate the relationship between LN metastasis and primary tumor size. Results Intrapulmonary LN metastasis was detected in 22.7%(17/75) of patients. Positive LNs were detected in 21.7% (10/46) of T1b patients and 45% (11/24) of T1c patients, while no metastasis (0/5) was observed in T1a patients (P = 0.036). The mean longest diameter of the 17 involved intrapulmonary LNs was only 6.5 ± 2.1 mm, which was not significantly different to the size of negative intrapulmonary LNs (5.2 ± 1.4 mm). Conclusions Intrapulmonary LN metastasis is common in clinically staged IA peripheral adenocarcinoma of the lung. LN metastasis is related to tumor size, and this should be taken into account to determine appropriate surgical procedures and postoperative treatment. Computed tomography is not a reliable method to judge LN metastasis, particularly intrapulmonary LN metastasis

Teacher-assessment and equity

Indel marker experimental validation. (XLSX 16 kb