Journal of Genetics and Genomics

Molecular and evolutionary analyses of formyl peptide receptors suggest the absence of VNO-specific FPRs in primates

Hui Yang, Peng Shi

2010, 37(12): 771-778. doi: 10.1016/S1673-8527(09)60094-1

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Abstract:
Formyl peptide receptors (FPRs) were observed to expand in rodents and were recently suggested as candidate vomeronasal chemosensory receptors. Since vomeronasal chemosensory receptors usually underwent positive selection and evolved concordantly with the vomeronasal organ (VNO) morphology, we surveyed FPRs in primates in which VNO morphology is greatly diverse and thus it would provide us a clearer view of VNO-FPRs evolution. By screening available primate genome sequences, we obtained the FPR repertoires in representative primate species. As a result, we did not find FPR family size expansion in primates. Further analyses showed no evolutionary force variance between primates with or without VNO structure, which indicated that there was no functional divergence among primates FPRs. Our results suggest that primates lack the VNO-specific FPRs and the FPR expansion is not a common phenomenon in mammals outside rodent lineage, regardless of VNO complexity.

A genome wide association study between copy number variation (CNV) and human height in Chinese population

Xi Li, Lijun Tan, Xiaogang Liu, Shufeng Lei, Tielin Yang, Xiangding Chen, Fang Zhang, Yue Fang, Yan Guo, Liang Zhang, Han Yan, Feng Pan, Zhixin Zhang, Yumei Peng, Qi Zhou, Lina He, Xuezhen Zhu, Jing Cheng, Lishu Zhang, Yaozhong Liu, Qing Tian, Hongwen Deng

2010, 37(12): 779-785. doi: 10.1016/S1673-8527(09)60095-3

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Abstract:
Copy number variation (CNV) is a type of genetic variation which may have important roles in phenotypic variability and disease susceptibility. To hunt for genetic variants underlying human height variation, we performed a genome wide CNV association study for human height in 618 Chinese unrelated subjects using Affymetrix 500K array set. After adjusting for age and sex, we found that four CNVs at 6p21.3, 8p23.3-23.2, 9p23 and 16p12.1 were associated with human height (with borderline significant p value: 0.013, 0.011, 0.024, 0.049; respectively). However, after multiple tests correction, none of them was associated with human height. We observed that the gain of copy number (more than 2 copies) at 8p23.3-23.2 was associated with lower height (normal copy number vs. gain of copy number: 161.2 cm vs. 153.7 cm, p = 0.011), which accounted for 0.9% of height variation. Loss of copy number (less than 2 copies) at 6p21.3 was associated with 0.8% lower height (loss of copy numbervs. normal copy number: 154.5 cm vs. 161.1 cm, p = 0.013). Since no important genes influencing height located in CNVs at loci of 8p23.3-23.2 and 6p21.3, the two CNVs may cause the structural rearrangements of neighbored important candidate genes, thus regulates the variation of height. Our results expand our knowledge of the genetic factors underlying height variation and the biological regulation of human height.

Identification of a novel mutation in POU3F4 for prenatal diagnosis in a Chinese family with X-linked nonsyndromic hearing loss

Jianzhong Li, Jing Cheng, Yanping Lu, Yu Lu, Aiting Chen, Yi Sun, Dongyang Kang, Xin Zhang, Pu Dai, Dongyi Han, Huijun Yuan

2010, 37(12): 787-793. doi: 10.1016/S1673-8527(09)60096-5

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Abstract:
We present the clinical and genetic findings for a Chinese family with X-linked non-syndromic hearing loss in which the affected males showed congenital profound sensorineural hearing impairment. In two affected brothers, the computer tomography of temporal bone showed bilateral dilation of the internal auditory canal with fistulous communication between the lateral canal and the basal cochlear turn, which is consistent with the typical DFNX2 phenotype. A missense mutation (c.647G→A) in thePOU3F4 gene caused a substitution from glycine to glutamic acid at position 216 (p.G216E), and this mutation was found to consistently cosegregate with the deafness phenotype in the family. The mutation resulted in the loss of function of the POU3F4 by decreasing the affinity between the protein and DNA, as shown in silico by the structural analysis. Prenatal diagnosis of pregnant proband of this family revealed the c.647G→A mutation in DNA extracted from the amniotic fluid surrounding the fetus. The appropriate use of genetic testing and prenatal diagnosis plays a key role in reducing the recurrence of genetic defects in high-risk families.

Additive and additive × additive interaction make important contributions to spikelets per panicle in rice near isogenic (Oryza sativa L.) lines

Qin He, Kexin Zhang, Caiguo Xu, Yongzhong Xing

2010, 37(12): 795-803. doi: 10.1016/S1673-8527(09)60097-7

Abstract (94) HTML PDF (1)

Abstract:
Epistasis plays an important role in the genetic basis of rice yield traits. Taking interactions into account in breeding programs will help the development of high-yielding rice varieties. In this study, three sets of near isogenic lines (NILs) targeting three QTLs for spikelets per panicle (SPP), namely qSPP1, qSPP2 and qSPP7, which share the same Zhenshan 97 genetic background, were used to produce an F₂ population in which the three QTLs segregated simultaneously. The genotypes of the individual F₂ plants at the three QTLs were replaced with three markers that are closely linked to the corresponding QTLs. These QTLs were validated in the F₂ and F₃ populations at the single marker level. qSPP7 exhibited major pleiotropic effects on SPP, plant height and heading date. Multifactor analysis of variance was performed for the F₂ population and its progeny. Additive (additive interaction between qSPP2 and qSPP7 had significant effects on SPP in both the F₂ population and its progeny. Both additive and additive (additive interactions could explain about 73% of the total SPP phenotypic variance. The SPP performance of 27 three-locus combinations was ranked and favorable combinations were recommended for rice breeding in different ecosystems.

Expression of a cotton MADS-box gene is regulated in anther development and in response to phytohormone signaling

Su-Qiang Shao, Bing-Ying Li, Ze-Ting Zhang, Ying Zhou, Jia Jiang, Xue-Bao Li

2010, 37(12): 805-816. doi: 10.1016/S1673-8527(09)60098-9

Abstract (87) HTML PDF (1)

Abstract:
MADS-box gene family encodes a large number and variety of transcription regulators in plants. In this study, a cDNA, GhMADS9, encoding a typical MADS protein with 230 amino acids was isolated from cotton flower cDNA library. Subsequently, a 1,623 bp genomic DNA fragment of GhMADS9 gene was isolated in cotton by PCR. Compared with its cDNA sequence, six introns were found in GhMADS9 gene. Fluorescent microscopy indicated that GhMADS9 protein localized in the nucleus. Transactivation activity assay in yeast cells revealed that GhMADS9 protein did not show transcriptional activation. Quantitative RT-PCR analysis showed thatGhMADS9 was specially expressed in cotton anthers. Further in situ hybridization analysis demonstrated that strong expression of GhMADS9 gene was detected in developing pollens, but no or weak signals were found in the other anther tissues. Furthermore, GhMADS9 expression was dramatically up-regulated in anthers with abscisic acid (ABA) treatment, whereas its activity was down-regulated when treated by gibberellin (GA3). Collectively, our results suggest that GhMADS9 is a transcription factor and might be involved in cotton anther/pollen development and in response to ABA and GA3 signaling.

2010 Vol. 37, No. 12