Journal of Genetics and Genomics

ELE restrains empty glumes from developing into lemmas

Lilan Hong, Qian Qian, Keming Zhu, Ding Tang, Zejun Huang, Ling Gao, Ming Li, Minghong Gu, Zhukuan Cheng

2010, 37(2): 101-115. doi: 10.1016/S1673-8527(09)60029-1

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Abstract:
Although there is evident homology among reproductive organs when comparing Poaceae (grass) and eudicots, the identity of grass specific organs, such as lodicules, palea, lemma, and glumes has been the subject of a vast and largely inconclusive discussion. Here we provide some direct evidence to support the idea that the empty glumes of rice (Oryza sativa) are counterparts of lemmas. We show that the development of empty glumes is regulated by (), which belongs to a plant specific novel gene family. Mutations at the ELE locus cause elongated empty glumes, which mimic the lemmas and have the epidermal morphology of lemmas with four or five vascular bundles. As a nuclear-localized gene, ELE is specifically expressed at the empty glumes of immature spikelets, and its ectopic expression causes many floral development defects, including lemma-like palea, extra palea-like structures, elongated lodicules, extra stamens and stigmas. Our result suggests that empty glumes are lemmas of the sterile florets located at the lateral side of the rice spikelet, and ELE acts as a regulator restraining its growth to maintain its small size in wild-type plants.

The N-terminus of COX-1 and its effect on cyclooxygenase-1 catalytic activity

Yibing Xu, Sean Phipps, Michael J. Turner, Daniel L. Simmons

2010, 37(2): 117-123. doi: 10.1016/S1673-8527(09)60030-8

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Abstract:
Cyclooxygenases are encoded by COX-1 and COX-2. They share over sixty percent sequence identity in human and are similar to each other in their crystallographic structures. One major difference in the primary structure of these two isozymes is the presence of eight amino acids in the amino-terminal region of COX-1 that are not present in COX-2. The function of this amino acid sequence is unknown. In this study, a human COX-1 mutant (Δ7aa) with this sequence removed was studied in parallel with COX-1. Signal peptide cleavage, N-linked glycosylation, protein expression, distribution and dimerization were not affected by the mutation. The mutant was enzymatically active and showed the same sensitivity toward aspirin. The KM for the enzyme remained the same as COX-1. However, the V_max of the COX-1 mutant decreased by 3.3-fold. We conclude that the COX-1 specific amino-terminal sequence has a subtle but detectable effect on COX-1 catalysis.

BmSE, a SINE family with 3′ ends of (ATTT) repeats in domesticated silkworm (Bombyx mori)

Jinshan Xu, Tie Liu, Dong Li, Ze Zhang, Qinyou Xia, Zeyang Zhou

2010, 37(2): 125-135. doi: 10.1016/S1673-8527(09)60031-X

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Abstract:
Short interspersed elements (SINEs), which are mainly composed of Bm1, are abundant in the domesticated silkworm. A 294 bp novel SINE family, designated as BmSE, was identified by mining the database of the complete Bombyx mori genome. A representational BmSE element is flanked by an 11 bp target site duplication sequence posterior poly (A) at the 3′ end and has the sequence motifs of an internal promoter of RNA polymerase III, which are similar to that of Bm1. The repetitive elements of BmSE are widely distributed in all 28 chromosomes of the genome and share the common (ATTT) repeats at the ends. GC-content distribution shows that BmSE tends to accumulate preferably in the region of higher AT content than that of Bm1. A high proportion of the BmSEs are mapped to the coding sequence introns, whereas several elements are also present in the UTR of some transcripts, indicating that BmSEs are indeed exonized with UTRs. Of the 615 identified structural variants (SVs) of BmSE among the 40 domesticated and wild silkworms, only 230 SVs were found in the domesticated silkworms, indicating that many recent SV events of BmSE occurred after domestication, which was probably due to its mobilization. Our analysis might assist in developing BmSE as a potential marker and in understanding the evolutionary roles of SINEs in the domesticated silkworm.

Identification of differential genes in the ovary relative to the testis and their expression patterns in half-smooth tongue sole (Cynoglossus semilaevis)

Yeying Sun, Quanqi Zhang, Jie Qi, Yanjie Chen, Qiwang Zhong, Chunmei Li, Yan Yu, Shuo Li, Zhigang Wang

2010, 37(2): 137-145. doi: 10.1016/S1673-8527(09)60032-1

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Abstract:
Half-smooth tongue sole (Cynoglossus semilaevis) is a rare marine flatfish whose mature ovary and testis greatly differ in volume and weight. The length and weight of mature females are over twice greater than those of mature males. To obtain sufficient information on gonad differentiation and the relationship between gonad development and growth in the fish, we compared gene expression between the ovary and testis using suppression subtractive hybridization (SSH). Testis cDNAs are subtracted from ovary cDNAs and are used to establish an ovary testis-subtracted cDNA library. A total of 41 nonredundant clones are identified, including 20 known cDNAs, 9 uncharacterized cDNAs (EST clones), and 12 novel sequences. For selected genes such as ZPC, RacGAP, survivin, aquaporin, CPEB, O5, O15, and O18, gene expression patterns are analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR). The results confirm that these genes are only expressed in the ovary and not in the testis, or at higher levels in the ovary than in the testis. At the same time, expressions of certain genes such as ZPC, survivin, aquaporin, CPEB, and O15 are demonstrated to possess sexual dimorphism in the kidney or muscle, and spleen. The results suggest that these genes could play key roles not only in the ovary but in other female tissues as well.

Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.)

Qiang Fu, Peijiang Zhang, Lubin Tan, Zuofeng Zhu, Dan Ma, Yongcai Fu, Xinchun Zhan, Hongwei Cai, Chuanqing Sun

2010, 37(2): 147-157. doi: 10.1016/S1673-8527(09)60033-3

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Abstract:
Using an accession of common wild rice (Oryza rufipogon Griff.) collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two generations (BC₄F₂ and BC₄F₄), a total of 26 QTLs were detected by employing single point analysis and interval mapping in both generations. Of the 26 QTLs, the alleles of 10 (38.5%) QTLs originating from O. rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background. In addition, five QTLs controlling yield and its components were newly identified, indicating that there are potentially novel alleles in Yuanjiang common wild rice. Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1, 7 and 12. The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation, suggesting the pleiotropism or tight linkage. Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future.

The 8th International Bioinformatics Workshop (IBW2010)

2010, 37(2) doi: 10.1016/S1673-8527(10)60002-1

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Abstract:

2010 Vol. 37, No. 2