Journal of Genetics and Genomics

Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system

Yimian Ma, Luo Liu, Chengguang Zhu, Changhui Sun, Bo Xu, Jun Fang, Jiuyou Tang, Anding Luo, Shouyun Cao, Gupo Li, Qian Qian, Yongbiao Xue, Chengcai Chu

2009, 36(5): 267-276. doi: 10.1016/S1673-8527(08)60114-9

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Abstract:
About 25,000 rice T-DNA insertional mutant lines were generated using the vector pCAS04 which has both promoter-trapping and activation-tagging function. Southern blot analysis revealed that about 40% of these mutants were single copy integration and the average T-DNA insertion number was 2.28. By extensive phenotyping in the field, quite a number of agronomically important mutants were obtained. Histochemical GUS assay with 4,310 primary mutants revealed that the GUS-staining frequency was higher than that of the previous reports in various tissues and especially high in flowers. The T-DNA flanking sequences of some mutants were isolated and the T-DNA insertion sites were mapped to the rice genome. The flanking sequence analysis demonstrated the different integration pattern of the right border and left border into rice genome. Compared with Arabidopsis and poplar, it is much varied in the T-DNA border junctions in rice.

Gene expression profiles of the one-carbon metabolism pathway

Yin Leng Lee, Xinran Xu, Sylvan Wallenstein, Jia Chen

2009, 36(5): 277-282. doi: 10.1016/S1673-8527(08)60115-0

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One-carbon metabolism plays a critical role in both DNA methylation and DNA synthesis. Accumulating evidence has shown that interruptions of this pathway are associated with many disease outcomes including cardiovascular diseases and cancers. Mechanistic studies have been performed on genetic polymorphisms involved in one-carbon metabolism. However, expression profiles of these inter-related genes are not well-known. In this study, we examined the gene expression profiles of 11 one-carbon metabolizing genes by quantifying the mRNA level of the lymphocyte among 54 healthy individuals and explored the correlations of these genes. We found these genes were expressed in lymphocytes at moderate levels and showed significant inter-person variations. We also applied principle component analysis to explore potential patterns of expression. The components identified by the program agreed with existing knowledge about one-carbon metabolism. This study helps us better understand the biological functions of one-carbon metabolism.

The common MTHFR C677T and A1298C variants are not associated with the risk of non-syndromic cleft lip/palate in northern Venezuela

Mehmet A. Sözen, Marie M. Tolarova, Richard A. Spritz

2009, 36(5): 283-288. doi: 10.1016/S1673-8527(08)60116-2

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Non-syndromic cleft lip with or without cleft palate (nsCL/P) is among the most common major birth defects, with complex inheritance involving multiple genes and environmental factors. Numerous studies of MTHFR, encoding methylenetetrahydrofolate reductase, which catalyzes the rate-limiting step of folic acid biosynthesis, have shown inconsistent association of two common hypomorphic allelic variants, C677T and A1298C, in nsCL/P patients and, in some cases, their mothers. We have studied the MTHFR C677T and A1298C polymorphisms in nsCL/P patients, their mothers, and population-matched controls from northern Venezuela. We found no evidence for contribution of the MTHFR C677T and A1298C variants to the risk of nsCL/P in northern Venezuela. Overall, our findings fail to support a causal role of either the MTHFR C677T or A1298C variants in the pathogenesis of nsCL/P in northern Venezuela.

BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity

Lian Wang, Danling Pan, Xihao Hu, Jinyu Xiao, Yangyang Gao, Huifang Zhang, Yan Zhang, Juan Liu, Shanfeng Zhu

2009, 36(5): 289-296. doi: 10.1016/S1673-8527(08)60117-4

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Effective identification of major histocompatibility complex (MHC) molecules restricted peptides is a critical step in discovering immune epitopes. Although many online servers have been built to predict class II MHC-peptide binding affinity, they have been trained on different datasets, and thus fail in providing a unified comparison of various methods. In this paper, we present our implementation of seven popular predictive methods, namely SMM-align, ARB, SVR-pairwise, Gibbs sampler, ProPred, LP-top2, and MHCPred, on a single web server named BiodMHC (http://biod.whu.edu.cn/BiodMHC/index.html, the software is available upon request). Using a standard measure of AUC (Area Under the receiver operating characteristic Curves), we compare these methods by means of not only cross validation but also prediction on independent test datasets. We find that SMM-align, ProPred, SVR-pairwise, ARB, and Gibbs sampler are the five best-performing methods. For the binding affinity prediction of class II MHC-peptide, BiodMHC provides a convenient online platform for researchers to obtain binding information simultaneously using various methods.

Mapping QTLs for heading synchrony in a doubled haploid population of rice in two environments

Liangyong Ma, Changdeng Yang, Dali Zeng, Jing Cai, Ximing Li, Zhijuan Ji, Yingwu Xia, Qian Qian, Jinsong Bao

2009, 36(5): 297-304. doi: 10.1016/S1673-8527(08)60118-6

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Simultaneous heading of plants within the same rice variety, also refer to heading synchrony, is an important factor that affects simultaneous ripening of the variety. Understanding of the genetic basis of heading synchrony may contribute to molecular breeding of rice with simultaneous heading and ripening. In the present study, a doubled haploid (DH) population, derived from a cross between Chunjiang 06 and TN1 was used to analyze quantitative trait locus (QTL) for heading synchrony related traits, i.e., early heading date (EHD), late heading date (LHD), heading asynchrony (HAS), and tiller number (PN). A total of 19 QTLs for four traits distributed on nine chromosomes were detected in two environments. One QTL, qHAS-8 for HAS, explained 27.7% of the phenotypic variation, co-located with the QTLs for EHD and LHD, but it was only significant under long-day conditions in Hangzhou, China. The other three QTLs, qHAS-6, qHAS-9, and qHAS-10, were identified under short-day conditions in Hainan, China, each of which explained about 11% of the phenotypic variation. Two of them, qHAS-6 and qHAS-9, were co-located with the QTLs for EHD and LHD. Two QTLs, qPN-4 and qPN-5 for PN, were detected in Hangzhou, and qPN-5 was also detected in Hainan. However, none of them was co-located with QTLs for EHD, LHD, and HAS, suggesting that PN and HAS were controlled by different genetic factors. The results of this study can be useful in marker assisted breeding for improvement of heading synchrony.

Assessing indica-japonica differentiation of improved rice varieties using microsatellite markers

Yongwen Qi, Hongliang Zhang, Dongling Zhang, Meixing Wang, Junli Sun, Li Ding, Fenghua Wang, Zichao Li

2009, 36(5): 305-312. doi: 10.1016/S1673-8527(08)60119-8

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To assess the indica-japonica differentiation of improved rice varieties, a total of 512 modern varieties including 301 indica and 211 japonica accessions were analyzed using 36 microsatellites. The Fst coefficients ranged from 0.002 to 0.730 among the loci with an average of 0.315. Significant differentiation was detected at 94.4% of the loci studied (P < 0.05, pairwise Fst tests), indicating that there was a high level of indica-japonica differentiation within the improved varieties. At 18 loci, about 74%–98% of the alleles of indica and japonica accessions were distributed in two ranges of amplicon length. Linkage disequilibrium analysis showed that the distribution trends were significantly nonrandomly associated. Using the differentiation trends at the 18 loci, microsatellite index (MI) was proposed for discrimination of the two subspecies. When rice accessions with MI value greater than zero were classified as indica, and those with MI value smaller than zero were classified as japonica, about 96.1% of the accessions could be classified. This result agrees with the classification based on morphological-physiological characters, indicating that this method is feasible and effective.

Induction and transmission of wheat-Haynaldia villosa chromosomal translocations

Yaping Cao, Tongde Bie, Xiue Wang, Peidu Chen

2009, 36(5): 313-320. doi: 10.1016/S1673-8527(08)60120-4

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In order to develop more wheat-Haynaldia villosa translocations involving different chromosomes and chromosome segments of H. villosa, T. durum-H. villosa amphiploid was irradiated with ⁶⁰Co γ-rays at doses of 800, 1,200, and 1,600 rad. Pollen collected from the spikes 1, 2, and 3 days after irradiation were transferred to emasculated spikes of the common wheat cv. ‘Chinese Spring’. Genomic in situ hybridization was used to identify wheat-H. villosa chromosome translocations in the M₁ generation. Transmission of the identified translocation chromosomes was analyzed in the BC₁, BC₂, and BC₃ generations. The results indicated that all three irradiation doses were highly efficient for inducing wheat-alien translocations without affecting the viability of the M₁ seeds. Within the range of 800–1,600 rad, both the efficiency of translocation induction and the frequency of interstitial chromosome breakage-fusion increased as the irradiation dosage increased. A higher translocation induction frequency was observed using pollen collected from the spikes 1 day after irradiation over that of 2 or 3 days after irradiation. More than 70% of the translocations detected in the M₁ generation were transmitted to the BC₁ through the female gametes. All translocations recovered in the BC₁ generation were recovered in the following BC₂, and BC₃ generations. The transmission ability of different translocation types in different genetic backgrounds showed an order of ‘whole-arm translocation > small alien segment translocation > large alien segment translocation', through either male or female gametes. In general, the transmission ability through the female gametes was higher than that through the male gametes. By this approach, 14 translocation lines that involved different H. villosa chromosomes have been identified in the BC₃ using EST-STS markers, and eight of them were homozygous.

Instructions for authors

2009, 36(5): 321-324. doi: 10.1016/S1673-8527(09)60010-2

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2009 Vol. 36, No. 5